Hdac1

UniProt ID: O09106
Organism: Mus musculus
Review Status: COMPLETE
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Gene Description

Histone deacetylase 1 (HDAC1) is a zinc-dependent metalloenzyme (EC 3.5.1.98) that catalyzes the removal of acetyl groups from lysine residues on histones and non-histone proteins. HDAC1 functions as the catalytic subunit of multiple co-repressor complexes including NuRD, SIN3, and CoREST, mediating transcriptional repression through chromatin compaction. It also has experimentally supported decrotonylase activity; current delactylase annotation is similarity-based rather than direct mouse experimental evidence. HDAC1 is essential for embryonic development and plays roles in cell cycle regulation, differentiation, and numerous signaling pathways.

Existing Annotations Review

GO Term Evidence Action Reason
GO:0004407 histone deacetylase activity
IBA
GO_REF:0000033 		ACCEPT
Summary: HDAC1 is a zinc-dependent histone deacetylase (EC 3.5.1.98) that catalyzes removal of acetyl groups from N-acetyl-lysine residues on histones H2A, H2B, H3, and H4. This is the core enzymatic function of HDAC1, well established by direct biochemical assays (PMID:10615135, PMID:21960634, PMID:30279482).
Reason: Histone deacetylase activity is the primary enzymatic function of HDAC1, supported by multiple direct experimental studies demonstrating catalytic activity on histone substrates.
Supporting Evidence:
PMID:10615135
Here we show that Dnmt1 is itself associated with histone deacetylase activity in vivo
PMID:30279482
A ternary complex of HDAC1/CoREST1/LSD1 is able to hydrolyse both histone H3 Lys18-acetyl (H3K18ac) and H3 Lys18-crotonyl (H3K18cr) peptide substrates
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD, Sin3, CoREST, and related chromatin-repressor complexes.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
HDAC1 is a class I Zn2+-dependent histone/protein deacetylase that removes acetyl groups from lysine residues on histone tails and non-histone proteins.
GO:0031507 heterochromatin formation
IBA
GO_REF:0000033 		ACCEPT
Summary: HDAC1 contributes to heterochromatin formation through its deacetylase activity. It has been localized to heterochromatic regions including pericentromeric heterochromatin (PMID:14643676, PMID:14519686).
Reason: HDAC1 deacetylation promotes chromatin compaction and is involved in heterochromatin maintenance. IBA annotation from phylogenetic analysis is appropriate. Supported by localization to heterochromatin in mouse cells.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD, Sin3, CoREST, and related chromatin-repressor complexes.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylase that catalyzes the deacetylation of lysine residues on the N-terminal part of the core histones.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein corepressor complexes, especially SIN3, NuRD, and CoREST.
GO:0016581 NuRD complex
IBA
GO_REF:0000033 		ACCEPT
Summary: HDAC1 is a core catalytic subunit of the NuRD (nucleosome remodeling and deacetylase) complex. Proteomic studies show approximately 49% of cellular HDAC1 in ESCs is in the NuRD complex (deep research review). Well supported by mass spectrometry identification (PMID:27806305) and multiple interaction studies.
Reason: NuRD complex membership is a core aspect of HDAC1 function. HDAC1 serves as the catalytic deacetylase subunit within NuRD. Extensively validated by proteomics and co-immunoprecipitation studies.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD, Sin3, CoREST, and related chromatin-repressor complexes.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylase that catalyzes the deacetylation of lysine residues on the N-terminal part of the core histones.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein corepressor complexes, especially SIN3, NuRD, and CoREST.
GO:0004407 histone deacetylase activity
IEA
GO_REF:0000120 		ACCEPT
Summary: HDAC1 is a zinc-dependent histone deacetylase (EC 3.5.1.98) that catalyzes removal of acetyl groups from N-acetyl-lysine residues on histones H2A, H2B, H3, and H4. This is the core enzymatic function of HDAC1, well established by direct biochemical assays (PMID:10615135, PMID:21960634, PMID:30279482).
Reason: Histone deacetylase activity is the primary enzymatic function of HDAC1, supported by multiple direct experimental studies demonstrating catalytic activity on histone substrates.
Supporting Evidence:
PMID:10615135
Here we show that Dnmt1 is itself associated with histone deacetylase activity in vivo
PMID:30279482
A ternary complex of HDAC1/CoREST1/LSD1 is able to hydrolyse both histone H3 Lys18-acetyl (H3K18ac) and H3 Lys18-crotonyl (H3K18cr) peptide substrates
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD, Sin3, CoREST, and related chromatin-repressor complexes.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
HDAC1 is a class I Zn2+-dependent histone/protein deacetylase that removes acetyl groups from lysine residues on histone tails and non-histone proteins.
GO:0005634 nucleus
IEA
GO_REF:0000120 		ACCEPT
Summary: HDAC1 is predominantly nuclear, consistent with its function in chromatin modification and transcriptional regulation. Nuclear localization confirmed by multiple methods including immunofluorescence (PMID:11115394).
Reason: Nuclear localization is a well-established core feature of HDAC1. It is a Class I HDAC that is predominantly nuclear.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD, Sin3, CoREST, and related chromatin-repressor complexes.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylase that catalyzes the deacetylation of lysine residues on the N-terminal part of the core histones.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
Class I HDACs, including HDAC1, are predominantly or exclusively nuclear, consistent with chromatin accessibility and transcriptional control roles.
GO:0017053 transcription repressor complex
IEA
GO_REF:0000117 		ACCEPT
Summary: HDAC1 functions within transcription repressor complexes including NuRD, SIN3, and CoREST, which mediate transcriptional repression through histone deacetylation.
Reason: HDAC1 is a core catalytic subunit of several transcription repressor complexes. This is a correct and informative annotation.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD, Sin3, CoREST, and related chromatin-repressor complexes.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylase that catalyzes the deacetylation of lysine residues on the N-terminal part of the core histones.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein corepressor complexes, especially SIN3, NuRD, and CoREST.
GO:0030178 negative regulation of Wnt signaling pathway
IEA
GO_REF:0000117 		MODIFY
Summary: HDAC1 negatively regulates Wnt signaling. The more specific term GO:0090090 is already annotated.
Reason: The more specific term GO:0090090 (negative regulation of canonical Wnt signaling pathway) is already annotated and is more appropriate.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
The broader Wnt term is less precise than the canonical Wnt signaling annotation already present for HDAC1-dependent repression.
file:mouse/Hdac1/Hdac1-uniprot.txt
HDAC1 functions as a chromatin-modifying corepressor complex subunit.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
The report supports HDAC1 as a chromatin deacetylase whose developmental, signaling, cell-cycle, DNA-damage, and pathway phenotypes are context-specific downstream outputs.
GO:0035851 Krueppel-associated box domain binding
IEA
GO_REF:0000117 		ACCEPT
Summary: HDAC1 binds to KRAB domain-containing zinc finger proteins, demonstrated for ZNF431 (PMID:21177534).
Reason: IEA transfer consistent with direct experimental evidence for KRAB domain binding.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD, Sin3, CoREST, and related chromatin-repressor complexes.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylase that catalyzes the deacetylation of lysine residues on the N-terminal part of the core histones.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein corepressor complexes, especially SIN3, NuRD, and CoREST.
GO:0060789 hair follicle placode formation
IEA
GO_REF:0000117 		KEEP AS NON CORE
Summary: HDAC1/2 are required for hair follicle placode formation (PMID:21093383).
Reason: Specific epidermal phenotype. Pleiotropic downstream effect.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 has many developmental and signaling consequences through chromatin deacetylation; these are non-core outputs of the core enzymatic function.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylation gives a tag for epigenetic repression and plays an important role in transcriptional regulation, cell cycle progression and developmental events.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
The report supports HDAC1 as a chromatin deacetylase whose developmental, signaling, cell-cycle, DNA-damage, and pathway phenotypes are context-specific downstream outputs.
GO:0061029 eyelid development in camera-type eye
IEA
GO_REF:0000117 		KEEP AS NON CORE
Summary: HDAC1/2 conditional knockout in epidermis affects eyelid development (PMID:21093383).
Reason: Specific developmental phenotype. Pleiotropic downstream effect.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 has many developmental and signaling consequences through chromatin deacetylation; these are non-core outputs of the core enzymatic function.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylation gives a tag for epigenetic repression and plays an important role in transcriptional regulation, cell cycle progression and developmental events.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
The report supports HDAC1 as a chromatin deacetylase whose developmental, signaling, cell-cycle, DNA-damage, and pathway phenotypes are context-specific downstream outputs.
GO:0061198 fungiform papilla formation
IEA
GO_REF:0000117 		KEEP AS NON CORE
Summary: HDAC1/2 conditional loss in epidermis affects fungiform papilla formation (PMID:21093383).
Reason: Specific developmental phenotype. Pleiotropic downstream effect.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 has many developmental and signaling consequences through chromatin deacetylation; these are non-core outputs of the core enzymatic function.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylation gives a tag for epigenetic repression and plays an important role in transcriptional regulation, cell cycle progression and developmental events.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
The report supports HDAC1 as a chromatin deacetylase whose developmental, signaling, cell-cycle, DNA-damage, and pathway phenotypes are context-specific downstream outputs.
GO:0141221 histone deacetylase activity, hydrolytic mechanism
IEA
GO_REF:0000120 		ACCEPT
Summary: HDAC1 uses a zinc-dependent hydrolytic mechanism to remove acetyl groups from histones. This is a more specific child term of GO:0004407 that specifies the catalytic mechanism.
Reason: HDAC1 is a Class I HDAC that uses a zinc-dependent hydrolytic mechanism (as opposed to NAD+-dependent sirtuins). Well established from structural and biochemical studies.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD, Sin3, CoREST, and related chromatin-repressor complexes.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylase that catalyzes the deacetylation of lysine residues on the N-terminal part of the core histones.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
HDAC1 is a class I Zn2+-dependent histone/protein deacetylase that removes acetyl groups from lysine residues on histone tails and non-histone proteins.
GO:0160008 protein decrotonylase activity
IEA
GO_REF:0000116 		MODIFY
Summary: HDAC1 can remove crotonyl groups from lysine residues on proteins. Demonstrated by Kelly et al. (PMID:30279482) for histone substrates.
Reason: The cited evidence supports histone decrotonylase activity, not a broad protein decrotonylase role as the primary accepted term.
Proposed replacements: histone decrotonylase activity
Supporting Evidence:
PMID:30279482
Genetic deletion of HDAC1/2 in ES cells increases global levels of histone crotonylation and causes an 85% reduction in total decrotonylase activity
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD, Sin3, CoREST, and related chromatin-repressor complexes.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein corepressor complexes, especially SIN3, NuRD, and CoREST.
GO:2001243 negative regulation of intrinsic apoptotic signaling pathway
IEA
GO_REF:0000117 		ACCEPT
Summary: HDAC1 negatively regulates the intrinsic apoptotic signaling pathway. HDAC1/2 double knockout in epidermis leads to increased apoptosis (PMID:21093383).
Reason: HDAC1/2 directly mediate transcriptional repression through chromatin deacetylation and suppress p53 activity in this system, so negative regulation of intrinsic apoptotic signaling is a direct chromatin-repressor output rather than only a distal phenotype.
Supporting Evidence:
PMID:21093383
HDAC1/2 directly mediate repressive functions of p63 and suppress p53 activity.
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 can deacetylate p53, reducing p53 activity and thereby modulating apoptosis and DNA damage responses.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylation gives a tag for epigenetic repression and plays an important role in transcriptional regulation, cell cycle progression and developmental events.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein corepressor complexes.
GO:0005515 protein binding
IPI
PMID:10615135
DNA methyltransferase Dnmt1 associates with histone deacetyl... 		REMOVE
Summary: Protein binding annotation based on physical interaction evidence from PMID:10615135. HDAC1 is known to interact with a very large number of proteins as it functions within multiple co-repressor complexes (NuRD, SIN3, CoREST) and binds many transcription factors.
Reason: Per curation guidelines, protein binding (GO:0005515) is uninformative and should be replaced with more specific molecular function terms. HDAC1 physically interacts with many proteins, but this generic term does not convey functional information. More specific annotations such as histone deacetylase binding, transcription corepressor binding, NF-kappaB binding, and DNA-binding transcription factor binding are already present.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
Generic protein binding and weakly mechanistic interaction annotations are less informative than HDAC1 deacetylase activity and defined corepressor-complex membership.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylases act via the formation of large multiprotein complexes.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
The report supports specific enzymatic and chromatin-complex annotations for HDAC1 rather than generic binding or weakly localized annotations.
GO:0005515 protein binding
IPI
PMID:11931769
The phosphorylation status of nuclear NF-kappa B determines ... 		REMOVE
Summary: Protein binding annotation based on physical interaction evidence from PMID:11931769. HDAC1 is known to interact with a very large number of proteins as it functions within multiple co-repressor complexes (NuRD, SIN3, CoREST) and binds many transcription factors.
Reason: Per curation guidelines, protein binding (GO:0005515) is uninformative and should be replaced with more specific molecular function terms. HDAC1 physically interacts with many proteins, but this generic term does not convey functional information. More specific annotations such as histone deacetylase binding, transcription corepressor binding, NF-kappaB binding, and DNA-binding transcription factor binding are already present.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
Generic protein binding and weakly mechanistic interaction annotations are less informative than HDAC1 deacetylase activity and defined corepressor-complex membership.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylases act via the formation of large multiprotein complexes.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
The report supports specific enzymatic and chromatin-complex annotations for HDAC1 rather than generic binding or weakly localized annotations.
GO:0005515 protein binding
IPI
PMID:15337766
Leukemia/lymphoma-related factor, a POZ domain-containing tr... 		REMOVE
Summary: Protein binding annotation based on physical interaction evidence from PMID:15337766. HDAC1 is known to interact with a very large number of proteins as it functions within multiple co-repressor complexes (NuRD, SIN3, CoREST) and binds many transcription factors.
Reason: Per curation guidelines, protein binding (GO:0005515) is uninformative and should be replaced with more specific molecular function terms. HDAC1 physically interacts with many proteins, but this generic term does not convey functional information. More specific annotations such as histone deacetylase binding, transcription corepressor binding, NF-kappaB binding, and DNA-binding transcription factor binding are already present.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
Generic protein binding and weakly mechanistic interaction annotations are less informative than HDAC1 deacetylase activity and defined corepressor-complex membership.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylases act via the formation of large multiprotein complexes.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
The report supports specific enzymatic and chromatin-complex annotations for HDAC1 rather than generic binding or weakly localized annotations.
GO:0005515 protein binding
IPI
PMID:16407974
ETO2 coordinates cellular proliferation and differentiation ... 		REMOVE
Summary: Protein binding annotation based on physical interaction evidence from PMID:16407974. HDAC1 is known to interact with a very large number of proteins as it functions within multiple co-repressor complexes (NuRD, SIN3, CoREST) and binds many transcription factors.
Reason: Per curation guidelines, protein binding (GO:0005515) is uninformative and should be replaced with more specific molecular function terms. HDAC1 physically interacts with many proteins, but this generic term does not convey functional information. More specific annotations such as histone deacetylase binding, transcription corepressor binding, NF-kappaB binding, and DNA-binding transcription factor binding are already present.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
Generic protein binding and weakly mechanistic interaction annotations are less informative than HDAC1 deacetylase activity and defined corepressor-complex membership.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylases act via the formation of large multiprotein complexes.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
The report supports specific enzymatic and chromatin-complex annotations for HDAC1 rather than generic binding or weakly localized annotations.
GO:0005515 protein binding
IPI
PMID:17056544
The transcriptional repressor cAMP response element modulato... 		REMOVE
Summary: Protein binding annotation based on physical interaction evidence from PMID:17056544. HDAC1 is known to interact with a very large number of proteins as it functions within multiple co-repressor complexes (NuRD, SIN3, CoREST) and binds many transcription factors.
Reason: Per curation guidelines, protein binding (GO:0005515) is uninformative and should be replaced with more specific molecular function terms. HDAC1 physically interacts with many proteins, but this generic term does not convey functional information. More specific annotations such as histone deacetylase binding, transcription corepressor binding, NF-kappaB binding, and DNA-binding transcription factor binding are already present.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
Generic protein binding and weakly mechanistic interaction annotations are less informative than HDAC1 deacetylase activity and defined corepressor-complex membership.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylases act via the formation of large multiprotein complexes.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
The report supports specific enzymatic and chromatin-complex annotations for HDAC1 rather than generic binding or weakly localized annotations.
GO:0005515 protein binding
IPI
PMID:17568773
Foxh1 recruits Gsc to negatively regulate Mixl1 expression d... 		REMOVE
Summary: Protein binding annotation based on physical interaction evidence from PMID:17568773. HDAC1 is known to interact with a very large number of proteins as it functions within multiple co-repressor complexes (NuRD, SIN3, CoREST) and binds many transcription factors.
Reason: Per curation guidelines, protein binding (GO:0005515) is uninformative and should be replaced with more specific molecular function terms. HDAC1 physically interacts with many proteins, but this generic term does not convey functional information. More specific annotations such as histone deacetylase binding, transcription corepressor binding, NF-kappaB binding, and DNA-binding transcription factor binding are already present.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
Generic protein binding and weakly mechanistic interaction annotations are less informative than HDAC1 deacetylase activity and defined corepressor-complex membership.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylases act via the formation of large multiprotein complexes.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
The report supports specific enzymatic and chromatin-complex annotations for HDAC1 rather than generic binding or weakly localized annotations.
GO:0005515 protein binding
IPI
PMID:19424149
HDAC2 negatively regulates memory formation and synaptic pla... 		REMOVE
Summary: Protein binding annotation based on physical interaction evidence from PMID:19424149. HDAC1 is known to interact with a very large number of proteins as it functions within multiple co-repressor complexes (NuRD, SIN3, CoREST) and binds many transcription factors.
Reason: Per curation guidelines, protein binding (GO:0005515) is uninformative and should be replaced with more specific molecular function terms. HDAC1 physically interacts with many proteins, but this generic term does not convey functional information. More specific annotations such as histone deacetylase binding, transcription corepressor binding, NF-kappaB binding, and DNA-binding transcription factor binding are already present.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
Generic protein binding and weakly mechanistic interaction annotations are less informative than HDAC1 deacetylase activity and defined corepressor-complex membership.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylases act via the formation of large multiprotein complexes.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
The report supports specific enzymatic and chromatin-complex annotations for HDAC1 rather than generic binding or weakly localized annotations.
GO:0005515 protein binding
IPI
PMID:19497860
LSD1-mediated epigenetic modification is required for TAL1 f... 		REMOVE
Summary: Protein binding annotation based on physical interaction evidence from PMID:19497860. HDAC1 is known to interact with a very large number of proteins as it functions within multiple co-repressor complexes (NuRD, SIN3, CoREST) and binds many transcription factors.
Reason: Per curation guidelines, protein binding (GO:0005515) is uninformative and should be replaced with more specific molecular function terms. HDAC1 physically interacts with many proteins, but this generic term does not convey functional information. More specific annotations such as histone deacetylase binding, transcription corepressor binding, NF-kappaB binding, and DNA-binding transcription factor binding are already present.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
Generic protein binding and weakly mechanistic interaction annotations are less informative than HDAC1 deacetylase activity and defined corepressor-complex membership.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylases act via the formation of large multiprotein complexes.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
The report supports specific enzymatic and chromatin-complex annotations for HDAC1 rather than generic binding or weakly localized annotations.
GO:0005515 protein binding
IPI
PMID:20404188
Histone deacetylase 1 (HDAC1), but not HDAC2, controls embry... 		REMOVE
Summary: Protein binding annotation based on physical interaction evidence from PMID:20404188. HDAC1 is known to interact with a very large number of proteins as it functions within multiple co-repressor complexes (NuRD, SIN3, CoREST) and binds many transcription factors.
Reason: Per curation guidelines, protein binding (GO:0005515) is uninformative and should be replaced with more specific molecular function terms. HDAC1 physically interacts with many proteins, but this generic term does not convey functional information. More specific annotations such as histone deacetylase binding, transcription corepressor binding, NF-kappaB binding, and DNA-binding transcription factor binding are already present.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
Generic protein binding and weakly mechanistic interaction annotations are less informative than HDAC1 deacetylase activity and defined corepressor-complex membership.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylases act via the formation of large multiprotein complexes.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
The report supports specific enzymatic and chromatin-complex annotations for HDAC1 rather than generic binding or weakly localized annotations.
GO:0005515 protein binding
IPI
PMID:20596014
Chromatin regulation by Brg1 underlies heart muscle developm... 		REMOVE
Summary: Protein binding annotation based on physical interaction evidence from PMID:20596014. HDAC1 is known to interact with a very large number of proteins as it functions within multiple co-repressor complexes (NuRD, SIN3, CoREST) and binds many transcription factors.
Reason: Per curation guidelines, protein binding (GO:0005515) is uninformative and should be replaced with more specific molecular function terms. HDAC1 physically interacts with many proteins, but this generic term does not convey functional information. More specific annotations such as histone deacetylase binding, transcription corepressor binding, NF-kappaB binding, and DNA-binding transcription factor binding are already present.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
Generic protein binding and weakly mechanistic interaction annotations are less informative than HDAC1 deacetylase activity and defined corepressor-complex membership.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylases act via the formation of large multiprotein complexes.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
The report supports specific enzymatic and chromatin-complex annotations for HDAC1 rather than generic binding or weakly localized annotations.
GO:0005515 protein binding
IPI
PMID:21177534
A novel KRAB domain-containing zinc finger transcription fac... 		REMOVE
Summary: Protein binding annotation based on physical interaction evidence from PMID:21177534. HDAC1 is known to interact with a very large number of proteins as it functions within multiple co-repressor complexes (NuRD, SIN3, CoREST) and binds many transcription factors.
Reason: Per curation guidelines, protein binding (GO:0005515) is uninformative and should be replaced with more specific molecular function terms. HDAC1 physically interacts with many proteins, but this generic term does not convey functional information. More specific annotations such as histone deacetylase binding, transcription corepressor binding, NF-kappaB binding, and DNA-binding transcription factor binding are already present.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
Generic protein binding and weakly mechanistic interaction annotations are less informative than HDAC1 deacetylase activity and defined corepressor-complex membership.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylases act via the formation of large multiprotein complexes.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
The report supports specific enzymatic and chromatin-complex annotations for HDAC1 rather than generic binding or weakly localized annotations.
GO:0005515 protein binding
IPI
PMID:21448134
KDM5B regulates embryonic stem cell self-renewal and repress... 		REMOVE
Summary: Protein binding annotation based on physical interaction evidence from PMID:21448134. HDAC1 is known to interact with a very large number of proteins as it functions within multiple co-repressor complexes (NuRD, SIN3, CoREST) and binds many transcription factors.
Reason: Per curation guidelines, protein binding (GO:0005515) is uninformative and should be replaced with more specific molecular function terms. HDAC1 physically interacts with many proteins, but this generic term does not convey functional information. More specific annotations such as histone deacetylase binding, transcription corepressor binding, NF-kappaB binding, and DNA-binding transcription factor binding are already present.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
Generic protein binding and weakly mechanistic interaction annotations are less informative than HDAC1 deacetylase activity and defined corepressor-complex membership.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylases act via the formation of large multiprotein complexes.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
The report supports specific enzymatic and chromatin-complex annotations for HDAC1 rather than generic binding or weakly localized annotations.
GO:0005515 protein binding
IPI
PMID:22297846
Enhancer decommissioning by LSD1 during embryonic stem cell ... 		REMOVE
Summary: Protein binding annotation based on physical interaction evidence from PMID:22297846. HDAC1 is known to interact with a very large number of proteins as it functions within multiple co-repressor complexes (NuRD, SIN3, CoREST) and binds many transcription factors.
Reason: Per curation guidelines, protein binding (GO:0005515) is uninformative and should be replaced with more specific molecular function terms. HDAC1 physically interacts with many proteins, but this generic term does not convey functional information. More specific annotations such as histone deacetylase binding, transcription corepressor binding, NF-kappaB binding, and DNA-binding transcription factor binding are already present.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
Generic protein binding and weakly mechanistic interaction annotations are less informative than HDAC1 deacetylase activity and defined corepressor-complex membership.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylases act via the formation of large multiprotein complexes.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
The report supports specific enzymatic and chromatin-complex annotations for HDAC1 rather than generic binding or weakly localized annotations.
GO:0005515 protein binding
IPI
PMID:22334647
Protooncogene Ski cooperates with the chromatin-remodeling f... 		REMOVE
Summary: Protein binding annotation based on physical interaction evidence from PMID:22334647. HDAC1 is known to interact with a very large number of proteins as it functions within multiple co-repressor complexes (NuRD, SIN3, CoREST) and binds many transcription factors.
Reason: Per curation guidelines, protein binding (GO:0005515) is uninformative and should be replaced with more specific molecular function terms. HDAC1 physically interacts with many proteins, but this generic term does not convey functional information. More specific annotations such as histone deacetylase binding, transcription corepressor binding, NF-kappaB binding, and DNA-binding transcription factor binding are already present.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
Generic protein binding and weakly mechanistic interaction annotations are less informative than HDAC1 deacetylase activity and defined corepressor-complex membership.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylases act via the formation of large multiprotein complexes.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
The report supports specific enzymatic and chromatin-complex annotations for HDAC1 rather than generic binding or weakly localized annotations.
GO:0005515 protein binding
IPI
PMID:22918830
Histone deacetylase-1 (HDAC1) is a molecular switch between ... 		REMOVE
Summary: Protein binding annotation based on physical interaction evidence from PMID:22918830. HDAC1 is known to interact with a very large number of proteins as it functions within multiple co-repressor complexes (NuRD, SIN3, CoREST) and binds many transcription factors.
Reason: Per curation guidelines, protein binding (GO:0005515) is uninformative and should be replaced with more specific molecular function terms. HDAC1 physically interacts with many proteins, but this generic term does not convey functional information. More specific annotations such as histone deacetylase binding, transcription corepressor binding, NF-kappaB binding, and DNA-binding transcription factor binding are already present.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
Generic protein binding and weakly mechanistic interaction annotations are less informative than HDAC1 deacetylase activity and defined corepressor-complex membership.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylases act via the formation of large multiprotein complexes.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
The report supports specific enzymatic and chromatin-complex annotations for HDAC1 rather than generic binding or weakly localized annotations.
GO:0005515 protein binding
IPI
PMID:24240174
Divergent roles of HDAC1 and HDAC2 in the regulation of epid... 		REMOVE
Summary: Protein binding annotation based on physical interaction evidence from PMID:24240174. HDAC1 is known to interact with a very large number of proteins as it functions within multiple co-repressor complexes (NuRD, SIN3, CoREST) and binds many transcription factors.
Reason: Per curation guidelines, protein binding (GO:0005515) is uninformative and should be replaced with more specific molecular function terms. HDAC1 physically interacts with many proteins, but this generic term does not convey functional information. More specific annotations such as histone deacetylase binding, transcription corepressor binding, NF-kappaB binding, and DNA-binding transcription factor binding are already present.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
Generic protein binding and weakly mechanistic interaction annotations are less informative than HDAC1 deacetylase activity and defined corepressor-complex membership.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylases act via the formation of large multiprotein complexes.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
The report supports specific enzymatic and chromatin-complex annotations for HDAC1 rather than generic binding or weakly localized annotations.
GO:0005515 protein binding
IPI
PMID:24736997
A novel protein, CHRONO, functions as a core component of th... 		REMOVE
Summary: Protein binding annotation based on physical interaction evidence from PMID:24736997. HDAC1 is known to interact with a very large number of proteins as it functions within multiple co-repressor complexes (NuRD, SIN3, CoREST) and binds many transcription factors.
Reason: Per curation guidelines, protein binding (GO:0005515) is uninformative and should be replaced with more specific molecular function terms. HDAC1 physically interacts with many proteins, but this generic term does not convey functional information. More specific annotations such as histone deacetylase binding, transcription corepressor binding, NF-kappaB binding, and DNA-binding transcription factor binding are already present.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
Generic protein binding and weakly mechanistic interaction annotations are less informative than HDAC1 deacetylase activity and defined corepressor-complex membership.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylases act via the formation of large multiprotein complexes.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
The report supports specific enzymatic and chromatin-complex annotations for HDAC1 rather than generic binding or weakly localized annotations.
GO:0005515 protein binding
IPI
PMID:26816381
Transcription factors LRF and BCL11A independently repress e... 		REMOVE
Summary: Protein binding annotation based on physical interaction evidence from PMID:26816381. HDAC1 is known to interact with a very large number of proteins as it functions within multiple co-repressor complexes (NuRD, SIN3, CoREST) and binds many transcription factors.
Reason: Per curation guidelines, protein binding (GO:0005515) is uninformative and should be replaced with more specific molecular function terms. HDAC1 physically interacts with many proteins, but this generic term does not convey functional information. More specific annotations such as histone deacetylase binding, transcription corepressor binding, NF-kappaB binding, and DNA-binding transcription factor binding are already present.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
Generic protein binding and weakly mechanistic interaction annotations are less informative than HDAC1 deacetylase activity and defined corepressor-complex membership.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylases act via the formation of large multiprotein complexes.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
The report supports specific enzymatic and chromatin-complex annotations for HDAC1 rather than generic binding or weakly localized annotations.
GO:0005515 protein binding
IPI
PMID:26974661
C/EBPα creates elite cells for iPSC reprogramming by upregul... 		REMOVE
Summary: Protein binding annotation based on physical interaction evidence from PMID:26974661. HDAC1 is known to interact with a very large number of proteins as it functions within multiple co-repressor complexes (NuRD, SIN3, CoREST) and binds many transcription factors.
Reason: Per curation guidelines, protein binding (GO:0005515) is uninformative and should be replaced with more specific molecular function terms. HDAC1 physically interacts with many proteins, but this generic term does not convey functional information. More specific annotations such as histone deacetylase binding, transcription corepressor binding, NF-kappaB binding, and DNA-binding transcription factor binding are already present.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
Generic protein binding and weakly mechanistic interaction annotations are less informative than HDAC1 deacetylase activity and defined corepressor-complex membership.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylases act via the formation of large multiprotein complexes.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
The report supports specific enzymatic and chromatin-complex annotations for HDAC1 rather than generic binding or weakly localized annotations.
GO:0005515 protein binding
IPI
PMID:30726206
Genes encoding SATB2-interacting proteins in adult cerebral ... 		REMOVE
Summary: Protein binding annotation based on physical interaction evidence from PMID:30726206. HDAC1 is known to interact with a very large number of proteins as it functions within multiple co-repressor complexes (NuRD, SIN3, CoREST) and binds many transcription factors.
Reason: Per curation guidelines, protein binding (GO:0005515) is uninformative and should be replaced with more specific molecular function terms. HDAC1 physically interacts with many proteins, but this generic term does not convey functional information. More specific annotations such as histone deacetylase binding, transcription corepressor binding, NF-kappaB binding, and DNA-binding transcription factor binding are already present.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
Generic protein binding and weakly mechanistic interaction annotations are less informative than HDAC1 deacetylase activity and defined corepressor-complex membership.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylases act via the formation of large multiprotein complexes.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
The report supports specific enzymatic and chromatin-complex annotations for HDAC1 rather than generic binding or weakly localized annotations.
GO:0000118 histone deacetylase complex
IEA
GO_REF:0000107 		ACCEPT
Summary: HDAC1 is a core component of multiple histone deacetylase complexes including NuRD, SIN3, and CoREST. This is a general parent term encompassing all such complexes.
Reason: HDAC1 is the defining catalytic subunit of multiple HDAC complexes. This broader term is appropriate as a parent annotation alongside the more specific NuRD and SIN3 complex terms.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD, Sin3, CoREST, and related chromatin-repressor complexes.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylase that catalyzes the deacetylation of lysine residues on the N-terminal part of the core histones.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
HDAC1 is a class I Zn2+-dependent histone/protein deacetylase that removes acetyl groups from lysine residues on histone tails and non-histone proteins.
GO:0000122 negative regulation of transcription by RNA polymerase II
IEA
GO_REF:0000107 		ACCEPT
Summary: HDAC1 negatively regulates transcription by RNA polymerase II through histone deacetylation at target gene promoters. This is a core biological process annotation for HDAC1.
Reason: Negative regulation of pol II transcription is a primary biological function of HDAC1. Supported by multiple lines of evidence (PMID:8917507, PMID:9271381, PMID:21093383).
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD, Sin3, CoREST, and related chromatin-repressor complexes.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylase that catalyzes the deacetylation of lysine residues on the N-terminal part of the core histones.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein corepressor complexes, especially SIN3, NuRD, and CoREST.
GO:0000785 chromatin
IEA
GO_REF:0000120 		ACCEPT
Summary: HDAC1 is a chromatin-associated protein that modifies histone tails as part of co-repressor complexes.
Reason: HDAC1 is a histone-modifying enzyme that directly acts on chromatin. Association with chromatin is inherent to its function.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD, Sin3, CoREST, and related chromatin-repressor complexes.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylase that catalyzes the deacetylation of lysine residues on the N-terminal part of the core histones.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein corepressor complexes, especially SIN3, NuRD, and CoREST.
GO:0000978 RNA polymerase II cis-regulatory region sequence-specific DNA binding
IEA
GO_REF:0000107 		MODIFY
Summary: Annotation suggests HDAC1 has sequence-specific DNA binding at RNA pol II cis-regulatory regions. However, HDAC1 does not have intrinsic sequence-specific DNA binding - it is recruited to promoters by transcription factors.
Reason: Replace direct sequence-specific DNA binding with promoter-specific chromatin binding, which captures HDAC1 recruitment to promoter chromatin without implying intrinsic DNA-binding specificity.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 is recruited to chromatin by DNA-binding factors but is not itself a sequence-specific DNA-binding transcription factor.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylase that catalyzes the deacetylation of lysine residues on core histones.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
The report supports HDAC1 as a chromatin deacetylase whose developmental, signaling, cell-cycle, DNA-damage, and pathway phenotypes are context-specific downstream outputs.
GO:0000979 RNA polymerase II core promoter sequence-specific DNA binding
IEA
GO_REF:0000107 		MODIFY
Summary: This implies sequence-specific core promoter DNA binding by HDAC1, which is not supported. HDAC1 is recruited to core promoters via protein-protein interactions.
Reason: Replace direct sequence-specific DNA binding with promoter-specific chromatin binding, which captures HDAC1 recruitment to promoter chromatin without implying intrinsic DNA-binding specificity.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 is recruited to chromatin by DNA-binding factors but is not itself a sequence-specific DNA-binding transcription factor.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylase that catalyzes the deacetylation of lysine residues on core histones.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
The report supports HDAC1 as a chromatin deacetylase whose developmental, signaling, cell-cycle, DNA-damage, and pathway phenotypes are context-specific downstream outputs.
GO:0001046 core promoter sequence-specific DNA binding
IEA
GO_REF:0000107 		MODIFY
Summary: This implies HDAC1 has core promoter sequence-specific DNA binding, which is not supported by its known biochemistry.
Reason: Replace direct sequence-specific DNA binding with promoter-specific chromatin binding, which captures HDAC1 recruitment to promoter chromatin without implying intrinsic DNA-binding specificity.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 is recruited to chromatin by DNA-binding factors but is not itself a sequence-specific DNA-binding transcription factor.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylase that catalyzes the deacetylation of lysine residues on core histones.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
The report supports HDAC1 as a chromatin deacetylase whose developmental, signaling, cell-cycle, DNA-damage, and pathway phenotypes are context-specific downstream outputs.
GO:0001222 transcription corepressor binding
IEA
GO_REF:0000107 		ACCEPT
Summary: HDAC1 binds to transcription corepressors including SIN3A, SIN3B, CoREST, NCoR, and SMRT as part of its recruitment to target genes.
Reason: HDAC1 physically interacts with multiple corepressor scaffold proteins. This binding is essential for its function in transcriptional repression complexes.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD, Sin3, CoREST, and related chromatin-repressor complexes.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylase that catalyzes the deacetylation of lysine residues on the N-terminal part of the core histones.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein corepressor complexes, especially SIN3, NuRD, and CoREST.
GO:0001975 response to amphetamine
IEA
GO_REF:0000107 		KEEP AS NON CORE
Summary: IEA annotation suggesting HDAC1 involvement in response to amphetamine.
Reason: Highly context-specific phenotype likely representing downstream pleiotropic effects.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 has many developmental and signaling consequences through chromatin deacetylation; these are non-core outputs of the core enzymatic function.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylation gives a tag for epigenetic repression and plays an important role in transcriptional regulation, cell cycle progression and developmental events.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
The report supports HDAC1 as a chromatin deacetylase whose developmental, signaling, cell-cycle, DNA-damage, and pathway phenotypes are context-specific downstream outputs.
GO:0002039 p53 binding
IEA
GO_REF:0000107 		ACCEPT
Summary: HDAC1 binds to and deacetylates the tumor suppressor p53, thereby modulating its activity and stability.
Reason: HDAC1 interaction with p53 is well established. HDAC1 deacetylates p53, leading to its inactivation and degradation. Functionally relevant interaction.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD, Sin3, CoREST, and related chromatin-repressor complexes.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylase that catalyzes the deacetylation of lysine residues on the N-terminal part of the core histones.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein corepressor complexes, especially SIN3, NuRD, and CoREST.
GO:0003682 chromatin binding
IEA
GO_REF:0000120 		ACCEPT
Summary: HDAC1 binds chromatin as part of its function in co-repressor complexes. ChIP experiments have confirmed HDAC1 occupancy at promoters and other regulatory regions.
Reason: Chromatin binding is well supported by extensive ChIP-seq and ChIP-qPCR data showing HDAC1 occupancy at promoters, enhancers, and heterochromatic regions.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD, Sin3, CoREST, and related chromatin-repressor complexes.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylase that catalyzes the deacetylation of lysine residues on the N-terminal part of the core histones.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein corepressor complexes, especially SIN3, NuRD, and CoREST.
GO:0003714 transcription corepressor activity
IEA
GO_REF:0000107 		ACCEPT
Summary: HDAC1 functions as a transcription corepressor by deacetylating histones at target gene promoters, leading to chromatin compaction and transcriptional silencing.
Reason: Transcription corepressor activity is a core function of HDAC1. It mediates transcriptional repression through histone deacetylation when recruited to target promoters by sequence-specific repressors.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD, Sin3, CoREST, and related chromatin-repressor complexes.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylase that catalyzes the deacetylation of lysine residues on the N-terminal part of the core histones.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein corepressor complexes, especially SIN3, NuRD, and CoREST.
GO:0005654 nucleoplasm
IEA
GO_REF:0000120 		ACCEPT
Summary: HDAC1 is localized to the nucleoplasm where it functions as part of chromatin-modifying complexes.
Reason: Nucleoplasm localization is consistent with HDAC1 function in chromatin modification.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD, Sin3, CoREST, and related chromatin-repressor complexes.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylase that catalyzes the deacetylation of lysine residues on the N-terminal part of the core histones.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
Class I HDACs, including HDAC1, are predominantly or exclusively nuclear, consistent with chromatin accessibility and transcriptional control roles.
GO:0005829 cytosol
IEA
GO_REF:0000107 		KEEP AS NON CORE
Summary: GOA includes a cytosol annotation, but HDAC1 is primarily a nuclear chromatin deacetylase/corepressor-complex subunit.
Reason: Cytosol is, at most, a minor inferred localization and should not be treated as a core HDAC1 cellular-component annotation.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-uniprot.txt
GO; GO:0005829; C:cytosol; ISO:GO_Central.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
Class I HDACs, including HDAC1, are predominantly or exclusively nuclear, consistent with chromatin accessibility and transcriptional control roles.
GO:0006325 chromatin organization
IEA
GO_REF:0000107 		ACCEPT
Summary: HDAC1 plays a role in chromatin organization through histone deacetylation, which promotes nucleosome compaction.
Reason: Chromatin organization is a direct consequence of HDAC1 enzymatic activity.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD, Sin3, CoREST, and related chromatin-repressor complexes.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylase that catalyzes the deacetylation of lysine residues on the N-terminal part of the core histones.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein corepressor complexes, especially SIN3, NuRD, and CoREST.
GO:0006338 chromatin remodeling
IEA
GO_REF:0000107 		ACCEPT
Summary: HDAC1 is a subunit of the NuRD complex which combines histone deacetylation with ATP-dependent nucleosome remodeling (via CHD3/4).
Reason: HDAC1 participates in chromatin remodeling as a component of the NuRD complex.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD, Sin3, CoREST, and related chromatin-repressor complexes.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylase that catalyzes the deacetylation of lysine residues on the N-terminal part of the core histones.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein corepressor complexes, especially SIN3, NuRD, and CoREST.
GO:0006346 DNA methylation-dependent constitutive heterochromatin formation
IEA
GO_REF:0000107 		ACCEPT
Summary: HDAC1 cooperates with DNA methyltransferases (DNMT1, DNMT3A) and methyl-CpG binding proteins to establish constitutive heterochromatin (PMID:10615135).
Reason: HDAC1 interaction with DNMT1 and localization to heterochromatin support its role in DNA methylation-dependent heterochromatin formation.
Supporting Evidence:
PMID:10615135
Here we show that Dnmt1 is itself associated with histone deacetylase activity in vivo
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD, Sin3, CoREST, and related chromatin-repressor complexes.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein corepressor complexes, especially SIN3, NuRD, and CoREST.
GO:0006357 regulation of transcription by RNA polymerase II
IEA
GO_REF:0000107 		ACCEPT
Summary: HDAC1 regulates RNA polymerase II transcription, primarily through repression but also through modulation of chromatin dynamics.
Reason: HDAC1 is clearly involved in regulating pol II transcription. General parent term encompassing both positive and negative regulation.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD, Sin3, CoREST, and related chromatin-repressor complexes.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylase that catalyzes the deacetylation of lysine residues on the N-terminal part of the core histones.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein corepressor complexes, especially SIN3, NuRD, and CoREST.
GO:0008284 positive regulation of cell population proliferation
IEA
GO_REF:0000120 		KEEP AS NON CORE
Summary: HDAC1 promotes cell proliferation by repressing cell cycle inhibitors through the Rb-HDAC1 complex.
Reason: Well-documented pro-proliferative role but downstream biological consequence of deacetylase activity.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 has many developmental and signaling consequences through chromatin deacetylation; these are non-core outputs of the core enzymatic function.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylation gives a tag for epigenetic repression and plays an important role in transcriptional regulation, cell cycle progression and developmental events.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
The report supports HDAC1 as a chromatin deacetylase whose developmental, signaling, cell-cycle, DNA-damage, and pathway phenotypes are context-specific downstream outputs.
GO:0008285 negative regulation of cell population proliferation
IEA
GO_REF:0000107 		KEEP AS NON CORE
Summary: HDAC1 can also negatively regulate cell proliferation in certain contexts.
Reason: Context-dependent downstream effect rather than a core function.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 has many developmental and signaling consequences through chromatin deacetylation; these are non-core outputs of the core enzymatic function.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylation gives a tag for epigenetic repression and plays an important role in transcriptional regulation, cell cycle progression and developmental events.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
The report supports HDAC1 as a chromatin deacetylase whose developmental, signaling, cell-cycle, DNA-damage, and pathway phenotypes are context-specific downstream outputs.
GO:0009410 response to xenobiotic stimulus
IEA
GO_REF:0000107 		KEEP AS NON CORE
Summary: IEA annotation suggesting HDAC1 involvement in xenobiotic response.
Reason: Downstream pleiotropic effect. Not core.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 has many developmental and signaling consequences through chromatin deacetylation; these are non-core outputs of the core enzymatic function.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylation gives a tag for epigenetic repression and plays an important role in transcriptional regulation, cell cycle progression and developmental events.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
The report supports HDAC1 as a chromatin deacetylase whose developmental, signaling, cell-cycle, DNA-damage, and pathway phenotypes are context-specific downstream outputs.
GO:0010628 positive regulation of gene expression
IEA
GO_REF:0000107 		KEEP AS NON CORE
Summary: HDAC1 can positively regulate gene expression in certain contexts, likely through indirect mechanisms.
Reason: Secondary, context-dependent effect. HDAC1 is primarily a repressor.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 has many developmental and signaling consequences through chromatin deacetylation; these are non-core outputs of the core enzymatic function.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylation gives a tag for epigenetic repression and plays an important role in transcriptional regulation, cell cycle progression and developmental events.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
The report supports HDAC1 as a chromatin deacetylase whose developmental, signaling, cell-cycle, DNA-damage, and pathway phenotypes are context-specific downstream outputs.
GO:0010629 negative regulation of gene expression
IEA
GO_REF:0000107 		ACCEPT
Summary: HDAC1 negatively regulates gene expression through histone deacetylation and chromatin compaction.
Reason: Negative regulation of gene expression is a core function of HDAC1.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD, Sin3, CoREST, and related chromatin-repressor complexes.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylase that catalyzes the deacetylation of lysine residues on the N-terminal part of the core histones.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein corepressor complexes, especially SIN3, NuRD, and CoREST.
GO:0016581 NuRD complex
IEA
GO_REF:0000107 		ACCEPT
Summary: HDAC1 is a core catalytic subunit of the NuRD (nucleosome remodeling and deacetylase) complex. Proteomic studies show approximately 49% of cellular HDAC1 in ESCs is in the NuRD complex (deep research review). Well supported by mass spectrometry identification (PMID:27806305) and multiple interaction studies.
Reason: NuRD complex membership is a core aspect of HDAC1 function. HDAC1 serves as the catalytic deacetylase subunit within NuRD. Extensively validated by proteomics and co-immunoprecipitation studies.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD, Sin3, CoREST, and related chromatin-repressor complexes.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylase that catalyzes the deacetylation of lysine residues on the N-terminal part of the core histones.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein corepressor complexes, especially SIN3, NuRD, and CoREST.
GO:0019213 deacetylase activity
IEA
GO_REF:0000107 		ACCEPT
Summary: General deacetylase activity. HDAC1 has broad deacetylase activity on both histone and non-histone substrates.
Reason: HDAC1 has well-established deacetylase activity. While GO:0004407 (histone deacetylase activity) is more specific, this broader term is also correct as HDAC1 can deacetylate non-histone proteins. Acceptable as a parent-level annotation.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD, Sin3, CoREST, and related chromatin-repressor complexes.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylase that catalyzes the deacetylation of lysine residues on the N-terminal part of the core histones.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
HDAC1 is a class I Zn2+-dependent histone/protein deacetylase that removes acetyl groups from lysine residues on histone tails and non-histone proteins.
GO:0019899 enzyme binding
IEA
GO_REF:0000107 		ACCEPT
Summary: HDAC1 binds various enzymes including DNA methyltransferases (DNMT1, DNMT3A), histone methyltransferases (SUV39H1, SETDB1, SMYD2), and kinases.
Reason: HDAC1 interacts with multiple enzymes as part of chromatin-modifying networks. While somewhat general, this captures a real aspect of HDAC1 function.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD, Sin3, CoREST, and related chromatin-repressor complexes.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylase that catalyzes the deacetylation of lysine residues on the N-terminal part of the core histones.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein corepressor complexes, especially SIN3, NuRD, and CoREST.
GO:0031000 response to caffeine
IEA
GO_REF:0000107 		KEEP AS NON CORE
Summary: IEA annotation suggesting HDAC1 involvement in caffeine response.
Reason: Highly specific stimulus-response annotation. Downstream pleiotropic effect.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 has many developmental and signaling consequences through chromatin deacetylation; these are non-core outputs of the core enzymatic function.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylation gives a tag for epigenetic repression and plays an important role in transcriptional regulation, cell cycle progression and developmental events.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
The report supports HDAC1 as a chromatin deacetylase whose developmental, signaling, cell-cycle, DNA-damage, and pathway phenotypes are context-specific downstream outputs.
GO:0032496 response to lipopolysaccharide
IEA
GO_REF:0000107 		KEEP AS NON CORE
Summary: HDAC1 may be involved in LPS response through NF-kappaB signaling regulation.
Reason: Downstream inflammatory pathway effect.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 has many developmental and signaling consequences through chromatin deacetylation; these are non-core outputs of the core enzymatic function.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylation gives a tag for epigenetic repression and plays an important role in transcriptional regulation, cell cycle progression and developmental events.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
The report supports HDAC1 as a chromatin deacetylase whose developmental, signaling, cell-cycle, DNA-damage, and pathway phenotypes are context-specific downstream outputs.
GO:0032732 positive regulation of interleukin-1 production
IEA
GO_REF:0000107 		KEEP AS NON CORE
Summary: IEA annotation for HDAC1 in IL-1 production.
Reason: Downstream immune/inflammatory pathway effect.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 has many developmental and signaling consequences through chromatin deacetylation; these are non-core outputs of the core enzymatic function.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylation gives a tag for epigenetic repression and plays an important role in transcriptional regulation, cell cycle progression and developmental events.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
The report supports HDAC1 as a chromatin deacetylase whose developmental, signaling, cell-cycle, DNA-damage, and pathway phenotypes are context-specific downstream outputs.
GO:0032760 positive regulation of tumor necrosis factor production
IEA
GO_REF:0000107 		KEEP AS NON CORE
Summary: IEA annotation for HDAC1 in TNF production regulation.
Reason: Downstream immune/inflammatory pathway effect.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 has many developmental and signaling consequences through chromatin deacetylation; these are non-core outputs of the core enzymatic function.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylation gives a tag for epigenetic repression and plays an important role in transcriptional regulation, cell cycle progression and developmental events.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
The report supports HDAC1 as a chromatin deacetylase whose developmental, signaling, cell-cycle, DNA-damage, and pathway phenotypes are context-specific downstream outputs.
GO:0032991 protein-containing complex
IEA
GO_REF:0000120 		ACCEPT
Summary: HDAC1 is found in protein-containing complexes (NuRD, SIN3, CoREST). Very general cellular component annotation.
Reason: HDAC1 is found in protein-containing complexes. Correct as a root-level CC annotation alongside more specific complex terms.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD, Sin3, CoREST, and related chromatin-repressor complexes.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylase that catalyzes the deacetylation of lysine residues on the N-terminal part of the core histones.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein corepressor complexes, especially SIN3, NuRD, and CoREST.
GO:0033558 protein lysine deacetylase activity
IEA
GO_REF:0000120 		ACCEPT
Summary: HDAC1 removes acetyl groups from lysine residues on proteins, including both histone and non-histone substrates such as NR1D2, RELA, SP1, SP3, STAT3, ZNF76, and TSHZ3 (UniProt).
Reason: HDAC1 has well-documented protein lysine deacetylase activity on both histone and non-histone targets. This is a core function.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD, Sin3, CoREST, and related chromatin-repressor complexes.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylase that catalyzes the deacetylation of lysine residues on the N-terminal part of the core histones.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
HDAC1 is a class I Zn2+-dependent histone/protein deacetylase that removes acetyl groups from lysine residues on histone tails and non-histone proteins.
GO:0034599 cellular response to oxidative stress
IEA
GO_REF:0000107 		KEEP AS NON CORE
Summary: HDAC1 may participate in cellular response to oxidative stress.
Reason: Downstream context-specific process.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 has many developmental and signaling consequences through chromatin deacetylation; these are non-core outputs of the core enzymatic function.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylation gives a tag for epigenetic repression and plays an important role in transcriptional regulation, cell cycle progression and developmental events.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
The report supports HDAC1 as a chromatin deacetylase whose developmental, signaling, cell-cycle, DNA-damage, and pathway phenotypes are context-specific downstream outputs.
GO:0036120 cellular response to platelet-derived growth factor stimulus
IEA
GO_REF:0000107 		KEEP AS NON CORE
Summary: IEA annotation for HDAC1 in PDGF response.
Reason: Specific growth factor signaling context. Not core.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 has many developmental and signaling consequences through chromatin deacetylation; these are non-core outputs of the core enzymatic function.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylation gives a tag for epigenetic repression and plays an important role in transcriptional regulation, cell cycle progression and developmental events.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
The report supports HDAC1 as a chromatin deacetylase whose developmental, signaling, cell-cycle, DNA-damage, and pathway phenotypes are context-specific downstream outputs.
GO:0042826 histone deacetylase binding
IEA
GO_REF:0000107 		ACCEPT
Summary: HDAC1 binds to other histone deacetylases, particularly HDAC2 (forming heterodimers) and class II HDACs like HDAC7 and HDAC9.
Reason: HDAC1 forms heterodimers with HDAC2 as the catalytic core of NuRD, SIN3, and CoREST complexes. It also interacts with class II HDACs (HDAC7, HDAC9). Well documented.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD, Sin3, CoREST, and related chromatin-repressor complexes.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylase that catalyzes the deacetylation of lysine residues on the N-terminal part of the core histones.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
HDAC1 is a class I Zn2+-dependent histone/protein deacetylase that removes acetyl groups from lysine residues on histone tails and non-histone proteins.
GO:0043524 negative regulation of neuron apoptotic process
IEA
GO_REF:0000107 		KEEP AS NON CORE
Summary: HDAC1 has a neuroprotective role in certain contexts, preventing neuron apoptosis.
Reason: Context-specific downstream effect of HDAC1 in neurons.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 has many developmental and signaling consequences through chromatin deacetylation; these are non-core outputs of the core enzymatic function.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylation gives a tag for epigenetic repression and plays an important role in transcriptional regulation, cell cycle progression and developmental events.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
The report supports HDAC1 as a chromatin deacetylase whose developmental, signaling, cell-cycle, DNA-damage, and pathway phenotypes are context-specific downstream outputs.
GO:0043922 host-mediated suppression of viral transcription
IEA
GO_REF:0000107 		KEEP AS NON CORE
Summary: HDAC1 participates in host-mediated suppression of viral transcription by deacetylating histones at integrated viral promoters.
Reason: Context-specific application of general transcriptional repression function.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 has many developmental and signaling consequences through chromatin deacetylation; these are non-core outputs of the core enzymatic function.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylation gives a tag for epigenetic repression and plays an important role in transcriptional regulation, cell cycle progression and developmental events.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
The report supports HDAC1 as a chromatin deacetylase whose developmental, signaling, cell-cycle, DNA-damage, and pathway phenotypes are context-specific downstream outputs.
GO:0044877 protein-containing complex binding
IEA
GO_REF:0000107 		KEEP AS NON CORE
Summary: HDAC1 functions within protein-containing corepressor complexes, but this binding term is much less informative than the specific NuRD, SIN3, and CoREST complex annotations.
Reason: The annotation is directionally true but too generic to represent the core molecular function; specific complex membership and catalytic terms carry the curatorial signal.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD, Sin3, CoREST, and related chromatin-repressor complexes.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylase that catalyzes the deacetylation of lysine residues on the N-terminal part of the core histones.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein corepressor complexes, especially SIN3, NuRD, and CoREST.
GO:0045814 negative regulation of gene expression, epigenetic
IEA
GO_REF:0000107 		ACCEPT
Summary: HDAC1 mediates epigenetic gene silencing through histone deacetylation.
Reason: HDAC1-mediated histone deacetylation is a classical epigenetic mechanism of gene silencing. Core function.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD, Sin3, CoREST, and related chromatin-repressor complexes.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylase that catalyzes the deacetylation of lysine residues on the N-terminal part of the core histones.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein corepressor complexes, especially SIN3, NuRD, and CoREST.
GO:0045892 negative regulation of DNA-templated transcription
IEA
GO_REF:0000120 		ACCEPT
Summary: HDAC1 negatively regulates DNA-templated transcription through its histone deacetylase activity as part of co-repressor complexes.
Reason: Transcriptional repression is a core function of HDAC1. Well supported by extensive literature.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD, Sin3, CoREST, and related chromatin-repressor complexes.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylase that catalyzes the deacetylation of lysine residues on the N-terminal part of the core histones.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein corepressor complexes, especially SIN3, NuRD, and CoREST.
GO:0045893 positive regulation of DNA-templated transcription
IEA
GO_REF:0000107 		KEEP AS NON CORE
Summary: Although HDAC1 is primarily a transcriptional repressor, it can indirectly promote transcription of certain genes in specific contexts.
Reason: HDAC1 is primarily a repressor, but there is evidence that it can positively regulate transcription indirectly. This is a secondary, context-dependent function.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 has many developmental and signaling consequences through chromatin deacetylation; these are non-core outputs of the core enzymatic function.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylation gives a tag for epigenetic repression and plays an important role in transcriptional regulation, cell cycle progression and developmental events.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
The report supports HDAC1 as a chromatin deacetylase whose developmental, signaling, cell-cycle, DNA-damage, and pathway phenotypes are context-specific downstream outputs.
GO:0045944 positive regulation of transcription by RNA polymerase II
IEA
GO_REF:0000107 		KEEP AS NON CORE
Summary: HDAC1 can positively regulate RNA pol II transcription in certain contexts, likely through indirect mechanisms.
Reason: Not a core function of HDAC1 but documented in specific contexts.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 has many developmental and signaling consequences through chromatin deacetylation; these are non-core outputs of the core enzymatic function.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylation gives a tag for epigenetic repression and plays an important role in transcriptional regulation, cell cycle progression and developmental events.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
The report supports HDAC1 as a chromatin deacetylase whose developmental, signaling, cell-cycle, DNA-damage, and pathway phenotypes are context-specific downstream outputs.
GO:0046676 negative regulation of insulin secretion
IEA
GO_REF:0000107 		KEEP AS NON CORE
Summary: IEA annotation suggesting HDAC1 negatively regulates insulin secretion.
Reason: Downstream metabolic/endocrine effect.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 has many developmental and signaling consequences through chromatin deacetylation; these are non-core outputs of the core enzymatic function.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylation gives a tag for epigenetic repression and plays an important role in transcriptional regulation, cell cycle progression and developmental events.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
The report supports HDAC1 as a chromatin deacetylase whose developmental, signaling, cell-cycle, DNA-damage, and pathway phenotypes are context-specific downstream outputs.
GO:0048471 perinuclear region of cytoplasm
IEA
GO_REF:0000107 		MARK AS OVER ANNOTATED
Summary: Perinuclear cytoplasmic localization is an orthology-derived/minor subcellular annotation, whereas HDAC1's supported role is predominantly nuclear chromatin regulation.
Reason: This weak cytoplasmic sublocalization should not be accepted as a central HDAC1 localization when the evidence supports nuclear chromatin/corepressor complexes.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-uniprot.txt
GO; GO:0048471; C:perinuclear region of cytoplasm; ISO:GO_Central.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
Class I HDACs, including HDAC1, are predominantly or exclusively nuclear, consistent with chromatin accessibility and transcriptional control roles.
GO:0048661 positive regulation of smooth muscle cell proliferation
IEA
GO_REF:0000107 		KEEP AS NON CORE
Summary: IEA annotation for HDAC1 in smooth muscle cell proliferation.
Reason: Specific tissue context. Not core.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 has many developmental and signaling consequences through chromatin deacetylation; these are non-core outputs of the core enzymatic function.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylation gives a tag for epigenetic repression and plays an important role in transcriptional regulation, cell cycle progression and developmental events.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
The report supports HDAC1 as a chromatin deacetylase whose developmental, signaling, cell-cycle, DNA-damage, and pathway phenotypes are context-specific downstream outputs.
GO:0048714 positive regulation of oligodendrocyte differentiation
IEA
GO_REF:0000120 		KEEP AS NON CORE
Summary: HDAC1/2 positively regulate oligodendrocyte differentiation, likely by repressing inhibitors of myelination (PMID:19503085).
Reason: Cell-type-specific developmental process rather than a core function.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 has many developmental and signaling consequences through chromatin deacetylation; these are non-core outputs of the core enzymatic function.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylation gives a tag for epigenetic repression and plays an important role in transcriptional regulation, cell cycle progression and developmental events.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
The report supports HDAC1 as a chromatin deacetylase whose developmental, signaling, cell-cycle, DNA-damage, and pathway phenotypes are context-specific downstream outputs.
GO:0051059 NF-kappaB binding
IEA
GO_REF:0000120 		ACCEPT
Summary: HDAC1 directly binds to the NF-kappaB subunit RelA/p65 and deacetylates it, attenuating NF-kappaB transcriptional activity.
Reason: The HDAC1-NF-kappaB/p65 interaction is directly demonstrated and functionally characterized. HDAC1 deacetylates Lys-310 of RELA, inhibiting NF-kappaB activity (UniProt).
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD, Sin3, CoREST, and related chromatin-repressor complexes.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylase that catalyzes the deacetylation of lysine residues on the N-terminal part of the core histones.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein corepressor complexes, especially SIN3, NuRD, and CoREST.
GO:0055093 response to hyperoxia
IEA
GO_REF:0000107 		KEEP AS NON CORE
Summary: IEA annotation for HDAC1 in hyperoxia response.
Reason: Very specific stress response. Downstream pleiotropic effect.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 has many developmental and signaling consequences through chromatin deacetylation; these are non-core outputs of the core enzymatic function.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylation gives a tag for epigenetic repression and plays an important role in transcriptional regulation, cell cycle progression and developmental events.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
The report supports HDAC1 as a chromatin deacetylase whose developmental, signaling, cell-cycle, DNA-damage, and pathway phenotypes are context-specific downstream outputs.
GO:0060766 negative regulation of androgen receptor signaling pathway
IEA
GO_REF:0000107 		KEEP AS NON CORE
Summary: HDAC1 negatively regulates androgen receptor signaling.
Reason: Specific hormonal signaling context. Not core.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 has many developmental and signaling consequences through chromatin deacetylation; these are non-core outputs of the core enzymatic function.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylation gives a tag for epigenetic repression and plays an important role in transcriptional regulation, cell cycle progression and developmental events.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
The report supports HDAC1 as a chromatin deacetylase whose developmental, signaling, cell-cycle, DNA-damage, and pathway phenotypes are context-specific downstream outputs.
GO:0061629 RNA polymerase II-specific DNA-binding transcription factor binding
IEA
GO_REF:0000107 		ACCEPT
Summary: HDAC1 binds RNA polymerase II-specific transcription factors that recruit it to target genes for transcriptional repression.
Reason: This is a more specific version of DNA-binding transcription factor binding, appropriate given that HDAC1 primarily regulates RNA pol II-transcribed genes through interactions with pol II-specific TFs.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD, Sin3, CoREST, and related chromatin-repressor complexes.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylase that catalyzes the deacetylation of lysine residues on the N-terminal part of the core histones.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein corepressor complexes, especially SIN3, NuRD, and CoREST.
GO:0070822 Sin3-type complex
IEA
GO_REF:0000107 		ACCEPT
Summary: HDAC1 is a core catalytic subunit of the SIN3 co-repressor complex. Approximately 15% of cellular HDAC1 in ESCs is in the SIN3A complex. Confirmed by multiple studies including PMID:11909966 and PMID:28554894.
Reason: SIN3 complex membership is a core function of HDAC1. The SIN3-HDAC complex is one of the three major HDAC1-containing co-repressor complexes.
Supporting Evidence:
PMID:28554894
Sin3a is the central scaffold protein of the prototypical Hdac1/2 chromatin repressor complex
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD, Sin3, CoREST, and related chromatin-repressor complexes.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein corepressor complexes, especially SIN3, NuRD, and CoREST.
GO:0071356 cellular response to tumor necrosis factor
IEA
GO_REF:0000107 		KEEP AS NON CORE
Summary: HDAC1 participates in TNF response, potentially through NF-kappaB regulation.
Reason: Downstream inflammatory signaling context.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 has many developmental and signaling consequences through chromatin deacetylation; these are non-core outputs of the core enzymatic function.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylation gives a tag for epigenetic repression and plays an important role in transcriptional regulation, cell cycle progression and developmental events.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
The report supports HDAC1 as a chromatin deacetylase whose developmental, signaling, cell-cycle, DNA-damage, and pathway phenotypes are context-specific downstream outputs.
GO:0090090 negative regulation of canonical Wnt signaling pathway
IEA
GO_REF:0000107 		KEEP AS NON CORE
Summary: HDAC1/2 negatively regulate canonical Wnt signaling by deacetylating histones at Wnt target gene promoters. Demonstrated in neural development.
Reason: Well-supported role in neural development but represents a downstream biological consequence rather than a core molecular function.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 has many developmental and signaling consequences through chromatin deacetylation; these are non-core outputs of the core enzymatic function.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylation gives a tag for epigenetic repression and plays an important role in transcriptional regulation, cell cycle progression and developmental events.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
The report supports HDAC1 as a chromatin deacetylase whose developmental, signaling, cell-cycle, DNA-damage, and pathway phenotypes are context-specific downstream outputs.
GO:0140297 DNA-binding transcription factor binding
IEA
GO_REF:0000120 		ACCEPT
Summary: HDAC1 binds numerous DNA-binding transcription factors as part of its recruitment to target genes. Documented interactions include MyoD, YY1, KLF1, NR4A2, INSM1, and many others.
Reason: HDAC1 interaction with DNA-binding transcription factors is central to its biological function - this is how it is recruited to specific genomic loci.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD, Sin3, CoREST, and related chromatin-repressor complexes.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylase that catalyzes the deacetylation of lysine residues on the N-terminal part of the core histones.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein corepressor complexes, especially SIN3, NuRD, and CoREST.
GO:0160009 histone decrotonylase activity
IEA
GO_REF:0000120 		ACCEPT
Summary: HDAC1 can remove crotonyl modifications from histone lysine residues. Directly demonstrated by Kelly et al. (PMID:30279482) showing HDAC1/2 complexes are important histone decrotonylases in vivo.
Reason: Directly supported by experimental evidence. Genetic deletion of HDAC1/2 in ES cells increases global histone crotonylation and causes an 85% reduction in total decrotonylase activity (PMID:30279482).
Supporting Evidence:
PMID:30279482
Genetic deletion of HDAC1/2 in ES cells increases global levels of histone crotonylation and causes an 85% reduction in total decrotonylase activity
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD, Sin3, CoREST, and related chromatin-repressor complexes.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein corepressor complexes, especially SIN3, NuRD, and CoREST.
GO:0160216 protein lysine delactylase activity
IEA
GO_REF:0000120 		KEEP AS NON CORE
Summary: UniProt/GOA includes protein lysine delactylase activity for HDAC1, but this row is similarity-based; the accessible experimental paper supports HDAC1/2 decrotonylase activity, not direct mouse delactylase activity.
Reason: Do not treat delactylase activity as a direct/core Hdac1 function here. The stronger experimental support is for histone deacetylase and decrotonylase activity.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-uniprot.txt
GO; GO:0160216; F:protein lysine delactylase activity; ISS:UniProtKB.
PMID:30279482
A ternary complex of HDAC1/CoREST1/LSD1 is able to hydrolyse both histone H3 Lys18-acetyl (H3K18ac) and H3 Lys18-crotonyl (H3K18cr) peptide substrates
GO:2000343 positive regulation of chemokine (C-X-C motif) ligand 2 production
IEA
GO_REF:0000107 		KEEP AS NON CORE
Summary: IEA annotation for HDAC1 in CXCL2 production.
Reason: Downstream immune/inflammatory pathway effect.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 has many developmental and signaling consequences through chromatin deacetylation; these are non-core outputs of the core enzymatic function.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylation gives a tag for epigenetic repression and plays an important role in transcriptional regulation, cell cycle progression and developmental events.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
The report supports HDAC1 as a chromatin deacetylase whose developmental, signaling, cell-cycle, DNA-damage, and pathway phenotypes are context-specific downstream outputs.
GO:2000676 positive regulation of type B pancreatic cell apoptotic process
IEA
GO_REF:0000107 		KEEP AS NON CORE
Summary: IEA annotation for HDAC1 in beta cell apoptosis.
Reason: Very specific downstream effect in pancreatic biology.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 has many developmental and signaling consequences through chromatin deacetylation; these are non-core outputs of the core enzymatic function.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylation gives a tag for epigenetic repression and plays an important role in transcriptional regulation, cell cycle progression and developmental events.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
The report supports HDAC1 as a chromatin deacetylase whose developmental, signaling, cell-cycle, DNA-damage, and pathway phenotypes are context-specific downstream outputs.
GO:0032991 protein-containing complex
ISO
GO_REF:0000096 		ACCEPT
Summary: HDAC1 is found in protein-containing complexes (NuRD, SIN3, CoREST). Very general cellular component annotation.
Reason: HDAC1 is found in protein-containing complexes. Correct as a root-level CC annotation alongside more specific complex terms.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD, Sin3, CoREST, and related chromatin-repressor complexes.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylase that catalyzes the deacetylation of lysine residues on the N-terminal part of the core histones.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein corepressor complexes, especially SIN3, NuRD, and CoREST.
GO:1990904 ribonucleoprotein complex
IDA
PMID:21874018
lincRNAs act in the circuitry controlling pluripotency and d... 		KEEP AS NON CORE
Summary: HDAC1 was detected in lincRNA-associated chromatin regulatory complexes in mouse ESCs, supporting a non-core ribonucleoprotein-complex context rather than a primary HDAC1 cellular component.
Reason: The cited study shows HDAC1-containing chromatin regulatory complexes can associate with lincRNAs, but HDAC1 is primarily a nuclear deacetylase in NuRD/SIN3/CoREST and related complexes.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 has many developmental and signaling consequences through chromatin deacetylation; these are non-core outputs of the core enzymatic function.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylation gives a tag for epigenetic repression and plays an important role in transcriptional regulation, cell cycle progression and developmental events.
PMID:21874018
and HDAC1) histone modifications, as well as a chromatin-associated DNA binding protein (YY1)
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
PMID:21874018 supports HDAC1 association with lincRNA-containing chromatin regulatory complexes in mouse ESCs, but this is a non-core context relative to HDAC1 deacetylase and chromatin-complex functions.
GO:0006325 chromatin organization
ISO
GO_REF:0000119 		ACCEPT
Summary: HDAC1 plays a role in chromatin organization through histone deacetylation, which promotes nucleosome compaction.
Reason: Chromatin organization is a direct consequence of HDAC1 enzymatic activity.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD, Sin3, CoREST, and related chromatin-repressor complexes.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylase that catalyzes the deacetylation of lysine residues on the N-terminal part of the core histones.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein corepressor complexes, especially SIN3, NuRD, and CoREST.
GO:0017053 transcription repressor complex
ISO
GO_REF:0000119 		ACCEPT
Summary: HDAC1 functions within transcription repressor complexes including NuRD, SIN3, and CoREST, which mediate transcriptional repression through histone deacetylation.
Reason: HDAC1 is a core catalytic subunit of several transcription repressor complexes. This is a correct and informative annotation.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD, Sin3, CoREST, and related chromatin-repressor complexes.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylase that catalyzes the deacetylation of lysine residues on the N-terminal part of the core histones.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein corepressor complexes, especially SIN3, NuRD, and CoREST.
GO:0000118 histone deacetylase complex
ISO
GO_REF:0000119 		ACCEPT
Summary: HDAC1 is a core component of multiple histone deacetylase complexes including NuRD, SIN3, and CoREST. This is a general parent term encompassing all such complexes.
Reason: HDAC1 is the defining catalytic subunit of multiple HDAC complexes. This broader term is appropriate as a parent annotation alongside the more specific NuRD and SIN3 complex terms.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD, Sin3, CoREST, and related chromatin-repressor complexes.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylase that catalyzes the deacetylation of lysine residues on the N-terminal part of the core histones.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
HDAC1 is a class I Zn2+-dependent histone/protein deacetylase that removes acetyl groups from lysine residues on histone tails and non-histone proteins.
GO:0000122 negative regulation of transcription by RNA polymerase II
ISO
GO_REF:0000119 		ACCEPT
Summary: HDAC1 negatively regulates transcription by RNA polymerase II through histone deacetylation at target gene promoters. This is a core biological process annotation for HDAC1.
Reason: Negative regulation of pol II transcription is a primary biological function of HDAC1. Supported by multiple lines of evidence (PMID:8917507, PMID:9271381, PMID:21093383).
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD, Sin3, CoREST, and related chromatin-repressor complexes.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylase that catalyzes the deacetylation of lysine residues on the N-terminal part of the core histones.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein corepressor complexes, especially SIN3, NuRD, and CoREST.
GO:0000785 chromatin
ISO
GO_REF:0000096 		ACCEPT
Summary: HDAC1 is a chromatin-associated protein that modifies histone tails as part of co-repressor complexes.
Reason: HDAC1 is a histone-modifying enzyme that directly acts on chromatin. Association with chromatin is inherent to its function.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD, Sin3, CoREST, and related chromatin-repressor complexes.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylase that catalyzes the deacetylation of lysine residues on the N-terminal part of the core histones.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein corepressor complexes, especially SIN3, NuRD, and CoREST.
GO:0000785 chromatin
ISO
GO_REF:0000119 		ACCEPT
Summary: HDAC1 is a chromatin-associated protein that modifies histone tails as part of co-repressor complexes.
Reason: HDAC1 is a histone-modifying enzyme that directly acts on chromatin. Association with chromatin is inherent to its function.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD, Sin3, CoREST, and related chromatin-repressor complexes.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylase that catalyzes the deacetylation of lysine residues on the N-terminal part of the core histones.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein corepressor complexes, especially SIN3, NuRD, and CoREST.
GO:0000978 RNA polymerase II cis-regulatory region sequence-specific DNA binding
ISO
GO_REF:0000119 		MODIFY
Summary: Annotation suggests HDAC1 has sequence-specific DNA binding at RNA pol II cis-regulatory regions. However, HDAC1 does not have intrinsic sequence-specific DNA binding - it is recruited to promoters by transcription factors.
Reason: Replace direct sequence-specific DNA binding with promoter-specific chromatin binding, which captures HDAC1 recruitment to promoter chromatin without implying intrinsic DNA-binding specificity.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 is recruited to chromatin by DNA-binding factors but is not itself a sequence-specific DNA-binding transcription factor.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylase that catalyzes the deacetylation of lysine residues on core histones.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
The report supports HDAC1 as a chromatin deacetylase whose developmental, signaling, cell-cycle, DNA-damage, and pathway phenotypes are context-specific downstream outputs.
GO:0000979 RNA polymerase II core promoter sequence-specific DNA binding
ISO
GO_REF:0000119 		MODIFY
Summary: This implies sequence-specific core promoter DNA binding by HDAC1, which is not supported. HDAC1 is recruited to core promoters via protein-protein interactions.
Reason: Replace direct sequence-specific DNA binding with promoter-specific chromatin binding, which captures HDAC1 recruitment to promoter chromatin without implying intrinsic DNA-binding specificity.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 is recruited to chromatin by DNA-binding factors but is not itself a sequence-specific DNA-binding transcription factor.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylase that catalyzes the deacetylation of lysine residues on core histones.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
The report supports HDAC1 as a chromatin deacetylase whose developmental, signaling, cell-cycle, DNA-damage, and pathway phenotypes are context-specific downstream outputs.
GO:0001046 core promoter sequence-specific DNA binding
ISO
GO_REF:0000119 		MODIFY
Summary: This implies HDAC1 has core promoter sequence-specific DNA binding, which is not supported by its known biochemistry.
Reason: Replace direct sequence-specific DNA binding with promoter-specific chromatin binding, which captures HDAC1 recruitment to promoter chromatin without implying intrinsic DNA-binding specificity.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 is recruited to chromatin by DNA-binding factors but is not itself a sequence-specific DNA-binding transcription factor.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylase that catalyzes the deacetylation of lysine residues on core histones.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
The report supports HDAC1 as a chromatin deacetylase whose developmental, signaling, cell-cycle, DNA-damage, and pathway phenotypes are context-specific downstream outputs.
GO:0001222 transcription corepressor binding
ISO
GO_REF:0000119 		ACCEPT
Summary: HDAC1 binds to transcription corepressors including SIN3A, SIN3B, CoREST, NCoR, and SMRT as part of its recruitment to target genes.
Reason: HDAC1 physically interacts with multiple corepressor scaffold proteins. This binding is essential for its function in transcriptional repression complexes.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD, Sin3, CoREST, and related chromatin-repressor complexes.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylase that catalyzes the deacetylation of lysine residues on the N-terminal part of the core histones.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein corepressor complexes, especially SIN3, NuRD, and CoREST.
GO:0002039 p53 binding
ISO
GO_REF:0000119 		ACCEPT
Summary: HDAC1 binds to and deacetylates the tumor suppressor p53, thereby modulating its activity and stability.
Reason: HDAC1 interaction with p53 is well established. HDAC1 deacetylates p53, leading to its inactivation and degradation. Functionally relevant interaction.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD, Sin3, CoREST, and related chromatin-repressor complexes.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylase that catalyzes the deacetylation of lysine residues on the N-terminal part of the core histones.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein corepressor complexes, especially SIN3, NuRD, and CoREST.
GO:0003682 chromatin binding
ISO
GO_REF:0000096 		ACCEPT
Summary: HDAC1 binds chromatin as part of its function in co-repressor complexes. ChIP experiments have confirmed HDAC1 occupancy at promoters and other regulatory regions.
Reason: Chromatin binding is well supported by extensive ChIP-seq and ChIP-qPCR data showing HDAC1 occupancy at promoters, enhancers, and heterochromatic regions.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD, Sin3, CoREST, and related chromatin-repressor complexes.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylase that catalyzes the deacetylation of lysine residues on the N-terminal part of the core histones.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein corepressor complexes, especially SIN3, NuRD, and CoREST.
GO:0003714 transcription corepressor activity
ISO
GO_REF:0000119 		ACCEPT
Summary: HDAC1 functions as a transcription corepressor by deacetylating histones at target gene promoters, leading to chromatin compaction and transcriptional silencing.
Reason: Transcription corepressor activity is a core function of HDAC1. It mediates transcriptional repression through histone deacetylation when recruited to target promoters by sequence-specific repressors.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD, Sin3, CoREST, and related chromatin-repressor complexes.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylase that catalyzes the deacetylation of lysine residues on the N-terminal part of the core histones.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein corepressor complexes, especially SIN3, NuRD, and CoREST.
GO:0004407 histone deacetylase activity
ISO
GO_REF:0000119 		ACCEPT
Summary: HDAC1 is a zinc-dependent histone deacetylase (EC 3.5.1.98) that catalyzes removal of acetyl groups from N-acetyl-lysine residues on histones H2A, H2B, H3, and H4. This is the core enzymatic function of HDAC1, well established by direct biochemical assays (PMID:10615135, PMID:21960634, PMID:30279482).
Reason: Histone deacetylase activity is the primary enzymatic function of HDAC1, supported by multiple direct experimental studies demonstrating catalytic activity on histone substrates.
Supporting Evidence:
PMID:10615135
Here we show that Dnmt1 is itself associated with histone deacetylase activity in vivo
PMID:30279482
A ternary complex of HDAC1/CoREST1/LSD1 is able to hydrolyse both histone H3 Lys18-acetyl (H3K18ac) and H3 Lys18-crotonyl (H3K18cr) peptide substrates
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD, Sin3, CoREST, and related chromatin-repressor complexes.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
HDAC1 is a class I Zn2+-dependent histone/protein deacetylase that removes acetyl groups from lysine residues on histone tails and non-histone proteins.
GO:0005634 nucleus
ISO
GO_REF:0000096 		ACCEPT
Summary: HDAC1 is predominantly nuclear, consistent with its function in chromatin modification and transcriptional regulation. Nuclear localization confirmed by multiple methods including immunofluorescence (PMID:11115394).
Reason: Nuclear localization is a well-established core feature of HDAC1. It is a Class I HDAC that is predominantly nuclear.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD, Sin3, CoREST, and related chromatin-repressor complexes.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylase that catalyzes the deacetylation of lysine residues on the N-terminal part of the core histones.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
Class I HDACs, including HDAC1, are predominantly or exclusively nuclear, consistent with chromatin accessibility and transcriptional control roles.
GO:0005634 nucleus
ISO
GO_REF:0000119 		ACCEPT
Summary: HDAC1 is predominantly nuclear, consistent with its function in chromatin modification and transcriptional regulation. Nuclear localization confirmed by multiple methods including immunofluorescence (PMID:11115394).
Reason: Nuclear localization is a well-established core feature of HDAC1. It is a Class I HDAC that is predominantly nuclear.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD, Sin3, CoREST, and related chromatin-repressor complexes.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylase that catalyzes the deacetylation of lysine residues on the N-terminal part of the core histones.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
Class I HDACs, including HDAC1, are predominantly or exclusively nuclear, consistent with chromatin accessibility and transcriptional control roles.
GO:0005654 nucleoplasm
ISO
GO_REF:0000119 		ACCEPT
Summary: HDAC1 is localized to the nucleoplasm where it functions as part of chromatin-modifying complexes.
Reason: Nucleoplasm localization is consistent with HDAC1 function in chromatin modification.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD, Sin3, CoREST, and related chromatin-repressor complexes.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylase that catalyzes the deacetylation of lysine residues on the N-terminal part of the core histones.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
Class I HDACs, including HDAC1, are predominantly or exclusively nuclear, consistent with chromatin accessibility and transcriptional control roles.
GO:0005829 cytosol
ISO
GO_REF:0000119 		KEEP AS NON CORE
Summary: GOA includes a cytosol annotation, but HDAC1 is primarily a nuclear chromatin deacetylase/corepressor-complex subunit.
Reason: Cytosol is, at most, a minor inferred localization and should not be treated as a core HDAC1 cellular-component annotation.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-uniprot.txt
GO; GO:0005829; C:cytosol; ISO:GO_Central.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
Class I HDACs, including HDAC1, are predominantly or exclusively nuclear, consistent with chromatin accessibility and transcriptional control roles.
GO:0006338 chromatin remodeling
ISO
GO_REF:0000119 		ACCEPT
Summary: HDAC1 is a subunit of the NuRD complex which combines histone deacetylation with ATP-dependent nucleosome remodeling (via CHD3/4).
Reason: HDAC1 participates in chromatin remodeling as a component of the NuRD complex.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD, Sin3, CoREST, and related chromatin-repressor complexes.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylase that catalyzes the deacetylation of lysine residues on the N-terminal part of the core histones.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein corepressor complexes, especially SIN3, NuRD, and CoREST.
GO:0006346 DNA methylation-dependent constitutive heterochromatin formation
ISO
GO_REF:0000119 		ACCEPT
Summary: HDAC1 cooperates with DNA methyltransferases (DNMT1, DNMT3A) and methyl-CpG binding proteins to establish constitutive heterochromatin (PMID:10615135).
Reason: HDAC1 interaction with DNMT1 and localization to heterochromatin support its role in DNA methylation-dependent heterochromatin formation.
Supporting Evidence:
PMID:10615135
Here we show that Dnmt1 is itself associated with histone deacetylase activity in vivo
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD, Sin3, CoREST, and related chromatin-repressor complexes.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein corepressor complexes, especially SIN3, NuRD, and CoREST.
GO:0006357 regulation of transcription by RNA polymerase II
ISO
GO_REF:0000119 		ACCEPT
Summary: HDAC1 regulates RNA polymerase II transcription, primarily through repression but also through modulation of chromatin dynamics.
Reason: HDAC1 is clearly involved in regulating pol II transcription. General parent term encompassing both positive and negative regulation.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD, Sin3, CoREST, and related chromatin-repressor complexes.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylase that catalyzes the deacetylation of lysine residues on the N-terminal part of the core histones.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein corepressor complexes, especially SIN3, NuRD, and CoREST.
GO:0008284 positive regulation of cell population proliferation
ISO
GO_REF:0000119 		KEEP AS NON CORE
Summary: HDAC1 promotes cell proliferation by repressing cell cycle inhibitors through the Rb-HDAC1 complex.
Reason: Well-documented pro-proliferative role but downstream biological consequence of deacetylase activity.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 has many developmental and signaling consequences through chromatin deacetylation; these are non-core outputs of the core enzymatic function.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylation gives a tag for epigenetic repression and plays an important role in transcriptional regulation, cell cycle progression and developmental events.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
The report supports HDAC1 as a chromatin deacetylase whose developmental, signaling, cell-cycle, DNA-damage, and pathway phenotypes are context-specific downstream outputs.
GO:0010629 negative regulation of gene expression
ISO
GO_REF:0000119 		ACCEPT
Summary: HDAC1 negatively regulates gene expression through histone deacetylation and chromatin compaction.
Reason: Negative regulation of gene expression is a core function of HDAC1.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD, Sin3, CoREST, and related chromatin-repressor complexes.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylase that catalyzes the deacetylation of lysine residues on the N-terminal part of the core histones.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein corepressor complexes, especially SIN3, NuRD, and CoREST.
GO:0016581 NuRD complex
ISO
GO_REF:0000119 		ACCEPT
Summary: HDAC1 is a core catalytic subunit of the NuRD (nucleosome remodeling and deacetylase) complex. Proteomic studies show approximately 49% of cellular HDAC1 in ESCs is in the NuRD complex (deep research review). Well supported by mass spectrometry identification (PMID:27806305) and multiple interaction studies.
Reason: NuRD complex membership is a core aspect of HDAC1 function. HDAC1 serves as the catalytic deacetylase subunit within NuRD. Extensively validated by proteomics and co-immunoprecipitation studies.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD, Sin3, CoREST, and related chromatin-repressor complexes.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylase that catalyzes the deacetylation of lysine residues on the N-terminal part of the core histones.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein corepressor complexes, especially SIN3, NuRD, and CoREST.
GO:0019213 deacetylase activity
ISO
GO_REF:0000096 		ACCEPT
Summary: General deacetylase activity. HDAC1 has broad deacetylase activity on both histone and non-histone substrates.
Reason: HDAC1 has well-established deacetylase activity. While GO:0004407 (histone deacetylase activity) is more specific, this broader term is also correct as HDAC1 can deacetylate non-histone proteins. Acceptable as a parent-level annotation.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD, Sin3, CoREST, and related chromatin-repressor complexes.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylase that catalyzes the deacetylation of lysine residues on the N-terminal part of the core histones.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
HDAC1 is a class I Zn2+-dependent histone/protein deacetylase that removes acetyl groups from lysine residues on histone tails and non-histone proteins.
GO:0019899 enzyme binding
ISO
GO_REF:0000119 		ACCEPT
Summary: HDAC1 binds various enzymes including DNA methyltransferases (DNMT1, DNMT3A), histone methyltransferases (SUV39H1, SETDB1, SMYD2), and kinases.
Reason: HDAC1 interacts with multiple enzymes as part of chromatin-modifying networks. While somewhat general, this captures a real aspect of HDAC1 function.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD, Sin3, CoREST, and related chromatin-repressor complexes.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylase that catalyzes the deacetylation of lysine residues on the N-terminal part of the core histones.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein corepressor complexes, especially SIN3, NuRD, and CoREST.
GO:0032991 protein-containing complex
ISO
GO_REF:0000119 		ACCEPT
Summary: HDAC1 is found in protein-containing complexes (NuRD, SIN3, CoREST). Very general cellular component annotation.
Reason: HDAC1 is found in protein-containing complexes. Correct as a root-level CC annotation alongside more specific complex terms.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD, Sin3, CoREST, and related chromatin-repressor complexes.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylase that catalyzes the deacetylation of lysine residues on the N-terminal part of the core histones.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein corepressor complexes, especially SIN3, NuRD, and CoREST.
GO:0033148 positive regulation of intracellular estrogen receptor signaling pathway
ISO
GO_REF:0000119 		KEEP AS NON CORE
Summary: HDAC1 positively regulates estrogen receptor signaling. HDAC1 interacts with PHB2/REA (PMID:15140878, UniProt).
Reason: Specific hormonal signaling context.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 has many developmental and signaling consequences through chromatin deacetylation; these are non-core outputs of the core enzymatic function.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylation gives a tag for epigenetic repression and plays an important role in transcriptional regulation, cell cycle progression and developmental events.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
The report supports HDAC1 as a chromatin deacetylase whose developmental, signaling, cell-cycle, DNA-damage, and pathway phenotypes are context-specific downstream outputs.
GO:0033558 protein lysine deacetylase activity
ISO
GO_REF:0000119 		ACCEPT
Summary: HDAC1 removes acetyl groups from lysine residues on proteins, including both histone and non-histone substrates such as NR1D2, RELA, SP1, SP3, STAT3, ZNF76, and TSHZ3 (UniProt).
Reason: HDAC1 has well-documented protein lysine deacetylase activity on both histone and non-histone targets. This is a core function.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD, Sin3, CoREST, and related chromatin-repressor complexes.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylase that catalyzes the deacetylation of lysine residues on the N-terminal part of the core histones.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
HDAC1 is a class I Zn2+-dependent histone/protein deacetylase that removes acetyl groups from lysine residues on histone tails and non-histone proteins.
GO:0042826 histone deacetylase binding
ISO
GO_REF:0000119 		ACCEPT
Summary: HDAC1 binds to other histone deacetylases, particularly HDAC2 (forming heterodimers) and class II HDACs like HDAC7 and HDAC9.
Reason: HDAC1 forms heterodimers with HDAC2 as the catalytic core of NuRD, SIN3, and CoREST complexes. It also interacts with class II HDACs (HDAC7, HDAC9). Well documented.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD, Sin3, CoREST, and related chromatin-repressor complexes.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylase that catalyzes the deacetylation of lysine residues on the N-terminal part of the core histones.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
HDAC1 is a class I Zn2+-dependent histone/protein deacetylase that removes acetyl groups from lysine residues on histone tails and non-histone proteins.
GO:0043922 host-mediated suppression of viral transcription
ISO
GO_REF:0000119 		KEEP AS NON CORE
Summary: HDAC1 participates in host-mediated suppression of viral transcription by deacetylating histones at integrated viral promoters.
Reason: Context-specific application of general transcriptional repression function.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 has many developmental and signaling consequences through chromatin deacetylation; these are non-core outputs of the core enzymatic function.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylation gives a tag for epigenetic repression and plays an important role in transcriptional regulation, cell cycle progression and developmental events.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
The report supports HDAC1 as a chromatin deacetylase whose developmental, signaling, cell-cycle, DNA-damage, and pathway phenotypes are context-specific downstream outputs.
GO:0044877 protein-containing complex binding
ISO
GO_REF:0000096 		KEEP AS NON CORE
Summary: HDAC1 functions within protein-containing corepressor complexes, but this binding term is much less informative than the specific NuRD, SIN3, and CoREST complex annotations.
Reason: The annotation is directionally true but too generic to represent the core molecular function; specific complex membership and catalytic terms carry the curatorial signal.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD, Sin3, CoREST, and related chromatin-repressor complexes.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylase that catalyzes the deacetylation of lysine residues on the N-terminal part of the core histones.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein corepressor complexes, especially SIN3, NuRD, and CoREST.
GO:0045814 negative regulation of gene expression, epigenetic
ISO
GO_REF:0000119 		ACCEPT
Summary: HDAC1 mediates epigenetic gene silencing through histone deacetylation.
Reason: HDAC1-mediated histone deacetylation is a classical epigenetic mechanism of gene silencing. Core function.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD, Sin3, CoREST, and related chromatin-repressor complexes.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylase that catalyzes the deacetylation of lysine residues on the N-terminal part of the core histones.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein corepressor complexes, especially SIN3, NuRD, and CoREST.
GO:0045892 negative regulation of DNA-templated transcription
ISO
GO_REF:0000119 		ACCEPT
Summary: HDAC1 negatively regulates DNA-templated transcription through its histone deacetylase activity as part of co-repressor complexes.
Reason: Transcriptional repression is a core function of HDAC1. Well supported by extensive literature.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD, Sin3, CoREST, and related chromatin-repressor complexes.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylase that catalyzes the deacetylation of lysine residues on the N-terminal part of the core histones.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein corepressor complexes, especially SIN3, NuRD, and CoREST.
GO:0045893 positive regulation of DNA-templated transcription
ISO
GO_REF:0000119 		KEEP AS NON CORE
Summary: Although HDAC1 is primarily a transcriptional repressor, it can indirectly promote transcription of certain genes in specific contexts.
Reason: HDAC1 is primarily a repressor, but there is evidence that it can positively regulate transcription indirectly. This is a secondary, context-dependent function.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 has many developmental and signaling consequences through chromatin deacetylation; these are non-core outputs of the core enzymatic function.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylation gives a tag for epigenetic repression and plays an important role in transcriptional regulation, cell cycle progression and developmental events.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
The report supports HDAC1 as a chromatin deacetylase whose developmental, signaling, cell-cycle, DNA-damage, and pathway phenotypes are context-specific downstream outputs.
GO:0045944 positive regulation of transcription by RNA polymerase II
ISO
GO_REF:0000119 		KEEP AS NON CORE
Summary: HDAC1 can positively regulate RNA pol II transcription in certain contexts, likely through indirect mechanisms.
Reason: Not a core function of HDAC1 but documented in specific contexts.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 has many developmental and signaling consequences through chromatin deacetylation; these are non-core outputs of the core enzymatic function.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylation gives a tag for epigenetic repression and plays an important role in transcriptional regulation, cell cycle progression and developmental events.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
The report supports HDAC1 as a chromatin deacetylase whose developmental, signaling, cell-cycle, DNA-damage, and pathway phenotypes are context-specific downstream outputs.
GO:0048471 perinuclear region of cytoplasm
ISO
GO_REF:0000096 		MARK AS OVER ANNOTATED
Summary: Perinuclear cytoplasmic localization is an orthology-derived/minor subcellular annotation, whereas HDAC1's supported role is predominantly nuclear chromatin regulation.
Reason: This weak cytoplasmic sublocalization should not be accepted as a central HDAC1 localization when the evidence supports nuclear chromatin/corepressor complexes.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-uniprot.txt
GO; GO:0048471; C:perinuclear region of cytoplasm; ISO:GO_Central.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
Class I HDACs, including HDAC1, are predominantly or exclusively nuclear, consistent with chromatin accessibility and transcriptional control roles.
GO:0051059 NF-kappaB binding
ISO
GO_REF:0000119 		ACCEPT
Summary: HDAC1 directly binds to the NF-kappaB subunit RelA/p65 and deacetylates it, attenuating NF-kappaB transcriptional activity.
Reason: The HDAC1-NF-kappaB/p65 interaction is directly demonstrated and functionally characterized. HDAC1 deacetylates Lys-310 of RELA, inhibiting NF-kappaB activity (UniProt).
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD, Sin3, CoREST, and related chromatin-repressor complexes.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylase that catalyzes the deacetylation of lysine residues on the N-terminal part of the core histones.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein corepressor complexes, especially SIN3, NuRD, and CoREST.
GO:0060766 negative regulation of androgen receptor signaling pathway
ISO
GO_REF:0000119 		KEEP AS NON CORE
Summary: HDAC1 negatively regulates androgen receptor signaling.
Reason: Specific hormonal signaling context. Not core.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 has many developmental and signaling consequences through chromatin deacetylation; these are non-core outputs of the core enzymatic function.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylation gives a tag for epigenetic repression and plays an important role in transcriptional regulation, cell cycle progression and developmental events.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
The report supports HDAC1 as a chromatin deacetylase whose developmental, signaling, cell-cycle, DNA-damage, and pathway phenotypes are context-specific downstream outputs.
GO:0061629 RNA polymerase II-specific DNA-binding transcription factor binding
ISO
GO_REF:0000119 		ACCEPT
Summary: HDAC1 binds RNA polymerase II-specific transcription factors that recruit it to target genes for transcriptional repression.
Reason: This is a more specific version of DNA-binding transcription factor binding, appropriate given that HDAC1 primarily regulates RNA pol II-transcribed genes through interactions with pol II-specific TFs.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD, Sin3, CoREST, and related chromatin-repressor complexes.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylase that catalyzes the deacetylation of lysine residues on the N-terminal part of the core histones.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein corepressor complexes, especially SIN3, NuRD, and CoREST.
GO:0070822 Sin3-type complex
ISO
GO_REF:0000119 		ACCEPT
Summary: HDAC1 is a core catalytic subunit of the SIN3 co-repressor complex. Approximately 15% of cellular HDAC1 in ESCs is in the SIN3A complex. Confirmed by multiple studies including PMID:11909966 and PMID:28554894.
Reason: SIN3 complex membership is a core function of HDAC1. The SIN3-HDAC complex is one of the three major HDAC1-containing co-repressor complexes.
Supporting Evidence:
PMID:28554894
Sin3a is the central scaffold protein of the prototypical Hdac1/2 chromatin repressor complex
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD, Sin3, CoREST, and related chromatin-repressor complexes.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein corepressor complexes, especially SIN3, NuRD, and CoREST.
GO:0090090 negative regulation of canonical Wnt signaling pathway
ISO
GO_REF:0000119 		KEEP AS NON CORE
Summary: HDAC1/2 negatively regulate canonical Wnt signaling by deacetylating histones at Wnt target gene promoters. Demonstrated in neural development.
Reason: Well-supported role in neural development but represents a downstream biological consequence rather than a core molecular function.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 has many developmental and signaling consequences through chromatin deacetylation; these are non-core outputs of the core enzymatic function.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylation gives a tag for epigenetic repression and plays an important role in transcriptional regulation, cell cycle progression and developmental events.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
The report supports HDAC1 as a chromatin deacetylase whose developmental, signaling, cell-cycle, DNA-damage, and pathway phenotypes are context-specific downstream outputs.
GO:0140297 DNA-binding transcription factor binding
ISO
GO_REF:0000096 		ACCEPT
Summary: HDAC1 binds numerous DNA-binding transcription factors as part of its recruitment to target genes. Documented interactions include MyoD, YY1, KLF1, NR4A2, INSM1, and many others.
Reason: HDAC1 interaction with DNA-binding transcription factors is central to its biological function - this is how it is recruited to specific genomic loci.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD, Sin3, CoREST, and related chromatin-repressor complexes.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylase that catalyzes the deacetylation of lysine residues on the N-terminal part of the core histones.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein corepressor complexes, especially SIN3, NuRD, and CoREST.
GO:0140297 DNA-binding transcription factor binding
ISO
GO_REF:0000119 		ACCEPT
Summary: HDAC1 binds numerous DNA-binding transcription factors as part of its recruitment to target genes. Documented interactions include MyoD, YY1, KLF1, NR4A2, INSM1, and many others.
Reason: HDAC1 interaction with DNA-binding transcription factors is central to its biological function - this is how it is recruited to specific genomic loci.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD, Sin3, CoREST, and related chromatin-repressor complexes.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylase that catalyzes the deacetylation of lysine residues on the N-terminal part of the core histones.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein corepressor complexes, especially SIN3, NuRD, and CoREST.
GO:0160009 histone decrotonylase activity
ISO
GO_REF:0000119 		ACCEPT
Summary: HDAC1 can remove crotonyl modifications from histone lysine residues. Directly demonstrated by Kelly et al. (PMID:30279482) showing HDAC1/2 complexes are important histone decrotonylases in vivo.
Reason: Directly supported by experimental evidence. Genetic deletion of HDAC1/2 in ES cells increases global histone crotonylation and causes an 85% reduction in total decrotonylase activity (PMID:30279482).
Supporting Evidence:
PMID:30279482
Genetic deletion of HDAC1/2 in ES cells increases global levels of histone crotonylation and causes an 85% reduction in total decrotonylase activity
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD, Sin3, CoREST, and related chromatin-repressor complexes.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein corepressor complexes, especially SIN3, NuRD, and CoREST.
GO:0160216 protein lysine delactylase activity
ISO
GO_REF:0000119 		KEEP AS NON CORE
Summary: UniProt/GOA includes protein lysine delactylase activity for HDAC1, but this row is similarity-based; the accessible experimental paper supports HDAC1/2 decrotonylase activity, not direct mouse delactylase activity.
Reason: Do not treat delactylase activity as a direct/core Hdac1 function here. The stronger experimental support is for histone deacetylase and decrotonylase activity.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-uniprot.txt
GO; GO:0160216; F:protein lysine delactylase activity; ISS:UniProtKB.
PMID:30279482
A ternary complex of HDAC1/CoREST1/LSD1 is able to hydrolyse both histone H3 Lys18-acetyl (H3K18ac) and H3 Lys18-crotonyl (H3K18cr) peptide substrates
GO:0000122 negative regulation of transcription by RNA polymerase II
NAS
PMID:22865885
Family with sequence similarity 60A (FAM60A) protein is a ce... 		ACCEPT
Summary: HDAC1 negatively regulates transcription by RNA polymerase II through histone deacetylation at target gene promoters. This is a core biological process annotation for HDAC1.
Reason: Negative regulation of pol II transcription is a primary biological function of HDAC1. Supported by multiple lines of evidence (PMID:8917507, PMID:9271381, PMID:21093383).
Supporting Evidence:
PMID:22865885
The SIN3A-HDAC complex deacetylates histones thereby repressing gene transcription
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD, Sin3, CoREST, and related chromatin-repressor complexes.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein corepressor complexes, especially SIN3, NuRD, and CoREST.
GO:0000122 negative regulation of transcription by RNA polymerase II
NAS
PMID:9651585
SAP30, a novel protein conserved between human and yeast, is... 		ACCEPT
Summary: HDAC1 negatively regulates transcription by RNA polymerase II through histone deacetylation at target gene promoters. This is a core biological process annotation for HDAC1.
Reason: Negative regulation of pol II transcription is a primary biological function of HDAC1. Supported by multiple lines of evidence (PMID:8917507, PMID:9271381, PMID:21093383).
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD, Sin3, CoREST, and related chromatin-repressor complexes.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylase that catalyzes the deacetylation of lysine residues on the N-terminal part of the core histones.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein corepressor complexes, especially SIN3, NuRD, and CoREST.
GO:0005634 nucleus
NAS
PMID:28554894
Fam60a defines a variant Sin3a-Hdac complex in embryonic ste... 		ACCEPT
Summary: HDAC1 is predominantly nuclear, consistent with its function in chromatin modification and transcriptional regulation. Nuclear localization confirmed by multiple methods including immunofluorescence (PMID:11115394).
Reason: Nuclear localization is a well-established core feature of HDAC1. It is a Class I HDAC that is predominantly nuclear.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD, Sin3, CoREST, and related chromatin-repressor complexes.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylase that catalyzes the deacetylation of lysine residues on the N-terminal part of the core histones.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
Class I HDACs, including HDAC1, are predominantly or exclusively nuclear, consistent with chromatin accessibility and transcriptional control roles.
GO:0030336 negative regulation of cell migration
NAS
PMID:22984288
Human family with sequence similarity 60 member A (FAM60A) p... 		KEEP AS NON CORE
Summary: HDAC1 negatively regulates cell migration (PMID:22984288).
Reason: Downstream pleiotropic effect.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 has many developmental and signaling consequences through chromatin deacetylation; these are non-core outputs of the core enzymatic function.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylation gives a tag for epigenetic repression and plays an important role in transcriptional regulation, cell cycle progression and developmental events.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
The report supports HDAC1 as a chromatin deacetylase whose developmental, signaling, cell-cycle, DNA-damage, and pathway phenotypes are context-specific downstream outputs.
GO:0030512 negative regulation of transforming growth factor beta receptor signaling pathway
NAS
PMID:22984288
Human family with sequence similarity 60 member A (FAM60A) p... 		KEEP AS NON CORE
Summary: HDAC1 negatively regulates TGF-beta receptor signaling (PMID:22984288).
Reason: Specific signaling context.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 has many developmental and signaling consequences through chromatin deacetylation; these are non-core outputs of the core enzymatic function.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylation gives a tag for epigenetic repression and plays an important role in transcriptional regulation, cell cycle progression and developmental events.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
The report supports HDAC1 as a chromatin deacetylase whose developmental, signaling, cell-cycle, DNA-damage, and pathway phenotypes are context-specific downstream outputs.
GO:0042659 regulation of cell fate specification
NAS
PMID:22560079
NuRD suppresses pluripotency gene expression to promote tran... 		KEEP AS NON CORE
Summary: HDAC1 participates in regulation of cell fate specification through epigenetic gene regulation.
Reason: Broad developmental process. Pleiotropic downstream effect.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 has many developmental and signaling consequences through chromatin deacetylation; these are non-core outputs of the core enzymatic function.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylation gives a tag for epigenetic repression and plays an important role in transcriptional regulation, cell cycle progression and developmental events.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
The report supports HDAC1 as a chromatin deacetylase whose developmental, signaling, cell-cycle, DNA-damage, and pathway phenotypes are context-specific downstream outputs.
GO:0045892 negative regulation of DNA-templated transcription
NAS
PMID:22560079
NuRD suppresses pluripotency gene expression to promote tran... 		ACCEPT
Summary: HDAC1 negatively regulates DNA-templated transcription through its histone deacetylase activity as part of co-repressor complexes.
Reason: Transcriptional repression is a core function of HDAC1. Well supported by extensive literature.
Supporting Evidence:
PMID:22560079
the action of NuRD is sufficient to silence transcription of these pluripotency genes, allowing cells to exit self-renewal
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD, Sin3, CoREST, and related chromatin-repressor complexes.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein corepressor complexes, especially SIN3, NuRD, and CoREST.
GO:0045893 positive regulation of DNA-templated transcription
NAS
PMID:19927129
NuRD mediates activating and repressive functions of GATA-1 ... 		KEEP AS NON CORE
Summary: Although HDAC1 is primarily a transcriptional repressor, it can indirectly promote transcription of certain genes in specific contexts.
Reason: HDAC1 is primarily a repressor, but there is evidence that it can positively regulate transcription indirectly. This is a secondary, context-dependent function.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 has many developmental and signaling consequences through chromatin deacetylation; these are non-core outputs of the core enzymatic function.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylation gives a tag for epigenetic repression and plays an important role in transcriptional regulation, cell cycle progression and developmental events.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
The report supports HDAC1 as a chromatin deacetylase whose developmental, signaling, cell-cycle, DNA-damage, and pathway phenotypes are context-specific downstream outputs.
GO:1902455 negative regulation of stem cell population maintenance
NAS
PMID:28554894
Fam60a defines a variant Sin3a-Hdac complex in embryonic ste... 		KEEP AS NON CORE
Summary: HDAC1 negatively regulates stem cell maintenance in certain contexts (PMID:28554894).
Reason: Context-specific downstream effect.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 has many developmental and signaling consequences through chromatin deacetylation; these are non-core outputs of the core enzymatic function.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylation gives a tag for epigenetic repression and plays an important role in transcriptional regulation, cell cycle progression and developmental events.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
The report supports HDAC1 as a chromatin deacetylase whose developmental, signaling, cell-cycle, DNA-damage, and pathway phenotypes are context-specific downstream outputs.
GO:1902459 positive regulation of stem cell population maintenance
NAS
PMID:28554894
Fam60a defines a variant Sin3a-Hdac complex in embryonic ste... 		KEEP AS NON CORE
Summary: HDAC1 positively regulates stem cell maintenance as part of the variant Sin3a-Hdac complex in ESCs (PMID:28554894).
Reason: Context-specific downstream effect.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 has many developmental and signaling consequences through chromatin deacetylation; these are non-core outputs of the core enzymatic function.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylation gives a tag for epigenetic repression and plays an important role in transcriptional regulation, cell cycle progression and developmental events.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
The report supports HDAC1 as a chromatin deacetylase whose developmental, signaling, cell-cycle, DNA-damage, and pathway phenotypes are context-specific downstream outputs.
GO:2000736 regulation of stem cell differentiation
NAS
PMID:22560079
NuRD suppresses pluripotency gene expression to promote tran... 		KEEP AS NON CORE
Summary: HDAC1 participates in regulation of stem cell differentiation (PMID:28554894).
Reason: Downstream biological process affected by HDAC1 activity.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 has many developmental and signaling consequences through chromatin deacetylation; these are non-core outputs of the core enzymatic function.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylation gives a tag for epigenetic repression and plays an important role in transcriptional regulation, cell cycle progression and developmental events.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
The report supports HDAC1 as a chromatin deacetylase whose developmental, signaling, cell-cycle, DNA-damage, and pathway phenotypes are context-specific downstream outputs.
GO:0004407 histone deacetylase activity
TAS
Reactome:R-MMU-573376 		ACCEPT
Summary: HDAC1 is a zinc-dependent histone deacetylase (EC 3.5.1.98) that catalyzes removal of acetyl groups from N-acetyl-lysine residues on histones H2A, H2B, H3, and H4. This is the core enzymatic function of HDAC1, well established by direct biochemical assays (PMID:10615135, PMID:21960634, PMID:30279482).
Reason: Histone deacetylase activity is the primary enzymatic function of HDAC1, supported by multiple direct experimental studies demonstrating catalytic activity on histone substrates.
Supporting Evidence:
PMID:10615135
Here we show that Dnmt1 is itself associated with histone deacetylase activity in vivo
PMID:30279482
A ternary complex of HDAC1/CoREST1/LSD1 is able to hydrolyse both histone H3 Lys18-acetyl (H3K18ac) and H3 Lys18-crotonyl (H3K18cr) peptide substrates
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD, Sin3, CoREST, and related chromatin-repressor complexes.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
HDAC1 is a class I Zn2+-dependent histone/protein deacetylase that removes acetyl groups from lysine residues on histone tails and non-histone proteins.
GO:0160216 protein lysine delactylase activity
ISS
GO_REF:0000024 		KEEP AS NON CORE
Summary: UniProt/GOA includes protein lysine delactylase activity for HDAC1, but this row is similarity-based; the accessible experimental paper supports HDAC1/2 decrotonylase activity, not direct mouse delactylase activity.
Reason: Do not treat delactylase activity as a direct/core Hdac1 function here. The stronger experimental support is for histone deacetylase and decrotonylase activity.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-uniprot.txt
GO; GO:0160216; F:protein lysine delactylase activity; ISS:UniProtKB.
PMID:30279482
A ternary complex of HDAC1/CoREST1/LSD1 is able to hydrolyse both histone H3 Lys18-acetyl (H3K18ac) and H3 Lys18-crotonyl (H3K18cr) peptide substrates
GO:0005634 nucleus
IDA
PMID:11115394
Msx3 protein recruits histone deacetylase to down-regulate t... 		ACCEPT
Summary: HDAC1 is predominantly nuclear, consistent with its function in chromatin modification and transcriptional regulation. Nuclear localization confirmed by multiple methods including immunofluorescence (PMID:11115394).
Reason: Nuclear localization is a well-established core feature of HDAC1. It is a Class I HDAC that is predominantly nuclear.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD, Sin3, CoREST, and related chromatin-repressor complexes.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylase that catalyzes the deacetylation of lysine residues on the N-terminal part of the core histones.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
Class I HDACs, including HDAC1, are predominantly or exclusively nuclear, consistent with chromatin accessibility and transcriptional control roles.
GO:0005515 protein binding
IPI
PMID:33831416
The uncharacterized SANT and BTB domain-containing protein S... 		REMOVE
Summary: Protein binding annotation based on physical interaction evidence from PMID:33831416. HDAC1 is known to interact with a very large number of proteins as it functions within multiple co-repressor complexes (NuRD, SIN3, CoREST) and binds many transcription factors.
Reason: Per curation guidelines, protein binding (GO:0005515) is uninformative and should be replaced with more specific molecular function terms. HDAC1 physically interacts with many proteins, but this generic term does not convey functional information. More specific annotations such as histone deacetylase binding, transcription corepressor binding, NF-kappaB binding, and DNA-binding transcription factor binding are already present.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
Generic protein binding and weakly mechanistic interaction annotations are less informative than HDAC1 deacetylase activity and defined corepressor-complex membership.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylases act via the formation of large multiprotein complexes.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
The report supports specific enzymatic and chromatin-complex annotations for HDAC1 rather than generic binding or weakly localized annotations.
GO:0004407 histone deacetylase activity
IDA
PMID:30279482
Histone deacetylase (HDAC) 1 and 2 complexes regulate both h... 		ACCEPT
Summary: HDAC1 is a zinc-dependent histone deacetylase (EC 3.5.1.98) that catalyzes removal of acetyl groups from N-acetyl-lysine residues on histones H2A, H2B, H3, and H4. This is the core enzymatic function of HDAC1, well established by direct biochemical assays (PMID:10615135, PMID:21960634, PMID:30279482).
Reason: Histone deacetylase activity is the primary enzymatic function of HDAC1, supported by multiple direct experimental studies demonstrating catalytic activity on histone substrates.
Supporting Evidence:
PMID:10615135
Here we show that Dnmt1 is itself associated with histone deacetylase activity in vivo
PMID:30279482
A ternary complex of HDAC1/CoREST1/LSD1 is able to hydrolyse both histone H3 Lys18-acetyl (H3K18ac) and H3 Lys18-crotonyl (H3K18cr) peptide substrates
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD, Sin3, CoREST, and related chromatin-repressor complexes.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
HDAC1 is a class I Zn2+-dependent histone/protein deacetylase that removes acetyl groups from lysine residues on histone tails and non-histone proteins.
GO:0160009 histone decrotonylase activity
IDA
PMID:30279482
Histone deacetylase (HDAC) 1 and 2 complexes regulate both h... 		ACCEPT
Summary: HDAC1 can remove crotonyl modifications from histone lysine residues. Directly demonstrated by Kelly et al. (PMID:30279482) showing HDAC1/2 complexes are important histone decrotonylases in vivo.
Reason: Directly supported by experimental evidence. Genetic deletion of HDAC1/2 in ES cells increases global histone crotonylation and causes an 85% reduction in total decrotonylase activity (PMID:30279482).
Supporting Evidence:
PMID:30279482
Genetic deletion of HDAC1/2 in ES cells increases global levels of histone crotonylation and causes an 85% reduction in total decrotonylase activity
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD, Sin3, CoREST, and related chromatin-repressor complexes.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein corepressor complexes, especially SIN3, NuRD, and CoREST.
GO:0005515 protein binding
IPI
PMID:30228260
A variant NuRD complex containing PWWP2A/B excludes MBD2/3 t... 		REMOVE
Summary: Protein binding annotation based on physical interaction evidence from PMID:30228260. HDAC1 is known to interact with a very large number of proteins as it functions within multiple co-repressor complexes (NuRD, SIN3, CoREST) and binds many transcription factors.
Reason: Per curation guidelines, protein binding (GO:0005515) is uninformative and should be replaced with more specific molecular function terms. HDAC1 physically interacts with many proteins, but this generic term does not convey functional information. More specific annotations such as histone deacetylase binding, transcription corepressor binding, NF-kappaB binding, and DNA-binding transcription factor binding are already present.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
Generic protein binding and weakly mechanistic interaction annotations are less informative than HDAC1 deacetylase activity and defined corepressor-complex membership.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylases act via the formation of large multiprotein complexes.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
The report supports specific enzymatic and chromatin-complex annotations for HDAC1 rather than generic binding or weakly localized annotations.
GO:0005515 protein binding
IPI
PMID:34180153
PWWP2B Fine-Tunes Adipose Thermogenesis by Stabilizing HDACs... 		REMOVE
Summary: Protein binding annotation based on physical interaction evidence from PMID:34180153. HDAC1 is known to interact with a very large number of proteins as it functions within multiple co-repressor complexes (NuRD, SIN3, CoREST) and binds many transcription factors.
Reason: Per curation guidelines, protein binding (GO:0005515) is uninformative and should be replaced with more specific molecular function terms. HDAC1 physically interacts with many proteins, but this generic term does not convey functional information. More specific annotations such as histone deacetylase binding, transcription corepressor binding, NF-kappaB binding, and DNA-binding transcription factor binding are already present.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
Generic protein binding and weakly mechanistic interaction annotations are less informative than HDAC1 deacetylase activity and defined corepressor-complex membership.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylases act via the formation of large multiprotein complexes.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
The report supports specific enzymatic and chromatin-complex annotations for HDAC1 rather than generic binding or weakly localized annotations.
GO:0004407 histone deacetylase activity
IDA
PMID:10615135
DNA methyltransferase Dnmt1 associates with histone deacetyl... 		ACCEPT
Summary: HDAC1 is a zinc-dependent histone deacetylase (EC 3.5.1.98) that catalyzes removal of acetyl groups from N-acetyl-lysine residues on histones H2A, H2B, H3, and H4. This is the core enzymatic function of HDAC1, well established by direct biochemical assays (PMID:10615135, PMID:21960634, PMID:30279482).
Reason: Histone deacetylase activity is the primary enzymatic function of HDAC1, supported by multiple direct experimental studies demonstrating catalytic activity on histone substrates.
Supporting Evidence:
PMID:10615135
Here we show that Dnmt1 is itself associated with histone deacetylase activity in vivo
PMID:30279482
A ternary complex of HDAC1/CoREST1/LSD1 is able to hydrolyse both histone H3 Lys18-acetyl (H3K18ac) and H3 Lys18-crotonyl (H3K18cr) peptide substrates
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD, Sin3, CoREST, and related chromatin-repressor complexes.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
HDAC1 is a class I Zn2+-dependent histone/protein deacetylase that removes acetyl groups from lysine residues on histone tails and non-histone proteins.
GO:0140297 DNA-binding transcription factor binding
IPI
PMID:33795231
Regulation of otocyst patterning by Tbx2 and Tbx3 is require... 		ACCEPT
Summary: HDAC1 binds numerous DNA-binding transcription factors as part of its recruitment to target genes. Documented interactions include MyoD, YY1, KLF1, NR4A2, INSM1, and many others.
Reason: HDAC1 interaction with DNA-binding transcription factors is central to its biological function - this is how it is recruited to specific genomic loci.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD, Sin3, CoREST, and related chromatin-repressor complexes.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylase that catalyzes the deacetylation of lysine residues on the N-terminal part of the core histones.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein corepressor complexes, especially SIN3, NuRD, and CoREST.
GO:0140297 DNA-binding transcription factor binding
IPI
PMID:18486321
Acetylation and deacetylation regulate CCAAT/enhancer bindin... 		ACCEPT
Summary: HDAC1 binds numerous DNA-binding transcription factors as part of its recruitment to target genes. Documented interactions include MyoD, YY1, KLF1, NR4A2, INSM1, and many others.
Reason: HDAC1 interaction with DNA-binding transcription factors is central to its biological function - this is how it is recruited to specific genomic loci.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD, Sin3, CoREST, and related chromatin-repressor complexes.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylase that catalyzes the deacetylation of lysine residues on the N-terminal part of the core histones.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein corepressor complexes, especially SIN3, NuRD, and CoREST.
GO:0140297 DNA-binding transcription factor binding
TAS
PMID:12711221
Class II histone deacetylases: versatile regulators. 		ACCEPT
Summary: HDAC1 binds numerous DNA-binding transcription factors as part of its recruitment to target genes. Documented interactions include MyoD, YY1, KLF1, NR4A2, INSM1, and many others.
Reason: HDAC1 interaction with DNA-binding transcription factors is central to its biological function - this is how it is recruited to specific genomic loci.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD, Sin3, CoREST, and related chromatin-repressor complexes.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylase that catalyzes the deacetylation of lysine residues on the N-terminal part of the core histones.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein corepressor complexes, especially SIN3, NuRD, and CoREST.
GO:0005515 protein binding
IPI
PMID:30911105
Safeguard function of PU.1 shapes the inflammatory epigenome... 		REMOVE
Summary: Protein binding annotation based on physical interaction evidence from PMID:30911105. HDAC1 is known to interact with a very large number of proteins as it functions within multiple co-repressor complexes (NuRD, SIN3, CoREST) and binds many transcription factors.
Reason: Per curation guidelines, protein binding (GO:0005515) is uninformative and should be replaced with more specific molecular function terms. HDAC1 physically interacts with many proteins, but this generic term does not convey functional information. More specific annotations such as histone deacetylase binding, transcription corepressor binding, NF-kappaB binding, and DNA-binding transcription factor binding are already present.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
Generic protein binding and weakly mechanistic interaction annotations are less informative than HDAC1 deacetylase activity and defined corepressor-complex membership.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylases act via the formation of large multiprotein complexes.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
The report supports specific enzymatic and chromatin-complex annotations for HDAC1 rather than generic binding or weakly localized annotations.
GO:0003682 chromatin binding
IDA
PMID:15608638
Loss of silent-chromatin looping and impaired imprinting of ... 		ACCEPT
Summary: HDAC1 binds chromatin as part of its function in co-repressor complexes. ChIP experiments have confirmed HDAC1 occupancy at promoters and other regulatory regions.
Reason: Chromatin binding is well supported by extensive ChIP-seq and ChIP-qPCR data showing HDAC1 occupancy at promoters, enhancers, and heterochromatic regions.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD, Sin3, CoREST, and related chromatin-repressor complexes.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylase that catalyzes the deacetylation of lysine residues on the N-terminal part of the core histones.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein corepressor complexes, especially SIN3, NuRD, and CoREST.
GO:0005515 protein binding
IPI
PMID:12900441
Consequences of the depletion of zygotic and embryonic enhan... 		REMOVE
Summary: Protein binding annotation based on physical interaction evidence from PMID:12900441. HDAC1 is known to interact with a very large number of proteins as it functions within multiple co-repressor complexes (NuRD, SIN3, CoREST) and binds many transcription factors.
Reason: Per curation guidelines, protein binding (GO:0005515) is uninformative and should be replaced with more specific molecular function terms. HDAC1 physically interacts with many proteins, but this generic term does not convey functional information. More specific annotations such as histone deacetylase binding, transcription corepressor binding, NF-kappaB binding, and DNA-binding transcription factor binding are already present.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
Generic protein binding and weakly mechanistic interaction annotations are less informative than HDAC1 deacetylase activity and defined corepressor-complex membership.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylases act via the formation of large multiprotein complexes.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
The report supports specific enzymatic and chromatin-complex annotations for HDAC1 rather than generic binding or weakly localized annotations.
GO:0005515 protein binding
IPI
PMID:19796622
Uncovering early response of gene regulatory networks in ESC... 		REMOVE
Summary: Protein binding annotation based on physical interaction evidence from PMID:19796622. HDAC1 is known to interact with a very large number of proteins as it functions within multiple co-repressor complexes (NuRD, SIN3, CoREST) and binds many transcription factors.
Reason: Per curation guidelines, protein binding (GO:0005515) is uninformative and should be replaced with more specific molecular function terms. HDAC1 physically interacts with many proteins, but this generic term does not convey functional information. More specific annotations such as histone deacetylase binding, transcription corepressor binding, NF-kappaB binding, and DNA-binding transcription factor binding are already present.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
Generic protein binding and weakly mechanistic interaction annotations are less informative than HDAC1 deacetylase activity and defined corepressor-complex membership.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylases act via the formation of large multiprotein complexes.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
The report supports specific enzymatic and chromatin-complex annotations for HDAC1 rather than generic binding or weakly localized annotations.
GO:0003682 chromatin binding
IDA
PMID:17392792
Opposing LSD1 complexes function in developmental gene activ... 		ACCEPT
Summary: HDAC1 binds chromatin as part of its function in co-repressor complexes. ChIP experiments have confirmed HDAC1 occupancy at promoters and other regulatory regions.
Reason: Chromatin binding is well supported by extensive ChIP-seq and ChIP-qPCR data showing HDAC1 occupancy at promoters, enhancers, and heterochromatic regions.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD, Sin3, CoREST, and related chromatin-repressor complexes.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylase that catalyzes the deacetylation of lysine residues on the N-terminal part of the core histones.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein corepressor complexes, especially SIN3, NuRD, and CoREST.
GO:0005515 protein binding
IPI
PMID:15907476
REST and its corepressors mediate plasticity of neuronal gen... 		REMOVE
Summary: Protein binding annotation based on physical interaction evidence from PMID:15907476. HDAC1 is known to interact with a very large number of proteins as it functions within multiple co-repressor complexes (NuRD, SIN3, CoREST) and binds many transcription factors.
Reason: Per curation guidelines, protein binding (GO:0005515) is uninformative and should be replaced with more specific molecular function terms. HDAC1 physically interacts with many proteins, but this generic term does not convey functional information. More specific annotations such as histone deacetylase binding, transcription corepressor binding, NF-kappaB binding, and DNA-binding transcription factor binding are already present.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
Generic protein binding and weakly mechanistic interaction annotations are less informative than HDAC1 deacetylase activity and defined corepressor-complex membership.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylases act via the formation of large multiprotein complexes.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
The report supports specific enzymatic and chromatin-complex annotations for HDAC1 rather than generic binding or weakly localized annotations.
GO:0070888 E-box binding
IDA
PMID:24736997
A novel protein, CHRONO, functions as a core component of th... 		MODIFY
Summary: HDAC1 is recruited to E-box-containing circadian gene promoters, but the evidence is chromatin occupancy/repressor-complex recruitment rather than direct sequence-specific E-box motif binding by HDAC1.
Reason: Replace direct E-box binding with promoter-specific chromatin binding, which matches the ChIP/recruitment evidence.
Supporting Evidence:
PMID:24736997
The HDAC1 occupancies at the endogenous E-box of the Per2 promoter were detected in the WT MEF cells at 28, 36, 44, and 52 h after induction with dexamethasone
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein corepressor complexes, especially SIN3, NuRD, and CoREST.
GO:0005515 protein binding
IPI
PMID:17442941
Protein inhibitor of activated STAT 3 modulates osteoclastog... 		REMOVE
Summary: Protein binding annotation based on physical interaction evidence from PMID:17442941. HDAC1 is known to interact with a very large number of proteins as it functions within multiple co-repressor complexes (NuRD, SIN3, CoREST) and binds many transcription factors.
Reason: Per curation guidelines, protein binding (GO:0005515) is uninformative and should be replaced with more specific molecular function terms. HDAC1 physically interacts with many proteins, but this generic term does not convey functional information. More specific annotations such as histone deacetylase binding, transcription corepressor binding, NF-kappaB binding, and DNA-binding transcription factor binding are already present.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
Generic protein binding and weakly mechanistic interaction annotations are less informative than HDAC1 deacetylase activity and defined corepressor-complex membership.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylases act via the formation of large multiprotein complexes.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
The report supports specific enzymatic and chromatin-complex annotations for HDAC1 rather than generic binding or weakly localized annotations.
GO:0032991 protein-containing complex
IDA
PMID:19796622
Uncovering early response of gene regulatory networks in ESC... 		ACCEPT
Summary: HDAC1 is found in protein-containing complexes (NuRD, SIN3, CoREST). Very general cellular component annotation.
Reason: HDAC1 is found in protein-containing complexes. Correct as a root-level CC annotation alongside more specific complex terms.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
approximately 92% of cellular HDAC1 in ESCs was found in just three complexes, about 49% in the NuRD complex, 28% in CoREST, and 15% in SIN3A
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein corepressor complexes, especially SIN3, NuRD, and CoREST.
GO:0005515 protein binding
IPI
PMID:28554894
Fam60a defines a variant Sin3a-Hdac complex in embryonic ste... 		REMOVE
Summary: Protein binding annotation based on physical interaction evidence from PMID:28554894. HDAC1 is known to interact with a very large number of proteins as it functions within multiple co-repressor complexes (NuRD, SIN3, CoREST) and binds many transcription factors.
Reason: Per curation guidelines, protein binding (GO:0005515) is uninformative and should be replaced with more specific molecular function terms. HDAC1 physically interacts with many proteins, but this generic term does not convey functional information. More specific annotations such as histone deacetylase binding, transcription corepressor binding, NF-kappaB binding, and DNA-binding transcription factor binding are already present.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
Generic protein binding and weakly mechanistic interaction annotations are less informative than HDAC1 deacetylase activity and defined corepressor-complex membership.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylases act via the formation of large multiprotein complexes.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
The report supports specific enzymatic and chromatin-complex annotations for HDAC1 rather than generic binding or weakly localized annotations.
GO:0005515 protein binding
IPI
PMID:22770845
The polycomb group protein L3mbtl2 assembles an atypical PRC... 		REMOVE
Summary: Protein binding annotation based on physical interaction evidence from PMID:22770845. HDAC1 is known to interact with a very large number of proteins as it functions within multiple co-repressor complexes (NuRD, SIN3, CoREST) and binds many transcription factors.
Reason: Per curation guidelines, protein binding (GO:0005515) is uninformative and should be replaced with more specific molecular function terms. HDAC1 physically interacts with many proteins, but this generic term does not convey functional information. More specific annotations such as histone deacetylase binding, transcription corepressor binding, NF-kappaB binding, and DNA-binding transcription factor binding are already present.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
Generic protein binding and weakly mechanistic interaction annotations are less informative than HDAC1 deacetylase activity and defined corepressor-complex membership.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylases act via the formation of large multiprotein complexes.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
The report supports specific enzymatic and chromatin-complex annotations for HDAC1 rather than generic binding or weakly localized annotations.
GO:0005634 nucleus
IDA
PMID:22770845
The polycomb group protein L3mbtl2 assembles an atypical PRC... 		ACCEPT
Summary: HDAC1 is predominantly nuclear, consistent with its function in chromatin modification and transcriptional regulation. Nuclear localization confirmed by multiple methods including immunofluorescence (PMID:11115394).
Reason: Nuclear localization is a well-established core feature of HDAC1. It is a Class I HDAC that is predominantly nuclear.
Supporting Evidence:
PMID:22770845
key interactions (Ring1b, Mbd3, Hdac1, and Oct4) are not the result of proximity at promoters, as they were stable in the presence of ethidium bromide
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD, Sin3, CoREST, and related chromatin-repressor complexes.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
Class I HDACs, including HDAC1, are predominantly or exclusively nuclear, consistent with chromatin accessibility and transcriptional control roles.
GO:1990841 promoter-specific chromatin binding
IDA
PMID:22770845
The polycomb group protein L3mbtl2 assembles an atypical PRC... 		ACCEPT
Summary: HDAC1 binds to specific promoter regions as shown by ChIP experiments. HDAC1 occupancy has been demonstrated at the Per2 promoter E-box (PMID:21960634) and other gene promoters.
Reason: Directly supported by ChIP experiments showing HDAC1 at specific promoters.
Supporting Evidence:
PMID:21960634
Chromatin immunoprecipitation followed by quantitative PCR (ChIP-QPCR) analysis from mouse liver chromatin showed a nearly constant HDAC1 occupancy at the Per2 E-box
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD, Sin3, CoREST, and related chromatin-repressor complexes.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein corepressor complexes, especially SIN3, NuRD, and CoREST.
GO:0005515 protein binding
IPI
PMID:21454521
The developmental regulator protein Gon4l associates with pr... 		REMOVE
Summary: Protein binding annotation based on physical interaction evidence from PMID:21454521. HDAC1 is known to interact with a very large number of proteins as it functions within multiple co-repressor complexes (NuRD, SIN3, CoREST) and binds many transcription factors.
Reason: Per curation guidelines, protein binding (GO:0005515) is uninformative and should be replaced with more specific molecular function terms. HDAC1 physically interacts with many proteins, but this generic term does not convey functional information. More specific annotations such as histone deacetylase binding, transcription corepressor binding, NF-kappaB binding, and DNA-binding transcription factor binding are already present.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
Generic protein binding and weakly mechanistic interaction annotations are less informative than HDAC1 deacetylase activity and defined corepressor-complex membership.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylases act via the formation of large multiprotein complexes.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
The report supports specific enzymatic and chromatin-complex annotations for HDAC1 rather than generic binding or weakly localized annotations.
GO:0005515 protein binding
IPI
PMID:24335282
Analysis of the SWI/SNF chromatin-remodeling complex during ... 		REMOVE
Summary: Protein binding annotation based on physical interaction evidence from PMID:24335282. HDAC1 is known to interact with a very large number of proteins as it functions within multiple co-repressor complexes (NuRD, SIN3, CoREST) and binds many transcription factors.
Reason: Per curation guidelines, protein binding (GO:0005515) is uninformative and should be replaced with more specific molecular function terms. HDAC1 physically interacts with many proteins, but this generic term does not convey functional information. More specific annotations such as histone deacetylase binding, transcription corepressor binding, NF-kappaB binding, and DNA-binding transcription factor binding are already present.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
Generic protein binding and weakly mechanistic interaction annotations are less informative than HDAC1 deacetylase activity and defined corepressor-complex membership.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylases act via the formation of large multiprotein complexes.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
The report supports specific enzymatic and chromatin-complex annotations for HDAC1 rather than generic binding or weakly localized annotations.
GO:0004407 histone deacetylase activity
IDA
PMID:21960634
Histone lysine demethylase JARID1a activates CLOCK-BMAL1 and... 		ACCEPT
Summary: HDAC1 is a zinc-dependent histone deacetylase (EC 3.5.1.98) that catalyzes removal of acetyl groups from N-acetyl-lysine residues on histones H2A, H2B, H3, and H4. This is the core enzymatic function of HDAC1, well established by direct biochemical assays (PMID:10615135, PMID:21960634, PMID:30279482).
Reason: Histone deacetylase activity is the primary enzymatic function of HDAC1, supported by multiple direct experimental studies demonstrating catalytic activity on histone substrates.
Supporting Evidence:
PMID:10615135
Here we show that Dnmt1 is itself associated with histone deacetylase activity in vivo
PMID:30279482
A ternary complex of HDAC1/CoREST1/LSD1 is able to hydrolyse both histone H3 Lys18-acetyl (H3K18ac) and H3 Lys18-crotonyl (H3K18cr) peptide substrates
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD, Sin3, CoREST, and related chromatin-repressor complexes.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
HDAC1 is a class I Zn2+-dependent histone/protein deacetylase that removes acetyl groups from lysine residues on histone tails and non-histone proteins.
GO:0005515 protein binding
IPI
PMID:21960634
Histone lysine demethylase JARID1a activates CLOCK-BMAL1 and... 		REMOVE
Summary: Protein binding annotation based on physical interaction evidence from PMID:21960634. HDAC1 is known to interact with a very large number of proteins as it functions within multiple co-repressor complexes (NuRD, SIN3, CoREST) and binds many transcription factors.
Reason: Per curation guidelines, protein binding (GO:0005515) is uninformative and should be replaced with more specific molecular function terms. HDAC1 physically interacts with many proteins, but this generic term does not convey functional information. More specific annotations such as histone deacetylase binding, transcription corepressor binding, NF-kappaB binding, and DNA-binding transcription factor binding are already present.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
Generic protein binding and weakly mechanistic interaction annotations are less informative than HDAC1 deacetylase activity and defined corepressor-complex membership.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylases act via the formation of large multiprotein complexes.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
The report supports specific enzymatic and chromatin-complex annotations for HDAC1 rather than generic binding or weakly localized annotations.
GO:0045892 negative regulation of DNA-templated transcription
IDA
PMID:21960634
Histone lysine demethylase JARID1a activates CLOCK-BMAL1 and... 		ACCEPT
Summary: HDAC1 negatively regulates DNA-templated transcription through its histone deacetylase activity as part of co-repressor complexes.
Reason: Transcriptional repression is a core function of HDAC1. Well supported by extensive literature.
Supporting Evidence:
PMID:21960634
JARID1a increased histone acetylation by inhibiting histone deacetylase 1 function and enhanced transcription by CLOCK-BMAL1 in a demethylase-independent manner
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD, Sin3, CoREST, and related chromatin-repressor complexes.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein corepressor complexes, especially SIN3, NuRD, and CoREST.
GO:0043124 negative regulation of canonical NF-kappaB signal transduction
IGI
PMID:19805123
NF-kappaB activity is constitutively elevated in c-Abl null ... 		KEEP AS NON CORE
Summary: HDAC1 negatively regulates NF-kappaB signaling by deacetylating RelA/p65 at Lys-310.
Reason: Well-characterized regulatory mechanism but represents one of many signaling pathways where HDAC1 functions.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 has many developmental and signaling consequences through chromatin deacetylation; these are non-core outputs of the core enzymatic function.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylation gives a tag for epigenetic repression and plays an important role in transcriptional regulation, cell cycle progression and developmental events.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
The report supports HDAC1 as a chromatin deacetylase whose developmental, signaling, cell-cycle, DNA-damage, and pathway phenotypes are context-specific downstream outputs.
GO:0005515 protein binding
IPI
PMID:15226430
Circadian and light-induced transcription of clock gene Per1... 		REMOVE
Summary: Protein binding annotation based on physical interaction evidence from PMID:15226430. HDAC1 is known to interact with a very large number of proteins as it functions within multiple co-repressor complexes (NuRD, SIN3, CoREST) and binds many transcription factors.
Reason: Per curation guidelines, protein binding (GO:0005515) is uninformative and should be replaced with more specific molecular function terms. HDAC1 physically interacts with many proteins, but this generic term does not convey functional information. More specific annotations such as histone deacetylase binding, transcription corepressor binding, NF-kappaB binding, and DNA-binding transcription factor binding are already present.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
Generic protein binding and weakly mechanistic interaction annotations are less informative than HDAC1 deacetylase activity and defined corepressor-complex membership.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylases act via the formation of large multiprotein complexes.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
The report supports specific enzymatic and chromatin-complex annotations for HDAC1 rather than generic binding or weakly localized annotations.
GO:0032922 circadian regulation of gene expression
IDA
PMID:15226430
Circadian and light-induced transcription of clock gene Per1... 		KEEP AS NON CORE
Summary: HDAC1 participates in circadian gene regulation. Recruited to E-box elements at Per1/Per2 promoters by CRY1 and CIART/CHRONO (PMID:15226430, PMID:24736997).
Reason: HDAC1 has a documented role in circadian gene regulation but this is one of many biological contexts where it functions as a corepressor.
Supporting Evidence:
PMID:15226430
Mouse CRY1 (mCRY1) repressed transcription with HDACs and mSin3B, which was relieved by the HDAC inhibitor trichostatin A (TSA)
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 has many developmental and signaling consequences through chromatin deacetylation; these are non-core outputs of the core enzymatic function.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
The report supports HDAC1 as a chromatin deacetylase whose developmental, signaling, cell-cycle, DNA-damage, and pathway phenotypes are context-specific downstream outputs.
GO:0007623 circadian rhythm
IDA
PMID:24736997
A novel protein, CHRONO, functions as a core component of th... 		KEEP AS NON CORE
Summary: HDAC1 is involved in circadian rhythm regulation by mediating histone deacetylation at circadian gene promoters.
Reason: HDAC1 participates in circadian clock regulation but this is one of many biological contexts where it serves as a corepressor.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 has many developmental and signaling consequences through chromatin deacetylation; these are non-core outputs of the core enzymatic function.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylation gives a tag for epigenetic repression and plays an important role in transcriptional regulation, cell cycle progression and developmental events.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
The report supports HDAC1 as a chromatin deacetylase whose developmental, signaling, cell-cycle, DNA-damage, and pathway phenotypes are context-specific downstream outputs.
GO:0000976 transcription cis-regulatory region binding
IDA
PMID:24413057
Temporal orchestration of repressive chromatin modifiers by ... 		MODIFY
Summary: HDAC1 is recruited to E-box-containing circadian promoters as part of PER-associated repressor complexes, but the evidence shows promoter occupancy/recruitment rather than direct cis-regulatory DNA binding by HDAC1.
Reason: Replace the direct DNA-binding term with promoter-specific chromatin binding, which better matches the ChIP/recruitment evidence.
Supporting Evidence:
PMID:24413057
PER complexes containing HDAC1 or HP1gamma-Suv39h appeared to be physically separable. Circadian clock negative feedback by the PER complex thus involves dynamic, ordered recruitment of repressive chromatin modifiers to DNA-bound Clock-Bmal1.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein corepressor complexes, especially SIN3, NuRD, and CoREST.
GO:0005515 protein binding
IPI
PMID:24413057
Temporal orchestration of repressive chromatin modifiers by ... 		REMOVE
Summary: Protein binding annotation based on physical interaction evidence from PMID:24413057. HDAC1 is known to interact with a very large number of proteins as it functions within multiple co-repressor complexes (NuRD, SIN3, CoREST) and binds many transcription factors.
Reason: Per curation guidelines, protein binding (GO:0005515) is uninformative and should be replaced with more specific molecular function terms. HDAC1 physically interacts with many proteins, but this generic term does not convey functional information. More specific annotations such as histone deacetylase binding, transcription corepressor binding, NF-kappaB binding, and DNA-binding transcription factor binding are already present.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
Generic protein binding and weakly mechanistic interaction annotations are less informative than HDAC1 deacetylase activity and defined corepressor-complex membership.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylases act via the formation of large multiprotein complexes.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
The report supports specific enzymatic and chromatin-complex annotations for HDAC1 rather than generic binding or weakly localized annotations.
GO:0005515 protein binding
IPI
PMID:21931736
CHD5, a brain-specific paralog of Mi2 chromatin remodeling e... 		REMOVE
Summary: Protein binding annotation based on physical interaction evidence from PMID:21931736. HDAC1 is known to interact with a very large number of proteins as it functions within multiple co-repressor complexes (NuRD, SIN3, CoREST) and binds many transcription factors.
Reason: Per curation guidelines, protein binding (GO:0005515) is uninformative and should be replaced with more specific molecular function terms. HDAC1 physically interacts with many proteins, but this generic term does not convey functional information. More specific annotations such as histone deacetylase binding, transcription corepressor binding, NF-kappaB binding, and DNA-binding transcription factor binding are already present.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
Generic protein binding and weakly mechanistic interaction annotations are less informative than HDAC1 deacetylase activity and defined corepressor-complex membership.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylases act via the formation of large multiprotein complexes.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
The report supports specific enzymatic and chromatin-complex annotations for HDAC1 rather than generic binding or weakly localized annotations.
GO:0035851 Krueppel-associated box domain binding
IPI
PMID:21177534
A novel KRAB domain-containing zinc finger transcription fac... 		ACCEPT
Summary: HDAC1 binds to KRAB domain-containing zinc finger proteins. Demonstrated for ZNF431 (PMID:21177534), which recruits HDAC1 via its KRAB domain to repress target genes.
Reason: KRAB-ZFP interaction with HDAC1 is directly demonstrated by co-immunoprecipitation (PMID:21177534).
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD, Sin3, CoREST, and related chromatin-repressor complexes.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylase that catalyzes the deacetylation of lysine residues on the N-terminal part of the core histones.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein corepressor complexes, especially SIN3, NuRD, and CoREST.
GO:0005654 nucleoplasm
TAS
Reactome:R-MMU-573336 		ACCEPT
Summary: HDAC1 is localized to the nucleoplasm where it functions as part of chromatin-modifying complexes.
Reason: Nucleoplasm localization is consistent with HDAC1 function in chromatin modification.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD, Sin3, CoREST, and related chromatin-repressor complexes.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylase that catalyzes the deacetylation of lysine residues on the N-terminal part of the core histones.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
Class I HDACs, including HDAC1, are predominantly or exclusively nuclear, consistent with chromatin accessibility and transcriptional control roles.
GO:0005654 nucleoplasm
TAS
Reactome:R-MMU-573376 		ACCEPT
Summary: HDAC1 is localized to the nucleoplasm where it functions as part of chromatin-modifying complexes.
Reason: Nucleoplasm localization is consistent with HDAC1 function in chromatin modification.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD, Sin3, CoREST, and related chromatin-repressor complexes.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylase that catalyzes the deacetylation of lysine residues on the N-terminal part of the core histones.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
Class I HDACs, including HDAC1, are predominantly or exclusively nuclear, consistent with chromatin accessibility and transcriptional control roles.
GO:0005654 nucleoplasm
TAS
Reactome:R-MMU-573383 		ACCEPT
Summary: HDAC1 is localized to the nucleoplasm where it functions as part of chromatin-modifying complexes.
Reason: Nucleoplasm localization is consistent with HDAC1 function in chromatin modification.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD, Sin3, CoREST, and related chromatin-repressor complexes.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylase that catalyzes the deacetylation of lysine residues on the N-terminal part of the core histones.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
Class I HDACs, including HDAC1, are predominantly or exclusively nuclear, consistent with chromatin accessibility and transcriptional control roles.
GO:0005654 nucleoplasm
TAS
Reactome:R-MMU-8978954 		ACCEPT
Summary: HDAC1 is localized to the nucleoplasm where it functions as part of chromatin-modifying complexes.
Reason: Nucleoplasm localization is consistent with HDAC1 function in chromatin modification.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD, Sin3, CoREST, and related chromatin-repressor complexes.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylase that catalyzes the deacetylation of lysine residues on the N-terminal part of the core histones.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
Class I HDACs, including HDAC1, are predominantly or exclusively nuclear, consistent with chromatin accessibility and transcriptional control roles.
GO:0005654 nucleoplasm
TAS
Reactome:R-MMU-8978970 		ACCEPT
Summary: HDAC1 is localized to the nucleoplasm where it functions as part of chromatin-modifying complexes.
Reason: Nucleoplasm localization is consistent with HDAC1 function in chromatin modification.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD, Sin3, CoREST, and related chromatin-repressor complexes.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylase that catalyzes the deacetylation of lysine residues on the N-terminal part of the core histones.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
Class I HDACs, including HDAC1, are predominantly or exclusively nuclear, consistent with chromatin accessibility and transcriptional control roles.
GO:0005654 nucleoplasm
TAS
Reactome:R-MMU-8978980 		ACCEPT
Summary: HDAC1 is localized to the nucleoplasm where it functions as part of chromatin-modifying complexes.
Reason: Nucleoplasm localization is consistent with HDAC1 function in chromatin modification.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD, Sin3, CoREST, and related chromatin-repressor complexes.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylase that catalyzes the deacetylation of lysine residues on the N-terminal part of the core histones.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
Class I HDACs, including HDAC1, are predominantly or exclusively nuclear, consistent with chromatin accessibility and transcriptional control roles.
GO:0005654 nucleoplasm
TAS
Reactome:R-MMU-8978989 		ACCEPT
Summary: HDAC1 is localized to the nucleoplasm where it functions as part of chromatin-modifying complexes.
Reason: Nucleoplasm localization is consistent with HDAC1 function in chromatin modification.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD, Sin3, CoREST, and related chromatin-repressor complexes.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylase that catalyzes the deacetylation of lysine residues on the N-terminal part of the core histones.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
Class I HDACs, including HDAC1, are predominantly or exclusively nuclear, consistent with chromatin accessibility and transcriptional control roles.
GO:0005654 nucleoplasm
TAS
Reactome:R-MMU-9006133 		ACCEPT
Summary: HDAC1 is localized to the nucleoplasm where it functions as part of chromatin-modifying complexes.
Reason: Nucleoplasm localization is consistent with HDAC1 function in chromatin modification.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD, Sin3, CoREST, and related chromatin-repressor complexes.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylase that catalyzes the deacetylation of lysine residues on the N-terminal part of the core histones.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
Class I HDACs, including HDAC1, are predominantly or exclusively nuclear, consistent with chromatin accessibility and transcriptional control roles.
GO:0005654 nucleoplasm
TAS
Reactome:R-MMU-9017958 		ACCEPT
Summary: HDAC1 is localized to the nucleoplasm where it functions as part of chromatin-modifying complexes.
Reason: Nucleoplasm localization is consistent with HDAC1 function in chromatin modification.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD, Sin3, CoREST, and related chromatin-repressor complexes.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylase that catalyzes the deacetylation of lysine residues on the N-terminal part of the core histones.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
Class I HDACs, including HDAC1, are predominantly or exclusively nuclear, consistent with chromatin accessibility and transcriptional control roles.
GO:0005654 nucleoplasm
TAS
Reactome:R-MMU-9625109 		ACCEPT
Summary: HDAC1 is localized to the nucleoplasm where it functions as part of chromatin-modifying complexes.
Reason: Nucleoplasm localization is consistent with HDAC1 function in chromatin modification.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD, Sin3, CoREST, and related chromatin-repressor complexes.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylase that catalyzes the deacetylation of lysine residues on the N-terminal part of the core histones.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
Class I HDACs, including HDAC1, are predominantly or exclusively nuclear, consistent with chromatin accessibility and transcriptional control roles.
GO:0005654 nucleoplasm
TAS
Reactome:R-MMU-9727502 		ACCEPT
Summary: HDAC1 is localized to the nucleoplasm where it functions as part of chromatin-modifying complexes.
Reason: Nucleoplasm localization is consistent with HDAC1 function in chromatin modification.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD, Sin3, CoREST, and related chromatin-repressor complexes.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylase that catalyzes the deacetylation of lysine residues on the N-terminal part of the core histones.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
Class I HDACs, including HDAC1, are predominantly or exclusively nuclear, consistent with chromatin accessibility and transcriptional control roles.
GO:0005654 nucleoplasm
TAS
Reactome:R-MMU-9844527 		ACCEPT
Summary: HDAC1 is localized to the nucleoplasm where it functions as part of chromatin-modifying complexes.
Reason: Nucleoplasm localization is consistent with HDAC1 function in chromatin modification.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD, Sin3, CoREST, and related chromatin-repressor complexes.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylase that catalyzes the deacetylation of lysine residues on the N-terminal part of the core histones.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
Class I HDACs, including HDAC1, are predominantly or exclusively nuclear, consistent with chromatin accessibility and transcriptional control roles.
GO:0005654 nucleoplasm
TAS
Reactome:R-MMU-9845305 		ACCEPT
Summary: HDAC1 is localized to the nucleoplasm where it functions as part of chromatin-modifying complexes.
Reason: Nucleoplasm localization is consistent with HDAC1 function in chromatin modification.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD, Sin3, CoREST, and related chromatin-repressor complexes.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylase that catalyzes the deacetylation of lysine residues on the N-terminal part of the core histones.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
Class I HDACs, including HDAC1, are predominantly or exclusively nuclear, consistent with chromatin accessibility and transcriptional control roles.
GO:0005654 nucleoplasm
TAS
Reactome:R-NUL-573373 		ACCEPT
Summary: HDAC1 is localized to the nucleoplasm where it functions as part of chromatin-modifying complexes.
Reason: Nucleoplasm localization is consistent with HDAC1 function in chromatin modification.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD, Sin3, CoREST, and related chromatin-repressor complexes.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylase that catalyzes the deacetylation of lysine residues on the N-terminal part of the core histones.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
Class I HDACs, including HDAC1, are predominantly or exclusively nuclear, consistent with chromatin accessibility and transcriptional control roles.
GO:0005654 nucleoplasm
TAS
Reactome:R-NUL-573385 		ACCEPT
Summary: HDAC1 is localized to the nucleoplasm where it functions as part of chromatin-modifying complexes.
Reason: Nucleoplasm localization is consistent with HDAC1 function in chromatin modification.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD, Sin3, CoREST, and related chromatin-repressor complexes.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylase that catalyzes the deacetylation of lysine residues on the N-terminal part of the core histones.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
Class I HDACs, including HDAC1, are predominantly or exclusively nuclear, consistent with chromatin accessibility and transcriptional control roles.
GO:0005515 protein binding
IPI
PMID:11923873
Bop encodes a muscle-restricted protein containing MYND and ... 		REMOVE
Summary: Protein binding annotation based on physical interaction evidence from PMID:11923873. HDAC1 is known to interact with a very large number of proteins as it functions within multiple co-repressor complexes (NuRD, SIN3, CoREST) and binds many transcription factors.
Reason: Per curation guidelines, protein binding (GO:0005515) is uninformative and should be replaced with more specific molecular function terms. HDAC1 physically interacts with many proteins, but this generic term does not convey functional information. More specific annotations such as histone deacetylase binding, transcription corepressor binding, NF-kappaB binding, and DNA-binding transcription factor binding are already present.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
Generic protein binding and weakly mechanistic interaction annotations are less informative than HDAC1 deacetylase activity and defined corepressor-complex membership.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylases act via the formation of large multiprotein complexes.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
The report supports specific enzymatic and chromatin-complex annotations for HDAC1 rather than generic binding or weakly localized annotations.
GO:0005515 protein binding
IPI
PMID:11115394
Msx3 protein recruits histone deacetylase to down-regulate t... 		REMOVE
Summary: Protein binding annotation based on physical interaction evidence from PMID:11115394. HDAC1 is known to interact with a very large number of proteins as it functions within multiple co-repressor complexes (NuRD, SIN3, CoREST) and binds many transcription factors.
Reason: Per curation guidelines, protein binding (GO:0005515) is uninformative and should be replaced with more specific molecular function terms. HDAC1 physically interacts with many proteins, but this generic term does not convey functional information. More specific annotations such as histone deacetylase binding, transcription corepressor binding, NF-kappaB binding, and DNA-binding transcription factor binding are already present.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
Generic protein binding and weakly mechanistic interaction annotations are less informative than HDAC1 deacetylase activity and defined corepressor-complex membership.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylases act via the formation of large multiprotein complexes.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
The report supports specific enzymatic and chromatin-complex annotations for HDAC1 rather than generic binding or weakly localized annotations.
GO:2001243 negative regulation of intrinsic apoptotic signaling pathway
IGI
PMID:21093383
Hdac1 and Hdac2 act redundantly to control p63 and p53 funct... 		ACCEPT
Summary: HDAC1 negatively regulates the intrinsic apoptotic signaling pathway. HDAC1/2 double knockout in epidermis leads to increased apoptosis (PMID:21093383).
Reason: PMID:21093383 directly links HDAC1/2 chromatin repression to suppression of p53 activity in epidermal progenitors; this supports negative regulation of intrinsic apoptotic signaling as a direct output of HDAC1-containing repressor complexes.
Supporting Evidence:
PMID:21093383
Mutant embryos display increased levels of acetylated p53, which opposes p63 functions
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 can deacetylate p53, reducing p53 activity and thereby modulating apoptosis and DNA damage responses.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylation gives a tag for epigenetic repression and plays an important role in transcriptional regulation, cell cycle progression and developmental events.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein corepressor complexes.
GO:0005515 protein binding
IPI
PMID:21937600
Transposon mutagenesis with coat color genotyping identifies... 		REMOVE
Summary: Protein binding annotation based on physical interaction evidence from PMID:21937600. HDAC1 is known to interact with a very large number of proteins as it functions within multiple co-repressor complexes (NuRD, SIN3, CoREST) and binds many transcription factors.
Reason: Per curation guidelines, protein binding (GO:0005515) is uninformative and should be replaced with more specific molecular function terms. HDAC1 physically interacts with many proteins, but this generic term does not convey functional information. More specific annotations such as histone deacetylase binding, transcription corepressor binding, NF-kappaB binding, and DNA-binding transcription factor binding are already present.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
Generic protein binding and weakly mechanistic interaction annotations are less informative than HDAC1 deacetylase activity and defined corepressor-complex membership.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylases act via the formation of large multiprotein complexes.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
The report supports specific enzymatic and chromatin-complex annotations for HDAC1 rather than generic binding or weakly localized annotations.
GO:0005515 protein binding
IPI
PMID:19501046
Znhit1 causes cell cycle arrest and down-regulates CDK6 expr... 		REMOVE
Summary: Protein binding annotation based on physical interaction evidence from PMID:19501046. HDAC1 is known to interact with a very large number of proteins as it functions within multiple co-repressor complexes (NuRD, SIN3, CoREST) and binds many transcription factors.
Reason: Per curation guidelines, protein binding (GO:0005515) is uninformative and should be replaced with more specific molecular function terms. HDAC1 physically interacts with many proteins, but this generic term does not convey functional information. More specific annotations such as histone deacetylase binding, transcription corepressor binding, NF-kappaB binding, and DNA-binding transcription factor binding are already present.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
Generic protein binding and weakly mechanistic interaction annotations are less informative than HDAC1 deacetylase activity and defined corepressor-complex membership.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylases act via the formation of large multiprotein complexes.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
The report supports specific enzymatic and chromatin-complex annotations for HDAC1 rather than generic binding or weakly localized annotations.
GO:0005515 protein binding
IPI
PMID:11836251
Murine Sall1 represses transcription by recruiting a histone... 		REMOVE
Summary: Protein binding annotation based on physical interaction evidence from PMID:11836251. HDAC1 is known to interact with a very large number of proteins as it functions within multiple co-repressor complexes (NuRD, SIN3, CoREST) and binds many transcription factors.
Reason: Per curation guidelines, protein binding (GO:0005515) is uninformative and should be replaced with more specific molecular function terms. HDAC1 physically interacts with many proteins, but this generic term does not convey functional information. More specific annotations such as histone deacetylase binding, transcription corepressor binding, NF-kappaB binding, and DNA-binding transcription factor binding are already present.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
Generic protein binding and weakly mechanistic interaction annotations are less informative than HDAC1 deacetylase activity and defined corepressor-complex membership.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylases act via the formation of large multiprotein complexes.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
The report supports specific enzymatic and chromatin-complex annotations for HDAC1 rather than generic binding or weakly localized annotations.
GO:0005515 protein binding
IPI
PMID:22242125
Stress-induced C/EBP homology protein (CHOP) represses MyoD ... 		REMOVE
Summary: Protein binding annotation based on physical interaction evidence from PMID:22242125. HDAC1 is known to interact with a very large number of proteins as it functions within multiple co-repressor complexes (NuRD, SIN3, CoREST) and binds many transcription factors.
Reason: Per curation guidelines, protein binding (GO:0005515) is uninformative and should be replaced with more specific molecular function terms. HDAC1 physically interacts with many proteins, but this generic term does not convey functional information. More specific annotations such as histone deacetylase binding, transcription corepressor binding, NF-kappaB binding, and DNA-binding transcription factor binding are already present.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
Generic protein binding and weakly mechanistic interaction annotations are less informative than HDAC1 deacetylase activity and defined corepressor-complex membership.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylases act via the formation of large multiprotein complexes.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
The report supports specific enzymatic and chromatin-complex annotations for HDAC1 rather than generic binding or weakly localized annotations.
GO:0005515 protein binding
IPI
PMID:22075476
Metastasis-associated protein 3 (MTA3) regulates G2/M progre... 		REMOVE
Summary: Protein binding annotation based on physical interaction evidence from PMID:22075476. HDAC1 is known to interact with a very large number of proteins as it functions within multiple co-repressor complexes (NuRD, SIN3, CoREST) and binds many transcription factors.
Reason: Per curation guidelines, protein binding (GO:0005515) is uninformative and should be replaced with more specific molecular function terms. HDAC1 physically interacts with many proteins, but this generic term does not convey functional information. More specific annotations such as histone deacetylase binding, transcription corepressor binding, NF-kappaB binding, and DNA-binding transcription factor binding are already present.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
Generic protein binding and weakly mechanistic interaction annotations are less informative than HDAC1 deacetylase activity and defined corepressor-complex membership.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylases act via the formation of large multiprotein complexes.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
The report supports specific enzymatic and chromatin-complex annotations for HDAC1 rather than generic binding or weakly localized annotations.
GO:0016581 NuRD complex
IDA
PMID:22075476
Metastasis-associated protein 3 (MTA3) regulates G2/M progre... 		ACCEPT
Summary: HDAC1 is a core catalytic subunit of the NuRD (nucleosome remodeling and deacetylase) complex. Proteomic studies show approximately 49% of cellular HDAC1 in ESCs is in the NuRD complex (deep research review). Well supported by mass spectrometry identification (PMID:27806305) and multiple interaction studies.
Reason: NuRD complex membership is a core aspect of HDAC1 function. HDAC1 serves as the catalytic deacetylase subunit within NuRD. Extensively validated by proteomics and co-immunoprecipitation studies.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD, Sin3, CoREST, and related chromatin-repressor complexes.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylase that catalyzes the deacetylation of lysine residues on the N-terminal part of the core histones.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein corepressor complexes, especially SIN3, NuRD, and CoREST.
GO:0005634 nucleus
IDA
PMID:20720167
Metastasis tumor antigen 2 (MTA2) is involved in proper impr... 		ACCEPT
Summary: HDAC1 is predominantly nuclear, consistent with its function in chromatin modification and transcriptional regulation. Nuclear localization confirmed by multiple methods including immunofluorescence (PMID:11115394).
Reason: Nuclear localization is a well-established core feature of HDAC1. It is a Class I HDAC that is predominantly nuclear.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD, Sin3, CoREST, and related chromatin-repressor complexes.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylase that catalyzes the deacetylation of lysine residues on the N-terminal part of the core histones.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
Class I HDACs, including HDAC1, are predominantly or exclusively nuclear, consistent with chromatin accessibility and transcriptional control roles.
GO:0005634 nucleus
IDA
PMID:21874024
The ubiquitin ligase Peli1 negatively regulates T cell activ... 		ACCEPT
Summary: HDAC1 is predominantly nuclear, consistent with its function in chromatin modification and transcriptional regulation. Nuclear localization confirmed by multiple methods including immunofluorescence (PMID:11115394).
Reason: Nuclear localization is a well-established core feature of HDAC1. It is a Class I HDAC that is predominantly nuclear.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 is predominantly a nuclear protein, consistent with its role in modifying chromatin
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
Class I HDACs, including HDAC1, are predominantly or exclusively nuclear, consistent with chromatin accessibility and transcriptional control roles.
GO:0061629 RNA polymerase II-specific DNA-binding transcription factor binding
IPI
PMID:19235719
The homeobox gene Mohawk represses transcription by recruiti... 		ACCEPT
Summary: HDAC1 binds RNA polymerase II-specific transcription factors that recruit it to target genes for transcriptional repression.
Reason: This is a more specific version of DNA-binding transcription factor binding, appropriate given that HDAC1 primarily regulates RNA pol II-transcribed genes through interactions with pol II-specific TFs.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD, Sin3, CoREST, and related chromatin-repressor complexes.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylase that catalyzes the deacetylation of lysine residues on the N-terminal part of the core histones.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein corepressor complexes, especially SIN3, NuRD, and CoREST.
GO:0005667 transcription regulator complex
IDA
PMID:17707228
Epigenetic regulation of hematopoietic differentiation by Gf... 		ACCEPT
Summary: HDAC1 is a component of transcription regulator complexes. This is a broad parent term for the more specific NuRD, SIN3, and CoREST complexes.
Reason: Correct but very general. HDAC1 does function in transcription regulator complexes. More specific complex annotations (NuRD, SIN3) are also present.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD, Sin3, CoREST, and related chromatin-repressor complexes.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylase that catalyzes the deacetylation of lysine residues on the N-terminal part of the core histones.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein corepressor complexes, especially SIN3, NuRD, and CoREST.
GO:0005515 protein binding
IPI
PMID:20599664
A novel role for cardiac ankyrin repeat protein Ankrd1/CARP ... 		REMOVE
Summary: Protein binding annotation based on physical interaction evidence from PMID:20599664. HDAC1 is known to interact with a very large number of proteins as it functions within multiple co-repressor complexes (NuRD, SIN3, CoREST) and binds many transcription factors.
Reason: Per curation guidelines, protein binding (GO:0005515) is uninformative and should be replaced with more specific molecular function terms. HDAC1 physically interacts with many proteins, but this generic term does not convey functional information. More specific annotations such as histone deacetylase binding, transcription corepressor binding, NF-kappaB binding, and DNA-binding transcription factor binding are already present.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
Generic protein binding and weakly mechanistic interaction annotations are less informative than HDAC1 deacetylase activity and defined corepressor-complex membership.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylases act via the formation of large multiprotein complexes.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
The report supports specific enzymatic and chromatin-complex annotations for HDAC1 rather than generic binding or weakly localized annotations.
GO:0003682 chromatin binding
IDA
PMID:17905753
Adipose tissue mass is modulated by SLUG (SNAI2). 		ACCEPT
Summary: HDAC1 binds chromatin as part of its function in co-repressor complexes. ChIP experiments have confirmed HDAC1 occupancy at promoters and other regulatory regions.
Reason: Chromatin binding is well supported by extensive ChIP-seq and ChIP-qPCR data showing HDAC1 occupancy at promoters, enhancers, and heterochromatic regions.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD, Sin3, CoREST, and related chromatin-repressor complexes.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylase that catalyzes the deacetylation of lysine residues on the N-terminal part of the core histones.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein corepressor complexes, especially SIN3, NuRD, and CoREST.
GO:0045892 negative regulation of DNA-templated transcription
IDA
PMID:9271381
Identification of mouse histone deacetylase 1 as a growth fa... 		ACCEPT
Summary: HDAC1 negatively regulates DNA-templated transcription through its histone deacetylase activity as part of co-repressor complexes.
Reason: Transcriptional repression is a core function of HDAC1. Well supported by extensive literature.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD, Sin3, CoREST, and related chromatin-repressor complexes.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylase that catalyzes the deacetylation of lysine residues on the N-terminal part of the core histones.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein corepressor complexes, especially SIN3, NuRD, and CoREST.
GO:0005515 protein binding
IPI
PMID:19503085
HDAC1 and HDAC2 regulate oligodendrocyte differentiation by ... 		REMOVE
Summary: Protein binding annotation based on physical interaction evidence from PMID:19503085. HDAC1 is known to interact with a very large number of proteins as it functions within multiple co-repressor complexes (NuRD, SIN3, CoREST) and binds many transcription factors.
Reason: Per curation guidelines, protein binding (GO:0005515) is uninformative and should be replaced with more specific molecular function terms. HDAC1 physically interacts with many proteins, but this generic term does not convey functional information. More specific annotations such as histone deacetylase binding, transcription corepressor binding, NF-kappaB binding, and DNA-binding transcription factor binding are already present.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
Generic protein binding and weakly mechanistic interaction annotations are less informative than HDAC1 deacetylase activity and defined corepressor-complex membership.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylases act via the formation of large multiprotein complexes.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
The report supports specific enzymatic and chromatin-complex annotations for HDAC1 rather than generic binding or weakly localized annotations.
GO:0048714 positive regulation of oligodendrocyte differentiation
IGI
PMID:19503085
HDAC1 and HDAC2 regulate oligodendrocyte differentiation by ... 		KEEP AS NON CORE
Summary: HDAC1/2 positively regulate oligodendrocyte differentiation, likely by repressing inhibitors of myelination (PMID:19503085).
Reason: Cell-type-specific developmental process rather than a core function.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 has many developmental and signaling consequences through chromatin deacetylation; these are non-core outputs of the core enzymatic function.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylation gives a tag for epigenetic repression and plays an important role in transcriptional regulation, cell cycle progression and developmental events.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
The report supports HDAC1 as a chromatin deacetylase whose developmental, signaling, cell-cycle, DNA-damage, and pathway phenotypes are context-specific downstream outputs.
GO:0090090 negative regulation of canonical Wnt signaling pathway
IGI
PMID:19503085
HDAC1 and HDAC2 regulate oligodendrocyte differentiation by ... 		KEEP AS NON CORE
Summary: HDAC1/2 negatively regulate canonical Wnt signaling by deacetylating histones at Wnt target gene promoters. Demonstrated in neural development.
Reason: Well-supported role in neural development but represents a downstream biological consequence rather than a core molecular function.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 has many developmental and signaling consequences through chromatin deacetylation; these are non-core outputs of the core enzymatic function.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylation gives a tag for epigenetic repression and plays an important role in transcriptional regulation, cell cycle progression and developmental events.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
The report supports HDAC1 as a chromatin deacetylase whose developmental, signaling, cell-cycle, DNA-damage, and pathway phenotypes are context-specific downstream outputs.
GO:0016581 NuRD complex
IDA
PMID:11836251
Murine Sall1 represses transcription by recruiting a histone... 		ACCEPT
Summary: HDAC1 is a core catalytic subunit of the NuRD (nucleosome remodeling and deacetylase) complex. Proteomic studies show approximately 49% of cellular HDAC1 in ESCs is in the NuRD complex (deep research review). Well supported by mass spectrometry identification (PMID:27806305) and multiple interaction studies.
Reason: NuRD complex membership is a core aspect of HDAC1 function. HDAC1 serves as the catalytic deacetylase subunit within NuRD. Extensively validated by proteomics and co-immunoprecipitation studies.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD, Sin3, CoREST, and related chromatin-repressor complexes.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylase that catalyzes the deacetylation of lysine residues on the N-terminal part of the core histones.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein corepressor complexes, especially SIN3, NuRD, and CoREST.
GO:0000122 negative regulation of transcription by RNA polymerase II
IGI
PMID:21093383
Hdac1 and Hdac2 act redundantly to control p63 and p53 funct... 		ACCEPT
Summary: HDAC1 negatively regulates transcription by RNA polymerase II through histone deacetylation at target gene promoters. This is a core biological process annotation for HDAC1.
Reason: Negative regulation of pol II transcription is a primary biological function of HDAC1. Supported by multiple lines of evidence (PMID:8917507, PMID:9271381, PMID:21093383).
Supporting Evidence:
PMID:21093383
HDAC1/2 directly mediate repressive functions of p63 and suppress p53 activity
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD, Sin3, CoREST, and related chromatin-repressor complexes.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein corepressor complexes, especially SIN3, NuRD, and CoREST.
GO:0000785 chromatin
IDA
PMID:21093383
Hdac1 and Hdac2 act redundantly to control p63 and p53 funct... 		ACCEPT
Summary: HDAC1 is a chromatin-associated protein that modifies histone tails as part of co-repressor complexes.
Reason: HDAC1 is a histone-modifying enzyme that directly acts on chromatin. Association with chromatin is inherent to its function.
Supporting Evidence:
PMID:21093383
HDACs bind and are active at their promoter regions in normal undifferentiated keratinocytes
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD, Sin3, CoREST, and related chromatin-repressor complexes.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein corepressor complexes, especially SIN3, NuRD, and CoREST.
GO:0008284 positive regulation of cell population proliferation
IGI
PMID:21093383
Hdac1 and Hdac2 act redundantly to control p63 and p53 funct... 		KEEP AS NON CORE
Summary: HDAC1 promotes cell proliferation by repressing cell cycle inhibitors through the Rb-HDAC1 complex.
Reason: Well-documented pro-proliferative role but downstream biological consequence of deacetylase activity.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 has many developmental and signaling consequences through chromatin deacetylation; these are non-core outputs of the core enzymatic function.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylation gives a tag for epigenetic repression and plays an important role in transcriptional regulation, cell cycle progression and developmental events.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
The report supports HDAC1 as a chromatin deacetylase whose developmental, signaling, cell-cycle, DNA-damage, and pathway phenotypes are context-specific downstream outputs.
GO:0009913 epidermal cell differentiation
IGI
PMID:21093383
Hdac1 and Hdac2 act redundantly to control p63 and p53 funct... 		KEEP AS NON CORE
Summary: HDAC1/2 are required for proper epidermal cell differentiation (PMID:21093383).
Reason: Tissue-specific developmental process affected by HDAC1.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 has many developmental and signaling consequences through chromatin deacetylation; these are non-core outputs of the core enzymatic function.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylation gives a tag for epigenetic repression and plays an important role in transcriptional regulation, cell cycle progression and developmental events.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
The report supports HDAC1 as a chromatin deacetylase whose developmental, signaling, cell-cycle, DNA-damage, and pathway phenotypes are context-specific downstream outputs.
GO:0042475 odontogenesis of dentin-containing tooth
IGI
PMID:21093383
Hdac1 and Hdac2 act redundantly to control p63 and p53 funct... 		KEEP AS NON CORE
Summary: HDAC1/2 conditional knockout affects tooth development (PMID:21093383).
Reason: Highly specific downstream developmental phenotype.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 has many developmental and signaling consequences through chromatin deacetylation; these are non-core outputs of the core enzymatic function.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylation gives a tag for epigenetic repression and plays an important role in transcriptional regulation, cell cycle progression and developmental events.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
The report supports HDAC1 as a chromatin deacetylase whose developmental, signaling, cell-cycle, DNA-damage, and pathway phenotypes are context-specific downstream outputs.
GO:0042733 embryonic digit morphogenesis
IGI
PMID:21093383
Hdac1 and Hdac2 act redundantly to control p63 and p53 funct... 		KEEP AS NON CORE
Summary: HDAC1/2 conditional loss affects digit morphogenesis (PMID:21093383).
Reason: Pleiotropic downstream developmental effect.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 has many developmental and signaling consequences through chromatin deacetylation; these are non-core outputs of the core enzymatic function.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylation gives a tag for epigenetic repression and plays an important role in transcriptional regulation, cell cycle progression and developmental events.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
The report supports HDAC1 as a chromatin deacetylase whose developmental, signaling, cell-cycle, DNA-damage, and pathway phenotypes are context-specific downstream outputs.
GO:0043066 negative regulation of apoptotic process
IGI
PMID:21093383
Hdac1 and Hdac2 act redundantly to control p63 and p53 funct... 		KEEP AS NON CORE
Summary: HDAC1 negatively regulates apoptosis, in part through deacetylation and inactivation of p53.
Reason: Anti-apoptotic effects are a downstream consequence of HDAC1 activity.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 has many developmental and signaling consequences through chromatin deacetylation; these are non-core outputs of the core enzymatic function.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylation gives a tag for epigenetic repression and plays an important role in transcriptional regulation, cell cycle progression and developmental events.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
The report supports HDAC1 as a chromatin deacetylase whose developmental, signaling, cell-cycle, DNA-damage, and pathway phenotypes are context-specific downstream outputs.
GO:0060789 hair follicle placode formation
IGI
PMID:21093383
Hdac1 and Hdac2 act redundantly to control p63 and p53 funct... 		KEEP AS NON CORE
Summary: HDAC1/2 are required for hair follicle placode formation (PMID:21093383).
Reason: Specific epidermal phenotype. Pleiotropic downstream effect.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 has many developmental and signaling consequences through chromatin deacetylation; these are non-core outputs of the core enzymatic function.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylation gives a tag for epigenetic repression and plays an important role in transcriptional regulation, cell cycle progression and developmental events.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
The report supports HDAC1 as a chromatin deacetylase whose developmental, signaling, cell-cycle, DNA-damage, and pathway phenotypes are context-specific downstream outputs.
GO:0061029 eyelid development in camera-type eye
IGI
PMID:21093383
Hdac1 and Hdac2 act redundantly to control p63 and p53 funct... 		KEEP AS NON CORE
Summary: HDAC1/2 conditional knockout in epidermis affects eyelid development (PMID:21093383).
Reason: Specific developmental phenotype. Pleiotropic downstream effect.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 has many developmental and signaling consequences through chromatin deacetylation; these are non-core outputs of the core enzymatic function.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylation gives a tag for epigenetic repression and plays an important role in transcriptional regulation, cell cycle progression and developmental events.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
The report supports HDAC1 as a chromatin deacetylase whose developmental, signaling, cell-cycle, DNA-damage, and pathway phenotypes are context-specific downstream outputs.
GO:0061198 fungiform papilla formation
IGI
PMID:21093383
Hdac1 and Hdac2 act redundantly to control p63 and p53 funct... 		KEEP AS NON CORE
Summary: HDAC1/2 conditional loss in epidermis affects fungiform papilla formation (PMID:21093383).
Reason: Specific developmental phenotype. Pleiotropic downstream effect.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 has many developmental and signaling consequences through chromatin deacetylation; these are non-core outputs of the core enzymatic function.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylation gives a tag for epigenetic repression and plays an important role in transcriptional regulation, cell cycle progression and developmental events.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
The report supports HDAC1 as a chromatin deacetylase whose developmental, signaling, cell-cycle, DNA-damage, and pathway phenotypes are context-specific downstream outputs.
GO:0005515 protein binding
IPI
PMID:16805913
Identification and characterization of Smyd2: a split SET/MY... 		REMOVE
Summary: Protein binding annotation based on physical interaction evidence from PMID:16805913. HDAC1 is known to interact with a very large number of proteins as it functions within multiple co-repressor complexes (NuRD, SIN3, CoREST) and binds many transcription factors.
Reason: Per curation guidelines, protein binding (GO:0005515) is uninformative and should be replaced with more specific molecular function terms. HDAC1 physically interacts with many proteins, but this generic term does not convey functional information. More specific annotations such as histone deacetylase binding, transcription corepressor binding, NF-kappaB binding, and DNA-binding transcription factor binding are already present.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
Generic protein binding and weakly mechanistic interaction annotations are less informative than HDAC1 deacetylase activity and defined corepressor-complex membership.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylases act via the formation of large multiprotein complexes.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
The report supports specific enzymatic and chromatin-complex annotations for HDAC1 rather than generic binding or weakly localized annotations.
GO:0005515 protein binding
IPI
PMID:19144721
Pitx3 potentiates Nurr1 in dopamine neuron terminal differen... 		REMOVE
Summary: Protein binding annotation based on physical interaction evidence from PMID:19144721. HDAC1 is known to interact with a very large number of proteins as it functions within multiple co-repressor complexes (NuRD, SIN3, CoREST) and binds many transcription factors.
Reason: Per curation guidelines, protein binding (GO:0005515) is uninformative and should be replaced with more specific molecular function terms. HDAC1 physically interacts with many proteins, but this generic term does not convey functional information. More specific annotations such as histone deacetylase binding, transcription corepressor binding, NF-kappaB binding, and DNA-binding transcription factor binding are already present.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
Generic protein binding and weakly mechanistic interaction annotations are less informative than HDAC1 deacetylase activity and defined corepressor-complex membership.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylases act via the formation of large multiprotein complexes.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
The report supports specific enzymatic and chromatin-complex annotations for HDAC1 rather than generic binding or weakly localized annotations.
GO:0005667 transcription regulator complex
IPI
PMID:17182846
Cell fate determination factor DACH1 inhibits c-Jun-induced ... 		ACCEPT
Summary: HDAC1 is a component of transcription regulator complexes. This is a broad parent term for the more specific NuRD, SIN3, and CoREST complexes.
Reason: Correct but very general. HDAC1 does function in transcription regulator complexes. More specific complex annotations (NuRD, SIN3) are also present.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD, Sin3, CoREST, and related chromatin-repressor complexes.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylase that catalyzes the deacetylation of lysine residues on the N-terminal part of the core histones.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein corepressor complexes, especially SIN3, NuRD, and CoREST.
GO:0017053 transcription repressor complex
IPI
PMID:17182846
Cell fate determination factor DACH1 inhibits c-Jun-induced ... 		ACCEPT
Summary: HDAC1 functions within transcription repressor complexes including NuRD, SIN3, and CoREST, which mediate transcriptional repression through histone deacetylation.
Reason: HDAC1 is a core catalytic subunit of several transcription repressor complexes. This is a correct and informative annotation.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD, Sin3, CoREST, and related chromatin-repressor complexes.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylase that catalyzes the deacetylation of lysine residues on the N-terminal part of the core histones.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein corepressor complexes, especially SIN3, NuRD, and CoREST.
GO:0003682 chromatin binding
IDA
PMID:16109736
Adrenocorticotropic hormone-mediated signaling cascades coor... 		ACCEPT
Summary: HDAC1 binds chromatin as part of its function in co-repressor complexes. ChIP experiments have confirmed HDAC1 occupancy at promoters and other regulatory regions.
Reason: Chromatin binding is well supported by extensive ChIP-seq and ChIP-qPCR data showing HDAC1 occupancy at promoters, enhancers, and heterochromatic regions.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD, Sin3, CoREST, and related chromatin-repressor complexes.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylase that catalyzes the deacetylation of lysine residues on the N-terminal part of the core histones.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein corepressor complexes, especially SIN3, NuRD, and CoREST.
GO:0005515 protein binding
IPI
PMID:16109736
Adrenocorticotropic hormone-mediated signaling cascades coor... 		REMOVE
Summary: Protein binding annotation based on physical interaction evidence from PMID:16109736. HDAC1 is known to interact with a very large number of proteins as it functions within multiple co-repressor complexes (NuRD, SIN3, CoREST) and binds many transcription factors.
Reason: Per curation guidelines, protein binding (GO:0005515) is uninformative and should be replaced with more specific molecular function terms. HDAC1 physically interacts with many proteins, but this generic term does not convey functional information. More specific annotations such as histone deacetylase binding, transcription corepressor binding, NF-kappaB binding, and DNA-binding transcription factor binding are already present.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
Generic protein binding and weakly mechanistic interaction annotations are less informative than HDAC1 deacetylase activity and defined corepressor-complex membership.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylases act via the formation of large multiprotein complexes.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
The report supports specific enzymatic and chromatin-complex annotations for HDAC1 rather than generic binding or weakly localized annotations.
GO:0000122 negative regulation of transcription by RNA polymerase II
IDA
PMID:8917507
Transcriptional repression by YY1 is mediated by interaction... 		ACCEPT
Summary: HDAC1 negatively regulates transcription by RNA polymerase II through histone deacetylation at target gene promoters. This is a core biological process annotation for HDAC1.
Reason: Negative regulation of pol II transcription is a primary biological function of HDAC1. Supported by multiple lines of evidence (PMID:8917507, PMID:9271381, PMID:21093383).
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD, Sin3, CoREST, and related chromatin-repressor complexes.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylase that catalyzes the deacetylation of lysine residues on the N-terminal part of the core histones.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein corepressor complexes, especially SIN3, NuRD, and CoREST.
GO:0000122 negative regulation of transcription by RNA polymerase II
IDA
PMID:9271381
Identification of mouse histone deacetylase 1 as a growth fa... 		ACCEPT
Summary: HDAC1 negatively regulates transcription by RNA polymerase II through histone deacetylation at target gene promoters. This is a core biological process annotation for HDAC1.
Reason: Negative regulation of pol II transcription is a primary biological function of HDAC1. Supported by multiple lines of evidence (PMID:8917507, PMID:9271381, PMID:21093383).
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD, Sin3, CoREST, and related chromatin-repressor complexes.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylase that catalyzes the deacetylation of lysine residues on the N-terminal part of the core histones.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein corepressor complexes, especially SIN3, NuRD, and CoREST.
GO:0003714 transcription corepressor activity
IDA
PMID:8917507
Transcriptional repression by YY1 is mediated by interaction... 		ACCEPT
Summary: HDAC1 functions as a transcription corepressor by deacetylating histones at target gene promoters, leading to chromatin compaction and transcriptional silencing.
Reason: Transcription corepressor activity is a core function of HDAC1. It mediates transcriptional repression through histone deacetylation when recruited to target promoters by sequence-specific repressors.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD, Sin3, CoREST, and related chromatin-repressor complexes.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylase that catalyzes the deacetylation of lysine residues on the N-terminal part of the core histones.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein corepressor complexes, especially SIN3, NuRD, and CoREST.
GO:0005515 protein binding
IPI
PMID:8917507
Transcriptional repression by YY1 is mediated by interaction... 		REMOVE
Summary: Protein binding annotation based on physical interaction evidence from PMID:8917507. HDAC1 is known to interact with a very large number of proteins as it functions within multiple co-repressor complexes (NuRD, SIN3, CoREST) and binds many transcription factors.
Reason: Per curation guidelines, protein binding (GO:0005515) is uninformative and should be replaced with more specific molecular function terms. HDAC1 physically interacts with many proteins, but this generic term does not convey functional information. More specific annotations such as histone deacetylase binding, transcription corepressor binding, NF-kappaB binding, and DNA-binding transcription factor binding are already present.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
Generic protein binding and weakly mechanistic interaction annotations are less informative than HDAC1 deacetylase activity and defined corepressor-complex membership.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylases act via the formation of large multiprotein complexes.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
The report supports specific enzymatic and chromatin-complex annotations for HDAC1 rather than generic binding or weakly localized annotations.
GO:0021766 hippocampus development
IGI
PMID:19380719
Histone deacetylases 1 and 2 control the progression of neur... 		KEEP AS NON CORE
Summary: HDAC1 contributes to hippocampus development (PMID:19380719).
Reason: Specific developmental process affected by HDAC1 loss. Pleiotropic downstream effect.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 has many developmental and signaling consequences through chromatin deacetylation; these are non-core outputs of the core enzymatic function.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylation gives a tag for epigenetic repression and plays an important role in transcriptional regulation, cell cycle progression and developmental events.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
The report supports HDAC1 as a chromatin deacetylase whose developmental, signaling, cell-cycle, DNA-damage, and pathway phenotypes are context-specific downstream outputs.
GO:0030182 neuron differentiation
IGI
PMID:19380719
Histone deacetylases 1 and 2 control the progression of neur... 		KEEP AS NON CORE
Summary: HDAC1 is involved in neuron differentiation (PMID:19380719).
Reason: Downstream pleiotropic developmental effect.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 has many developmental and signaling consequences through chromatin deacetylation; these are non-core outputs of the core enzymatic function.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylation gives a tag for epigenetic repression and plays an important role in transcriptional regulation, cell cycle progression and developmental events.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
The report supports HDAC1 as a chromatin deacetylase whose developmental, signaling, cell-cycle, DNA-damage, and pathway phenotypes are context-specific downstream outputs.
GO:0005515 protein binding
IPI
PMID:12198165
The chromatin remodeling complex NoRC targets HDAC1 to the r... 		REMOVE
Summary: Protein binding annotation based on physical interaction evidence from PMID:12198165. HDAC1 is known to interact with a very large number of proteins as it functions within multiple co-repressor complexes (NuRD, SIN3, CoREST) and binds many transcription factors.
Reason: Per curation guidelines, protein binding (GO:0005515) is uninformative and should be replaced with more specific molecular function terms. HDAC1 physically interacts with many proteins, but this generic term does not convey functional information. More specific annotations such as histone deacetylase binding, transcription corepressor binding, NF-kappaB binding, and DNA-binding transcription factor binding are already present.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
Generic protein binding and weakly mechanistic interaction annotations are less informative than HDAC1 deacetylase activity and defined corepressor-complex membership.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylases act via the formation of large multiprotein complexes.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
The report supports specific enzymatic and chromatin-complex annotations for HDAC1 rather than generic binding or weakly localized annotations.
GO:0005515 protein binding
IPI
PMID:16085498
The PHD finger/bromodomain of NoRC interacts with acetylated... 		REMOVE
Summary: Protein binding annotation based on physical interaction evidence from PMID:16085498. HDAC1 is known to interact with a very large number of proteins as it functions within multiple co-repressor complexes (NuRD, SIN3, CoREST) and binds many transcription factors.
Reason: Per curation guidelines, protein binding (GO:0005515) is uninformative and should be replaced with more specific molecular function terms. HDAC1 physically interacts with many proteins, but this generic term does not convey functional information. More specific annotations such as histone deacetylase binding, transcription corepressor binding, NF-kappaB binding, and DNA-binding transcription factor binding are already present.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
Generic protein binding and weakly mechanistic interaction annotations are less informative than HDAC1 deacetylase activity and defined corepressor-complex membership.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylases act via the formation of large multiprotein complexes.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
The report supports specific enzymatic and chromatin-complex annotations for HDAC1 rather than generic binding or weakly localized annotations.
GO:0043025 neuronal cell body
IDA
PMID:18651664
Histone deacetylases 1 and 2 are expressed at distinct stage... 		ACCEPT
Summary: HDAC1 has been localized to neuronal cell bodies (PMID:18651664).
Reason: Neuronal cell body localization supported by IDA evidence.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD, Sin3, CoREST, and related chromatin-repressor complexes.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylase that catalyzes the deacetylation of lysine residues on the N-terminal part of the core histones.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein corepressor complexes, especially SIN3, NuRD, and CoREST.
GO:0005515 protein binding
IPI
PMID:16103876
Mnt transcriptional repressor is functionally regulated duri... 		REMOVE
Summary: Protein binding annotation based on physical interaction evidence from PMID:16103876. HDAC1 is known to interact with a very large number of proteins as it functions within multiple co-repressor complexes (NuRD, SIN3, CoREST) and binds many transcription factors.
Reason: Per curation guidelines, protein binding (GO:0005515) is uninformative and should be replaced with more specific molecular function terms. HDAC1 physically interacts with many proteins, but this generic term does not convey functional information. More specific annotations such as histone deacetylase binding, transcription corepressor binding, NF-kappaB binding, and DNA-binding transcription factor binding are already present.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
Generic protein binding and weakly mechanistic interaction annotations are less informative than HDAC1 deacetylase activity and defined corepressor-complex membership.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylases act via the formation of large multiprotein complexes.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
The report supports specific enzymatic and chromatin-complex annotations for HDAC1 rather than generic binding or weakly localized annotations.
GO:0005515 protein binding
IPI
PMID:9139821
Role for N-CoR and histone deacetylase in Sin3-mediated tran... 		REMOVE
Summary: Protein binding annotation based on physical interaction evidence from PMID:9139821. HDAC1 is known to interact with a very large number of proteins as it functions within multiple co-repressor complexes (NuRD, SIN3, CoREST) and binds many transcription factors.
Reason: Per curation guidelines, protein binding (GO:0005515) is uninformative and should be replaced with more specific molecular function terms. HDAC1 physically interacts with many proteins, but this generic term does not convey functional information. More specific annotations such as histone deacetylase binding, transcription corepressor binding, NF-kappaB binding, and DNA-binding transcription factor binding are already present.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
Generic protein binding and weakly mechanistic interaction annotations are less informative than HDAC1 deacetylase activity and defined corepressor-complex membership.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylases act via the formation of large multiprotein complexes.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
The report supports specific enzymatic and chromatin-complex annotations for HDAC1 rather than generic binding or weakly localized annotations.
GO:0003677 DNA binding
IDA
PMID:14593184
DNA methylation-related chromatin remodeling in activity-dep... 		MARK AS OVER ANNOTATED
Summary: General DNA binding annotation. HDAC1 associates with DNA through chromatin complexes rather than having intrinsic sequence-specific DNA binding.
Reason: HDAC1 does not have intrinsic DNA binding activity in the classical sense. It associates with DNA indirectly through chromatin complexes and recruitment by DNA-binding transcription factors. More appropriate terms like chromatin binding (GO:0003682) are already annotated.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 is recruited to chromatin by DNA-binding factors but is not itself a sequence-specific DNA-binding transcription factor.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylase that catalyzes the deacetylation of lysine residues on core histones.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
The report supports HDAC1 as a chromatin deacetylase whose developmental, signaling, cell-cycle, DNA-damage, and pathway phenotypes are context-specific downstream outputs.
GO:0003682 chromatin binding
IDA
PMID:16678101
Homeodomain-mediated beta-catenin-dependent switching events... 		ACCEPT
Summary: HDAC1 binds chromatin as part of its function in co-repressor complexes. ChIP experiments have confirmed HDAC1 occupancy at promoters and other regulatory regions.
Reason: Chromatin binding is well supported by extensive ChIP-seq and ChIP-qPCR data showing HDAC1 occupancy at promoters, enhancers, and heterochromatic regions.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD, Sin3, CoREST, and related chromatin-repressor complexes.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylase that catalyzes the deacetylation of lysine residues on the N-terminal part of the core histones.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein corepressor complexes, especially SIN3, NuRD, and CoREST.
GO:0003714 transcription corepressor activity
IDA
PMID:15509593
HNF1beta/TCF2 mutations impair transactivation potential thr... 		ACCEPT
Summary: HDAC1 functions as a transcription corepressor by deacetylating histones at target gene promoters, leading to chromatin compaction and transcriptional silencing.
Reason: Transcription corepressor activity is a core function of HDAC1. It mediates transcriptional repression through histone deacetylation when recruited to target promoters by sequence-specific repressors.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD, Sin3, CoREST, and related chromatin-repressor complexes.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylase that catalyzes the deacetylation of lysine residues on the N-terminal part of the core histones.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein corepressor complexes, especially SIN3, NuRD, and CoREST.
GO:0005515 protein binding
IPI
PMID:15509593
HNF1beta/TCF2 mutations impair transactivation potential thr... 		REMOVE
Summary: Protein binding annotation based on physical interaction evidence from PMID:15509593. HDAC1 is known to interact with a very large number of proteins as it functions within multiple co-repressor complexes (NuRD, SIN3, CoREST) and binds many transcription factors.
Reason: Per curation guidelines, protein binding (GO:0005515) is uninformative and should be replaced with more specific molecular function terms. HDAC1 physically interacts with many proteins, but this generic term does not convey functional information. More specific annotations such as histone deacetylase binding, transcription corepressor binding, NF-kappaB binding, and DNA-binding transcription factor binding are already present.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
Generic protein binding and weakly mechanistic interaction annotations are less informative than HDAC1 deacetylase activity and defined corepressor-complex membership.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylases act via the formation of large multiprotein complexes.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
The report supports specific enzymatic and chromatin-complex annotations for HDAC1 rather than generic binding or weakly localized annotations.
GO:0000792 heterochromatin
IDA
PMID:14643676
Expression and localization of components of the histone dea... 		ACCEPT
Summary: HDAC1 has been localized to heterochromatin regions by immunofluorescence/ChIP studies, consistent with its role in histone deacetylation and chromatin compaction.
Reason: HDAC1 localization to heterochromatin is experimentally validated and consistent with its function in promoting chromatin condensation through deacetylation.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD, Sin3, CoREST, and related chromatin-repressor complexes.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylase that catalyzes the deacetylation of lysine residues on the N-terminal part of the core histones.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein corepressor complexes, especially SIN3, NuRD, and CoREST.
GO:0005515 protein binding
IPI
PMID:16462733
The NuRD component Mbd3 is required for pluripotency of embr... 		REMOVE
Summary: Protein binding annotation based on physical interaction evidence from PMID:16462733. HDAC1 is known to interact with a very large number of proteins as it functions within multiple co-repressor complexes (NuRD, SIN3, CoREST) and binds many transcription factors.
Reason: Per curation guidelines, protein binding (GO:0005515) is uninformative and should be replaced with more specific molecular function terms. HDAC1 physically interacts with many proteins, but this generic term does not convey functional information. More specific annotations such as histone deacetylase binding, transcription corepressor binding, NF-kappaB binding, and DNA-binding transcription factor binding are already present.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
Generic protein binding and weakly mechanistic interaction annotations are less informative than HDAC1 deacetylase activity and defined corepressor-complex membership.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylases act via the formation of large multiprotein complexes.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
The report supports specific enzymatic and chromatin-complex annotations for HDAC1 rather than generic binding or weakly localized annotations.
GO:0016581 NuRD complex
IPI
PMID:16462733
The NuRD component Mbd3 is required for pluripotency of embr... 		ACCEPT
Summary: HDAC1 is a core catalytic subunit of the NuRD (nucleosome remodeling and deacetylase) complex. Proteomic studies show approximately 49% of cellular HDAC1 in ESCs is in the NuRD complex (deep research review). Well supported by mass spectrometry identification (PMID:27806305) and multiple interaction studies.
Reason: NuRD complex membership is a core aspect of HDAC1 function. HDAC1 serves as the catalytic deacetylase subunit within NuRD. Extensively validated by proteomics and co-immunoprecipitation studies.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD, Sin3, CoREST, and related chromatin-repressor complexes.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylase that catalyzes the deacetylation of lysine residues on the N-terminal part of the core histones.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein corepressor complexes, especially SIN3, NuRD, and CoREST.
GO:0005515 protein binding
IPI
PMID:11641275
The hairless gene mutated in congenital hair loss disorders ... 		REMOVE
Summary: Protein binding annotation based on physical interaction evidence from PMID:11641275. HDAC1 is known to interact with a very large number of proteins as it functions within multiple co-repressor complexes (NuRD, SIN3, CoREST) and binds many transcription factors.
Reason: Per curation guidelines, protein binding (GO:0005515) is uninformative and should be replaced with more specific molecular function terms. HDAC1 physically interacts with many proteins, but this generic term does not convey functional information. More specific annotations such as histone deacetylase binding, transcription corepressor binding, NF-kappaB binding, and DNA-binding transcription factor binding are already present.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
Generic protein binding and weakly mechanistic interaction annotations are less informative than HDAC1 deacetylase activity and defined corepressor-complex membership.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylases act via the formation of large multiprotein complexes.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
The report supports specific enzymatic and chromatin-complex annotations for HDAC1 rather than generic binding or weakly localized annotations.
GO:0016581 NuRD complex
IPI
PMID:14645126
Atrophin 2 recruits histone deacetylase and is required for ... 		ACCEPT
Summary: HDAC1 is a core catalytic subunit of the NuRD (nucleosome remodeling and deacetylase) complex. Proteomic studies show approximately 49% of cellular HDAC1 in ESCs is in the NuRD complex (deep research review). Well supported by mass spectrometry identification (PMID:27806305) and multiple interaction studies.
Reason: NuRD complex membership is a core aspect of HDAC1 function. HDAC1 serves as the catalytic deacetylase subunit within NuRD. Extensively validated by proteomics and co-immunoprecipitation studies.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD, Sin3, CoREST, and related chromatin-repressor complexes.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylase that catalyzes the deacetylation of lysine residues on the N-terminal part of the core histones.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein corepressor complexes, especially SIN3, NuRD, and CoREST.
GO:0007492 endoderm development
IDA
PMID:15060137
Regulation of mammalian epithelial differentiation and intes... 		KEEP AS NON CORE
Summary: HDAC1 plays a role in endoderm development (PMID:15060137).
Reason: Specific developmental process affected by HDAC1. Pleiotropic downstream effect.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 has many developmental and signaling consequences through chromatin deacetylation; these are non-core outputs of the core enzymatic function.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylation gives a tag for epigenetic repression and plays an important role in transcriptional regulation, cell cycle progression and developmental events.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
The report supports HDAC1 as a chromatin deacetylase whose developmental, signaling, cell-cycle, DNA-damage, and pathway phenotypes are context-specific downstream outputs.
GO:0007492 endoderm development
IMP
PMID:15060137
Regulation of mammalian epithelial differentiation and intes... 		KEEP AS NON CORE
Summary: HDAC1 plays a role in endoderm development (PMID:15060137).
Reason: Specific developmental process affected by HDAC1. Pleiotropic downstream effect.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 has many developmental and signaling consequences through chromatin deacetylation; these are non-core outputs of the core enzymatic function.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylation gives a tag for epigenetic repression and plays an important role in transcriptional regulation, cell cycle progression and developmental events.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
The report supports HDAC1 as a chromatin deacetylase whose developmental, signaling, cell-cycle, DNA-damage, and pathway phenotypes are context-specific downstream outputs.
GO:0000792 heterochromatin
IDA
PMID:14519686
Analysis of mammalian proteins involved in chromatin modific... 		ACCEPT
Summary: HDAC1 has been localized to heterochromatin regions by immunofluorescence/ChIP studies, consistent with its role in histone deacetylation and chromatin compaction.
Reason: HDAC1 localization to heterochromatin is experimentally validated and consistent with its function in promoting chromatin condensation through deacetylation.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD, Sin3, CoREST, and related chromatin-repressor complexes.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylase that catalyzes the deacetylation of lysine residues on the N-terminal part of the core histones.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein corepressor complexes, especially SIN3, NuRD, and CoREST.
GO:0000118 histone deacetylase complex
IPI
PMID:14645126
Atrophin 2 recruits histone deacetylase and is required for ... 		ACCEPT
Summary: HDAC1 is a core component of multiple histone deacetylase complexes including NuRD, SIN3, and CoREST. This is a general parent term encompassing all such complexes.
Reason: HDAC1 is the defining catalytic subunit of multiple HDAC complexes. This broader term is appropriate as a parent annotation alongside the more specific NuRD and SIN3 complex terms.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD, Sin3, CoREST, and related chromatin-repressor complexes.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylase that catalyzes the deacetylation of lysine residues on the N-terminal part of the core histones.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
HDAC1 is a class I Zn2+-dependent histone/protein deacetylase that removes acetyl groups from lysine residues on histone tails and non-histone proteins.
GO:0005515 protein binding
IPI
PMID:14645126
Atrophin 2 recruits histone deacetylase and is required for ... 		REMOVE
Summary: Protein binding annotation based on physical interaction evidence from PMID:14645126. HDAC1 is known to interact with a very large number of proteins as it functions within multiple co-repressor complexes (NuRD, SIN3, CoREST) and binds many transcription factors.
Reason: Per curation guidelines, protein binding (GO:0005515) is uninformative and should be replaced with more specific molecular function terms. HDAC1 physically interacts with many proteins, but this generic term does not convey functional information. More specific annotations such as histone deacetylase binding, transcription corepressor binding, NF-kappaB binding, and DNA-binding transcription factor binding are already present.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
Generic protein binding and weakly mechanistic interaction annotations are less informative than HDAC1 deacetylase activity and defined corepressor-complex membership.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylases act via the formation of large multiprotein complexes.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
The report supports specific enzymatic and chromatin-complex annotations for HDAC1 rather than generic binding or weakly localized annotations.
GO:0005515 protein binding
IPI
PMID:12529400
Homeodomain-interacting protein kinase 1 modulates Daxx loca... 		REMOVE
Summary: Protein binding annotation based on physical interaction evidence from PMID:12529400. HDAC1 is known to interact with a very large number of proteins as it functions within multiple co-repressor complexes (NuRD, SIN3, CoREST) and binds many transcription factors.
Reason: Per curation guidelines, protein binding (GO:0005515) is uninformative and should be replaced with more specific molecular function terms. HDAC1 physically interacts with many proteins, but this generic term does not convey functional information. More specific annotations such as histone deacetylase binding, transcription corepressor binding, NF-kappaB binding, and DNA-binding transcription factor binding are already present.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
Generic protein binding and weakly mechanistic interaction annotations are less informative than HDAC1 deacetylase activity and defined corepressor-complex membership.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylases act via the formation of large multiprotein complexes.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
The report supports specific enzymatic and chromatin-complex annotations for HDAC1 rather than generic binding or weakly localized annotations.
GO:0000118 histone deacetylase complex
TAS
PMID:12711221
Class II histone deacetylases: versatile regulators. 		ACCEPT
Summary: HDAC1 is a core component of multiple histone deacetylase complexes including NuRD, SIN3, and CoREST. This is a general parent term encompassing all such complexes.
Reason: HDAC1 is the defining catalytic subunit of multiple HDAC complexes. This broader term is appropriate as a parent annotation alongside the more specific NuRD and SIN3 complex terms.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD, Sin3, CoREST, and related chromatin-repressor complexes.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylase that catalyzes the deacetylation of lysine residues on the N-terminal part of the core histones.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
HDAC1 is a class I Zn2+-dependent histone/protein deacetylase that removes acetyl groups from lysine residues on histone tails and non-histone proteins.
GO:0005737 cytoplasm
TAS
PMID:12711221
Class II histone deacetylases: versatile regulators. 		KEEP AS NON CORE
Summary: HDAC1 has some cytoplasmic localization in addition to its predominant nuclear localization.
Reason: Cytoplasm is a minor localization relative to HDAC1's predominant nuclear chromatin/corepressor role and should not be treated as a core cellular-component call.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-uniprot.txt
GO; GO:0005737; C:cytoplasm; TAS:UniProtKB.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
Class I HDACs, including HDAC1, are predominantly or exclusively nuclear, consistent with chromatin accessibility and transcriptional control roles.
GO:0006325 chromatin organization
TAS
PMID:12711221
Class II histone deacetylases: versatile regulators. 		ACCEPT
Summary: HDAC1 plays a role in chromatin organization through histone deacetylation, which promotes nucleosome compaction.
Reason: Chromatin organization is a direct consequence of HDAC1 enzymatic activity.
Supporting Evidence:
file:mouse/Hdac1/Hdac1-deep-research-openai.md
HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD, Sin3, CoREST, and related chromatin-repressor complexes.
file:mouse/Hdac1/Hdac1-uniprot.txt
Histone deacetylase that catalyzes the deacetylation of lysine residues on the N-terminal part of the core histones.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein corepressor complexes, especially SIN3, NuRD, and CoREST.

Core Functions

Catalyzes zinc-dependent hydrolytic removal of acetyl groups from lysine residues on histones H2A, H2B, H3, and H4 as the catalytic subunit of the NuRD corepressor complex, mediating transcriptional repression through chromatin compaction. Approximately 49% of cellular HDAC1 resides in the NuRD complex in embryonic stem cells.

Molecular Function:
histone deacetylase activity
Directly Involved In:
negative regulation of transcription by RNA polymerase II chromatin organization
Cellular Locations:
chromatin nucleus
In Complex:
NuRD complex
Supporting Evidence:
  • file:mouse/Hdac1/Hdac1-uniprot.txt
    Histone deacetylase that catalyzes the deacetylation of lysine residues on the N-terminal part of the core histones.
  • file:mouse/Hdac1/Hdac1-deep-research-openai.md
    HDAC1 is a catalytic subunit of NuRD, Sin3, CoREST and related repressor complexes.
  • file:mouse/Hdac1/Hdac1-deep-research-falcon.md
    HDAC1 is a class I Zn2+-dependent histone/protein deacetylase that removes acetyl groups from lysine residues on histone tails and non-histone proteins.

Catalyzes histone deacetylation as the catalytic subunit of the Sin3 corepressor complex, which is recruited to target gene promoters by sequence-specific transcription factors and scaffold proteins SIN3A/SIN3B. Approximately 15% of cellular HDAC1 resides in the SIN3 complex.

Molecular Function:
histone deacetylase activity
Directly Involved In:
negative regulation of transcription by RNA polymerase II
Cellular Locations:
chromatin nucleus
In Complex:
Sin3-type complex
Supporting Evidence:
  • file:mouse/Hdac1/Hdac1-uniprot.txt
    Histone deacetylase that catalyzes the deacetylation of lysine residues on the N-terminal part of the core histones.
  • file:mouse/Hdac1/Hdac1-deep-research-openai.md
    HDAC1 is a catalytic subunit of NuRD, Sin3, CoREST and related repressor complexes.
  • file:mouse/Hdac1/Hdac1-deep-research-falcon.md
    HDAC1 is a class I Zn2+-dependent histone/protein deacetylase that removes acetyl groups from lysine residues on histone tails and non-histone proteins.

Catalyzes histone deacetylation as part of CoREST repressor complexes, including the HDAC1/CoREST1/LSD1 ternary complex that represses transcription through chromatin deacetylation and demethylase-associated corepression.

Molecular Function:
histone deacetylase activity
Directly Involved In:
negative regulation of transcription by RNA polymerase II
Cellular Locations:
chromatin nucleus
In Complex:
histone deacetylase complex
Supporting Evidence:
  • PMID:30279482
    A ternary complex of HDAC1/CoREST1/LSD1 is able to hydrolyse both histone H3 Lys18-acetyl (H3K18ac) and H3 Lys18-crotonyl (H3K18cr) peptide substrates
  • file:mouse/Hdac1/Hdac1-deep-research-openai.md
    HDAC1 is a catalytic subunit of NuRD, Sin3, CoREST and related repressor complexes.
  • file:mouse/Hdac1/Hdac1-deep-research-falcon.md
    HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein corepressor complexes, especially SIN3, NuRD, and CoREST.

Removes crotonyl groups from histone lysine residues in vivo. Genetic deletion of HDAC1/2 in ES cells causes an 85% reduction in total decrotonylase activity and increased global histone crotonylation.

Molecular Function:
histone decrotonylase activity
Cellular Locations:
nucleus
Supporting Evidence:
  • PMID:30279482
    Genetic deletion of HDAC1/2 in ES cells increases global levels of histone crotonylation and causes an 85% reduction in total decrotonylase activity
  • file:mouse/Hdac1/Hdac1-deep-research-openai.md
    HDAC1 is a catalytic subunit of chromatin corepressor complexes and mediates histone deacetylation-dependent transcriptional repression.
  • file:mouse/Hdac1/Hdac1-deep-research-falcon.md
    HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein corepressor complexes, especially SIN3, NuRD, and CoREST.

References

GO_REF:0000024
Method for ISS annotations
GO_REF:0000033
Phylogenetic Annotation (IBA)
GO_REF:0000096
UniProt-GOA annotation (ISO)
GO_REF:0000107
Automatic transfer of experimentally verified manual GO annotation data to orthologs using Ensembl Compara
GO_REF:0000116
Rhea-based UniProt to GO mapping
GO_REF:0000117
Automatic Gene Ontology annotation by MGI
GO_REF:0000119
Manual transfer of experimentally verified GO annotation data to orthologs by UniProt
GO_REF:0000120
UniProt-based electronic GO annotation (UniRule/ARBA/InterPro)
PMID:10615135
DNA methyltransferase Dnmt1 associates with histone deacetylase activity.
PMID:11115394
Msx3 protein recruits histone deacetylase to down-regulate the Msx1 promoter.
PMID:11641275
The hairless gene mutated in congenital hair loss disorders encodes a novel nuclear receptor corepressor.
PMID:11836251
Murine Sall1 represses transcription by recruiting a histone deacetylase complex.
PMID:11923873
Bop encodes a muscle-restricted protein containing MYND and SET domains and is essential for cardiac differentiation and morphogenesis.
PMID:11931769
The phosphorylation status of nuclear NF-kappa B determines its association with CBP/p300 or HDAC-1.
PMID:12198165
The chromatin remodeling complex NoRC targets HDAC1 to the ribosomal gene promoter and represses RNA polymerase I transcription.
PMID:12529400
Homeodomain-interacting protein kinase 1 modulates Daxx localization, phosphorylation, and transcriptional activity.
PMID:12711221
Class II histone deacetylases: versatile regulators.
PMID:12900441
Consequences of the depletion of zygotic and embryonic enhancer of zeste 2 during preimplantation mouse development.
PMID:14519686
Analysis of mammalian proteins involved in chromatin modification reveals new metaphase centromeric proteins and distinct chromosomal distribution patterns.
PMID:14593184
DNA methylation-related chromatin remodeling in activity-dependent BDNF gene regulation.
PMID:14643676
Expression and localization of components of the histone deacetylases multiprotein repressory complexes in the mouse preimplantation embryo.
PMID:14645126
Atrophin 2 recruits histone deacetylase and is required for the function of multiple signaling centers during mouse embryogenesis.
PMID:15060137
Regulation of mammalian epithelial differentiation and intestine development by class I histone deacetylases.
PMID:15226430
Circadian and light-induced transcription of clock gene Per1 depends on histone acetylation and deacetylation.
PMID:15337766
Leukemia/lymphoma-related factor, a POZ domain-containing transcriptional repressor, interacts with histone deacetylase-1 and inhibits cartilage oligomeric matrix protein gene expression and chondrogenesis.
PMID:15509593
HNF1beta/TCF2 mutations impair transactivation potential through altered co-regulator recruitment.
PMID:15608638
Loss of silent-chromatin looping and impaired imprinting of DLX5 in Rett syndrome.
PMID:15907476
REST and its corepressors mediate plasticity of neuronal gene chromatin throughout neurogenesis.
PMID:16085498
The PHD finger/bromodomain of NoRC interacts with acetylated histone H4K16 and is sufficient for rDNA silencing.
PMID:16103876
Mnt transcriptional repressor is functionally regulated during cell cycle progression.
PMID:16109736
Adrenocorticotropic hormone-mediated signaling cascades coordinate a cyclic pattern of steroidogenic factor 1-dependent transcriptional activation.
PMID:16407974
ETO2 coordinates cellular proliferation and differentiation during erythropoiesis.
PMID:16462733
The NuRD component Mbd3 is required for pluripotency of embryonic stem cells.
PMID:16678101
Homeodomain-mediated beta-catenin-dependent switching events dictate cell-lineage determination.
PMID:16805913
Identification and characterization of Smyd2: a split SET/MYND domain-containing histone H3 lysine 36-specific methyltransferase that interacts with the Sin3 histone deacetylase complex.
PMID:17056544
The transcriptional repressor cAMP response element modulator alpha interacts with histone deacetylase 1 to repress promoter activity.
PMID:17182846
Cell fate determination factor DACH1 inhibits c-Jun-induced contact-independent growth.
PMID:17392792
Opposing LSD1 complexes function in developmental gene activation and repression programmes.
PMID:17442941
Protein inhibitor of activated STAT 3 modulates osteoclastogenesis by down-regulation of NFATc1 and osteoclast-associated receptor.
PMID:17568773
Foxh1 recruits Gsc to negatively regulate Mixl1 expression during early mouse development.
PMID:17707228
Epigenetic regulation of hematopoietic differentiation by Gfi-1 and Gfi-1b is mediated by the cofactors CoREST and LSD1.
PMID:17905753
Adipose tissue mass is modulated by SLUG (SNAI2).
PMID:18486321
Acetylation and deacetylation regulate CCAAT/enhancer binding protein beta at K39 in mediating gene transcription.
PMID:18651664
Histone deacetylases 1 and 2 are expressed at distinct stages of neuro-glial development.
PMID:19144721
Pitx3 potentiates Nurr1 in dopamine neuron terminal differentiation through release of SMRT-mediated repression.
PMID:19235719
The homeobox gene Mohawk represses transcription by recruiting the sin3A/HDAC co-repressor complex.
PMID:19380719
Histone deacetylases 1 and 2 control the progression of neural precursors to neurons during brain development.
PMID:19424149
HDAC2 negatively regulates memory formation and synaptic plasticity.
PMID:19497860
LSD1-mediated epigenetic modification is required for TAL1 function and hematopoiesis.
PMID:19501046
Znhit1 causes cell cycle arrest and down-regulates CDK6 expression.
PMID:19503085
HDAC1 and HDAC2 regulate oligodendrocyte differentiation by disrupting the beta-catenin-TCF interaction.
PMID:19796622
Uncovering early response of gene regulatory networks in ESCs by systematic induction of transcription factors.
PMID:19805123
NF-kappaB activity is constitutively elevated in c-Abl null fibroblasts.
PMID:19927129
NuRD mediates activating and repressive functions of GATA-1 and FOG-1 during blood development.
PMID:20404188
Histone deacetylase 1 (HDAC1), but not HDAC2, controls embryonic stem cell differentiation.
PMID:20596014
Chromatin regulation by Brg1 underlies heart muscle development and disease.
PMID:20599664
A novel role for cardiac ankyrin repeat protein Ankrd1/CARP as a co-activator of the p53 tumor suppressor protein.
PMID:20720167
Metastasis tumor antigen 2 (MTA2) is involved in proper imprinted expression of H19 and Peg3 during mouse preimplantation development.
PMID:21093383
Hdac1 and Hdac2 act redundantly to control p63 and p53 functions in epidermal progenitor cells.
PMID:21177534
A novel KRAB domain-containing zinc finger transcription factor ZNF431 directly represses Patched1 transcription.
PMID:21448134
KDM5B regulates embryonic stem cell self-renewal and represses cryptic intragenic transcription.
PMID:21454521
The developmental regulator protein Gon4l associates with protein YY1, co-repressor Sin3a, and histone deacetylase 1 and mediates transcriptional repression.
PMID:21874018
lincRNAs act in the circuitry controlling pluripotency and differentiation.
PMID:21874024
The ubiquitin ligase Peli1 negatively regulates T cell activation and prevents autoimmunity.
PMID:21931736
CHD5, a brain-specific paralog of Mi2 chromatin remodeling enzymes, regulates expression of neuronal genes.
PMID:21937600
Transposon mutagenesis with coat color genotyping identifies an essential role for Skor2 in sonic hedgehog signaling and cerebellum development.
PMID:21960634
Histone lysine demethylase JARID1a activates CLOCK-BMAL1 and influences the circadian clock.
PMID:22075476
Metastasis-associated protein 3 (MTA3) regulates G2/M progression in proliferating mouse granulosa cells.
PMID:22242125
Stress-induced C/EBP homology protein (CHOP) represses MyoD transcription to delay myoblast differentiation.
PMID:22297846
Enhancer decommissioning by LSD1 during embryonic stem cell differentiation.
PMID:22334647
Protooncogene Ski cooperates with the chromatin-remodeling factor Satb2 in specifying callosal neurons.
PMID:22560079
NuRD suppresses pluripotency gene expression to promote transcriptional heterogeneity and lineage commitment.
PMID:22770845
The polycomb group protein L3mbtl2 assembles an atypical PRC1-family complex that is essential in pluripotent stem cells and early development.
PMID:22865885
Family with sequence similarity 60A (FAM60A) protein is a cell cycle-fluctuating regulator of the SIN3-HDAC1 histone deacetylase complex.
PMID:22918830
Histone deacetylase-1 (HDAC1) is a molecular switch between neuronal survival and death.
PMID:22984288
Human family with sequence similarity 60 member A (FAM60A) protein: a new subunit of the Sin3 deacetylase complex.
PMID:24240174
Divergent roles of HDAC1 and HDAC2 in the regulation of epidermal development and tumorigenesis.
PMID:24335282
Analysis of the SWI/SNF chromatin-remodeling complex during early heart development and BAF250a repression cardiac gene transcription during P19 cell differentiation.
PMID:24413057
Temporal orchestration of repressive chromatin modifiers by circadian clock Period complexes.
PMID:24736997
A novel protein, CHRONO, functions as a core component of the mammalian circadian clock.
PMID:26816381
Transcription factors LRF and BCL11A independently repress expression of fetal hemoglobin.
PMID:26974661
C/EBPα creates elite cells for iPSC reprogramming by upregulating Klf4 and increasing the levels of Lsd1 and Brd4.
PMID:28554894
Fam60a defines a variant Sin3a-Hdac complex in embryonic stem cells required for self-renewal.
PMID:30228260
A variant NuRD complex containing PWWP2A/B excludes MBD2/3 to regulate transcription at active genes.
PMID:30279482
Histone deacetylase (HDAC) 1 and 2 complexes regulate both histone acetylation and crotonylation in vivo.
PMID:30726206
Genes encoding SATB2-interacting proteins in adult cerebral cortex contribute to human cognitive ability.
PMID:30911105
Safeguard function of PU.1 shapes the inflammatory epigenome of neutrophils.
PMID:33795231
Regulation of otocyst patterning by Tbx2 and Tbx3 is required for inner ear morphogenesis in the mouse.
PMID:33831416
The uncharacterized SANT and BTB domain-containing protein SANBR inhibits class switch recombination.
PMID:34180153
PWWP2B Fine-Tunes Adipose Thermogenesis by Stabilizing HDACs in a NuRD Subcomplex.
PMID:8917507
Transcriptional repression by YY1 is mediated by interaction with a mammalian homolog of the yeast global regulator RPD3.
PMID:9139821
Role for N-CoR and histone deacetylase in Sin3-mediated transcriptional repression.
PMID:9271381
Identification of mouse histone deacetylase 1 as a growth factor-inducible gene.
PMID:9651585
SAP30, a novel protein conserved between human and yeast, is a component of a histone deacetylase complex.
Reactome:R-MMU-573336
Reactome pathway annotation
Reactome:R-MMU-573376
Reactome pathway annotation
Reactome:R-MMU-573383
Reactome pathway annotation
Reactome:R-MMU-8978954
Reactome pathway annotation
Reactome:R-MMU-8978970
Reactome pathway annotation
Reactome:R-MMU-8978980
Reactome pathway annotation
Reactome:R-MMU-8978989
Reactome pathway annotation
Reactome:R-MMU-9006133
Reactome pathway annotation
Reactome:R-MMU-9017958
Reactome pathway annotation
Reactome:R-MMU-9625109
Reactome pathway annotation
Reactome:R-MMU-9727502
Reactome pathway annotation
Reactome:R-MMU-9844527
Reactome pathway annotation
Reactome:R-MMU-9845305
Reactome pathway annotation
Reactome:R-NUL-573373
Reactome pathway annotation
Reactome:R-NUL-573385
Reactome pathway annotation
file:mouse/Hdac1/Hdac1-uniprot.txt
UniProt record for mouse Hdac1
  • Hdac1 is a histone/protein deacetylase and deacylase in corepressor complexes.
    "Histone deacetylase that catalyzes the deacetylation of lysine residues on the N-terminal part of the core histones."
file:mouse/Hdac1/Hdac1-deep-research-openai.md
OpenAI deep research report on mouse Hdac1
  • HDAC1 is a catalytic subunit of NuRD, Sin3, CoREST and related chromatin-repressor complexes.
file:mouse/Hdac1/Hdac1-deep-research-falcon.md
Falcon deep research report on mouse Hdac1
  • HDAC1 is a complex-integrated nuclear lysine deacetylase in SIN3, NuRD, CoREST, and related chromatin regulatory complexes.
    "HDAC1 is best annotated as a complex-integrated nuclear lysine deacetylase; modern evidence supports that most HDAC1 is embedded in corepressor complexes that specify function and genomic binding."

Deep Research

Falcon

(Hdac1-deep-research-falcon.md)
Research Report: Mouse **Hdac1** (UniProt **O09106**) — Functional Annotation Falcon Edison Scientific Literature 31 citations 2026-05-03T14:19:40.748240

The research report should be a detailed narrative explaining the function, biological processes, and localization of the gene product. Citations should be given for all claims.

You should prioritize authoritative reviews and primary scientific literature when conducting research. You can supplement
this with annotations you find in gene/protein databases, but these can be outdated or inaccurate.

We are specifically interested in the primary function of the gene - for enzymes, what reaction is catalyzed, and what is the substrate specificity? For transporters, what is the substrate? For structural proteins or adapters, what is the broader structural role? For signaling molecules, what is the role in the pathway.

We are interested in where in or outside the cell the gene product carries out its function.

We are also interested in the signaling or biochemical pathways in which the gene functions. We are less interested in broad pleiotropic effects, except where these elucidate the precise role.

Include evidence where possible. We are interested in both experimental evidence as well as inference from structure, evolution, or bioinformatic analysis. Precise studies should be prioritized over high-throughput, where available.

Research Report: Mouse Hdac1 (UniProt O09106) — Functional Annotation

0) Target verification (critical identity checks)

The requested target is Mus musculus Hdac1, encoding histone deacetylase 1 (HDAC1), a class I Zn2+-dependent histone deacetylase that functions predominantly as the catalytic subunit of nuclear multiprotein corepressor complexes (e.g., SIN3, NuRD, CoREST). This identity is consistent across multiple retrieved sources that discuss mouse Hdac1/HDAC1 biology and class I HDAC biochemistry. (english2025rapiddegradationof pages 1-2, curcio2024thehistonedeacetylase pages 3-4, zhu2024hdac1andhdac2 pages 1-2)

Important limitation: the retrieved full texts did not explicitly mention the UniProt accession O09106; therefore, the accession-to-gene mapping is taken from the user-provided UniProt context and cross-validated by concordant gene/protein descriptions in the literature rather than by a direct UniProt citation within the retrieved papers. (english2025rapiddegradationof pages 1-2, curcio2024thehistonedeacetylase pages 3-4)

1) Key concepts and definitions (current understanding)

1.1 What HDAC1 is

HDAC1 is a class I histone deacetylase (HDAC)—a Zn2+-dependent metalloenzyme class that removes acetyl groups from lysine residues in histone tails and many non-histone proteins, typically linking deacetylation to chromatin compaction and transcriptional regulation. Class I HDACs are generally described as predominantly/exclusively nuclear. (curcio2024thehistonedeacetylase pages 3-4, barrett2024hdacactivityis pages 1-2, castiello2025newfrontiersfor pages 42-45)

1.2 Enzymatic activity and mechanism

Class I/II/IV HDACs catalyze deacetylation via Zn2+-dependent hydrolysis in a conserved active-site channel; mechanistic descriptions emphasize a metal-activated water nucleophile and general acid–base chemistry. (shi2024advancesintargeting pages 1-2, curcio2024thehistonedeacetylase pages 3-4)

A recent structural review table summarizing class I HDACs reports HDAC1 Zn2+ coordination residues as His140, His141, Asp176, Asp264, and lists HDAC1 association with Sin3 and NuRD complexes (with CoREST also noted elsewhere in the same review). (curcio2024thehistonedeacetylase media 2e20e924)

1.3 Substrate scope (histone and non-histone)

HDAC1 is described as deacetylating lysines on core histones (H2A/H2B/H3/H4) (sadia2025epigeneticregulationthrough pages 4-6) and is also linked to non-histone substrates; for example, a review describes p53 as a deacetylation target of HDAC1-containing complexes. (castiello2025newfrontiersfor pages 42-45)

2) Molecular function, complexes, and localization

2.1 Complex-centric biology of HDAC1

A central modern view is that class I HDACs—including HDAC1—act within multiprotein complexes that dictate genomic targeting, substrate selection, and regulatory function. Reviews and primary studies consistently cite SIN3, NuRD, and CoREST as key HDAC1/2-containing assemblies. (castiello2025newfrontiersfor pages 42-45, curcio2024thehistonedeacetylase pages 3-4, barrett2024hdacactivityis pages 1-2)

Quantitative complex distribution in mouse cells (high-value statistic): In mouse embryonic stem cells, HDAC1-Flag co-immunoprecipitation/mass spectrometry estimated that 92% of HDAC1 resides in three complexes—NuRD (49%), CoREST (28%), and SIN3 (15%)—providing a quantitative basis for annotating HDAC1 as a complex-dedicated enzyme rather than a solitary deacetylase. (alshehri2025mutationsonthe pages 1-5, alshehri2025mutationsonthe pages 8-10)

2.2 Nuclear localization

Class I HDACs, including HDAC1, are described as predominantly or exclusively nuclear, consistent with roles in chromatin accessibility and transcriptional control. (curcio2024thehistonedeacetylase pages 3-4, castiello2025newfrontiersfor pages 42-45, sadia2025epigeneticregulationthrough pages 4-6)

3) Biological processes and pathways (mouse-focused)

3.1 Neurodevelopment: HDAC1/2 control of Wnt signaling (2024 primary evidence)

A 2024 mouse neurodevelopment study (iScience; publication date: Sep 2024; URL: https://doi.org/10.1016/j.isci.2024.110600) reports that HDAC1 and HDAC2 act as epigenetic repressors of Wnt signaling during early neocortical development. Conditional depletion of HDAC1/2 from neuroepithelial progenitors (NPs) upregulated Wnt pathway genes, impaired NP-to-radial glial progenitor (RGP) transition, and produced proliferative rosette structures; multi-omics identified Wnt9a as a key HDAC1/2-regulated target, and a Wnt inhibitor partially rescued cortical defects (supporting causality). (zhu2024hdac1andhdac2 pages 1-2)

This provides a pathway-level functional annotation: Hdac1 participates in transcriptional programs that restrain Wnt signaling to enable correct neural progenitor state transitions. (zhu2024hdac1andhdac2 pages 1-2)

3.2 Cell-cycle repression models refined by 2024 evidence

A 2024 Nature Communications paper (publication date: May 2024; URL: https://doi.org/10.1038/s41467-024-48724-0) re-examines long-standing models in which HDAC complexes (often recruited via RB or DREAM) are required to repress cell-cycle genes. In arrested cells, the study reports that HDAC activity is dispensable for DREAM/E2F:RB-dependent repression in their tested settings; HDAC inhibition increased histone acetylation at targets but did not broadly derepress RB/DREAM target genes. This refines “HDAC = required for repression” assumptions in certain cell-cycle contexts. (barrett2024hdacactivityis pages 1-2)

4) Recent developments and latest research (prioritizing 2023–2024)

4.1 Structural annotation improvements (2024 review + table)

A 2024 Pharmaceuticals review (publication date: May 2024; URL: https://doi.org/10.3390/ph17050620) summarizes class I HDAC structural features and nuclear localization and provides a table-level mapping of HDAC1 Zn2+ coordination residues and its principal complexes. This supports up-to-date mechanistic annotation of active-site chemistry and complex membership that can be incorporated into functional annotation pipelines. (curcio2024thehistonedeacetylase pages 3-4, curcio2024thehistonedeacetylase media 2e20e924)

4.2 Complex stoichiometry/abundance as a functional concept (quantitative proteomics; mouse ESCs)

Quantitative proteomics in mouse ESCs provides a near “complex census” for HDAC1, supporting the current understanding that HDAC1’s biological specificity arises from complex assembly (NuRD/CoREST/SIN3 dominating) and that specific surface residues tune complex binding. (alshehri2025mutationsonthe pages 1-5, alshehri2025mutationsonthe pages 8-10)

4.3 Rapid perturbation experiments (functional genomics; mouse ESC-derived system)

A Nucleic Acids Research study (publication date: Jun 2025; URL: https://doi.org/10.1093/nar/gkae1223) introduced acute, isoform-specific depletion of HDAC1 (in ESCs lacking HDAC2) using the dTAG system. Although outside the requested 2023–2024 window, it provides unusually direct mechanistic evidence:

  • HDAC1 depletion occurred in <1 hour.
  • Histone acetylation increased within 2 hours, with H2BK5 and H2BK11 among the most sensitive.
  • Differential gene expression after HDAC1 loss showed time-dependent directionality: 275 up vs 15 down (2 h); 1,153 up vs 443 down (6 h); 1,146 up vs 967 down (24 h).
  • Upregulated genes gained H2BK5ac/H3K27ac around TSSs; strong downregulated genes were linked to reduced acetylation/accessibility at super-enhancers.

These data support a nuanced annotation: HDAC1 contributes to both gene repression and maintenance of active transcriptional programs at specific regulatory elements. (english2025rapiddegradationof pages 1-2)

5) Current applications and real-world implementations (HDAC1-relevant)

5.1 HDAC inhibitors as tools and therapies (2024 reviews)

Multiple 2024 reviews emphasize that clinical agents often target class I or pan-HDACs, rather than HDAC1 alone, due to isoform similarity and shared complex biology; these reviews also emphasize challenges including toxicity, heterogeneity, and off-target effects—especially in solid tumors. (shi2024advancesintargeting pages 1-2, theodoropoulou2024histonedeacetylase(hdac) pages 1-3)

A 2024 Biomolecules perspective (publication date: Dec 2024; URL: https://doi.org/10.3390/biom14121605) highlights HDAC inhibitors beyond oncology and notes the FDA approval of givinostat for Duchenne muscular dystrophy (first non-cancer HDACi indication). (theodoropoulou2024histonedeacetylase(hdac) pages 1-3)

5.2 Selected ClinicalTrials.gov implementations (trial metadata; URLs by NCT)

The following trials exemplify how HDAC inhibition (often affecting HDAC1/2) is implemented clinically:

  • NCT01528501 (Panobinostat/LBH589; Phase II; terminated; planned enrollment 28)
  • Indication: chemo-refractory metastatic adenocarcinoma of stomach/esophagogastric junction/lower esophagus with tumor overexpression of ≥1 class I HDAC by IHC.
  • Dosing: oral panobinostat 20 mg three times weekly on a 21-day cycle; endpoints included ORR, PFS, OS, 1-year survival, and safety.

  • URL: https://clinicaltrials.gov/study/NCT01528501 (NCT01528501 chunk 1)

  • NCT00357162 (Belinostat/PXD101; Phase II; completed; enrollment 21)

  • Indication: myelodysplastic syndromes.
  • Dosing: IV belinostat days 1–5 of 21-day cycles; outcomes included CR/PR/hematologic improvement and correlative assays (histone acetylation; gene expression; DNA methylation).
  • URL: https://clinicaltrials.gov/study/NCT00357162 (NCT00357162 chunk 1)

5.3 Reported response statistics from a 2024 authoritative review

A 2024 review on peripheral T-cell lymphomas (publication date: Sep 2024; URL: https://doi.org/10.3390/cancers16193359) reports outcome statistics for a combination regimen in Hodgkin lymphoma: vorinostat + pembrolizumab with ORR 100%, CR 44%, 6-month PFS 80%, 6-month OS 100% (as summarized in the review). These effects are consistent with clinical interest in combining HDAC inhibition (often affecting HDAC1/2) with immunotherapy. (irimia2024histonedeacetylaseinhibitors pages 6-8)

6) Expert synthesis / authoritative interpretation

  1. HDAC1 is best annotated as a “complex-integrated nuclear lysine deacetylase”: modern quantitative and structural evidence supports that most HDAC1 is physically embedded in a limited set of corepressor complexes that specify function and genomic binding (NuRD/CoREST/SIN3 dominating in mouse ESCs). (alshehri2025mutationsonthe pages 1-5, curcio2024thehistonedeacetylase media 2e20e924)

  2. Pathway specificity often arises from transcriptional network context rather than enzyme chemistry alone: in vivo mouse neurodevelopment data link Hdac1/2 directly to Wnt program suppression to enable progenitor transitions. (zhu2024hdac1andhdac2 pages 1-2)

  3. HDAC activity is not universally required for all repression modalities, as shown by recent tests of DREAM/E2F:RB models; thus functional annotation should distinguish between “HDAC recruitment” and “HDAC catalytic dependence,” which can diverge by locus and cellular state. (barrett2024hdacactivityis pages 1-2)

7) Evidence-backed statistics and data highlights (recent + high-confidence)

  • Complex distribution in mouse ESCs: NuRD 49%, CoREST 28%, SIN3 15% (92% total in these three complexes). (alshehri2025mutationsonthe pages 1-5)
  • Active-site Zn2+ coordination residues for HDAC1 (structural table): His140, His141, Asp176, Asp264. (curcio2024thehistonedeacetylase media 2e20e924)
  • Acute HDAC1 depletion transcriptomic effects (ESC system): 2 h 275 up / 15 down; 6 h 1,153 up / 443 down; 24 h 1,146 up / 967 down. (english2025rapiddegradationof pages 1-2)
  • Trial enrollment examples: NCT00357162 (belinostat) 21 participants; NCT01528501 (panobinostat) planned 28 participants. (NCT00357162 chunk 1, NCT01528501 chunk 1)
  • Review-reported clinical outcomes (HL combo): ORR 100%, CR 44%, 6-mo PFS 80%, 6-mo OS 100% for vorinostat+pembrolizumab as summarized in a 2024 review. (irimia2024histonedeacetylaseinhibitors pages 6-8)

8) Summary table (for functional annotation pipelines)

Category Key points (1-3 concise bullets) Best supporting sources (citation IDs)
Identity • Target matches mouse Hdac1 / histone deacetylase 1 in the class I HDAC family. • Functions as a Zn²⁺-dependent histone deacetylase within chromatin-regulatory complexes rather than as a largely free enzyme. • HDAC1/2 are closely related “sister enzymes” with ~83% sequence similarity / ~80% homology reported in reviews. (castiello2025newfrontiersfor pages 42-45, english2025rapiddegradationof pages 1-2, sadia2025epigeneticregulationthrough pages 4-6, curcio2024thehistonedeacetylase pages 3-4)
Enzymatic activity • Catalyzes hydrolytic removal of acetyl groups from ε-N-acetyl-lysine on proteins; class I HDACs are Zn²⁺-dependent amidohydrolases/metalloenzymes. • Mechanism uses a metal-water nucleophile in a conserved catalytic channel. • HDAC1 active-site Zn²⁺ coordination residues summarized as His140, His141, Asp176, Asp264 in a recent structural table. (castiello2025newfrontiersfor pages 42-45, zrimsek2022quantitativeacetylomicsuncover pages 1-2, curcio2024thehistonedeacetylase pages 3-4, curcio2024thehistonedeacetylase media 2e20e924)
Substrates • Primary histone substrates include lysines on H2A, H2B, H3, H4. • Non-histone substrates are also important; p53 is a documented deacetylation target in HDAC1-containing complexes. • After acute HDAC1 degradation in ESCs, histone marks H2BK5ac and H2BK11ac were among the most sensitive to change. (castiello2025newfrontiersfor pages 42-45, sadia2025epigeneticregulationthrough pages 4-6, english2025rapiddegradationof pages 1-2)
Complexes • HDAC1 is a catalytic/structural component of SIN3, NuRD, CoREST and also MiDAC/MIER/RERE-associated assemblies. • In mouse ESCs, quantitative proteomics estimated 92% of HDAC1 in three major complexes: NuRD 49%, CoREST 28%, SIN3 15%. • Complex assembly depends on specific HDAC1 surface residues; e.g., Y48E disrupts binding to all tested complexes except SIN3. (alshehri2025mutationsonthe pages 8-10, alshehri2025mutationsonthe pages 1-5, curcio2024thehistonedeacetylase media 2e20e924)
Localization • Class I HDACs, including HDAC1, are reported as predominantly/exclusively nuclear. • Functional localization is chromatin-associated, consistent with residence in large multiprotein corepressor complexes. • Nuclear localization aligns with regulation of promoter/TSS acetylation and enhancer states. (castiello2025newfrontiersfor pages 42-45, sadia2025epigeneticregulationthrough pages 4-6, curcio2024thehistonedeacetylase pages 3-4, english2025rapiddegradationof pages 1-2)
Pathways • Canonical role is regulation of chromatin accessibility, transcriptional repression/activation balance, cell-cycle control, genomic stability, and DNA-damage responses. • In mouse neurodevelopment, HDAC1/2 repress Wnt signaling; loss upregulates Wnt-pathway genes and identifies Wnt9a as a key regulated target. • Recent evidence also suggests some cell-cycle repression by DREAM/E2F:RB can occur without requiring HDAC catalytic activity, refining pathway models. (zhu2024hdac1andhdac2 pages 1-2, barrett2024hdacactivityis pages 1-2, shi2024advancesintargeting pages 1-2, zrimsek2022quantitativeacetylomicsuncover pages 1-2)
Mouse in vivo evidence • Mouse studies support essential developmental roles for Hdac1, including proliferation control and hematopoietic/neurodevelopmental functions. • In developing cortex, HDAC1/2 depletion impairs neuroepithelial-to-radial glial progenitor transition and causes rosette-like proliferative abnormalities. • Mouse knockout-based analyses indicate HDAC1/2 contribute >50% of total cellular deacetylase activity in some contexts. (zhu2024hdac1andhdac2 pages 1-2, english2025rapiddegradationof pages 1-2, irimia2024histonedeacetylaseinhibitors pages 6-8)
Recent mechanistic findings • Acute HDAC1 degradation in ESCs occurs in <1 h and increases histone acetylation within 2 h. • Differential expression after degradation: 275 up / 15 down genes at 2 h; 1,153 up / 443 down at 6 h; 1,146 up / 967 down at 24 h. • Upregulated genes gain H2BK5ac/H3K27ac near TSSs, whereas strong downregulation associates with reduced super-enhancer acetylation—supporting dual roles in repression and active transcription support. (english2025rapiddegradationof pages 1-2)
Applications/HDACi clinical • HDAC1 is not targeted alone in routine practice; most real-world drugs hit class I or pan-HDACs. • Approved HDACi cited in recent reviews include vorinostat, romidepsin, belinostat, panobinostat; givinostat became the first FDA-approved non-cancer HDACi indication (DMD). • Example trial implementations: NCT00020579 entinostat/MS-275 phase I, 75 participants; NCT00357162 belinostat phase II in MDS, 21 participants; NCT01528501 panobinostat phase II in HDAC-positive gastric/esophagogastric cancer, planned 28 participants, terminated; review-reported combo outcome in Hodgkin lymphoma for vorinostat+pembrolizumab: ORR 100%, CR 44%, 6-mo PFS 80%, 6-mo OS 100%. (theodoropoulou2024histonedeacetylase(hdac) pages 1-3, NCT01528501 chunk 1, NCT00357162 chunk 1, irimia2024histonedeacetylaseinhibitors pages 6-8, zhou2024roleofhistone pages 3-5)

Table: This table summarizes the functional annotation of mouse Hdac1/HDAC1, including enzymatic role, substrates, complexes, localization, pathways, mouse evidence, recent mechanistic findings, and HDAC inhibitor applications. It highlights quantitative findings useful for evidence-based gene function reporting.

9) Supporting figure/table excerpt

A useful, compact summary of HDAC1 active-site Zn2+ ligands and complex membership is captured in a cropped table from Curcio et al. 2024. (curcio2024thehistonedeacetylase media 2e20e924)

Key references (URLs + publication dates from retrieved evidence)

  • Curcio A. et al. The Histone Deacetylase Family: Structural Features… Pharmaceuticals (May 2024). https://doi.org/10.3390/ph17050620 (curcio2024thehistonedeacetylase pages 3-4, curcio2024thehistonedeacetylase media 2e20e924)
  • Zhu Y. et al. HDAC1 and HDAC2 orchestrate Wnt signaling… iScience (Sep 2024). https://doi.org/10.1016/j.isci.2024.110600 (zhu2024hdac1andhdac2 pages 1-2)
  • Barrett A.K. et al. HDAC activity is dispensable for repression of cell-cycle genes… Nature Communications (May 2024). https://doi.org/10.1038/s41467-024-48724-0 (barrett2024hdacactivityis pages 1-2)
  • Shi M-Q. et al. Advances in targeting histone deacetylase for treatment of solid tumors J Hematol Oncol (May 2024). https://doi.org/10.1186/s13045-024-01551-8 (shi2024advancesintargeting pages 1-2)
  • Theodoropoulou M.A. et al. HDAC inhibitors… fibrotic and inflammatory diseases Biomolecules (Dec 2024). https://doi.org/10.3390/biom14121605 (theodoropoulou2024histonedeacetylase(hdac) pages 1-3)
  • Irimia R., Piccaluga P.P. HDAC inhibitors for peripheral T-cell lymphomas Cancers (Sep 2024). https://doi.org/10.3390/cancers16193359 (irimia2024histonedeacetylaseinhibitors pages 6-8)
  • ClinicalTrials.gov: NCT01528501 (Panobinostat; Phase II; terminated; planned n=28). https://clinicaltrials.gov/study/NCT01528501 (NCT01528501 chunk 1)
  • ClinicalTrials.gov: NCT00357162 (Belinostat; Phase II; completed; n=21). https://clinicaltrials.gov/study/NCT00357162 (NCT00357162 chunk 1)

References

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  3. (zhu2024hdac1andhdac2 pages 1-2): Yue Zhu, Yunyun Huang, Tianxiang Tang, and Yunli Xie. Hdac1 and hdac2 orchestrate wnt signaling to regulate neural progenitor transition during brain development. iScience, 27:110600, Sep 2024. URL: https://doi.org/10.1016/j.isci.2024.110600, doi:10.1016/j.isci.2024.110600. This article has 1 citations and is from a peer-reviewed journal.

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  7. (curcio2024thehistonedeacetylase media 2e20e924): Antonio Curcio, Roberta Rocca, Stefano Alcaro, and Anna Artese. The histone deacetylase family: structural features and application of combined computational methods. Pharmaceuticals, 17:620, May 2024. URL: https://doi.org/10.3390/ph17050620, doi:10.3390/ph17050620. This article has 64 citations.

  8. (sadia2025epigeneticregulationthrough pages 4-6): Khulah Sadia, Annalisa Castagna, Silvia Udali, Francesca Ambrosani, Patrizia Pattini, Ruggero Beri, Giuseppe Argentino, Maria Masutti, Sara Moruzzi, and Simonetta Friso. Epigenetic regulation through histone deacetylation: implications and therapeutic potential in hepatocellular carcinoma. Cells, 14:1337, Aug 2025. URL: https://doi.org/10.3390/cells14171337, doi:10.3390/cells14171337. This article has 12 citations.

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  10. (alshehri2025mutationsonthe pages 8-10): Ahmad Alshehri, India-May Baker, David M English, Louise Fairall, Mark O Collins, John WR Schwabe, and Shaun M Cowley. Mutations on the surface of hdac1 reveal molecular determinants of specific complex assembly and their requirement for gene regulation. bioRxiv, Feb 2025. URL: https://doi.org/10.1101/2025.02.24.639909, doi:10.1101/2025.02.24.639909. This article has 4 citations.

  11. (theodoropoulou2024histonedeacetylase(hdac) pages 1-3): Maria A. Theodoropoulou, Christiana Mantzourani, and George Kokotos. Histone deacetylase (hdac) inhibitors as a novel therapeutic option against fibrotic and inflammatory diseases. Biomolecules, 14:1605, Dec 2024. URL: https://doi.org/10.3390/biom14121605, doi:10.3390/biom14121605. This article has 14 citations.

  12. (NCT01528501 chunk 1): Histone Deacetylases - Gastric Cancer (HDAC-GaCa-2008). Technical University of Munich. 2009. ClinicalTrials.gov Identifier: NCT01528501

  13. (NCT00357162 chunk 1): Belinostat in Treating Patients With Myelodysplastic Syndromes. National Cancer Institute (NCI). 2006. ClinicalTrials.gov Identifier: NCT00357162

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  16. (zhou2024roleofhistone pages 3-5): Chunxiao Zhou, Dengke Zhao, Chunyan Wu, Zhimin Wu, Wen Zhang, Shilv Chen, Xindong Zhao, and Shaoling Wu. Role of histone deacetylase inhibitors in non-neoplastic diseases. Heliyon, 10:e33997, Jul 2024. URL: https://doi.org/10.1016/j.heliyon.2024.e33997, doi:10.1016/j.heliyon.2024.e33997. This article has 21 citations.

Citations

  1. sadia2025epigeneticregulationthrough pages 4-6
  2. castiello2025newfrontiersfor pages 42-45
  3. barrett2024hdacactivityis pages 1-2
  4. english2025rapiddegradationof pages 1-2
  5. irimia2024histonedeacetylaseinhibitors pages 6-8
  6. alshehri2025mutationsonthe pages 1-5
  7. shi2024advancesintargeting pages 1-2
  8. curcio2024thehistonedeacetylase pages 3-4
  9. alshehri2025mutationsonthe pages 8-10
  10. zrimsek2022quantitativeacetylomicsuncover pages 1-2
  11. zhou2024roleofhistone pages 3-5
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OpenAI

(Hdac1-deep-research-openai.md)
Histone Deacetylase 1 (HDAC1) – Function, Mechanisms, and Roles in Mouse Biology OpenAI o3-deep-research-2025-06-26 99 citations 2026-03-20T01:13:48.676989

Histone Deacetylase 1 (HDAC1) – Function, Mechanisms, and Roles in Mouse Biology

Overview and Enzymatic Function

Histone deacetylase 1 (HDAC1) is a zinc-dependent metalloenzyme involved in epigenetic regulation. It catalyzes the removal of acetyl groups from ε-N-acetyl lysine residues on histone proteins, producing deacetylated lysine and acetate (enzyme.expasy.org) (enzyme.expasy.org). By reversing the acetylation of histone tails (a modification associated with open chromatin), HDAC1 promotes chromatin compaction and transcriptional repression. HDAC1 is evolutionarily conserved (the mammalian homolog of yeast Rpd3) and can also deacetylate certain non-histone proteins involved in gene expression (www.degruyterbrill.com). This enzyme is classified as EC 3.5.1.98 (histone deacetylase), reflecting its amidohydrolase activity on N^6^-acetyl-lysine groups (enzyme.expasy.org).

Biochemically, HDAC1 belongs to Class I HDACs, which also includes HDAC2, HDAC3, and HDAC8 (pmc.ncbi.nlm.nih.gov). Class I HDACs are ubiquitously expressed and predominantly nuclear enzymes (pmc.ncbi.nlm.nih.gov). HDAC1 requires a Zn^2+ cofactor at its active site for catalysis and operates via a charge-relay mechanism to hydrolyze the amide bond of acetyl-lysine. The net reaction removes the acetyl group from histone lysines (e.g. on H3 and H4 tails), opposing the activity of histone acetyltransferases (HATs) (enzyme.expasy.org). This deacetylation generally causes the DNA to wrap more tightly around nucleosomes, limiting access of transcription factors and thereby downregulating gene expression (pmc.ncbi.nlm.nih.gov). Notably, HDAC1 shows broad substrate specificity for acetylated lysines on core histones; recent high-resolution studies indicate HDAC1 regulates the majority of acetylation sites on core histones, with certain lysines on H2B being especially sensitive to HDAC1 loss (academic.oup.com).

In addition to classical deacetylation, new research (2023) has revealed that HDAC1 (together with its close paralogs HDAC2 and HDAC3) can act on other acyl modifications such as lysine succinylation. While lysine succinylation was previously thought to be removed mainly by NAD^+^-dependent sirtuins, a 2023 study showed that class I HDACs, particularly HDAC1/2/3, are the principal histone desuccinylases in mammalian cells (pmc.ncbi.nlm.nih.gov) (pmc.ncbi.nlm.nih.gov). Inhibiting or knocking down HDAC1/2/3 caused a marked increase in global histone succinylation, whereas ectopic expression of active HDAC1/2/3 reduced succinylation levels (pmc.ncbi.nlm.nih.gov) (pmc.ncbi.nlm.nih.gov). This finding expands the functional repertoire of HDAC1 beyond deacetylation, suggesting it can remove larger acyl groups (like succinyl) from lysines, thereby influencing chromatin structure and gene activity in additional ways.

Cellular Localization and Complexes

HDAC1 is predominantly a nuclear protein, consistent with its role in modifying chromatin. It is enriched in the nucleus and often associated with heterochromatin regions (www.ncbi.nlm.nih.gov). Within the nucleus, HDAC1 does not typically act alone; instead, it functions as part of multi-protein complexes that target it to specific genes. In cells, HDAC1 and the closely related HDAC2 usually form a heterodimer that serves as the catalytic core of several large co-repressor complexes (pmc.ncbi.nlm.nih.gov). Major HDAC1-containing complexes include:

  • SIN3A complex – scaffolded by the Sin3 adaptor protein
  • NuRD complex (nucleosome remodeling and deacetylase) – containing Mi-2/CHD4, MTA proteins, RbAp46/48, etc.
  • CoREST complex – associated with the CoREST/LSD1 repressor for neuron-specific genes
  • Other less abundant HDAC1 complexes (e.g. MiDAC, MIER, and RERE complexes) identified in various contexts (pmc.ncbi.nlm.nih.gov).

Proteomic analysis in mouse embryonic stem cells (ESCs) showed that the vast majority of HDAC1 is sequestered in a few complexes. Strikingly, ~92% of cellular HDAC1 in ESCs was found in just three complexes: about 49% in the NuRD complex, 28% in CoREST, and 15% in SIN3A, with only a minor fraction unbound or in smaller assemblies (pmc.ncbi.nlm.nih.gov). This underscores that HDAC1’s in vivo function is tightly linked to these co-repressor complexes, which provide targeting specificity. The adapter proteins in each complex recruit HDAC1 to particular genomic sites – for example, SIN3A complexes bind DNA through sequence-specific repressors, and NuRD can be recruited via methylated DNA or transcription factors (pmc.ncbi.nlm.nih.gov). HDAC1/2 serve not only as catalytic subunits in these complexes but also as structural components stabilizing complex assembly (pmc.ncbi.nlm.nih.gov).

Because of the critical role of these interactions, specific surface residues on HDAC1 mediate its binding to different complex proteins. A recent 2025 structure-function study demonstrated that mutating a single amino acid on HDAC1’s surface (Tyr48) disrupted its incorporation into most complexes except SIN3, highlighting how distinct interfaces on HDAC1 are required for complex-specific interactions (pmc.ncbi.nlm.nih.gov). This kind of evidence shows that HDAC1’s function and regulation depend on its partners, and disrupting those partnerships can profoundly alter which genes HDAC1 can target.

Biological Roles and Processes

HDAC1 is a global regulator of gene expression with widespread effects on cell fate, proliferation, and development. By deacetylating histones, HDAC1 generally represses transcription, and it plays a key role in maintaining the balance between gene activation and silencing in many pathways. Gene ontology annotations and experimental studies indicate HDAC1 is involved in numerous biological processes:

  • Embryonic Development: HDAC1 is essential for early development. Mouse embryos completely lacking Hdac1 die during early embryogenesis, reflecting severe proliferation and differentiation defects. In early blastocysts, HDAC1 and HDAC2 have redundant roles – only when both are disrupted do embryos fail to form a proper blastocyst, with increased apoptosis linked to hyperacetylation of p53 (pubmed.ncbi.nlm.nih.gov) (pubmed.ncbi.nlm.nih.gov). However, later in development and in specific lineages, HDAC1 has unique, non-redundant functions. For example, in the developing brain, HDAC1 is somewhat more critical than HDAC2: one study found that a single copy of Hdac2 could not fully rescue brain development if Hdac1 was completely knocked out, indicating Hdac1 provides functions that Hdac2 cannot wholly compensate (pubmed.ncbi.nlm.nih.gov). Conversely, a single Hdac1 allele was more capable of offsetting the loss of Hdac2, underscoring the dominant role of HDAC1 in neurodevelopment (pubmed.ncbi.nlm.nih.gov).

  • Neurogenesis and Differentiation: HDAC1 is highly expressed in the nervous system and influences neural progenitor differentiation. It is required for proper nervous system development and has been linked to specific events like oligodendrocyte maturation (www.ncbi.nlm.nih.gov). A recent study (Zhu et al., 2024) showed that HDAC1 (together with HDAC2) regulates the transition of neural stem cells during cortex development by restraining Wnt signaling (pmc.ncbi.nlm.nih.gov). Conditional deletion of Hdac1/2 in early neuroepithelial progenitors led to aberrant activation of Wnt-target genes, which in turn blocked the normal progression of these progenitors into radial glial cells and caused cortical architectural defects (pmc.ncbi.nlm.nih.gov). This finding illustrates a precise role: HDAC1/2-mediated deacetylation keeps Wnt pathway genes in check during neurogenesis. In line with this, administering a Wnt inhibitor could partially rescue the neurodevelopmental defects caused by HDAC1/2 loss (pmc.ncbi.nlm.nih.gov). HDAC1 also supports the differentiation of glial cells – for instance, oligodendrocyte differentiation (formation of myelinating glia) is positively regulated by HDAC1 activity (www.ncbi.nlm.nih.gov), likely through repression of inhibitors of myelination. Consistent with these roles, neuronal survival and memory processes can be affected by HDAC1 levels: in aging and disease models, imbalanced Class I HDAC activity is linked to cognitive deficits, and HDAC inhibitors are being studied to modulate memory-related gene expression (pmc.ncbi.nlm.nih.gov) (pubmed.ncbi.nlm.nih.gov) (Brain Res. 2024).

  • Immune Cell Development: HDAC1 is also crucial in the hematopoietic and immune systems. A 2024 study demonstrated that HDAC1 controls the development of certain dendritic cell (DC) subsets and thereby influences immune responses (pubmed.ncbi.nlm.nih.gov). Mice lacking Hdac1 in early blood progenitors had severely reduced production of plasmacytoid dendritic cells (pDCs) and a subset of conventional DCs, while other lineages (like cDC1) were unaffected (pubmed.ncbi.nlm.nih.gov). Notably, deleting Hdac2 in the same context had little effect on DC development, highlighting a non-redundant requirement for HDAC1 in this lineage (pubmed.ncbi.nlm.nih.gov). The HDAC1-deficient DC progenitors showed abnormal gene expression and chromatin accessibility, indicating HDAC1’s deacetylase activity is needed to properly program the DC differentiation transcriptional network (pubmed.ncbi.nlm.nih.gov). In human cells as well, knocking down HDAC1 impaired DC differentiation (pubmed.ncbi.nlm.nih.gov). This specialized role in the immune system suggests HDAC1 helps enforce the epigenetic programs that generate functional immune cells, and loss of HDAC1 may weaken immune surveillance (the study also linked HDAC1-deficient DCs to poor anti-tumor immunity (pubmed.ncbi.nlm.nih.gov)).

  • Cell Cycle and Proliferation: HDAC1 has long been known to interact with cell cycle regulators. It partners with the Retinoblastoma (Rb) tumor suppressor and E2F transcription factors to repress E2F-responsive genes during cell cycle exit (pmc.ncbi.nlm.nih.gov). In G₀/G₁ phase, Rb recruits HDAC1 (via Sin3 or NuRD complexes) to promoters of S-phase genes (cyclins, replication factors), leading to local histone H4 deacetylation and gene silencing (pubmed.ncbi.nlm.nih.gov) (pmc.ncbi.nlm.nih.gov). This Rb–HDAC1–E2F complex is important for enforcing cell cycle checkpoints. When cells are stimulated to divide, Rb is inactivated, HDAC1 is released, histones become acetylated, and E2F target genes are activated. If HDAC1 is lost, cells show inappropriate expression of cell-cycle genes and often a failure to properly exit the cell cycle. Indeed, HDAC1-null mouse embryos exhibit proliferation defects and increased apoptosis in proliferative tissues (pubmed.ncbi.nlm.nih.gov) (pubmed.ncbi.nlm.nih.gov), partly due to misregulation of cell-cycle inhibitors and hyperactivation of p53. Thus, HDAC1 plays a pro-proliferative role by repressing anti-proliferative genes under normal conditions. Consistent with this, many cancers show HDAC1 overexpression as a strategy to silence tumor suppressor genes and promote uncontrolled growth (www.degruyterbrill.com).

  • Gene Silencing and DNA Methylation: HDAC1 often works in concert with DNA methyltransferases and other epigenetic silencers. For example, in some contexts HDAC1 is part of a repressor complex with DNMT1 (maintenance DNA methyltransferase), Rb, and E2F, which together maintain methylation and deacetylation at tumor suppressor gene promoters (www.nature.com). HDAC1’s deacetylation can facilitate DNA methylation and vice versa, creating a repressive chromatin state. In cancer cells, simultaneous inhibition of HDAC1/2 and DNMTs synergistically reactivates silenced genes (pubmed.ncbi.nlm.nih.gov), underscoring that HDAC1 is a key executor of long-term gene silencing programs. HDAC1 is also located at heterochromatic regions like pericentromeres, where it helps maintain condensed, transcriptionally inactive chromatin (often in tandem with methyl-binding proteins and histone methyltransferases).

  • Direct Regulation of Transcription Factors: Beyond chromatin-centric functions, HDAC1 can directly interact with and deacetylate several transcription factors, modulating their activity. For instance, the NF-κB family member RelA/p65 is acetylated in active states; HDAC1 binds to the Rel homology domain of p65 and deacetylates it, which attenuates NF-κB’s transcriptional activity (pmc.ncbi.nlm.nih.gov) (pmc.ncbi.nlm.nih.gov). In a classic study, overexpression of HDAC1/2 was shown to repress NF-κB-dependent genes by this mechanism, and HDAC1–p65 interaction was required for turning off inflammatory gene expression after a stimulus (pmc.ncbi.nlm.nih.gov) (pmc.ncbi.nlm.nih.gov). Similarly, HDAC1 interacts with the muscle-specific transcription factor MyoD to repress muscle gene expression in undifferentiated cells (pmc.ncbi.nlm.nih.gov). Deacetylation of MyoD by HDAC1 keeps it in an inactive state until differentiation signals downregulate HDAC1, allowing MyoD to activate muscle genes. Another important target is the tumor suppressor p53: acetylation of p53 enhances its stability and activity, and HDAC1 (often in complex with MDM2 ubiquitin ligase) can deacetylate p53, leading to p53 inactivation and degradation (pubmed.ncbi.nlm.nih.gov). This HDAC1–p53 axis is one way that cells modulate apoptosis and DNA damage responses. In summary, HDAC1 influences several signaling pathways (Wnt, NF-κB, p53, MyoD, etc.) by deacetylating key factors or their histone targets, thereby integrating epigenetic control with cell signaling and fate decisions.

It is important to note that while HDAC1 is generally associated with transcriptional repression, its activity can sometimes positively influence gene expression in indirect ways. For example, an acute degradation study (2021, Nucleic Acids Res.) of HDAC1 in cells revealed an unexpected finding: for a subset of genes, removing HDAC1 caused reduced transcription, correlated with a loss of acetylation at certain super-enhancers (academic.oup.com). One explanation is that HDAC1 helps maintain a dynamic acetylation turnover at these regulatory regions; in its absence, aberrant hyperacetylation of certain factors or feedback mechanisms might lead to decreased net acetylation and gene activity (academic.oup.com). This nuance underscores that HDAC1’s role is context-dependent – while it is a repressor by nature, proper levels of HDAC1 activity are also required for normal activation of some genes (likely by preventing overshooting acetylation that could trigger compensatory shut-off). Nonetheless, the overarching role of HDAC1 is to enforce appropriate gene expression programs – shutting genes off when they should be silent and allowing activation when needed, in coordination with other chromatin modifiers.

Pathophysiology and Clinical Relevance

Given HDAC1’s fundamental role in regulating cell proliferation, differentiation, and survival, it is not surprising that its dysfunction is implicated in disease, especially cancer. HDAC1 is frequently overexpressed in tumors of diverse types (including breast, lung, and liver cancers), and high HDAC1 levels often correlate with poor patient prognosis (pmc.ncbi.nlm.nih.gov). By recruiting HDAC1, cancer cells can aberrantly silence tumor suppressor genes and DNA damage response genes. For example, overexpression of HDAC1 has been noted in aggressive subtypes of lung cancer and linked to increased metastasis and worse outcomes (pubmed.ncbi.nlm.nih.gov) (www.degruyterbrill.com). HDAC1 can also promote oncogenic traits by deacetylating and inactivating p53, as mentioned, which reduces apoptosis in cancer cells. In hepatocellular carcinoma (HCC) and other cancers, broad evidence shows that HDACs orchestrate multiple hallmarks of cancer – cell cycle progression, evasion of apoptosis, enhanced migration/invasion, metabolic rewiring – through their control of histone and non-histone acetylation (www.degruyterbrill.com). Consequently, HDAC1 has become a prominent therapeutic target in oncology.

HDAC Inhibitors (HDACi) are a class of epigenetic drugs designed to block the activity of HDAC1 and related enzymes. By inhibiting HDAC1, these drugs cause accumulation of acetylated histones, leading to reactivation of suppressed genes (such as those regulating cell cycle arrest or apoptosis in cancer cells). Several HDAC inhibitors have reached clinical use. The first FDA-approved HDAC inhibitor was Vorinostat (SAHA), approved in 2006 for cutaneous T-cell lymphoma; vorinostat inhibits Class I HDACs (including HDAC1) and causes growth arrest and cell death in cancer cells (pmc.ncbi.nlm.nih.gov). Since then, other HDAC1-targeting drugs have been approved: Romidepsin, a cyclic peptide that selectively targets HDAC1/2, is used for certain lymphomas; and the hydroxamate inhibitors Panobinostat and Belinostat were approved for multiple myeloma and T-cell lymphoma, respectively (pmc.ncbi.nlm.nih.gov) (pmc.ncbi.nlm.nih.gov). (Panobinostat’s approval was later withdrawn in 2022 due to safety concerns (pmc.ncbi.nlm.nih.gov), but it demonstrated the potent effect of HDAC1/2 inhibition in refractory myeloma.) These inhibitors have shown efficacy in hematologic cancers by inducing apoptosis and cell-cycle arrest. However, their success in solid tumors has been limited when used alone (pmc.ncbi.nlm.nih.gov). As a result, HDAC inhibitors are often used in combination therapies – for example, HDAC1 blockade can sensitize tumors to other treatments. In one study, romidepsin (an HDAC1/2 inhibitor) not only killed biliary tract cancer cells but also enhanced their response to standard chemotherapy (cisplatin) (pmc.ncbi.nlm.nih.gov).

Beyond cancer, modulation of HDAC1 is being explored in neurodegenerative and psychiatric disorders. Because HDAC1 helps silence genes, HDAC inhibitors can potentially boost expression of neuroprotective or memory-related genes. Indeed, preclinical studies in mice suggest that inhibiting Class I HDACs can alleviate cognitive deficits caused by acute stress or in Alzheimer’s models (pubmed.ncbi.nlm.nih.gov) (pubmed.ncbi.nlm.nih.gov). There is also interest in HDAC1 in aging and neurological diseases: for instance, HDAC1 dysfunction has been linked to DNA damage accumulation in neurons, and HDAC1 activation (in the correct context) might promote DNA repair in neurodegeneration (academic.oup.com). However, because HDAC1 is ubiquitously required, systemic inhibition carries risks (e.g. bone marrow suppression, GI toxicity). To minimize side effects, next-generation approaches include developing isoform-selective HDAC1/2 inhibitors or targeted HDAC1 degraders (PROTACs) (pmc.ncbi.nlm.nih.gov) that could degrade HDAC1 specifically in certain tissues or contexts. As of 2023, multiple Class I HDAC inhibitors selective for HDAC1-3 are in clinical trials for cancers and other diseases (pmc.ncbi.nlm.nih.gov) (pmc.ncbi.nlm.nih.gov), and eight class I-selective agents were noted to be in trials ranging from Phase I to III (pmc.ncbi.nlm.nih.gov). The continued therapeutic interest underlines HDAC1’s importance: it is a double-edged sword – necessary for normal cell function but also a driver of pathology when misregulated.

Conclusion

HDAC1 (histone deacetylase 1) is a key epigenetic regulator in mice (and other mammals) that enforces transcriptional control by deacetylating histones and other proteins. It functions at the nexus of chromatin remodeling, cell cycle control, and developmental signaling. HDAC1 is mainly nuclear and acts within multi-unit co-repressor complexes (such as NuRD, SIN3A, and CoREST) that target it to specific genes (pmc.ncbi.nlm.nih.gov) (pmc.ncbi.nlm.nih.gov). Its primary biochemical activity is the removal of acetyl groups from histone lysines (enzyme.expasy.org), which leads to chromatin condensation and gene repression. This activity is critical for numerous processes: it helps progenitor cells exit the cell cycle and differentiate at the correct time, maintains stem cell pluripotency until differentiation cues arrive, and safeguards genome stability by regulating DNA repair genes and checkpoint proteins. HDAC1 is also adaptable – recent insights show it can erase other acyl modifications like succinylation (pmc.ncbi.nlm.nih.gov) (pmc.ncbi.nlm.nih.gov), reflecting a broader role in post-translational modification homeostasis.

At the organism level, HDAC1 is indispensable. Mice require HDAC1 for normal embryogenesis, as it supports proper lineage specification and prevents excess apoptotic cell death in early development (pubmed.ncbi.nlm.nih.gov) (pubmed.ncbi.nlm.nih.gov). In specialized cells, HDAC1 helps orchestrate developmental programs (neural differentiation via Wnt repression (pmc.ncbi.nlm.nih.gov), immune lineage commitment in dendritic cells (pubmed.ncbi.nlm.nih.gov), etc.) and maintains the silenced state of genes that should not be expressed (e.g. imprinted genes or tissue-specific genes in other cell types). When HDAC1 function is lost or imbalanced, cells typically exhibit aberrant gene expression – either unscheduled activation of genes or failure to activate others – leading to defects like developmental anomalies or cell death. This precise control is also exploited by diseases: cancer cells, for instance, often hijack HDAC1 to broadly repress anti-tumor pathways. As a result, HDAC1 has become a prominent drug target, and inhibiting its activity can reactivate latent gene expression programs to therapeutic benefit in cancer and possibly neurological disorders. Conversely, excessive HDAC1 inhibition can be detrimental, given its role in normal cell viability and identity.

In summary, HDAC1 serves as a molecular switch for gene regulation, working in chromatin complexes to ensure genes are turned “off” when they should be, but also enabling correct gene “on” states in response to developmental cues. Its importance is evident from both fundamental biology and translational medicine perspectives. Ongoing research (2023–2024) continues to uncover new facets of HDAC1 biology – from novel enzymatic capabilities (pmc.ncbi.nlm.nih.gov) to specific roles in complex diseases – solidifying HDAC1 as a central player in the epigenetic regulation of cell function and a critical link between the genome, chromatin state, and cellular phenotype.

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  33. AnnotationURLCitation(end_index=13398, start_index=13215, title='The histone deacetylase HDAC1 controls dendritic cell development and anti-tumor immunity - PubMed', type='url_citation', url='https://pubmed.ncbi.nlm.nih.gov/38829740/#:~:text=deacetylation%20on%20DCs%20by%20genetically,HDAC1%20controls%20expression%2C%20chromatin%20accessibility')
  34. AnnotationURLCitation(end_index=13684, start_index=13548, title='The histone deacetylase HDAC1 controls dendritic cell development and anti-tumor immunity - PubMed', type='url_citation', url='https://pubmed.ncbi.nlm.nih.gov/38829740/#:~:text=these%20processes%20is%20unclear,pDC%20and%20mature%20pDC')
  35. AnnotationURLCitation(end_index=14082, start_index=13899, title='The histone deacetylase HDAC1 controls dendritic cell development and anti-tumor immunity - PubMed', type='url_citation', url='https://pubmed.ncbi.nlm.nih.gov/38829740/#:~:text=deacetylation%20on%20DCs%20by%20genetically,HDAC1%20controls%20expression%2C%20chromatin%20accessibility')
  36. AnnotationURLCitation(end_index=14283, start_index=14156, title='The histone deacetylase HDAC1 controls dendritic cell development and anti-tumor immunity - PubMed', type='url_citation', url='https://pubmed.ncbi.nlm.nih.gov/38829740/#:~:text=not%20critical%20for%20DC%20development%2C,Multi')
  37. AnnotationURLCitation(end_index=14729, start_index=14540, title='The histone deacetylase HDAC1 controls dendritic cell development and anti-tumor immunity - PubMed', type='url_citation', url='https://pubmed.ncbi.nlm.nih.gov/38829740/#:~:text=development%2C%20generating%20different%20subsets,HDAC1%20controls%20expression%2C%20chromatin%20accessibility')
  38. AnnotationURLCitation(end_index=15113, start_index=14982, title='Cell cycle-dependent recruitment of HDAC-1 correlates with deacetylation of histone H4 on an Rb–E2F target promoter - PMC', type='url_citation', url='https://pmc.ncbi.nlm.nih.gov/articles/PMC1084028/#:~:text=histone%20H4%20on%20an%20Rb%E2%80%93E2F,1%20can')
  39. AnnotationURLCitation(end_index=15380, start_index=15301, title='E2F mediates cell cycle-dependent transcriptional repression in vivo by recruitment of an HDAC1/mSin3B corepressor complex - PubMed', type='url_citation', url='https://pubmed.ncbi.nlm.nih.gov/11959842/#:~:text=')
  40. AnnotationURLCitation(end_index=15512, start_index=15381, title='Cell cycle-dependent recruitment of HDAC-1 correlates with deacetylation of histone H4 on an Rb–E2F target promoter - PMC', type='url_citation', url='https://pmc.ncbi.nlm.nih.gov/articles/PMC1084028/#:~:text=histone%20H4%20on%20an%20Rb%E2%80%93E2F,1%20can')
  41. AnnotationURLCitation(end_index=16098, start_index=15973, title='Essential roles of HDAC1 and 2 in lineage development and genome-wide DNA methylation during mouse preimplantation development - PubMed', type='url_citation', url='https://pubmed.ncbi.nlm.nih.gov/31533525/#:~:text=individually,an%20increase%20in%20global%20DNA')
  42. AnnotationURLCitation(end_index=16226, start_index=16099, title='Essential roles of HDAC1 and 2 in lineage development and genome-wide DNA methylation during mouse preimplantation development - PubMed', type='url_citation', url='https://pubmed.ncbi.nlm.nih.gov/31533525/#:~:text=HDAC1%2F2,are%20core%20components%20of%20several')
  43. AnnotationURLCitation(end_index=16756, start_index=16561, title='A comprehensive review of histone deacetylases: implicati...', type='url_citation', url='https://www.degruyterbrill.com/document/doi/10.1515/oncologie-2025-0419/html#:~:text=that%20HDACs%20orchestrate%20crucial%20oncogenic,The%20aberrant%20expression%20and')
  44. AnnotationURLCitation(end_index=17250, start_index=17111, title='DNMT1 forms a complex with Rb, E2F1 and HDAC1 and represses transcription from E2F-responsive promoters | Nature Genetics', type='url_citation', url='https://www.nature.com/articles/ng0700_338#:~:text=DNMT1%20forms%20a%20complex%20with,with%20Rb%2C%20E2F1%20and%20HDAC1')
  45. AnnotationURLCitation(end_index=17598, start_index=17465, title='The NuRD complex cooperates with DNMTs to maintain silencing of key colorectal tumor suppressor genes - PubMed', type='url_citation', url='https://pubmed.ncbi.nlm.nih.gov/23708667/#:~:text=colorectal%20tumor%20suppressor%20genes%20,CONT1%20and')
  46. AnnotationURLCitation(end_index=18427, start_index=18300, title='The p65 (RelA) Subunit of NF-κB Interacts with the Histone Deacetylase (HDAC) Corepressors HDAC1 and HDAC2 To Negatively Regulate Gene Expression - PMC', type='url_citation', url='https://pmc.ncbi.nlm.nih.gov/articles/PMC99882/#:~:text=were%20mutated,%CE%BAB%20directly%20but%20can')
  47. AnnotationURLCitation(end_index=18582, start_index=18428, title='The p65 (RelA) Subunit of NF-κB Interacts with the Histone Deacetylase (HDAC) Corepressors HDAC1 and HDAC2 To Negatively Regulate Gene Expression - PMC', type='url_citation', url='https://pmc.ncbi.nlm.nih.gov/articles/PMC99882/#:~:text=match%20at%20L87%20association%20of,of%20expression%20of%20these%20genes')
  48. AnnotationURLCitation(end_index=18924, start_index=18797, title='The p65 (RelA) Subunit of NF-κB Interacts with the Histone Deacetylase (HDAC) Corepressors HDAC1 and HDAC2 To Negatively Regulate Gene Expression - PMC', type='url_citation', url='https://pmc.ncbi.nlm.nih.gov/articles/PMC99882/#:~:text=were%20mutated,%CE%BAB%20directly%20but%20can')
  49. AnnotationURLCitation(end_index=19070, start_index=18925, title='The p65 (RelA) Subunit of NF-κB Interacts with the Histone Deacetylase (HDAC) Corepressors HDAC1 and HDAC2 To Negatively Regulate Gene Expression - PMC', type='url_citation', url='https://pmc.ncbi.nlm.nih.gov/articles/PMC99882/#:~:text=dependent%20reporter%20gene,an%20increased%20basal%20level%20of')
  50. AnnotationURLCitation(end_index=19341, start_index=19214, title='The p65 (RelA) Subunit of NF-κB Interacts with the Histone Deacetylase (HDAC) Corepressors HDAC1 and HDAC2 To Negatively Regulate Gene Expression - PMC', type='url_citation', url='https://pmc.ncbi.nlm.nih.gov/articles/PMC99882/#:~:text=%2814%29,interact%20with%20the%20MyoD%20basic')
  51. AnnotationURLCitation(end_index=19817, start_index=19729, title='MDM2-HDAC1-mediated deacetylation of p53 is required for its degradation - PubMed', type='url_citation', url='https://pubmed.ncbi.nlm.nih.gov/12426395/#:~:text=MDM2,lane')
  52. AnnotationURLCitation(end_index=20737, start_index=20571, title='Rapid degradation of histone deacetylase 1 (HDAC1) reveals essential roles in both gene repression and active transcription | Nucleic Acids Research | Oxford Academic', type='url_citation', url='https://academic.oup.com/nar/article-abstract/doi/10.1093/nar/gkae1223/7929376#:~:text=In%20conclusion%2C%20these%20results%20show,Providing%20a')
  53. AnnotationURLCitation(end_index=21152, start_index=20986, title='Rapid degradation of histone deacetylase 1 (HDAC1) reveals essential roles in both gene repression and active transcription | Nucleic Acids Research | Oxford Academic', type='url_citation', url='https://academic.oup.com/nar/article-abstract/doi/10.1093/nar/gkae1223/7929376#:~:text=In%20conclusion%2C%20these%20results%20show,Providing%20a')
  54. AnnotationURLCitation(end_index=22246, start_index=22069, title='HDAC1: a promising target for cancer treatment: insights from a thorough analysis of tumor functions - PMC', type='url_citation', url='https://pmc.ncbi.nlm.nih.gov/articles/PMC11543092/#:~:text=HDAC1%20exhibited%20high%20expression%20in,migration%20were%20significantly%20inhibited%20by')
  55. AnnotationURLCitation(end_index=22633, start_index=22503, title='HDAC1: a promising target for cancer treatment: insights from a thorough analysis of tumor functions - PubMed', type='url_citation', url='https://pubmed.ncbi.nlm.nih.gov/39525004/#:~:text=,numerous%20tumors%2C%20and%20strong%20correlations')
  56. AnnotationURLCitation(end_index=22829, start_index=22634, title='A comprehensive review of histone deacetylases: implicati...', type='url_citation', url='https://www.degruyterbrill.com/document/doi/10.1515/oncologie-2025-0419/html#:~:text=that%20HDACs%20orchestrate%20crucial%20oncogenic,The%20aberrant%20expression%20and')
  57. AnnotationURLCitation(end_index=23449, start_index=23254, title='A comprehensive review of histone deacetylases: implicati...', type='url_citation', url='https://www.degruyterbrill.com/document/doi/10.1515/oncologie-2025-0419/html#:~:text=that%20HDACs%20orchestrate%20crucial%20oncogenic,The%20aberrant%20expression%20and')
  58. AnnotationURLCitation(end_index=24219, start_index=24119, title='HDAC inhibitors as anticancer drugs: chemical diversity, clinical trials, challenges and perspectives - PMC', type='url_citation', url='https://pmc.ncbi.nlm.nih.gov/articles/PMC12805814/#:~:text=IV.,have%20been')
  59. AnnotationURLCitation(end_index=24679, start_index=24515, title='HDAC inhibitors as anticancer drugs: chemical diversity, clinical trials, challenges and perspectives - PMC', type='url_citation', url='https://pmc.ncbi.nlm.nih.gov/articles/PMC12805814/#:~:text=This%20class%20showed%20inhibition%20of,hence%20panobinostat%20is%20no%20longer')
  60. AnnotationURLCitation(end_index=24820, start_index=24680, title='HDAC inhibitors as anticancer drugs: chemical diversity, clinical trials, challenges and perspectives - PMC', type='url_citation', url='https://pmc.ncbi.nlm.nih.gov/articles/PMC12805814/#:~:text=was%20vorinostat%20or%20suberoylanilide%20hydroxamic,23')
  61. AnnotationURLCitation(end_index=25024, start_index=24898, title='HDAC inhibitors as anticancer drugs: chemical diversity, clinical trials, challenges and perspectives - PMC', type='url_citation', url='https://pmc.ncbi.nlm.nih.gov/articles/PMC12805814/#:~:text=approved%20for%20multiple%20myeloma%20,42')
  62. AnnotationURLCitation(end_index=25462, start_index=25287, title='HDAC inhibitors as anticancer drugs: chemical diversity, clinical trials, challenges and perspectives - PMC', type='url_citation', url='https://pmc.ncbi.nlm.nih.gov/articles/PMC12805814/#:~:text=from%20clinical%20trials%20showed%20that,effective%20against%20lymphomas%20and%20leukemias')
  63. AnnotationURLCitation(end_index=25935, start_index=25770, title='HDAC Screening Identifies the HDAC Class I Inhibitor Romidepsin as a Promising Epigenetic Drug for Biliary Tract Cancer - PMC', type='url_citation', url='https://pmc.ncbi.nlm.nih.gov/articles/PMC8345689/#:~:text=study%2C%20we%20demonstrate%20that%20histone,able%20to%20demonstrate%20that%20BTC')
  64. AnnotationURLCitation(end_index=26438, start_index=26327, title='Class I histone deacetylases inhibition reverses memory impairment induced by acute stress in mice - PubMed', type='url_citation', url='https://pubmed.ncbi.nlm.nih.gov/38635564/#:~:text=by%20acute%20stress%20in%20mice,')
  65. AnnotationURLCitation(end_index=26605, start_index=26439, title='Class 1 histone deacetylases differentially modulate memory and synaptic genes in a spatial and temporal manner in aged and APP/PS1 mice - PubMed', type='url_citation', url='https://pubmed.ncbi.nlm.nih.gov/38642789/#:~:text=Class%201%20histone%20deacetylases%20differentially,synaptic%20genes%20in%20a%20spatial')
  66. AnnotationURLCitation(end_index=27056, start_index=26858, title='Rapid degradation of histone deacetylase 1 (HDAC1) reveals essential roles in both gene repression and active transcription | Nucleic Acids Research | Oxford Academic', type='url_citation', url='https://academic.oup.com/nar/article-abstract/doi/10.1093/nar/gkae1223/7929376#:~:text=In%20conclusion%2C%20our%20results%20have,early%20consequences%20of%20HDAC1%20degradation')
  67. AnnotationURLCitation(end_index=27511, start_index=27341, title='HDAC1/2 Inhibitor Romidepsin Suppresses DEN-Induced Hepatocellular Carcinogenesis in Mice - PMC', type='url_citation', url='https://pmc.ncbi.nlm.nih.gov/articles/PMC7304783/#:~:text=HDAC1%2F2%20Inhibitor%20Romidepsin%20Suppresses%20DEN,The%20same%20mouse%20model%20was')
  68. AnnotationURLCitation(end_index=27852, start_index=27707, title='Medicinal chemistry advances in targeting class I histone deacetylases - PMC', type='url_citation', url='https://pmc.ncbi.nlm.nih.gov/articles/PMC10497394/#:~:text=match%20at%20L112%20Class%20I,an%20emphasis%20on%20class%20I')
  69. AnnotationURLCitation(end_index=28005, start_index=27853, title='Medicinal chemistry advances in targeting class I histone deacetylases - PMC', type='url_citation', url='https://pmc.ncbi.nlm.nih.gov/articles/PMC10497394/#:~:text=Class%20I%20HDACs%20are%20attractive,an%20emphasis%20on%20class%20I')
  70. AnnotationURLCitation(end_index=28249, start_index=28097, title='Medicinal chemistry advances in targeting class I histone deacetylases - PMC', type='url_citation', url='https://pmc.ncbi.nlm.nih.gov/articles/PMC10497394/#:~:text=With%20regards%20to%20class%20I,which%20are%20class%20I%20selective')
  71. AnnotationURLCitation(end_index=29014, start_index=28865, title='The p65 (RelA) Subunit of NF-κB Interacts with the Histone Deacetylase (HDAC) Corepressors HDAC1 and HDAC2 To Negatively Regulate Gene Expression - PMC', type='url_citation', url='https://pmc.ncbi.nlm.nih.gov/articles/PMC99882/#:~:text=HDAC1%20and%20HDAC2%20are%20class,and%20HDAC2%20can%20regulate%20NF')
  72. AnnotationURLCitation(end_index=29173, start_index=29015, title='Mutations on the surface of HDAC1 reveal molecular determinants of specific complex assembly and their requirement for gene regulation - PMC', type='url_citation', url='https://pmc.ncbi.nlm.nih.gov/articles/PMC12448893/#:~:text=Histone%20deacetylase%201%20and%202,showed%20that%20retention%20of%20SIN3')
  73. AnnotationURLCitation(end_index=29382, start_index=29261, title='ENZYME - 3.5.1.98 histone deacetylase', type='url_citation', url='https://enzyme.expasy.org/EC/3.5.1.98#:~:text=,sequence%20similarity%20and%20domain%20organization')
  74. AnnotationURLCitation(end_index=30010, start_index=29838, title='HDAC1/2/3 are major histone desuccinylases critical for promoter desuccinylation - PMC', type='url_citation', url='https://pmc.ncbi.nlm.nih.gov/articles/PMC10425439/#:~:text=believed%20to%20be%20catalyzed%20by,elevation%20of%20promoter%20histone%20succinylation')
  75. AnnotationURLCitation(end_index=30191, start_index=30011, title='HDAC1/2/3 are major histone desuccinylases critical for promoter desuccinylation - PMC', type='url_citation', url='https://pmc.ncbi.nlm.nih.gov/articles/PMC10425439/#:~:text=desuccinylase%20activity%20in%20vitro,histone%20desuccinylases%20particularly%20important%20for')
  76. AnnotationURLCitation(end_index=30638, start_index=30470, title='Essential roles of HDAC1 and 2 in lineage development and genome-wide DNA methylation during mouse preimplantation development - PubMed', type='url_citation', url='https://pubmed.ncbi.nlm.nih.gov/31533525/#:~:text=role%20of%20histone%20modifications%20in,gene%20expression%20changes%2C%20a%20substantial')
  77. AnnotationURLCitation(end_index=30766, start_index=30639, title='Essential roles of HDAC1 and 2 in lineage development and genome-wide DNA methylation during mouse preimplantation development - PubMed', type='url_citation', url='https://pubmed.ncbi.nlm.nih.gov/31533525/#:~:text=HDAC1%2F2,are%20core%20components%20of%20several')
  78. AnnotationURLCitation(end_index=31068, start_index=30880, title='HDAC1 and HDAC2 orchestrate Wnt signaling to regulate neural progenitor transition during brain development - PMC', type='url_citation', url='https://pmc.ncbi.nlm.nih.gov/articles/PMC11367519/#:~:text=neural%20differentiation%2C%20yet%20the%20governing,rescued%20the%20disrupted%20cortical%20architecture')
  79. AnnotationURLCitation(end_index=31298, start_index=31115, title='The histone deacetylase HDAC1 controls dendritic cell development and anti-tumor immunity - PubMed', type='url_citation', url='https://pubmed.ncbi.nlm.nih.gov/38829740/#:~:text=deacetylation%20on%20DCs%20by%20genetically,HDAC1%20controls%20expression%2C%20chromatin%20accessibility')
  80. AnnotationURLCitation(end_index=32749, start_index=32577, title='HDAC1/2/3 are major histone desuccinylases critical for promoter desuccinylation - PMC', type='url_citation', url='https://pmc.ncbi.nlm.nih.gov/articles/PMC10425439/#:~:text=believed%20to%20be%20catalyzed%20by,elevation%20of%20promoter%20histone%20succinylation')
  81. AnnotationURLCitation(end_index=33276, start_index=33128, title='Medicinal chemistry advances in targeting class I histone deacetylases - PMC', type='url_citation', url='https://pmc.ncbi.nlm.nih.gov/articles/PMC10497394/#:~:text=Histone%20deacetylases%20,via%20histone%20acetyl%20transferases')
  82. AnnotationURLCitation(end_index=33424, start_index=33303, title='ENZYME - 3.5.1.98 histone deacetylase', type='url_citation', url='https://enzyme.expasy.org/EC/3.5.1.98#:~:text=,sequence%20similarity%20and%20domain%20organization')
  83. AnnotationURLCitation(end_index=33558, start_index=33425, title='ENZYME - 3.5.1.98 histone deacetylase', type='url_citation', url='https://enzyme.expasy.org/EC/3.5.1.98#:~:text=Reaction%20catalysed%20,histone%5D%20%2B%20acetate%20Comment%28s')
  84. AnnotationURLCitation(end_index=33786, start_index=33637, title='The p65 (RelA) Subunit of NF-κB Interacts with the Histone Deacetylase (HDAC) Corepressors HDAC1 and HDAC2 To Negatively Regulate Gene Expression - PMC', type='url_citation', url='https://pmc.ncbi.nlm.nih.gov/articles/PMC99882/#:~:text=HDAC1%20and%20HDAC2%20are%20class,and%20HDAC2%20can%20regulate%20NF')
  85. AnnotationURLCitation(end_index=33993, start_index=33835, title='Mutations on the surface of HDAC1 reveal molecular determinants of specific complex assembly and their requirement for gene regulation - PMC', type='url_citation', url='https://pmc.ncbi.nlm.nih.gov/articles/PMC12448893/#:~:text=Histone%20deacetylase%201%20and%202,showed%20that%20retention%20of%20SIN3')
  86. AnnotationURLCitation(end_index=34264, start_index=34108, title='Hdac1 histone deacetylase 1 [Mus musculus (house mouse)] - Gene - NCBI', type='url_citation', url='https://www.ncbi.nlm.nih.gov/gene/433759#:~:text=Enables%20several%20functions%2C%20including%20E,Orthologous%20to%20human%20HDAC1')
  87. AnnotationURLCitation(end_index=34486, start_index=34298, title='HDAC1 and HDAC2 orchestrate Wnt signaling to regulate neural progenitor transition during brain development - PMC', type='url_citation', url='https://pmc.ncbi.nlm.nih.gov/articles/PMC11367519/#:~:text=neural%20differentiation%2C%20yet%20the%20governing,rescued%20the%20disrupted%20cortical%20architecture')
  88. AnnotationURLCitation(end_index=34746, start_index=34557, title='The histone deacetylase HDAC1 controls dendritic cell development and anti-tumor immunity - PubMed', type='url_citation', url='https://pubmed.ncbi.nlm.nih.gov/38829740/#:~:text=development%2C%20generating%20different%20subsets,HDAC1%20controls%20expression%2C%20chromatin%20accessibility')
  89. AnnotationURLCitation(end_index=34960, start_index=34833, title='The p65 (RelA) Subunit of NF-κB Interacts with the Histone Deacetylase (HDAC) Corepressors HDAC1 and HDAC2 To Negatively Regulate Gene Expression - PMC', type='url_citation', url='https://pmc.ncbi.nlm.nih.gov/articles/PMC99882/#:~:text=were%20mutated,%CE%BAB%20directly%20but%20can')
  90. AnnotationURLCitation(end_index=35088, start_index=34961, title='The p65 (RelA) Subunit of NF-κB Interacts with the Histone Deacetylase (HDAC) Corepressors HDAC1 and HDAC2 To Negatively Regulate Gene Expression - PMC', type='url_citation', url='https://pmc.ncbi.nlm.nih.gov/articles/PMC99882/#:~:text=%2814%29,interact%20with%20the%20MyoD%20basic')
  91. AnnotationURLCitation(end_index=35423, start_index=35290, title='The NuRD complex cooperates with DNMTs to maintain silencing of key colorectal tumor suppressor genes - PubMed', type='url_citation', url='https://pubmed.ncbi.nlm.nih.gov/23708667/#:~:text=colorectal%20tumor%20suppressor%20genes%20,CONT1%20and')
  92. AnnotationURLCitation(end_index=35662, start_index=35490, title='HDAC1/2/3 are major histone desuccinylases critical for promoter desuccinylation - PMC', type='url_citation', url='https://pmc.ncbi.nlm.nih.gov/articles/PMC10425439/#:~:text=believed%20to%20be%20catalyzed%20by,elevation%20of%20promoter%20histone%20succinylation')
  93. AnnotationURLCitation(end_index=35843, start_index=35663, title='HDAC1/2/3 are major histone desuccinylases critical for promoter desuccinylation - PMC', type='url_citation', url='https://pmc.ncbi.nlm.nih.gov/articles/PMC10425439/#:~:text=desuccinylase%20activity%20in%20vitro,histone%20desuccinylases%20particularly%20important%20for')
  94. AnnotationURLCitation(end_index=36087, start_index=35919, title='Essential roles of HDAC1 and 2 in lineage development and genome-wide DNA methylation during mouse preimplantation development - PubMed', type='url_citation', url='https://pubmed.ncbi.nlm.nih.gov/31533525/#:~:text=role%20of%20histone%20modifications%20in,gene%20expression%20changes%2C%20a%20substantial')
  95. AnnotationURLCitation(end_index=36215, start_index=36088, title='Essential roles of HDAC1 and 2 in lineage development and genome-wide DNA methylation during mouse preimplantation development - PubMed', type='url_citation', url='https://pubmed.ncbi.nlm.nih.gov/31533525/#:~:text=HDAC1%2F2,are%20core%20components%20of%20several')
  96. AnnotationURLCitation(end_index=36419, start_index=36285, title='A single allele of Hdac2 but not Hdac1 is sufficient for normal mouse brain development in the absence of its paralog - PubMed', type='url_citation', url='https://pubmed.ncbi.nlm.nih.gov/24449838/#:~:text=HDAC1%20and%20HDAC2%2C%20we%20expressed,brains%20showed')
  97. AnnotationURLCitation(end_index=36676, start_index=36499, title='HDAC1: a promising target for cancer treatment: insights from a thorough analysis of tumor functions - PMC', type='url_citation', url='https://pmc.ncbi.nlm.nih.gov/articles/PMC11543092/#:~:text=HDAC1%20exhibited%20high%20expression%20in,migration%20were%20significantly%20inhibited%20by')
  98. AnnotationURLCitation(end_index=36908, start_index=36713, title='A comprehensive review of histone deacetylases: implicati...', type='url_citation', url='https://www.degruyterbrill.com/document/doi/10.1515/oncologie-2025-0419/html#:~:text=that%20HDACs%20orchestrate%20crucial%20oncogenic,The%20aberrant%20expression%20and')
  99. AnnotationURLCitation(end_index=37040, start_index=36940, title='HDAC inhibitors as anticancer drugs: chemical diversity, clinical trials, challenges and perspectives - PMC', type='url_citation', url='https://pmc.ncbi.nlm.nih.gov/articles/PMC12805814/#:~:text=IV.,have%20been')

📄 View Raw YAML

 
id: O09106
gene_symbol: Hdac1
product_type: PROTEIN
status: COMPLETE
taxon:
  id: NCBITaxon:10090
  label: Mus musculus
description: Histone deacetylase 1 (HDAC1) is a zinc-dependent metalloenzyme (EC 3.5.1.98) that
  catalyzes the removal of acetyl groups from lysine residues on histones and non-histone proteins.
  HDAC1 functions as the catalytic subunit of multiple co-repressor complexes including NuRD, SIN3,
  and CoREST, mediating transcriptional repression through chromatin compaction. It also has
  experimentally supported decrotonylase activity; current delactylase annotation is similarity-based
  rather than direct mouse experimental evidence. HDAC1 is essential for embryonic development and
  plays roles in cell cycle regulation, differentiation, and numerous signaling pathways.
existing_annotations:
- term:
    id: GO:0004407
    label: histone deacetylase activity
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    summary: HDAC1 is a zinc-dependent histone deacetylase (EC 3.5.1.98) that catalyzes removal of
      acetyl groups from N-acetyl-lysine residues on histones H2A, H2B, H3, and H4. This is the core
      enzymatic function of HDAC1, well established by direct biochemical assays (PMID:10615135,
      PMID:21960634, PMID:30279482).
    action: ACCEPT
    reason: Histone deacetylase activity is the primary enzymatic function of HDAC1, supported by
      multiple direct experimental studies demonstrating catalytic activity on histone substrates.
    supported_by:
    - reference_id: PMID:10615135
      supporting_text: Here we show that Dnmt1 is itself associated with histone deacetylase
        activity in vivo
    - reference_id: PMID:30279482
      supporting_text: A ternary complex of HDAC1/CoREST1/LSD1 is able to hydrolyse both histone H3
        Lys18-acetyl (H3K18ac) and H3 Lys18-crotonyl (H3K18cr) peptide substrates
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD,
        Sin3, CoREST, and related chromatin-repressor complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: HDAC1 is a class I Zn2+-dependent histone/protein deacetylase that removes
        acetyl groups from lysine residues on histone tails and non-histone proteins.
- term:
    id: GO:0031507
    label: heterochromatin formation
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    summary: HDAC1 contributes to heterochromatin formation through its deacetylase activity. It has
      been localized to heterochromatic regions including pericentromeric heterochromatin
      (PMID:14643676, PMID:14519686).
    action: ACCEPT
    reason: HDAC1 deacetylation promotes chromatin compaction and is involved in heterochromatin
      maintenance. IBA annotation from phylogenetic analysis is appropriate. Supported by
      localization to heterochromatin in mouse cells.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD,
        Sin3, CoREST, and related chromatin-repressor complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylase that catalyzes the deacetylation of lysine residues on
        the N-terminal part of the core histones.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein
        corepressor complexes, especially SIN3, NuRD, and CoREST.
- term:
    id: GO:0016581
    label: NuRD complex
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    summary: HDAC1 is a core catalytic subunit of the NuRD (nucleosome remodeling and deacetylase)
      complex. Proteomic studies show approximately 49% of cellular HDAC1 in ESCs is in the NuRD
      complex (deep research review). Well supported by mass spectrometry identification
      (PMID:27806305) and multiple interaction studies.
    action: ACCEPT
    reason: NuRD complex membership is a core aspect of HDAC1 function. HDAC1 serves as the
      catalytic deacetylase subunit within NuRD. Extensively validated by proteomics and
      co-immunoprecipitation studies.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD,
        Sin3, CoREST, and related chromatin-repressor complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylase that catalyzes the deacetylation of lysine residues on
        the N-terminal part of the core histones.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein
        corepressor complexes, especially SIN3, NuRD, and CoREST.
- term:
    id: GO:0004407
    label: histone deacetylase activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  review:
    summary: HDAC1 is a zinc-dependent histone deacetylase (EC 3.5.1.98) that catalyzes removal of
      acetyl groups from N-acetyl-lysine residues on histones H2A, H2B, H3, and H4. This is the core
      enzymatic function of HDAC1, well established by direct biochemical assays (PMID:10615135,
      PMID:21960634, PMID:30279482).
    action: ACCEPT
    reason: Histone deacetylase activity is the primary enzymatic function of HDAC1, supported by
      multiple direct experimental studies demonstrating catalytic activity on histone substrates.
    supported_by:
    - reference_id: PMID:10615135
      supporting_text: Here we show that Dnmt1 is itself associated with histone deacetylase
        activity in vivo
    - reference_id: PMID:30279482
      supporting_text: A ternary complex of HDAC1/CoREST1/LSD1 is able to hydrolyse both histone H3
        Lys18-acetyl (H3K18ac) and H3 Lys18-crotonyl (H3K18cr) peptide substrates
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD,
        Sin3, CoREST, and related chromatin-repressor complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: HDAC1 is a class I Zn2+-dependent histone/protein deacetylase that removes
        acetyl groups from lysine residues on histone tails and non-histone proteins.
- term:
    id: GO:0005634
    label: nucleus
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  review:
    summary: HDAC1 is predominantly nuclear, consistent with its function in chromatin modification
      and transcriptional regulation. Nuclear localization confirmed by multiple methods including
      immunofluorescence (PMID:11115394).
    action: ACCEPT
    reason: Nuclear localization is a well-established core feature of HDAC1. It is a Class I HDAC
      that is predominantly nuclear.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD,
        Sin3, CoREST, and related chromatin-repressor complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylase that catalyzes the deacetylation of lysine residues on
        the N-terminal part of the core histones.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: Class I HDACs, including HDAC1, are predominantly or exclusively nuclear,
        consistent with chromatin accessibility and transcriptional control roles.
- term:
    id: GO:0017053
    label: transcription repressor complex
  evidence_type: IEA
  original_reference_id: GO_REF:0000117
  review:
    summary: HDAC1 functions within transcription repressor complexes including NuRD, SIN3, and
      CoREST, which mediate transcriptional repression through histone deacetylation.
    action: ACCEPT
    reason: HDAC1 is a core catalytic subunit of several transcription repressor complexes. This is
      a correct and informative annotation.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD,
        Sin3, CoREST, and related chromatin-repressor complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylase that catalyzes the deacetylation of lysine residues on
        the N-terminal part of the core histones.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein
        corepressor complexes, especially SIN3, NuRD, and CoREST.
- term:
    id: GO:0030178
    label: negative regulation of Wnt signaling pathway
  evidence_type: IEA
  original_reference_id: GO_REF:0000117
  review:
    summary: HDAC1 negatively regulates Wnt signaling. The more specific term GO:0090090 is already
      annotated.
    action: MODIFY
    reason: The more specific term GO:0090090 (negative regulation of canonical Wnt signaling
      pathway) is already annotated and is more appropriate.
    proposed_replacement_terms:
    - id: GO:0090090
      label: negative regulation of canonical Wnt signaling pathway
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: The broader Wnt term is less precise than the canonical Wnt signaling
        annotation already present for HDAC1-dependent repression.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: HDAC1 functions as a chromatin-modifying corepressor complex subunit.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: The report supports HDAC1 as a chromatin deacetylase whose developmental,
        signaling, cell-cycle, DNA-damage, and pathway phenotypes are context-specific downstream
        outputs.
- term:
    id: GO:0035851
    label: Krueppel-associated box domain binding
  evidence_type: IEA
  original_reference_id: GO_REF:0000117
  review:
    summary: HDAC1 binds to KRAB domain-containing zinc finger proteins, demonstrated for ZNF431
      (PMID:21177534).
    action: ACCEPT
    reason: IEA transfer consistent with direct experimental evidence for KRAB domain binding.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD,
        Sin3, CoREST, and related chromatin-repressor complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylase that catalyzes the deacetylation of lysine residues on
        the N-terminal part of the core histones.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein
        corepressor complexes, especially SIN3, NuRD, and CoREST.
- term:
    id: GO:0060789
    label: hair follicle placode formation
  evidence_type: IEA
  original_reference_id: GO_REF:0000117
  review:
    summary: HDAC1/2 are required for hair follicle placode formation (PMID:21093383).
    action: KEEP_AS_NON_CORE
    reason: Specific epidermal phenotype. Pleiotropic downstream effect.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 has many developmental and signaling consequences through chromatin
        deacetylation; these are non-core outputs of the core enzymatic function.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylation gives a tag for epigenetic repression and plays an
        important role in transcriptional regulation, cell cycle progression and developmental
        events.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: The report supports HDAC1 as a chromatin deacetylase whose developmental,
        signaling, cell-cycle, DNA-damage, and pathway phenotypes are context-specific downstream
        outputs.
- term:
    id: GO:0061029
    label: eyelid development in camera-type eye
  evidence_type: IEA
  original_reference_id: GO_REF:0000117
  review:
    summary: HDAC1/2 conditional knockout in epidermis affects eyelid development (PMID:21093383).
    action: KEEP_AS_NON_CORE
    reason: Specific developmental phenotype. Pleiotropic downstream effect.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 has many developmental and signaling consequences through chromatin
        deacetylation; these are non-core outputs of the core enzymatic function.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylation gives a tag for epigenetic repression and plays an
        important role in transcriptional regulation, cell cycle progression and developmental
        events.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: The report supports HDAC1 as a chromatin deacetylase whose developmental,
        signaling, cell-cycle, DNA-damage, and pathway phenotypes are context-specific downstream
        outputs.
- term:
    id: GO:0061198
    label: fungiform papilla formation
  evidence_type: IEA
  original_reference_id: GO_REF:0000117
  review:
    summary: HDAC1/2 conditional loss in epidermis affects fungiform papilla formation
      (PMID:21093383).
    action: KEEP_AS_NON_CORE
    reason: Specific developmental phenotype. Pleiotropic downstream effect.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 has many developmental and signaling consequences through chromatin
        deacetylation; these are non-core outputs of the core enzymatic function.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylation gives a tag for epigenetic repression and plays an
        important role in transcriptional regulation, cell cycle progression and developmental
        events.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: The report supports HDAC1 as a chromatin deacetylase whose developmental,
        signaling, cell-cycle, DNA-damage, and pathway phenotypes are context-specific downstream
        outputs.
- term:
    id: GO:0141221
    label: histone deacetylase activity, hydrolytic mechanism
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  review:
    summary: HDAC1 uses a zinc-dependent hydrolytic mechanism to remove acetyl groups from histones.
      This is a more specific child term of GO:0004407 that specifies the catalytic mechanism.
    action: ACCEPT
    reason: HDAC1 is a Class I HDAC that uses a zinc-dependent hydrolytic mechanism (as opposed to
      NAD+-dependent sirtuins). Well established from structural and biochemical studies.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD,
        Sin3, CoREST, and related chromatin-repressor complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylase that catalyzes the deacetylation of lysine residues on
        the N-terminal part of the core histones.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: HDAC1 is a class I Zn2+-dependent histone/protein deacetylase that removes
        acetyl groups from lysine residues on histone tails and non-histone proteins.
- term:
    id: GO:0160008
    label: protein decrotonylase activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000116
  review:
    summary: HDAC1 can remove crotonyl groups from lysine residues on proteins. Demonstrated by
      Kelly et al. (PMID:30279482) for histone substrates.
    action: MODIFY
    reason: The cited evidence supports histone decrotonylase activity, not a broad protein
      decrotonylase role as the primary accepted term.
    proposed_replacement_terms:
    - id: GO:0160009
      label: histone decrotonylase activity
    supported_by:
    - reference_id: PMID:30279482
      supporting_text: Genetic deletion of HDAC1/2 in ES cells increases global levels of histone
        crotonylation and causes an 85% reduction in total decrotonylase activity
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD,
        Sin3, CoREST, and related chromatin-repressor complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein
        corepressor complexes, especially SIN3, NuRD, and CoREST.
- term:
    id: GO:2001243
    label: negative regulation of intrinsic apoptotic signaling pathway
  evidence_type: IEA
  original_reference_id: GO_REF:0000117
  review:
    summary: HDAC1 negatively regulates the intrinsic apoptotic signaling pathway. HDAC1/2 double
      knockout in epidermis leads to increased apoptosis (PMID:21093383).
    action: ACCEPT
    reason: HDAC1/2 directly mediate transcriptional repression through chromatin deacetylation
      and suppress p53 activity in this system, so negative regulation of intrinsic apoptotic
      signaling is a direct chromatin-repressor output rather than only a distal phenotype.
    supported_by:
    - reference_id: PMID:21093383
      supporting_text: HDAC1/2 directly mediate repressive functions of p63 and suppress p53 activity.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 can deacetylate p53, reducing p53 activity and thereby modulating
        apoptosis and DNA damage responses.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylation gives a tag for epigenetic repression and plays an
        important role in transcriptional regulation, cell cycle progression and developmental
        events.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein
        corepressor complexes.
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:10615135
  review:
    summary: Protein binding annotation based on physical interaction evidence from PMID:10615135.
      HDAC1 is known to interact with a very large number of proteins as it functions within
      multiple co-repressor complexes (NuRD, SIN3, CoREST) and binds many transcription factors.
    action: REMOVE
    reason: Per curation guidelines, protein binding (GO:0005515) is uninformative and should be
      replaced with more specific molecular function terms. HDAC1 physically interacts with many
      proteins, but this generic term does not convey functional information. More specific
      annotations such as histone deacetylase binding, transcription corepressor binding, NF-kappaB
      binding, and DNA-binding transcription factor binding are already present.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: Generic protein binding and weakly mechanistic interaction annotations are
        less informative than HDAC1 deacetylase activity and defined corepressor-complex membership.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylases act via the formation of large multiprotein complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: The report supports specific enzymatic and chromatin-complex annotations for
        HDAC1 rather than generic binding or weakly localized annotations.
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:11931769
  review:
    summary: Protein binding annotation based on physical interaction evidence from PMID:11931769.
      HDAC1 is known to interact with a very large number of proteins as it functions within
      multiple co-repressor complexes (NuRD, SIN3, CoREST) and binds many transcription factors.
    action: REMOVE
    reason: Per curation guidelines, protein binding (GO:0005515) is uninformative and should be
      replaced with more specific molecular function terms. HDAC1 physically interacts with many
      proteins, but this generic term does not convey functional information. More specific
      annotations such as histone deacetylase binding, transcription corepressor binding, NF-kappaB
      binding, and DNA-binding transcription factor binding are already present.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: Generic protein binding and weakly mechanistic interaction annotations are
        less informative than HDAC1 deacetylase activity and defined corepressor-complex membership.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylases act via the formation of large multiprotein complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: The report supports specific enzymatic and chromatin-complex annotations for
        HDAC1 rather than generic binding or weakly localized annotations.
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:15337766
  review:
    summary: Protein binding annotation based on physical interaction evidence from PMID:15337766.
      HDAC1 is known to interact with a very large number of proteins as it functions within
      multiple co-repressor complexes (NuRD, SIN3, CoREST) and binds many transcription factors.
    action: REMOVE
    reason: Per curation guidelines, protein binding (GO:0005515) is uninformative and should be
      replaced with more specific molecular function terms. HDAC1 physically interacts with many
      proteins, but this generic term does not convey functional information. More specific
      annotations such as histone deacetylase binding, transcription corepressor binding, NF-kappaB
      binding, and DNA-binding transcription factor binding are already present.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: Generic protein binding and weakly mechanistic interaction annotations are
        less informative than HDAC1 deacetylase activity and defined corepressor-complex membership.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylases act via the formation of large multiprotein complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: The report supports specific enzymatic and chromatin-complex annotations for
        HDAC1 rather than generic binding or weakly localized annotations.
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:16407974
  review:
    summary: Protein binding annotation based on physical interaction evidence from PMID:16407974.
      HDAC1 is known to interact with a very large number of proteins as it functions within
      multiple co-repressor complexes (NuRD, SIN3, CoREST) and binds many transcription factors.
    action: REMOVE
    reason: Per curation guidelines, protein binding (GO:0005515) is uninformative and should be
      replaced with more specific molecular function terms. HDAC1 physically interacts with many
      proteins, but this generic term does not convey functional information. More specific
      annotations such as histone deacetylase binding, transcription corepressor binding, NF-kappaB
      binding, and DNA-binding transcription factor binding are already present.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: Generic protein binding and weakly mechanistic interaction annotations are
        less informative than HDAC1 deacetylase activity and defined corepressor-complex membership.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylases act via the formation of large multiprotein complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: The report supports specific enzymatic and chromatin-complex annotations for
        HDAC1 rather than generic binding or weakly localized annotations.
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:17056544
  review:
    summary: Protein binding annotation based on physical interaction evidence from PMID:17056544.
      HDAC1 is known to interact with a very large number of proteins as it functions within
      multiple co-repressor complexes (NuRD, SIN3, CoREST) and binds many transcription factors.
    action: REMOVE
    reason: Per curation guidelines, protein binding (GO:0005515) is uninformative and should be
      replaced with more specific molecular function terms. HDAC1 physically interacts with many
      proteins, but this generic term does not convey functional information. More specific
      annotations such as histone deacetylase binding, transcription corepressor binding, NF-kappaB
      binding, and DNA-binding transcription factor binding are already present.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: Generic protein binding and weakly mechanistic interaction annotations are
        less informative than HDAC1 deacetylase activity and defined corepressor-complex membership.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylases act via the formation of large multiprotein complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: The report supports specific enzymatic and chromatin-complex annotations for
        HDAC1 rather than generic binding or weakly localized annotations.
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:17568773
  review:
    summary: Protein binding annotation based on physical interaction evidence from PMID:17568773.
      HDAC1 is known to interact with a very large number of proteins as it functions within
      multiple co-repressor complexes (NuRD, SIN3, CoREST) and binds many transcription factors.
    action: REMOVE
    reason: Per curation guidelines, protein binding (GO:0005515) is uninformative and should be
      replaced with more specific molecular function terms. HDAC1 physically interacts with many
      proteins, but this generic term does not convey functional information. More specific
      annotations such as histone deacetylase binding, transcription corepressor binding, NF-kappaB
      binding, and DNA-binding transcription factor binding are already present.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: Generic protein binding and weakly mechanistic interaction annotations are
        less informative than HDAC1 deacetylase activity and defined corepressor-complex membership.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylases act via the formation of large multiprotein complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: The report supports specific enzymatic and chromatin-complex annotations for
        HDAC1 rather than generic binding or weakly localized annotations.
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:19424149
  review:
    summary: Protein binding annotation based on physical interaction evidence from PMID:19424149.
      HDAC1 is known to interact with a very large number of proteins as it functions within
      multiple co-repressor complexes (NuRD, SIN3, CoREST) and binds many transcription factors.
    action: REMOVE
    reason: Per curation guidelines, protein binding (GO:0005515) is uninformative and should be
      replaced with more specific molecular function terms. HDAC1 physically interacts with many
      proteins, but this generic term does not convey functional information. More specific
      annotations such as histone deacetylase binding, transcription corepressor binding, NF-kappaB
      binding, and DNA-binding transcription factor binding are already present.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: Generic protein binding and weakly mechanistic interaction annotations are
        less informative than HDAC1 deacetylase activity and defined corepressor-complex membership.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylases act via the formation of large multiprotein complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: The report supports specific enzymatic and chromatin-complex annotations for
        HDAC1 rather than generic binding or weakly localized annotations.
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:19497860
  review:
    summary: Protein binding annotation based on physical interaction evidence from PMID:19497860.
      HDAC1 is known to interact with a very large number of proteins as it functions within
      multiple co-repressor complexes (NuRD, SIN3, CoREST) and binds many transcription factors.
    action: REMOVE
    reason: Per curation guidelines, protein binding (GO:0005515) is uninformative and should be
      replaced with more specific molecular function terms. HDAC1 physically interacts with many
      proteins, but this generic term does not convey functional information. More specific
      annotations such as histone deacetylase binding, transcription corepressor binding, NF-kappaB
      binding, and DNA-binding transcription factor binding are already present.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: Generic protein binding and weakly mechanistic interaction annotations are
        less informative than HDAC1 deacetylase activity and defined corepressor-complex membership.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylases act via the formation of large multiprotein complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: The report supports specific enzymatic and chromatin-complex annotations for
        HDAC1 rather than generic binding or weakly localized annotations.
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:20404188
  review:
    summary: Protein binding annotation based on physical interaction evidence from PMID:20404188.
      HDAC1 is known to interact with a very large number of proteins as it functions within
      multiple co-repressor complexes (NuRD, SIN3, CoREST) and binds many transcription factors.
    action: REMOVE
    reason: Per curation guidelines, protein binding (GO:0005515) is uninformative and should be
      replaced with more specific molecular function terms. HDAC1 physically interacts with many
      proteins, but this generic term does not convey functional information. More specific
      annotations such as histone deacetylase binding, transcription corepressor binding, NF-kappaB
      binding, and DNA-binding transcription factor binding are already present.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: Generic protein binding and weakly mechanistic interaction annotations are
        less informative than HDAC1 deacetylase activity and defined corepressor-complex membership.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylases act via the formation of large multiprotein complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: The report supports specific enzymatic and chromatin-complex annotations for
        HDAC1 rather than generic binding or weakly localized annotations.
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:20596014
  review:
    summary: Protein binding annotation based on physical interaction evidence from PMID:20596014.
      HDAC1 is known to interact with a very large number of proteins as it functions within
      multiple co-repressor complexes (NuRD, SIN3, CoREST) and binds many transcription factors.
    action: REMOVE
    reason: Per curation guidelines, protein binding (GO:0005515) is uninformative and should be
      replaced with more specific molecular function terms. HDAC1 physically interacts with many
      proteins, but this generic term does not convey functional information. More specific
      annotations such as histone deacetylase binding, transcription corepressor binding, NF-kappaB
      binding, and DNA-binding transcription factor binding are already present.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: Generic protein binding and weakly mechanistic interaction annotations are
        less informative than HDAC1 deacetylase activity and defined corepressor-complex membership.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylases act via the formation of large multiprotein complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: The report supports specific enzymatic and chromatin-complex annotations for
        HDAC1 rather than generic binding or weakly localized annotations.
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:21177534
  review:
    summary: Protein binding annotation based on physical interaction evidence from PMID:21177534.
      HDAC1 is known to interact with a very large number of proteins as it functions within
      multiple co-repressor complexes (NuRD, SIN3, CoREST) and binds many transcription factors.
    action: REMOVE
    reason: Per curation guidelines, protein binding (GO:0005515) is uninformative and should be
      replaced with more specific molecular function terms. HDAC1 physically interacts with many
      proteins, but this generic term does not convey functional information. More specific
      annotations such as histone deacetylase binding, transcription corepressor binding, NF-kappaB
      binding, and DNA-binding transcription factor binding are already present.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: Generic protein binding and weakly mechanistic interaction annotations are
        less informative than HDAC1 deacetylase activity and defined corepressor-complex membership.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylases act via the formation of large multiprotein complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: The report supports specific enzymatic and chromatin-complex annotations for
        HDAC1 rather than generic binding or weakly localized annotations.
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:21448134
  review:
    summary: Protein binding annotation based on physical interaction evidence from PMID:21448134.
      HDAC1 is known to interact with a very large number of proteins as it functions within
      multiple co-repressor complexes (NuRD, SIN3, CoREST) and binds many transcription factors.
    action: REMOVE
    reason: Per curation guidelines, protein binding (GO:0005515) is uninformative and should be
      replaced with more specific molecular function terms. HDAC1 physically interacts with many
      proteins, but this generic term does not convey functional information. More specific
      annotations such as histone deacetylase binding, transcription corepressor binding, NF-kappaB
      binding, and DNA-binding transcription factor binding are already present.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: Generic protein binding and weakly mechanistic interaction annotations are
        less informative than HDAC1 deacetylase activity and defined corepressor-complex membership.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylases act via the formation of large multiprotein complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: The report supports specific enzymatic and chromatin-complex annotations for
        HDAC1 rather than generic binding or weakly localized annotations.
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:22297846
  review:
    summary: Protein binding annotation based on physical interaction evidence from PMID:22297846.
      HDAC1 is known to interact with a very large number of proteins as it functions within
      multiple co-repressor complexes (NuRD, SIN3, CoREST) and binds many transcription factors.
    action: REMOVE
    reason: Per curation guidelines, protein binding (GO:0005515) is uninformative and should be
      replaced with more specific molecular function terms. HDAC1 physically interacts with many
      proteins, but this generic term does not convey functional information. More specific
      annotations such as histone deacetylase binding, transcription corepressor binding, NF-kappaB
      binding, and DNA-binding transcription factor binding are already present.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: Generic protein binding and weakly mechanistic interaction annotations are
        less informative than HDAC1 deacetylase activity and defined corepressor-complex membership.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylases act via the formation of large multiprotein complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: The report supports specific enzymatic and chromatin-complex annotations for
        HDAC1 rather than generic binding or weakly localized annotations.
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:22334647
  review:
    summary: Protein binding annotation based on physical interaction evidence from PMID:22334647.
      HDAC1 is known to interact with a very large number of proteins as it functions within
      multiple co-repressor complexes (NuRD, SIN3, CoREST) and binds many transcription factors.
    action: REMOVE
    reason: Per curation guidelines, protein binding (GO:0005515) is uninformative and should be
      replaced with more specific molecular function terms. HDAC1 physically interacts with many
      proteins, but this generic term does not convey functional information. More specific
      annotations such as histone deacetylase binding, transcription corepressor binding, NF-kappaB
      binding, and DNA-binding transcription factor binding are already present.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: Generic protein binding and weakly mechanistic interaction annotations are
        less informative than HDAC1 deacetylase activity and defined corepressor-complex membership.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylases act via the formation of large multiprotein complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: The report supports specific enzymatic and chromatin-complex annotations for
        HDAC1 rather than generic binding or weakly localized annotations.
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:22918830
  review:
    summary: Protein binding annotation based on physical interaction evidence from PMID:22918830.
      HDAC1 is known to interact with a very large number of proteins as it functions within
      multiple co-repressor complexes (NuRD, SIN3, CoREST) and binds many transcription factors.
    action: REMOVE
    reason: Per curation guidelines, protein binding (GO:0005515) is uninformative and should be
      replaced with more specific molecular function terms. HDAC1 physically interacts with many
      proteins, but this generic term does not convey functional information. More specific
      annotations such as histone deacetylase binding, transcription corepressor binding, NF-kappaB
      binding, and DNA-binding transcription factor binding are already present.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: Generic protein binding and weakly mechanistic interaction annotations are
        less informative than HDAC1 deacetylase activity and defined corepressor-complex membership.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylases act via the formation of large multiprotein complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: The report supports specific enzymatic and chromatin-complex annotations for
        HDAC1 rather than generic binding or weakly localized annotations.
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:24240174
  review:
    summary: Protein binding annotation based on physical interaction evidence from PMID:24240174.
      HDAC1 is known to interact with a very large number of proteins as it functions within
      multiple co-repressor complexes (NuRD, SIN3, CoREST) and binds many transcription factors.
    action: REMOVE
    reason: Per curation guidelines, protein binding (GO:0005515) is uninformative and should be
      replaced with more specific molecular function terms. HDAC1 physically interacts with many
      proteins, but this generic term does not convey functional information. More specific
      annotations such as histone deacetylase binding, transcription corepressor binding, NF-kappaB
      binding, and DNA-binding transcription factor binding are already present.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: Generic protein binding and weakly mechanistic interaction annotations are
        less informative than HDAC1 deacetylase activity and defined corepressor-complex membership.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylases act via the formation of large multiprotein complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: The report supports specific enzymatic and chromatin-complex annotations for
        HDAC1 rather than generic binding or weakly localized annotations.
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:24736997
  review:
    summary: Protein binding annotation based on physical interaction evidence from PMID:24736997.
      HDAC1 is known to interact with a very large number of proteins as it functions within
      multiple co-repressor complexes (NuRD, SIN3, CoREST) and binds many transcription factors.
    action: REMOVE
    reason: Per curation guidelines, protein binding (GO:0005515) is uninformative and should be
      replaced with more specific molecular function terms. HDAC1 physically interacts with many
      proteins, but this generic term does not convey functional information. More specific
      annotations such as histone deacetylase binding, transcription corepressor binding, NF-kappaB
      binding, and DNA-binding transcription factor binding are already present.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: Generic protein binding and weakly mechanistic interaction annotations are
        less informative than HDAC1 deacetylase activity and defined corepressor-complex membership.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylases act via the formation of large multiprotein complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: The report supports specific enzymatic and chromatin-complex annotations for
        HDAC1 rather than generic binding or weakly localized annotations.
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:26816381
  review:
    summary: Protein binding annotation based on physical interaction evidence from PMID:26816381.
      HDAC1 is known to interact with a very large number of proteins as it functions within
      multiple co-repressor complexes (NuRD, SIN3, CoREST) and binds many transcription factors.
    action: REMOVE
    reason: Per curation guidelines, protein binding (GO:0005515) is uninformative and should be
      replaced with more specific molecular function terms. HDAC1 physically interacts with many
      proteins, but this generic term does not convey functional information. More specific
      annotations such as histone deacetylase binding, transcription corepressor binding, NF-kappaB
      binding, and DNA-binding transcription factor binding are already present.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: Generic protein binding and weakly mechanistic interaction annotations are
        less informative than HDAC1 deacetylase activity and defined corepressor-complex membership.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylases act via the formation of large multiprotein complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: The report supports specific enzymatic and chromatin-complex annotations for
        HDAC1 rather than generic binding or weakly localized annotations.
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:26974661
  review:
    summary: Protein binding annotation based on physical interaction evidence from PMID:26974661.
      HDAC1 is known to interact with a very large number of proteins as it functions within
      multiple co-repressor complexes (NuRD, SIN3, CoREST) and binds many transcription factors.
    action: REMOVE
    reason: Per curation guidelines, protein binding (GO:0005515) is uninformative and should be
      replaced with more specific molecular function terms. HDAC1 physically interacts with many
      proteins, but this generic term does not convey functional information. More specific
      annotations such as histone deacetylase binding, transcription corepressor binding, NF-kappaB
      binding, and DNA-binding transcription factor binding are already present.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: Generic protein binding and weakly mechanistic interaction annotations are
        less informative than HDAC1 deacetylase activity and defined corepressor-complex membership.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylases act via the formation of large multiprotein complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: The report supports specific enzymatic and chromatin-complex annotations for
        HDAC1 rather than generic binding or weakly localized annotations.
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:30726206
  review:
    summary: Protein binding annotation based on physical interaction evidence from PMID:30726206.
      HDAC1 is known to interact with a very large number of proteins as it functions within
      multiple co-repressor complexes (NuRD, SIN3, CoREST) and binds many transcription factors.
    action: REMOVE
    reason: Per curation guidelines, protein binding (GO:0005515) is uninformative and should be
      replaced with more specific molecular function terms. HDAC1 physically interacts with many
      proteins, but this generic term does not convey functional information. More specific
      annotations such as histone deacetylase binding, transcription corepressor binding, NF-kappaB
      binding, and DNA-binding transcription factor binding are already present.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: Generic protein binding and weakly mechanistic interaction annotations are
        less informative than HDAC1 deacetylase activity and defined corepressor-complex membership.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylases act via the formation of large multiprotein complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: The report supports specific enzymatic and chromatin-complex annotations for
        HDAC1 rather than generic binding or weakly localized annotations.
- term:
    id: GO:0000118
    label: histone deacetylase complex
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  review:
    summary: HDAC1 is a core component of multiple histone deacetylase complexes including NuRD,
      SIN3, and CoREST. This is a general parent term encompassing all such complexes.
    action: ACCEPT
    reason: HDAC1 is the defining catalytic subunit of multiple HDAC complexes. This broader term is
      appropriate as a parent annotation alongside the more specific NuRD and SIN3 complex terms.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD,
        Sin3, CoREST, and related chromatin-repressor complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylase that catalyzes the deacetylation of lysine residues on
        the N-terminal part of the core histones.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: HDAC1 is a class I Zn2+-dependent histone/protein deacetylase that removes
        acetyl groups from lysine residues on histone tails and non-histone proteins.
- term:
    id: GO:0000122
    label: negative regulation of transcription by RNA polymerase II
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  review:
    summary: HDAC1 negatively regulates transcription by RNA polymerase II through histone
      deacetylation at target gene promoters. This is a core biological process annotation for
      HDAC1.
    action: ACCEPT
    reason: Negative regulation of pol II transcription is a primary biological function of HDAC1.
      Supported by multiple lines of evidence (PMID:8917507, PMID:9271381, PMID:21093383).
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD,
        Sin3, CoREST, and related chromatin-repressor complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylase that catalyzes the deacetylation of lysine residues on
        the N-terminal part of the core histones.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein
        corepressor complexes, especially SIN3, NuRD, and CoREST.
- term:
    id: GO:0000785
    label: chromatin
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  review:
    summary: HDAC1 is a chromatin-associated protein that modifies histone tails as part of
      co-repressor complexes.
    action: ACCEPT
    reason: HDAC1 is a histone-modifying enzyme that directly acts on chromatin. Association with
      chromatin is inherent to its function.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD,
        Sin3, CoREST, and related chromatin-repressor complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylase that catalyzes the deacetylation of lysine residues on
        the N-terminal part of the core histones.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein
        corepressor complexes, especially SIN3, NuRD, and CoREST.
- term:
    id: GO:0000978
    label: RNA polymerase II cis-regulatory region sequence-specific DNA binding
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  review:
    summary: Annotation suggests HDAC1 has sequence-specific DNA binding at RNA pol II
      cis-regulatory regions. However, HDAC1 does not have intrinsic sequence-specific DNA binding -
      it is recruited to promoters by transcription factors.
    action: MODIFY
    reason: Replace direct sequence-specific DNA binding with promoter-specific chromatin binding,
      which captures HDAC1 recruitment to promoter chromatin without implying intrinsic DNA-binding
      specificity.
    proposed_replacement_terms:
    - id: GO:1990841
      label: promoter-specific chromatin binding
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 is recruited to chromatin by DNA-binding factors but is not itself a
        sequence-specific DNA-binding transcription factor.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylase that catalyzes the deacetylation of lysine residues on
        core histones.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: The report supports HDAC1 as a chromatin deacetylase whose developmental,
        signaling, cell-cycle, DNA-damage, and pathway phenotypes are context-specific downstream
        outputs.
- term:
    id: GO:0000979
    label: RNA polymerase II core promoter sequence-specific DNA binding
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  review:
    summary: This implies sequence-specific core promoter DNA binding by HDAC1, which is not
      supported. HDAC1 is recruited to core promoters via protein-protein interactions.
    action: MODIFY
    reason: Replace direct sequence-specific DNA binding with promoter-specific chromatin binding,
      which captures HDAC1 recruitment to promoter chromatin without implying intrinsic DNA-binding
      specificity.
    proposed_replacement_terms:
    - id: GO:1990841
      label: promoter-specific chromatin binding
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 is recruited to chromatin by DNA-binding factors but is not itself a
        sequence-specific DNA-binding transcription factor.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylase that catalyzes the deacetylation of lysine residues on
        core histones.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: The report supports HDAC1 as a chromatin deacetylase whose developmental,
        signaling, cell-cycle, DNA-damage, and pathway phenotypes are context-specific downstream
        outputs.
- term:
    id: GO:0001046
    label: core promoter sequence-specific DNA binding
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  review:
    summary: This implies HDAC1 has core promoter sequence-specific DNA binding, which is not
      supported by its known biochemistry.
    action: MODIFY
    reason: Replace direct sequence-specific DNA binding with promoter-specific chromatin binding,
      which captures HDAC1 recruitment to promoter chromatin without implying intrinsic DNA-binding
      specificity.
    proposed_replacement_terms:
    - id: GO:1990841
      label: promoter-specific chromatin binding
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 is recruited to chromatin by DNA-binding factors but is not itself a
        sequence-specific DNA-binding transcription factor.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylase that catalyzes the deacetylation of lysine residues on
        core histones.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: The report supports HDAC1 as a chromatin deacetylase whose developmental,
        signaling, cell-cycle, DNA-damage, and pathway phenotypes are context-specific downstream
        outputs.
- term:
    id: GO:0001222
    label: transcription corepressor binding
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  review:
    summary: HDAC1 binds to transcription corepressors including SIN3A, SIN3B, CoREST, NCoR, and
      SMRT as part of its recruitment to target genes.
    action: ACCEPT
    reason: HDAC1 physically interacts with multiple corepressor scaffold proteins. This binding is
      essential for its function in transcriptional repression complexes.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD,
        Sin3, CoREST, and related chromatin-repressor complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylase that catalyzes the deacetylation of lysine residues on
        the N-terminal part of the core histones.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein
        corepressor complexes, especially SIN3, NuRD, and CoREST.
- term:
    id: GO:0001975
    label: response to amphetamine
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  review:
    summary: IEA annotation suggesting HDAC1 involvement in response to amphetamine.
    action: KEEP_AS_NON_CORE
    reason: Highly context-specific phenotype likely representing downstream pleiotropic effects.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 has many developmental and signaling consequences through chromatin
        deacetylation; these are non-core outputs of the core enzymatic function.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylation gives a tag for epigenetic repression and plays an
        important role in transcriptional regulation, cell cycle progression and developmental
        events.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: The report supports HDAC1 as a chromatin deacetylase whose developmental,
        signaling, cell-cycle, DNA-damage, and pathway phenotypes are context-specific downstream
        outputs.
- term:
    id: GO:0002039
    label: p53 binding
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  review:
    summary: HDAC1 binds to and deacetylates the tumor suppressor p53, thereby modulating its
      activity and stability.
    action: ACCEPT
    reason: HDAC1 interaction with p53 is well established. HDAC1 deacetylates p53, leading to its
      inactivation and degradation. Functionally relevant interaction.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD,
        Sin3, CoREST, and related chromatin-repressor complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylase that catalyzes the deacetylation of lysine residues on
        the N-terminal part of the core histones.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein
        corepressor complexes, especially SIN3, NuRD, and CoREST.
- term:
    id: GO:0003682
    label: chromatin binding
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  review:
    summary: HDAC1 binds chromatin as part of its function in co-repressor complexes. ChIP
      experiments have confirmed HDAC1 occupancy at promoters and other regulatory regions.
    action: ACCEPT
    reason: Chromatin binding is well supported by extensive ChIP-seq and ChIP-qPCR data showing
      HDAC1 occupancy at promoters, enhancers, and heterochromatic regions.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD,
        Sin3, CoREST, and related chromatin-repressor complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylase that catalyzes the deacetylation of lysine residues on
        the N-terminal part of the core histones.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein
        corepressor complexes, especially SIN3, NuRD, and CoREST.
- term:
    id: GO:0003714
    label: transcription corepressor activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  review:
    summary: HDAC1 functions as a transcription corepressor by deacetylating histones at target gene
      promoters, leading to chromatin compaction and transcriptional silencing.
    action: ACCEPT
    reason: Transcription corepressor activity is a core function of HDAC1. It mediates
      transcriptional repression through histone deacetylation when recruited to target promoters by
      sequence-specific repressors.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD,
        Sin3, CoREST, and related chromatin-repressor complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylase that catalyzes the deacetylation of lysine residues on
        the N-terminal part of the core histones.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein
        corepressor complexes, especially SIN3, NuRD, and CoREST.
- term:
    id: GO:0005654
    label: nucleoplasm
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  review:
    summary: HDAC1 is localized to the nucleoplasm where it functions as part of chromatin-modifying
      complexes.
    action: ACCEPT
    reason: Nucleoplasm localization is consistent with HDAC1 function in chromatin modification.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD,
        Sin3, CoREST, and related chromatin-repressor complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylase that catalyzes the deacetylation of lysine residues on
        the N-terminal part of the core histones.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: Class I HDACs, including HDAC1, are predominantly or exclusively nuclear,
        consistent with chromatin accessibility and transcriptional control roles.
- term:
    id: GO:0005829
    label: cytosol
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  review:
    summary: GOA includes a cytosol annotation, but HDAC1 is primarily a nuclear chromatin
      deacetylase/corepressor-complex subunit.
    action: KEEP_AS_NON_CORE
    reason: Cytosol is, at most, a minor inferred localization and should not be treated as a core
      HDAC1 cellular-component annotation.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: 'GO; GO:0005829; C:cytosol; ISO:GO_Central.'
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: Class I HDACs, including HDAC1, are predominantly or exclusively nuclear,
        consistent with chromatin accessibility and transcriptional control roles.
- term:
    id: GO:0006325
    label: chromatin organization
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  review:
    summary: HDAC1 plays a role in chromatin organization through histone deacetylation, which
      promotes nucleosome compaction.
    action: ACCEPT
    reason: Chromatin organization is a direct consequence of HDAC1 enzymatic activity.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD,
        Sin3, CoREST, and related chromatin-repressor complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylase that catalyzes the deacetylation of lysine residues on
        the N-terminal part of the core histones.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein
        corepressor complexes, especially SIN3, NuRD, and CoREST.
- term:
    id: GO:0006338
    label: chromatin remodeling
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  review:
    summary: HDAC1 is a subunit of the NuRD complex which combines histone deacetylation with
      ATP-dependent nucleosome remodeling (via CHD3/4).
    action: ACCEPT
    reason: HDAC1 participates in chromatin remodeling as a component of the NuRD complex.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD,
        Sin3, CoREST, and related chromatin-repressor complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylase that catalyzes the deacetylation of lysine residues on
        the N-terminal part of the core histones.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein
        corepressor complexes, especially SIN3, NuRD, and CoREST.
- term:
    id: GO:0006346
    label: DNA methylation-dependent constitutive heterochromatin formation
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  review:
    summary: HDAC1 cooperates with DNA methyltransferases (DNMT1, DNMT3A) and methyl-CpG binding
      proteins to establish constitutive heterochromatin (PMID:10615135).
    action: ACCEPT
    reason: HDAC1 interaction with DNMT1 and localization to heterochromatin support its role in DNA
      methylation-dependent heterochromatin formation.
    supported_by:
    - reference_id: PMID:10615135
      supporting_text: Here we show that Dnmt1 is itself associated with histone deacetylase
        activity in vivo
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD,
        Sin3, CoREST, and related chromatin-repressor complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein
        corepressor complexes, especially SIN3, NuRD, and CoREST.
- term:
    id: GO:0006357
    label: regulation of transcription by RNA polymerase II
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  review:
    summary: HDAC1 regulates RNA polymerase II transcription, primarily through repression but also
      through modulation of chromatin dynamics.
    action: ACCEPT
    reason: HDAC1 is clearly involved in regulating pol II transcription. General parent term
      encompassing both positive and negative regulation.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD,
        Sin3, CoREST, and related chromatin-repressor complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylase that catalyzes the deacetylation of lysine residues on
        the N-terminal part of the core histones.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein
        corepressor complexes, especially SIN3, NuRD, and CoREST.
- term:
    id: GO:0008284
    label: positive regulation of cell population proliferation
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  review:
    summary: HDAC1 promotes cell proliferation by repressing cell cycle inhibitors through the
      Rb-HDAC1 complex.
    action: KEEP_AS_NON_CORE
    reason: Well-documented pro-proliferative role but downstream biological consequence of
      deacetylase activity.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 has many developmental and signaling consequences through chromatin
        deacetylation; these are non-core outputs of the core enzymatic function.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylation gives a tag for epigenetic repression and plays an
        important role in transcriptional regulation, cell cycle progression and developmental
        events.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: The report supports HDAC1 as a chromatin deacetylase whose developmental,
        signaling, cell-cycle, DNA-damage, and pathway phenotypes are context-specific downstream
        outputs.
- term:
    id: GO:0008285
    label: negative regulation of cell population proliferation
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  review:
    summary: HDAC1 can also negatively regulate cell proliferation in certain contexts.
    action: KEEP_AS_NON_CORE
    reason: Context-dependent downstream effect rather than a core function.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 has many developmental and signaling consequences through chromatin
        deacetylation; these are non-core outputs of the core enzymatic function.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylation gives a tag for epigenetic repression and plays an
        important role in transcriptional regulation, cell cycle progression and developmental
        events.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: The report supports HDAC1 as a chromatin deacetylase whose developmental,
        signaling, cell-cycle, DNA-damage, and pathway phenotypes are context-specific downstream
        outputs.
- term:
    id: GO:0009410
    label: response to xenobiotic stimulus
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  review:
    summary: IEA annotation suggesting HDAC1 involvement in xenobiotic response.
    action: KEEP_AS_NON_CORE
    reason: Downstream pleiotropic effect. Not core.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 has many developmental and signaling consequences through chromatin
        deacetylation; these are non-core outputs of the core enzymatic function.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylation gives a tag for epigenetic repression and plays an
        important role in transcriptional regulation, cell cycle progression and developmental
        events.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: The report supports HDAC1 as a chromatin deacetylase whose developmental,
        signaling, cell-cycle, DNA-damage, and pathway phenotypes are context-specific downstream
        outputs.
- term:
    id: GO:0010628
    label: positive regulation of gene expression
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  review:
    summary: HDAC1 can positively regulate gene expression in certain contexts, likely through
      indirect mechanisms.
    action: KEEP_AS_NON_CORE
    reason: Secondary, context-dependent effect. HDAC1 is primarily a repressor.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 has many developmental and signaling consequences through chromatin
        deacetylation; these are non-core outputs of the core enzymatic function.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylation gives a tag for epigenetic repression and plays an
        important role in transcriptional regulation, cell cycle progression and developmental
        events.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: The report supports HDAC1 as a chromatin deacetylase whose developmental,
        signaling, cell-cycle, DNA-damage, and pathway phenotypes are context-specific downstream
        outputs.
- term:
    id: GO:0010629
    label: negative regulation of gene expression
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  review:
    summary: HDAC1 negatively regulates gene expression through histone deacetylation and chromatin
      compaction.
    action: ACCEPT
    reason: Negative regulation of gene expression is a core function of HDAC1.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD,
        Sin3, CoREST, and related chromatin-repressor complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylase that catalyzes the deacetylation of lysine residues on
        the N-terminal part of the core histones.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein
        corepressor complexes, especially SIN3, NuRD, and CoREST.
- term:
    id: GO:0016581
    label: NuRD complex
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  review:
    summary: HDAC1 is a core catalytic subunit of the NuRD (nucleosome remodeling and deacetylase)
      complex. Proteomic studies show approximately 49% of cellular HDAC1 in ESCs is in the NuRD
      complex (deep research review). Well supported by mass spectrometry identification
      (PMID:27806305) and multiple interaction studies.
    action: ACCEPT
    reason: NuRD complex membership is a core aspect of HDAC1 function. HDAC1 serves as the
      catalytic deacetylase subunit within NuRD. Extensively validated by proteomics and
      co-immunoprecipitation studies.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD,
        Sin3, CoREST, and related chromatin-repressor complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylase that catalyzes the deacetylation of lysine residues on
        the N-terminal part of the core histones.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein
        corepressor complexes, especially SIN3, NuRD, and CoREST.
- term:
    id: GO:0019213
    label: deacetylase activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  review:
    summary: General deacetylase activity. HDAC1 has broad deacetylase activity on both histone and
      non-histone substrates.
    action: ACCEPT
    reason: HDAC1 has well-established deacetylase activity. While GO:0004407 (histone deacetylase
      activity) is more specific, this broader term is also correct as HDAC1 can deacetylate
      non-histone proteins. Acceptable as a parent-level annotation.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD,
        Sin3, CoREST, and related chromatin-repressor complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylase that catalyzes the deacetylation of lysine residues on
        the N-terminal part of the core histones.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: HDAC1 is a class I Zn2+-dependent histone/protein deacetylase that removes
        acetyl groups from lysine residues on histone tails and non-histone proteins.
- term:
    id: GO:0019899
    label: enzyme binding
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  review:
    summary: HDAC1 binds various enzymes including DNA methyltransferases (DNMT1, DNMT3A), histone
      methyltransferases (SUV39H1, SETDB1, SMYD2), and kinases.
    action: ACCEPT
    reason: HDAC1 interacts with multiple enzymes as part of chromatin-modifying networks. While
      somewhat general, this captures a real aspect of HDAC1 function.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD,
        Sin3, CoREST, and related chromatin-repressor complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylase that catalyzes the deacetylation of lysine residues on
        the N-terminal part of the core histones.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein
        corepressor complexes, especially SIN3, NuRD, and CoREST.
- term:
    id: GO:0031000
    label: response to caffeine
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  review:
    summary: IEA annotation suggesting HDAC1 involvement in caffeine response.
    action: KEEP_AS_NON_CORE
    reason: Highly specific stimulus-response annotation. Downstream pleiotropic effect.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 has many developmental and signaling consequences through chromatin
        deacetylation; these are non-core outputs of the core enzymatic function.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylation gives a tag for epigenetic repression and plays an
        important role in transcriptional regulation, cell cycle progression and developmental
        events.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: The report supports HDAC1 as a chromatin deacetylase whose developmental,
        signaling, cell-cycle, DNA-damage, and pathway phenotypes are context-specific downstream
        outputs.
- term:
    id: GO:0032496
    label: response to lipopolysaccharide
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  review:
    summary: HDAC1 may be involved in LPS response through NF-kappaB signaling regulation.
    action: KEEP_AS_NON_CORE
    reason: Downstream inflammatory pathway effect.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 has many developmental and signaling consequences through chromatin
        deacetylation; these are non-core outputs of the core enzymatic function.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylation gives a tag for epigenetic repression and plays an
        important role in transcriptional regulation, cell cycle progression and developmental
        events.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: The report supports HDAC1 as a chromatin deacetylase whose developmental,
        signaling, cell-cycle, DNA-damage, and pathway phenotypes are context-specific downstream
        outputs.
- term:
    id: GO:0032732
    label: positive regulation of interleukin-1 production
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  review:
    summary: IEA annotation for HDAC1 in IL-1 production.
    action: KEEP_AS_NON_CORE
    reason: Downstream immune/inflammatory pathway effect.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 has many developmental and signaling consequences through chromatin
        deacetylation; these are non-core outputs of the core enzymatic function.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylation gives a tag for epigenetic repression and plays an
        important role in transcriptional regulation, cell cycle progression and developmental
        events.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: The report supports HDAC1 as a chromatin deacetylase whose developmental,
        signaling, cell-cycle, DNA-damage, and pathway phenotypes are context-specific downstream
        outputs.
- term:
    id: GO:0032760
    label: positive regulation of tumor necrosis factor production
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  review:
    summary: IEA annotation for HDAC1 in TNF production regulation.
    action: KEEP_AS_NON_CORE
    reason: Downstream immune/inflammatory pathway effect.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 has many developmental and signaling consequences through chromatin
        deacetylation; these are non-core outputs of the core enzymatic function.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylation gives a tag for epigenetic repression and plays an
        important role in transcriptional regulation, cell cycle progression and developmental
        events.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: The report supports HDAC1 as a chromatin deacetylase whose developmental,
        signaling, cell-cycle, DNA-damage, and pathway phenotypes are context-specific downstream
        outputs.
- term:
    id: GO:0032991
    label: protein-containing complex
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  review:
    summary: HDAC1 is found in protein-containing complexes (NuRD, SIN3, CoREST). Very general
      cellular component annotation.
    action: ACCEPT
    reason: HDAC1 is found in protein-containing complexes. Correct as a root-level CC annotation
      alongside more specific complex terms.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD,
        Sin3, CoREST, and related chromatin-repressor complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylase that catalyzes the deacetylation of lysine residues on
        the N-terminal part of the core histones.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein
        corepressor complexes, especially SIN3, NuRD, and CoREST.
- term:
    id: GO:0033558
    label: protein lysine deacetylase activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  review:
    summary: HDAC1 removes acetyl groups from lysine residues on proteins, including both histone
      and non-histone substrates such as NR1D2, RELA, SP1, SP3, STAT3, ZNF76, and TSHZ3 (UniProt).
    action: ACCEPT
    reason: HDAC1 has well-documented protein lysine deacetylase activity on both histone and
      non-histone targets. This is a core function.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD,
        Sin3, CoREST, and related chromatin-repressor complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylase that catalyzes the deacetylation of lysine residues on
        the N-terminal part of the core histones.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: HDAC1 is a class I Zn2+-dependent histone/protein deacetylase that removes
        acetyl groups from lysine residues on histone tails and non-histone proteins.
- term:
    id: GO:0034599
    label: cellular response to oxidative stress
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  review:
    summary: HDAC1 may participate in cellular response to oxidative stress.
    action: KEEP_AS_NON_CORE
    reason: Downstream context-specific process.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 has many developmental and signaling consequences through chromatin
        deacetylation; these are non-core outputs of the core enzymatic function.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylation gives a tag for epigenetic repression and plays an
        important role in transcriptional regulation, cell cycle progression and developmental
        events.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: The report supports HDAC1 as a chromatin deacetylase whose developmental,
        signaling, cell-cycle, DNA-damage, and pathway phenotypes are context-specific downstream
        outputs.
- term:
    id: GO:0036120
    label: cellular response to platelet-derived growth factor stimulus
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  review:
    summary: IEA annotation for HDAC1 in PDGF response.
    action: KEEP_AS_NON_CORE
    reason: Specific growth factor signaling context. Not core.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 has many developmental and signaling consequences through chromatin
        deacetylation; these are non-core outputs of the core enzymatic function.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylation gives a tag for epigenetic repression and plays an
        important role in transcriptional regulation, cell cycle progression and developmental
        events.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: The report supports HDAC1 as a chromatin deacetylase whose developmental,
        signaling, cell-cycle, DNA-damage, and pathway phenotypes are context-specific downstream
        outputs.
- term:
    id: GO:0042826
    label: histone deacetylase binding
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  review:
    summary: HDAC1 binds to other histone deacetylases, particularly HDAC2 (forming heterodimers)
      and class II HDACs like HDAC7 and HDAC9.
    action: ACCEPT
    reason: HDAC1 forms heterodimers with HDAC2 as the catalytic core of NuRD, SIN3, and CoREST
      complexes. It also interacts with class II HDACs (HDAC7, HDAC9). Well documented.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD,
        Sin3, CoREST, and related chromatin-repressor complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylase that catalyzes the deacetylation of lysine residues on
        the N-terminal part of the core histones.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: HDAC1 is a class I Zn2+-dependent histone/protein deacetylase that removes
        acetyl groups from lysine residues on histone tails and non-histone proteins.
- term:
    id: GO:0043524
    label: negative regulation of neuron apoptotic process
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  review:
    summary: HDAC1 has a neuroprotective role in certain contexts, preventing neuron apoptosis.
    action: KEEP_AS_NON_CORE
    reason: Context-specific downstream effect of HDAC1 in neurons.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 has many developmental and signaling consequences through chromatin
        deacetylation; these are non-core outputs of the core enzymatic function.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylation gives a tag for epigenetic repression and plays an
        important role in transcriptional regulation, cell cycle progression and developmental
        events.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: The report supports HDAC1 as a chromatin deacetylase whose developmental,
        signaling, cell-cycle, DNA-damage, and pathway phenotypes are context-specific downstream
        outputs.
- term:
    id: GO:0043922
    label: host-mediated suppression of viral transcription
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  review:
    summary: HDAC1 participates in host-mediated suppression of viral transcription by deacetylating
      histones at integrated viral promoters.
    action: KEEP_AS_NON_CORE
    reason: Context-specific application of general transcriptional repression function.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 has many developmental and signaling consequences through chromatin
        deacetylation; these are non-core outputs of the core enzymatic function.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylation gives a tag for epigenetic repression and plays an
        important role in transcriptional regulation, cell cycle progression and developmental
        events.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: The report supports HDAC1 as a chromatin deacetylase whose developmental,
        signaling, cell-cycle, DNA-damage, and pathway phenotypes are context-specific downstream
        outputs.
- term:
    id: GO:0044877
    label: protein-containing complex binding
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  review:
    summary: HDAC1 functions within protein-containing corepressor complexes, but this binding term
      is much less informative than the specific NuRD, SIN3, and CoREST complex annotations.
    action: KEEP_AS_NON_CORE
    reason: The annotation is directionally true but too generic to represent the core molecular
      function; specific complex membership and catalytic terms carry the curatorial signal.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD,
        Sin3, CoREST, and related chromatin-repressor complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylase that catalyzes the deacetylation of lysine residues on
        the N-terminal part of the core histones.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein
        corepressor complexes, especially SIN3, NuRD, and CoREST.
- term:
    id: GO:0045814
    label: negative regulation of gene expression, epigenetic
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  review:
    summary: HDAC1 mediates epigenetic gene silencing through histone deacetylation.
    action: ACCEPT
    reason: HDAC1-mediated histone deacetylation is a classical epigenetic mechanism of gene
      silencing. Core function.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD,
        Sin3, CoREST, and related chromatin-repressor complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylase that catalyzes the deacetylation of lysine residues on
        the N-terminal part of the core histones.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein
        corepressor complexes, especially SIN3, NuRD, and CoREST.
- term:
    id: GO:0045892
    label: negative regulation of DNA-templated transcription
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  review:
    summary: HDAC1 negatively regulates DNA-templated transcription through its histone deacetylase
      activity as part of co-repressor complexes.
    action: ACCEPT
    reason: Transcriptional repression is a core function of HDAC1. Well supported by extensive
      literature.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD,
        Sin3, CoREST, and related chromatin-repressor complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylase that catalyzes the deacetylation of lysine residues on
        the N-terminal part of the core histones.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein
        corepressor complexes, especially SIN3, NuRD, and CoREST.
- term:
    id: GO:0045893
    label: positive regulation of DNA-templated transcription
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  review:
    summary: Although HDAC1 is primarily a transcriptional repressor, it can indirectly promote
      transcription of certain genes in specific contexts.
    action: KEEP_AS_NON_CORE
    reason: HDAC1 is primarily a repressor, but there is evidence that it can positively regulate
      transcription indirectly. This is a secondary, context-dependent function.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 has many developmental and signaling consequences through chromatin
        deacetylation; these are non-core outputs of the core enzymatic function.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylation gives a tag for epigenetic repression and plays an
        important role in transcriptional regulation, cell cycle progression and developmental
        events.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: The report supports HDAC1 as a chromatin deacetylase whose developmental,
        signaling, cell-cycle, DNA-damage, and pathway phenotypes are context-specific downstream
        outputs.
- term:
    id: GO:0045944
    label: positive regulation of transcription by RNA polymerase II
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  review:
    summary: HDAC1 can positively regulate RNA pol II transcription in certain contexts, likely
      through indirect mechanisms.
    action: KEEP_AS_NON_CORE
    reason: Not a core function of HDAC1 but documented in specific contexts.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 has many developmental and signaling consequences through chromatin
        deacetylation; these are non-core outputs of the core enzymatic function.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylation gives a tag for epigenetic repression and plays an
        important role in transcriptional regulation, cell cycle progression and developmental
        events.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: The report supports HDAC1 as a chromatin deacetylase whose developmental,
        signaling, cell-cycle, DNA-damage, and pathway phenotypes are context-specific downstream
        outputs.
- term:
    id: GO:0046676
    label: negative regulation of insulin secretion
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  review:
    summary: IEA annotation suggesting HDAC1 negatively regulates insulin secretion.
    action: KEEP_AS_NON_CORE
    reason: Downstream metabolic/endocrine effect.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 has many developmental and signaling consequences through chromatin
        deacetylation; these are non-core outputs of the core enzymatic function.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylation gives a tag for epigenetic repression and plays an
        important role in transcriptional regulation, cell cycle progression and developmental
        events.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: The report supports HDAC1 as a chromatin deacetylase whose developmental,
        signaling, cell-cycle, DNA-damage, and pathway phenotypes are context-specific downstream
        outputs.
- term:
    id: GO:0048471
    label: perinuclear region of cytoplasm
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  review:
    summary: Perinuclear cytoplasmic localization is an orthology-derived/minor subcellular
      annotation, whereas HDAC1's supported role is predominantly nuclear chromatin regulation.
    action: MARK_AS_OVER_ANNOTATED
    reason: This weak cytoplasmic sublocalization should not be accepted as a central HDAC1
      localization when the evidence supports nuclear chromatin/corepressor complexes.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: 'GO; GO:0048471; C:perinuclear region of cytoplasm; ISO:GO_Central.'
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: Class I HDACs, including HDAC1, are predominantly or exclusively nuclear,
        consistent with chromatin accessibility and transcriptional control roles.
- term:
    id: GO:0048661
    label: positive regulation of smooth muscle cell proliferation
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  review:
    summary: IEA annotation for HDAC1 in smooth muscle cell proliferation.
    action: KEEP_AS_NON_CORE
    reason: Specific tissue context. Not core.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 has many developmental and signaling consequences through chromatin
        deacetylation; these are non-core outputs of the core enzymatic function.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylation gives a tag for epigenetic repression and plays an
        important role in transcriptional regulation, cell cycle progression and developmental
        events.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: The report supports HDAC1 as a chromatin deacetylase whose developmental,
        signaling, cell-cycle, DNA-damage, and pathway phenotypes are context-specific downstream
        outputs.
- term:
    id: GO:0048714
    label: positive regulation of oligodendrocyte differentiation
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  review:
    summary: HDAC1/2 positively regulate oligodendrocyte differentiation, likely by repressing
      inhibitors of myelination (PMID:19503085).
    action: KEEP_AS_NON_CORE
    reason: Cell-type-specific developmental process rather than a core function.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 has many developmental and signaling consequences through chromatin
        deacetylation; these are non-core outputs of the core enzymatic function.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylation gives a tag for epigenetic repression and plays an
        important role in transcriptional regulation, cell cycle progression and developmental
        events.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: The report supports HDAC1 as a chromatin deacetylase whose developmental,
        signaling, cell-cycle, DNA-damage, and pathway phenotypes are context-specific downstream
        outputs.
- term:
    id: GO:0051059
    label: NF-kappaB binding
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  review:
    summary: HDAC1 directly binds to the NF-kappaB subunit RelA/p65 and deacetylates it, attenuating
      NF-kappaB transcriptional activity.
    action: ACCEPT
    reason: The HDAC1-NF-kappaB/p65 interaction is directly demonstrated and functionally
      characterized. HDAC1 deacetylates Lys-310 of RELA, inhibiting NF-kappaB activity (UniProt).
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD,
        Sin3, CoREST, and related chromatin-repressor complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylase that catalyzes the deacetylation of lysine residues on
        the N-terminal part of the core histones.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein
        corepressor complexes, especially SIN3, NuRD, and CoREST.
- term:
    id: GO:0055093
    label: response to hyperoxia
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  review:
    summary: IEA annotation for HDAC1 in hyperoxia response.
    action: KEEP_AS_NON_CORE
    reason: Very specific stress response. Downstream pleiotropic effect.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 has many developmental and signaling consequences through chromatin
        deacetylation; these are non-core outputs of the core enzymatic function.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylation gives a tag for epigenetic repression and plays an
        important role in transcriptional regulation, cell cycle progression and developmental
        events.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: The report supports HDAC1 as a chromatin deacetylase whose developmental,
        signaling, cell-cycle, DNA-damage, and pathway phenotypes are context-specific downstream
        outputs.
- term:
    id: GO:0060766
    label: negative regulation of androgen receptor signaling pathway
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  review:
    summary: HDAC1 negatively regulates androgen receptor signaling.
    action: KEEP_AS_NON_CORE
    reason: Specific hormonal signaling context. Not core.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 has many developmental and signaling consequences through chromatin
        deacetylation; these are non-core outputs of the core enzymatic function.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylation gives a tag for epigenetic repression and plays an
        important role in transcriptional regulation, cell cycle progression and developmental
        events.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: The report supports HDAC1 as a chromatin deacetylase whose developmental,
        signaling, cell-cycle, DNA-damage, and pathway phenotypes are context-specific downstream
        outputs.
- term:
    id: GO:0061629
    label: RNA polymerase II-specific DNA-binding transcription factor binding
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  review:
    summary: HDAC1 binds RNA polymerase II-specific transcription factors that recruit it to target
      genes for transcriptional repression.
    action: ACCEPT
    reason: This is a more specific version of DNA-binding transcription factor binding, appropriate
      given that HDAC1 primarily regulates RNA pol II-transcribed genes through interactions with
      pol II-specific TFs.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD,
        Sin3, CoREST, and related chromatin-repressor complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylase that catalyzes the deacetylation of lysine residues on
        the N-terminal part of the core histones.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein
        corepressor complexes, especially SIN3, NuRD, and CoREST.
- term:
    id: GO:0070822
    label: Sin3-type complex
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  review:
    summary: HDAC1 is a core catalytic subunit of the SIN3 co-repressor complex. Approximately 15%
      of cellular HDAC1 in ESCs is in the SIN3A complex. Confirmed by multiple studies including
      PMID:11909966 and PMID:28554894.
    action: ACCEPT
    reason: SIN3 complex membership is a core function of HDAC1. The SIN3-HDAC complex is one of the
      three major HDAC1-containing co-repressor complexes.
    supported_by:
    - reference_id: PMID:28554894
      supporting_text: Sin3a is the central scaffold protein of the prototypical Hdac1/2 chromatin
        repressor complex
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD,
        Sin3, CoREST, and related chromatin-repressor complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein
        corepressor complexes, especially SIN3, NuRD, and CoREST.
- term:
    id: GO:0071356
    label: cellular response to tumor necrosis factor
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  review:
    summary: HDAC1 participates in TNF response, potentially through NF-kappaB regulation.
    action: KEEP_AS_NON_CORE
    reason: Downstream inflammatory signaling context.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 has many developmental and signaling consequences through chromatin
        deacetylation; these are non-core outputs of the core enzymatic function.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylation gives a tag for epigenetic repression and plays an
        important role in transcriptional regulation, cell cycle progression and developmental
        events.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: The report supports HDAC1 as a chromatin deacetylase whose developmental,
        signaling, cell-cycle, DNA-damage, and pathway phenotypes are context-specific downstream
        outputs.
- term:
    id: GO:0090090
    label: negative regulation of canonical Wnt signaling pathway
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  review:
    summary: HDAC1/2 negatively regulate canonical Wnt signaling by deacetylating histones at Wnt
      target gene promoters. Demonstrated in neural development.
    action: KEEP_AS_NON_CORE
    reason: Well-supported role in neural development but represents a downstream biological
      consequence rather than a core molecular function.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 has many developmental and signaling consequences through chromatin
        deacetylation; these are non-core outputs of the core enzymatic function.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylation gives a tag for epigenetic repression and plays an
        important role in transcriptional regulation, cell cycle progression and developmental
        events.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: The report supports HDAC1 as a chromatin deacetylase whose developmental,
        signaling, cell-cycle, DNA-damage, and pathway phenotypes are context-specific downstream
        outputs.
- term:
    id: GO:0140297
    label: DNA-binding transcription factor binding
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  review:
    summary: HDAC1 binds numerous DNA-binding transcription factors as part of its recruitment to
      target genes. Documented interactions include MyoD, YY1, KLF1, NR4A2, INSM1, and many others.
    action: ACCEPT
    reason: HDAC1 interaction with DNA-binding transcription factors is central to its biological
      function - this is how it is recruited to specific genomic loci.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD,
        Sin3, CoREST, and related chromatin-repressor complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylase that catalyzes the deacetylation of lysine residues on
        the N-terminal part of the core histones.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein
        corepressor complexes, especially SIN3, NuRD, and CoREST.
- term:
    id: GO:0160009
    label: histone decrotonylase activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  review:
    summary: HDAC1 can remove crotonyl modifications from histone lysine residues. Directly
      demonstrated by Kelly et al. (PMID:30279482) showing HDAC1/2 complexes are important histone
      decrotonylases in vivo.
    action: ACCEPT
    reason: Directly supported by experimental evidence. Genetic deletion of HDAC1/2 in ES cells
      increases global histone crotonylation and causes an 85% reduction in total decrotonylase
      activity (PMID:30279482).
    supported_by:
    - reference_id: PMID:30279482
      supporting_text: Genetic deletion of HDAC1/2 in ES cells increases global levels of histone
        crotonylation and causes an 85% reduction in total decrotonylase activity
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD,
        Sin3, CoREST, and related chromatin-repressor complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein
        corepressor complexes, especially SIN3, NuRD, and CoREST.
- term:
    id: GO:0160216
    label: protein lysine delactylase activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  review:
    summary: UniProt/GOA includes protein lysine delactylase activity for HDAC1, but this row is
      similarity-based; the accessible experimental paper supports HDAC1/2 decrotonylase activity,
      not direct mouse delactylase activity.
    action: KEEP_AS_NON_CORE
    reason: Do not treat delactylase activity as a direct/core Hdac1 function here. The stronger
      experimental support is for histone deacetylase and decrotonylase activity.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: 'GO; GO:0160216; F:protein lysine delactylase activity; ISS:UniProtKB.'
    - reference_id: PMID:30279482
      supporting_text: A ternary complex of HDAC1/CoREST1/LSD1 is able to hydrolyse both histone H3
        Lys18-acetyl (H3K18ac) and H3 Lys18-crotonyl (H3K18cr) peptide substrates
- term:
    id: GO:2000343
    label: positive regulation of chemokine (C-X-C motif) ligand 2 production
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  review:
    summary: IEA annotation for HDAC1 in CXCL2 production.
    action: KEEP_AS_NON_CORE
    reason: Downstream immune/inflammatory pathway effect.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 has many developmental and signaling consequences through chromatin
        deacetylation; these are non-core outputs of the core enzymatic function.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylation gives a tag for epigenetic repression and plays an
        important role in transcriptional regulation, cell cycle progression and developmental
        events.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: The report supports HDAC1 as a chromatin deacetylase whose developmental,
        signaling, cell-cycle, DNA-damage, and pathway phenotypes are context-specific downstream
        outputs.
- term:
    id: GO:2000676
    label: positive regulation of type B pancreatic cell apoptotic process
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  review:
    summary: IEA annotation for HDAC1 in beta cell apoptosis.
    action: KEEP_AS_NON_CORE
    reason: Very specific downstream effect in pancreatic biology.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 has many developmental and signaling consequences through chromatin
        deacetylation; these are non-core outputs of the core enzymatic function.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylation gives a tag for epigenetic repression and plays an
        important role in transcriptional regulation, cell cycle progression and developmental
        events.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: The report supports HDAC1 as a chromatin deacetylase whose developmental,
        signaling, cell-cycle, DNA-damage, and pathway phenotypes are context-specific downstream
        outputs.
- term:
    id: GO:0032991
    label: protein-containing complex
  evidence_type: ISO
  original_reference_id: GO_REF:0000096
  review:
    summary: HDAC1 is found in protein-containing complexes (NuRD, SIN3, CoREST). Very general
      cellular component annotation.
    action: ACCEPT
    reason: HDAC1 is found in protein-containing complexes. Correct as a root-level CC annotation
      alongside more specific complex terms.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD,
        Sin3, CoREST, and related chromatin-repressor complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylase that catalyzes the deacetylation of lysine residues on
        the N-terminal part of the core histones.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein
        corepressor complexes, especially SIN3, NuRD, and CoREST.
- term:
    id: GO:1990904
    label: ribonucleoprotein complex
  evidence_type: IDA
  original_reference_id: PMID:21874018
  review:
    summary: HDAC1 was detected in lincRNA-associated chromatin regulatory complexes in mouse ESCs,
      supporting a non-core ribonucleoprotein-complex context rather than a primary HDAC1 cellular
      component.
    action: KEEP_AS_NON_CORE
    reason: The cited study shows HDAC1-containing chromatin regulatory complexes can associate with
      lincRNAs, but HDAC1 is primarily a nuclear deacetylase in NuRD/SIN3/CoREST and related
      complexes.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 has many developmental and signaling consequences through chromatin
        deacetylation; these are non-core outputs of the core enzymatic function.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylation gives a tag for epigenetic repression and plays an
        important role in transcriptional regulation, cell cycle progression and developmental
        events.
    - reference_id: PMID:21874018
      supporting_text: and HDAC1) histone modifications, as well as a chromatin-associated DNA
        binding protein (YY1)
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: PMID:21874018 supports HDAC1 association with lincRNA-containing chromatin
        regulatory complexes in mouse ESCs, but this is a non-core context relative to HDAC1
        deacetylase and chromatin-complex functions.
- term:
    id: GO:0006325
    label: chromatin organization
  evidence_type: ISO
  original_reference_id: GO_REF:0000119
  review:
    summary: HDAC1 plays a role in chromatin organization through histone deacetylation, which
      promotes nucleosome compaction.
    action: ACCEPT
    reason: Chromatin organization is a direct consequence of HDAC1 enzymatic activity.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD,
        Sin3, CoREST, and related chromatin-repressor complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylase that catalyzes the deacetylation of lysine residues on
        the N-terminal part of the core histones.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein
        corepressor complexes, especially SIN3, NuRD, and CoREST.
- term:
    id: GO:0017053
    label: transcription repressor complex
  evidence_type: ISO
  original_reference_id: GO_REF:0000119
  review:
    summary: HDAC1 functions within transcription repressor complexes including NuRD, SIN3, and
      CoREST, which mediate transcriptional repression through histone deacetylation.
    action: ACCEPT
    reason: HDAC1 is a core catalytic subunit of several transcription repressor complexes. This is
      a correct and informative annotation.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD,
        Sin3, CoREST, and related chromatin-repressor complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylase that catalyzes the deacetylation of lysine residues on
        the N-terminal part of the core histones.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein
        corepressor complexes, especially SIN3, NuRD, and CoREST.
- term:
    id: GO:0000118
    label: histone deacetylase complex
  evidence_type: ISO
  original_reference_id: GO_REF:0000119
  review:
    summary: HDAC1 is a core component of multiple histone deacetylase complexes including NuRD,
      SIN3, and CoREST. This is a general parent term encompassing all such complexes.
    action: ACCEPT
    reason: HDAC1 is the defining catalytic subunit of multiple HDAC complexes. This broader term is
      appropriate as a parent annotation alongside the more specific NuRD and SIN3 complex terms.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD,
        Sin3, CoREST, and related chromatin-repressor complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylase that catalyzes the deacetylation of lysine residues on
        the N-terminal part of the core histones.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: HDAC1 is a class I Zn2+-dependent histone/protein deacetylase that removes
        acetyl groups from lysine residues on histone tails and non-histone proteins.
- term:
    id: GO:0000122
    label: negative regulation of transcription by RNA polymerase II
  evidence_type: ISO
  original_reference_id: GO_REF:0000119
  review:
    summary: HDAC1 negatively regulates transcription by RNA polymerase II through histone
      deacetylation at target gene promoters. This is a core biological process annotation for
      HDAC1.
    action: ACCEPT
    reason: Negative regulation of pol II transcription is a primary biological function of HDAC1.
      Supported by multiple lines of evidence (PMID:8917507, PMID:9271381, PMID:21093383).
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD,
        Sin3, CoREST, and related chromatin-repressor complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylase that catalyzes the deacetylation of lysine residues on
        the N-terminal part of the core histones.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein
        corepressor complexes, especially SIN3, NuRD, and CoREST.
- term:
    id: GO:0000785
    label: chromatin
  evidence_type: ISO
  original_reference_id: GO_REF:0000096
  review:
    summary: HDAC1 is a chromatin-associated protein that modifies histone tails as part of
      co-repressor complexes.
    action: ACCEPT
    reason: HDAC1 is a histone-modifying enzyme that directly acts on chromatin. Association with
      chromatin is inherent to its function.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD,
        Sin3, CoREST, and related chromatin-repressor complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylase that catalyzes the deacetylation of lysine residues on
        the N-terminal part of the core histones.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein
        corepressor complexes, especially SIN3, NuRD, and CoREST.
- term:
    id: GO:0000785
    label: chromatin
  evidence_type: ISO
  original_reference_id: GO_REF:0000119
  review:
    summary: HDAC1 is a chromatin-associated protein that modifies histone tails as part of
      co-repressor complexes.
    action: ACCEPT
    reason: HDAC1 is a histone-modifying enzyme that directly acts on chromatin. Association with
      chromatin is inherent to its function.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD,
        Sin3, CoREST, and related chromatin-repressor complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylase that catalyzes the deacetylation of lysine residues on
        the N-terminal part of the core histones.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein
        corepressor complexes, especially SIN3, NuRD, and CoREST.
- term:
    id: GO:0000978
    label: RNA polymerase II cis-regulatory region sequence-specific DNA binding
  evidence_type: ISO
  original_reference_id: GO_REF:0000119
  review:
    summary: Annotation suggests HDAC1 has sequence-specific DNA binding at RNA pol II
      cis-regulatory regions. However, HDAC1 does not have intrinsic sequence-specific DNA binding -
      it is recruited to promoters by transcription factors.
    action: MODIFY
    reason: Replace direct sequence-specific DNA binding with promoter-specific chromatin binding,
      which captures HDAC1 recruitment to promoter chromatin without implying intrinsic DNA-binding
      specificity.
    proposed_replacement_terms:
    - id: GO:1990841
      label: promoter-specific chromatin binding
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 is recruited to chromatin by DNA-binding factors but is not itself a
        sequence-specific DNA-binding transcription factor.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylase that catalyzes the deacetylation of lysine residues on
        core histones.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: The report supports HDAC1 as a chromatin deacetylase whose developmental,
        signaling, cell-cycle, DNA-damage, and pathway phenotypes are context-specific downstream
        outputs.
- term:
    id: GO:0000979
    label: RNA polymerase II core promoter sequence-specific DNA binding
  evidence_type: ISO
  original_reference_id: GO_REF:0000119
  review:
    summary: This implies sequence-specific core promoter DNA binding by HDAC1, which is not
      supported. HDAC1 is recruited to core promoters via protein-protein interactions.
    action: MODIFY
    reason: Replace direct sequence-specific DNA binding with promoter-specific chromatin binding,
      which captures HDAC1 recruitment to promoter chromatin without implying intrinsic DNA-binding
      specificity.
    proposed_replacement_terms:
    - id: GO:1990841
      label: promoter-specific chromatin binding
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 is recruited to chromatin by DNA-binding factors but is not itself a
        sequence-specific DNA-binding transcription factor.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylase that catalyzes the deacetylation of lysine residues on
        core histones.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: The report supports HDAC1 as a chromatin deacetylase whose developmental,
        signaling, cell-cycle, DNA-damage, and pathway phenotypes are context-specific downstream
        outputs.
- term:
    id: GO:0001046
    label: core promoter sequence-specific DNA binding
  evidence_type: ISO
  original_reference_id: GO_REF:0000119
  review:
    summary: This implies HDAC1 has core promoter sequence-specific DNA binding, which is not
      supported by its known biochemistry.
    action: MODIFY
    reason: Replace direct sequence-specific DNA binding with promoter-specific chromatin binding,
      which captures HDAC1 recruitment to promoter chromatin without implying intrinsic DNA-binding
      specificity.
    proposed_replacement_terms:
    - id: GO:1990841
      label: promoter-specific chromatin binding
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 is recruited to chromatin by DNA-binding factors but is not itself a
        sequence-specific DNA-binding transcription factor.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylase that catalyzes the deacetylation of lysine residues on
        core histones.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: The report supports HDAC1 as a chromatin deacetylase whose developmental,
        signaling, cell-cycle, DNA-damage, and pathway phenotypes are context-specific downstream
        outputs.
- term:
    id: GO:0001222
    label: transcription corepressor binding
  evidence_type: ISO
  original_reference_id: GO_REF:0000119
  review:
    summary: HDAC1 binds to transcription corepressors including SIN3A, SIN3B, CoREST, NCoR, and
      SMRT as part of its recruitment to target genes.
    action: ACCEPT
    reason: HDAC1 physically interacts with multiple corepressor scaffold proteins. This binding is
      essential for its function in transcriptional repression complexes.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD,
        Sin3, CoREST, and related chromatin-repressor complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylase that catalyzes the deacetylation of lysine residues on
        the N-terminal part of the core histones.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein
        corepressor complexes, especially SIN3, NuRD, and CoREST.
- term:
    id: GO:0002039
    label: p53 binding
  evidence_type: ISO
  original_reference_id: GO_REF:0000119
  review:
    summary: HDAC1 binds to and deacetylates the tumor suppressor p53, thereby modulating its
      activity and stability.
    action: ACCEPT
    reason: HDAC1 interaction with p53 is well established. HDAC1 deacetylates p53, leading to its
      inactivation and degradation. Functionally relevant interaction.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD,
        Sin3, CoREST, and related chromatin-repressor complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylase that catalyzes the deacetylation of lysine residues on
        the N-terminal part of the core histones.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein
        corepressor complexes, especially SIN3, NuRD, and CoREST.
- term:
    id: GO:0003682
    label: chromatin binding
  evidence_type: ISO
  original_reference_id: GO_REF:0000096
  review:
    summary: HDAC1 binds chromatin as part of its function in co-repressor complexes. ChIP
      experiments have confirmed HDAC1 occupancy at promoters and other regulatory regions.
    action: ACCEPT
    reason: Chromatin binding is well supported by extensive ChIP-seq and ChIP-qPCR data showing
      HDAC1 occupancy at promoters, enhancers, and heterochromatic regions.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD,
        Sin3, CoREST, and related chromatin-repressor complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylase that catalyzes the deacetylation of lysine residues on
        the N-terminal part of the core histones.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein
        corepressor complexes, especially SIN3, NuRD, and CoREST.
- term:
    id: GO:0003714
    label: transcription corepressor activity
  evidence_type: ISO
  original_reference_id: GO_REF:0000119
  review:
    summary: HDAC1 functions as a transcription corepressor by deacetylating histones at target gene
      promoters, leading to chromatin compaction and transcriptional silencing.
    action: ACCEPT
    reason: Transcription corepressor activity is a core function of HDAC1. It mediates
      transcriptional repression through histone deacetylation when recruited to target promoters by
      sequence-specific repressors.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD,
        Sin3, CoREST, and related chromatin-repressor complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylase that catalyzes the deacetylation of lysine residues on
        the N-terminal part of the core histones.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein
        corepressor complexes, especially SIN3, NuRD, and CoREST.
- term:
    id: GO:0004407
    label: histone deacetylase activity
  evidence_type: ISO
  original_reference_id: GO_REF:0000119
  review:
    summary: HDAC1 is a zinc-dependent histone deacetylase (EC 3.5.1.98) that catalyzes removal of
      acetyl groups from N-acetyl-lysine residues on histones H2A, H2B, H3, and H4. This is the core
      enzymatic function of HDAC1, well established by direct biochemical assays (PMID:10615135,
      PMID:21960634, PMID:30279482).
    action: ACCEPT
    reason: Histone deacetylase activity is the primary enzymatic function of HDAC1, supported by
      multiple direct experimental studies demonstrating catalytic activity on histone substrates.
    supported_by:
    - reference_id: PMID:10615135
      supporting_text: Here we show that Dnmt1 is itself associated with histone deacetylase
        activity in vivo
    - reference_id: PMID:30279482
      supporting_text: A ternary complex of HDAC1/CoREST1/LSD1 is able to hydrolyse both histone H3
        Lys18-acetyl (H3K18ac) and H3 Lys18-crotonyl (H3K18cr) peptide substrates
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD,
        Sin3, CoREST, and related chromatin-repressor complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: HDAC1 is a class I Zn2+-dependent histone/protein deacetylase that removes
        acetyl groups from lysine residues on histone tails and non-histone proteins.
- term:
    id: GO:0005634
    label: nucleus
  evidence_type: ISO
  original_reference_id: GO_REF:0000096
  review:
    summary: HDAC1 is predominantly nuclear, consistent with its function in chromatin modification
      and transcriptional regulation. Nuclear localization confirmed by multiple methods including
      immunofluorescence (PMID:11115394).
    action: ACCEPT
    reason: Nuclear localization is a well-established core feature of HDAC1. It is a Class I HDAC
      that is predominantly nuclear.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD,
        Sin3, CoREST, and related chromatin-repressor complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylase that catalyzes the deacetylation of lysine residues on
        the N-terminal part of the core histones.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: Class I HDACs, including HDAC1, are predominantly or exclusively nuclear,
        consistent with chromatin accessibility and transcriptional control roles.
- term:
    id: GO:0005634
    label: nucleus
  evidence_type: ISO
  original_reference_id: GO_REF:0000119
  review:
    summary: HDAC1 is predominantly nuclear, consistent with its function in chromatin modification
      and transcriptional regulation. Nuclear localization confirmed by multiple methods including
      immunofluorescence (PMID:11115394).
    action: ACCEPT
    reason: Nuclear localization is a well-established core feature of HDAC1. It is a Class I HDAC
      that is predominantly nuclear.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD,
        Sin3, CoREST, and related chromatin-repressor complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylase that catalyzes the deacetylation of lysine residues on
        the N-terminal part of the core histones.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: Class I HDACs, including HDAC1, are predominantly or exclusively nuclear,
        consistent with chromatin accessibility and transcriptional control roles.
- term:
    id: GO:0005654
    label: nucleoplasm
  evidence_type: ISO
  original_reference_id: GO_REF:0000119
  review:
    summary: HDAC1 is localized to the nucleoplasm where it functions as part of chromatin-modifying
      complexes.
    action: ACCEPT
    reason: Nucleoplasm localization is consistent with HDAC1 function in chromatin modification.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD,
        Sin3, CoREST, and related chromatin-repressor complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylase that catalyzes the deacetylation of lysine residues on
        the N-terminal part of the core histones.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: Class I HDACs, including HDAC1, are predominantly or exclusively nuclear,
        consistent with chromatin accessibility and transcriptional control roles.
- term:
    id: GO:0005829
    label: cytosol
  evidence_type: ISO
  original_reference_id: GO_REF:0000119
  review:
    summary: GOA includes a cytosol annotation, but HDAC1 is primarily a nuclear chromatin
      deacetylase/corepressor-complex subunit.
    action: KEEP_AS_NON_CORE
    reason: Cytosol is, at most, a minor inferred localization and should not be treated as a core
      HDAC1 cellular-component annotation.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: 'GO; GO:0005829; C:cytosol; ISO:GO_Central.'
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: Class I HDACs, including HDAC1, are predominantly or exclusively nuclear,
        consistent with chromatin accessibility and transcriptional control roles.
- term:
    id: GO:0006338
    label: chromatin remodeling
  evidence_type: ISO
  original_reference_id: GO_REF:0000119
  review:
    summary: HDAC1 is a subunit of the NuRD complex which combines histone deacetylation with
      ATP-dependent nucleosome remodeling (via CHD3/4).
    action: ACCEPT
    reason: HDAC1 participates in chromatin remodeling as a component of the NuRD complex.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD,
        Sin3, CoREST, and related chromatin-repressor complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylase that catalyzes the deacetylation of lysine residues on
        the N-terminal part of the core histones.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein
        corepressor complexes, especially SIN3, NuRD, and CoREST.
- term:
    id: GO:0006346
    label: DNA methylation-dependent constitutive heterochromatin formation
  evidence_type: ISO
  original_reference_id: GO_REF:0000119
  review:
    summary: HDAC1 cooperates with DNA methyltransferases (DNMT1, DNMT3A) and methyl-CpG binding
      proteins to establish constitutive heterochromatin (PMID:10615135).
    action: ACCEPT
    reason: HDAC1 interaction with DNMT1 and localization to heterochromatin support its role in DNA
      methylation-dependent heterochromatin formation.
    supported_by:
    - reference_id: PMID:10615135
      supporting_text: Here we show that Dnmt1 is itself associated with histone deacetylase
        activity in vivo
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD,
        Sin3, CoREST, and related chromatin-repressor complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein
        corepressor complexes, especially SIN3, NuRD, and CoREST.
- term:
    id: GO:0006357
    label: regulation of transcription by RNA polymerase II
  evidence_type: ISO
  original_reference_id: GO_REF:0000119
  review:
    summary: HDAC1 regulates RNA polymerase II transcription, primarily through repression but also
      through modulation of chromatin dynamics.
    action: ACCEPT
    reason: HDAC1 is clearly involved in regulating pol II transcription. General parent term
      encompassing both positive and negative regulation.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD,
        Sin3, CoREST, and related chromatin-repressor complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylase that catalyzes the deacetylation of lysine residues on
        the N-terminal part of the core histones.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein
        corepressor complexes, especially SIN3, NuRD, and CoREST.
- term:
    id: GO:0008284
    label: positive regulation of cell population proliferation
  evidence_type: ISO
  original_reference_id: GO_REF:0000119
  review:
    summary: HDAC1 promotes cell proliferation by repressing cell cycle inhibitors through the
      Rb-HDAC1 complex.
    action: KEEP_AS_NON_CORE
    reason: Well-documented pro-proliferative role but downstream biological consequence of
      deacetylase activity.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 has many developmental and signaling consequences through chromatin
        deacetylation; these are non-core outputs of the core enzymatic function.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylation gives a tag for epigenetic repression and plays an
        important role in transcriptional regulation, cell cycle progression and developmental
        events.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: The report supports HDAC1 as a chromatin deacetylase whose developmental,
        signaling, cell-cycle, DNA-damage, and pathway phenotypes are context-specific downstream
        outputs.
- term:
    id: GO:0010629
    label: negative regulation of gene expression
  evidence_type: ISO
  original_reference_id: GO_REF:0000119
  review:
    summary: HDAC1 negatively regulates gene expression through histone deacetylation and chromatin
      compaction.
    action: ACCEPT
    reason: Negative regulation of gene expression is a core function of HDAC1.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD,
        Sin3, CoREST, and related chromatin-repressor complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylase that catalyzes the deacetylation of lysine residues on
        the N-terminal part of the core histones.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein
        corepressor complexes, especially SIN3, NuRD, and CoREST.
- term:
    id: GO:0016581
    label: NuRD complex
  evidence_type: ISO
  original_reference_id: GO_REF:0000119
  review:
    summary: HDAC1 is a core catalytic subunit of the NuRD (nucleosome remodeling and deacetylase)
      complex. Proteomic studies show approximately 49% of cellular HDAC1 in ESCs is in the NuRD
      complex (deep research review). Well supported by mass spectrometry identification
      (PMID:27806305) and multiple interaction studies.
    action: ACCEPT
    reason: NuRD complex membership is a core aspect of HDAC1 function. HDAC1 serves as the
      catalytic deacetylase subunit within NuRD. Extensively validated by proteomics and
      co-immunoprecipitation studies.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD,
        Sin3, CoREST, and related chromatin-repressor complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylase that catalyzes the deacetylation of lysine residues on
        the N-terminal part of the core histones.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein
        corepressor complexes, especially SIN3, NuRD, and CoREST.
- term:
    id: GO:0019213
    label: deacetylase activity
  evidence_type: ISO
  original_reference_id: GO_REF:0000096
  review:
    summary: General deacetylase activity. HDAC1 has broad deacetylase activity on both histone and
      non-histone substrates.
    action: ACCEPT
    reason: HDAC1 has well-established deacetylase activity. While GO:0004407 (histone deacetylase
      activity) is more specific, this broader term is also correct as HDAC1 can deacetylate
      non-histone proteins. Acceptable as a parent-level annotation.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD,
        Sin3, CoREST, and related chromatin-repressor complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylase that catalyzes the deacetylation of lysine residues on
        the N-terminal part of the core histones.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: HDAC1 is a class I Zn2+-dependent histone/protein deacetylase that removes
        acetyl groups from lysine residues on histone tails and non-histone proteins.
- term:
    id: GO:0019899
    label: enzyme binding
  evidence_type: ISO
  original_reference_id: GO_REF:0000119
  review:
    summary: HDAC1 binds various enzymes including DNA methyltransferases (DNMT1, DNMT3A), histone
      methyltransferases (SUV39H1, SETDB1, SMYD2), and kinases.
    action: ACCEPT
    reason: HDAC1 interacts with multiple enzymes as part of chromatin-modifying networks. While
      somewhat general, this captures a real aspect of HDAC1 function.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD,
        Sin3, CoREST, and related chromatin-repressor complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylase that catalyzes the deacetylation of lysine residues on
        the N-terminal part of the core histones.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein
        corepressor complexes, especially SIN3, NuRD, and CoREST.
- term:
    id: GO:0032991
    label: protein-containing complex
  evidence_type: ISO
  original_reference_id: GO_REF:0000119
  review:
    summary: HDAC1 is found in protein-containing complexes (NuRD, SIN3, CoREST). Very general
      cellular component annotation.
    action: ACCEPT
    reason: HDAC1 is found in protein-containing complexes. Correct as a root-level CC annotation
      alongside more specific complex terms.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD,
        Sin3, CoREST, and related chromatin-repressor complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylase that catalyzes the deacetylation of lysine residues on
        the N-terminal part of the core histones.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein
        corepressor complexes, especially SIN3, NuRD, and CoREST.
- term:
    id: GO:0033148
    label: positive regulation of intracellular estrogen receptor signaling pathway
  evidence_type: ISO
  original_reference_id: GO_REF:0000119
  review:
    summary: HDAC1 positively regulates estrogen receptor signaling. HDAC1 interacts with PHB2/REA
      (PMID:15140878, UniProt).
    action: KEEP_AS_NON_CORE
    reason: Specific hormonal signaling context.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 has many developmental and signaling consequences through chromatin
        deacetylation; these are non-core outputs of the core enzymatic function.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylation gives a tag for epigenetic repression and plays an
        important role in transcriptional regulation, cell cycle progression and developmental
        events.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: The report supports HDAC1 as a chromatin deacetylase whose developmental,
        signaling, cell-cycle, DNA-damage, and pathway phenotypes are context-specific downstream
        outputs.
- term:
    id: GO:0033558
    label: protein lysine deacetylase activity
  evidence_type: ISO
  original_reference_id: GO_REF:0000119
  review:
    summary: HDAC1 removes acetyl groups from lysine residues on proteins, including both histone
      and non-histone substrates such as NR1D2, RELA, SP1, SP3, STAT3, ZNF76, and TSHZ3 (UniProt).
    action: ACCEPT
    reason: HDAC1 has well-documented protein lysine deacetylase activity on both histone and
      non-histone targets. This is a core function.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD,
        Sin3, CoREST, and related chromatin-repressor complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylase that catalyzes the deacetylation of lysine residues on
        the N-terminal part of the core histones.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: HDAC1 is a class I Zn2+-dependent histone/protein deacetylase that removes
        acetyl groups from lysine residues on histone tails and non-histone proteins.
- term:
    id: GO:0042826
    label: histone deacetylase binding
  evidence_type: ISO
  original_reference_id: GO_REF:0000119
  review:
    summary: HDAC1 binds to other histone deacetylases, particularly HDAC2 (forming heterodimers)
      and class II HDACs like HDAC7 and HDAC9.
    action: ACCEPT
    reason: HDAC1 forms heterodimers with HDAC2 as the catalytic core of NuRD, SIN3, and CoREST
      complexes. It also interacts with class II HDACs (HDAC7, HDAC9). Well documented.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD,
        Sin3, CoREST, and related chromatin-repressor complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylase that catalyzes the deacetylation of lysine residues on
        the N-terminal part of the core histones.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: HDAC1 is a class I Zn2+-dependent histone/protein deacetylase that removes
        acetyl groups from lysine residues on histone tails and non-histone proteins.
- term:
    id: GO:0043922
    label: host-mediated suppression of viral transcription
  evidence_type: ISO
  original_reference_id: GO_REF:0000119
  review:
    summary: HDAC1 participates in host-mediated suppression of viral transcription by deacetylating
      histones at integrated viral promoters.
    action: KEEP_AS_NON_CORE
    reason: Context-specific application of general transcriptional repression function.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 has many developmental and signaling consequences through chromatin
        deacetylation; these are non-core outputs of the core enzymatic function.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylation gives a tag for epigenetic repression and plays an
        important role in transcriptional regulation, cell cycle progression and developmental
        events.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: The report supports HDAC1 as a chromatin deacetylase whose developmental,
        signaling, cell-cycle, DNA-damage, and pathway phenotypes are context-specific downstream
        outputs.
- term:
    id: GO:0044877
    label: protein-containing complex binding
  evidence_type: ISO
  original_reference_id: GO_REF:0000096
  review:
    summary: HDAC1 functions within protein-containing corepressor complexes, but this binding term
      is much less informative than the specific NuRD, SIN3, and CoREST complex annotations.
    action: KEEP_AS_NON_CORE
    reason: The annotation is directionally true but too generic to represent the core molecular
      function; specific complex membership and catalytic terms carry the curatorial signal.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD,
        Sin3, CoREST, and related chromatin-repressor complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylase that catalyzes the deacetylation of lysine residues on
        the N-terminal part of the core histones.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein
        corepressor complexes, especially SIN3, NuRD, and CoREST.
- term:
    id: GO:0045814
    label: negative regulation of gene expression, epigenetic
  evidence_type: ISO
  original_reference_id: GO_REF:0000119
  review:
    summary: HDAC1 mediates epigenetic gene silencing through histone deacetylation.
    action: ACCEPT
    reason: HDAC1-mediated histone deacetylation is a classical epigenetic mechanism of gene
      silencing. Core function.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD,
        Sin3, CoREST, and related chromatin-repressor complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylase that catalyzes the deacetylation of lysine residues on
        the N-terminal part of the core histones.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein
        corepressor complexes, especially SIN3, NuRD, and CoREST.
- term:
    id: GO:0045892
    label: negative regulation of DNA-templated transcription
  evidence_type: ISO
  original_reference_id: GO_REF:0000119
  review:
    summary: HDAC1 negatively regulates DNA-templated transcription through its histone deacetylase
      activity as part of co-repressor complexes.
    action: ACCEPT
    reason: Transcriptional repression is a core function of HDAC1. Well supported by extensive
      literature.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD,
        Sin3, CoREST, and related chromatin-repressor complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylase that catalyzes the deacetylation of lysine residues on
        the N-terminal part of the core histones.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein
        corepressor complexes, especially SIN3, NuRD, and CoREST.
- term:
    id: GO:0045893
    label: positive regulation of DNA-templated transcription
  evidence_type: ISO
  original_reference_id: GO_REF:0000119
  review:
    summary: Although HDAC1 is primarily a transcriptional repressor, it can indirectly promote
      transcription of certain genes in specific contexts.
    action: KEEP_AS_NON_CORE
    reason: HDAC1 is primarily a repressor, but there is evidence that it can positively regulate
      transcription indirectly. This is a secondary, context-dependent function.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 has many developmental and signaling consequences through chromatin
        deacetylation; these are non-core outputs of the core enzymatic function.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylation gives a tag for epigenetic repression and plays an
        important role in transcriptional regulation, cell cycle progression and developmental
        events.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: The report supports HDAC1 as a chromatin deacetylase whose developmental,
        signaling, cell-cycle, DNA-damage, and pathway phenotypes are context-specific downstream
        outputs.
- term:
    id: GO:0045944
    label: positive regulation of transcription by RNA polymerase II
  evidence_type: ISO
  original_reference_id: GO_REF:0000119
  review:
    summary: HDAC1 can positively regulate RNA pol II transcription in certain contexts, likely
      through indirect mechanisms.
    action: KEEP_AS_NON_CORE
    reason: Not a core function of HDAC1 but documented in specific contexts.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 has many developmental and signaling consequences through chromatin
        deacetylation; these are non-core outputs of the core enzymatic function.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylation gives a tag for epigenetic repression and plays an
        important role in transcriptional regulation, cell cycle progression and developmental
        events.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: The report supports HDAC1 as a chromatin deacetylase whose developmental,
        signaling, cell-cycle, DNA-damage, and pathway phenotypes are context-specific downstream
        outputs.
- term:
    id: GO:0048471
    label: perinuclear region of cytoplasm
  evidence_type: ISO
  original_reference_id: GO_REF:0000096
  review:
    summary: Perinuclear cytoplasmic localization is an orthology-derived/minor subcellular
      annotation, whereas HDAC1's supported role is predominantly nuclear chromatin regulation.
    action: MARK_AS_OVER_ANNOTATED
    reason: This weak cytoplasmic sublocalization should not be accepted as a central HDAC1
      localization when the evidence supports nuclear chromatin/corepressor complexes.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: 'GO; GO:0048471; C:perinuclear region of cytoplasm; ISO:GO_Central.'
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: Class I HDACs, including HDAC1, are predominantly or exclusively nuclear,
        consistent with chromatin accessibility and transcriptional control roles.
- term:
    id: GO:0051059
    label: NF-kappaB binding
  evidence_type: ISO
  original_reference_id: GO_REF:0000119
  review:
    summary: HDAC1 directly binds to the NF-kappaB subunit RelA/p65 and deacetylates it, attenuating
      NF-kappaB transcriptional activity.
    action: ACCEPT
    reason: The HDAC1-NF-kappaB/p65 interaction is directly demonstrated and functionally
      characterized. HDAC1 deacetylates Lys-310 of RELA, inhibiting NF-kappaB activity (UniProt).
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD,
        Sin3, CoREST, and related chromatin-repressor complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylase that catalyzes the deacetylation of lysine residues on
        the N-terminal part of the core histones.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein
        corepressor complexes, especially SIN3, NuRD, and CoREST.
- term:
    id: GO:0060766
    label: negative regulation of androgen receptor signaling pathway
  evidence_type: ISO
  original_reference_id: GO_REF:0000119
  review:
    summary: HDAC1 negatively regulates androgen receptor signaling.
    action: KEEP_AS_NON_CORE
    reason: Specific hormonal signaling context. Not core.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 has many developmental and signaling consequences through chromatin
        deacetylation; these are non-core outputs of the core enzymatic function.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylation gives a tag for epigenetic repression and plays an
        important role in transcriptional regulation, cell cycle progression and developmental
        events.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: The report supports HDAC1 as a chromatin deacetylase whose developmental,
        signaling, cell-cycle, DNA-damage, and pathway phenotypes are context-specific downstream
        outputs.
- term:
    id: GO:0061629
    label: RNA polymerase II-specific DNA-binding transcription factor binding
  evidence_type: ISO
  original_reference_id: GO_REF:0000119
  review:
    summary: HDAC1 binds RNA polymerase II-specific transcription factors that recruit it to target
      genes for transcriptional repression.
    action: ACCEPT
    reason: This is a more specific version of DNA-binding transcription factor binding, appropriate
      given that HDAC1 primarily regulates RNA pol II-transcribed genes through interactions with
      pol II-specific TFs.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD,
        Sin3, CoREST, and related chromatin-repressor complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylase that catalyzes the deacetylation of lysine residues on
        the N-terminal part of the core histones.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein
        corepressor complexes, especially SIN3, NuRD, and CoREST.
- term:
    id: GO:0070822
    label: Sin3-type complex
  evidence_type: ISO
  original_reference_id: GO_REF:0000119
  review:
    summary: HDAC1 is a core catalytic subunit of the SIN3 co-repressor complex. Approximately 15%
      of cellular HDAC1 in ESCs is in the SIN3A complex. Confirmed by multiple studies including
      PMID:11909966 and PMID:28554894.
    action: ACCEPT
    reason: SIN3 complex membership is a core function of HDAC1. The SIN3-HDAC complex is one of the
      three major HDAC1-containing co-repressor complexes.
    supported_by:
    - reference_id: PMID:28554894
      supporting_text: Sin3a is the central scaffold protein of the prototypical Hdac1/2 chromatin
        repressor complex
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD,
        Sin3, CoREST, and related chromatin-repressor complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein
        corepressor complexes, especially SIN3, NuRD, and CoREST.
- term:
    id: GO:0090090
    label: negative regulation of canonical Wnt signaling pathway
  evidence_type: ISO
  original_reference_id: GO_REF:0000119
  review:
    summary: HDAC1/2 negatively regulate canonical Wnt signaling by deacetylating histones at Wnt
      target gene promoters. Demonstrated in neural development.
    action: KEEP_AS_NON_CORE
    reason: Well-supported role in neural development but represents a downstream biological
      consequence rather than a core molecular function.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 has many developmental and signaling consequences through chromatin
        deacetylation; these are non-core outputs of the core enzymatic function.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylation gives a tag for epigenetic repression and plays an
        important role in transcriptional regulation, cell cycle progression and developmental
        events.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: The report supports HDAC1 as a chromatin deacetylase whose developmental,
        signaling, cell-cycle, DNA-damage, and pathway phenotypes are context-specific downstream
        outputs.
- term:
    id: GO:0140297
    label: DNA-binding transcription factor binding
  evidence_type: ISO
  original_reference_id: GO_REF:0000096
  review:
    summary: HDAC1 binds numerous DNA-binding transcription factors as part of its recruitment to
      target genes. Documented interactions include MyoD, YY1, KLF1, NR4A2, INSM1, and many others.
    action: ACCEPT
    reason: HDAC1 interaction with DNA-binding transcription factors is central to its biological
      function - this is how it is recruited to specific genomic loci.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD,
        Sin3, CoREST, and related chromatin-repressor complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylase that catalyzes the deacetylation of lysine residues on
        the N-terminal part of the core histones.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein
        corepressor complexes, especially SIN3, NuRD, and CoREST.
- term:
    id: GO:0140297
    label: DNA-binding transcription factor binding
  evidence_type: ISO
  original_reference_id: GO_REF:0000119
  review:
    summary: HDAC1 binds numerous DNA-binding transcription factors as part of its recruitment to
      target genes. Documented interactions include MyoD, YY1, KLF1, NR4A2, INSM1, and many others.
    action: ACCEPT
    reason: HDAC1 interaction with DNA-binding transcription factors is central to its biological
      function - this is how it is recruited to specific genomic loci.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD,
        Sin3, CoREST, and related chromatin-repressor complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylase that catalyzes the deacetylation of lysine residues on
        the N-terminal part of the core histones.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein
        corepressor complexes, especially SIN3, NuRD, and CoREST.
- term:
    id: GO:0160009
    label: histone decrotonylase activity
  evidence_type: ISO
  original_reference_id: GO_REF:0000119
  review:
    summary: HDAC1 can remove crotonyl modifications from histone lysine residues. Directly
      demonstrated by Kelly et al. (PMID:30279482) showing HDAC1/2 complexes are important histone
      decrotonylases in vivo.
    action: ACCEPT
    reason: Directly supported by experimental evidence. Genetic deletion of HDAC1/2 in ES cells
      increases global histone crotonylation and causes an 85% reduction in total decrotonylase
      activity (PMID:30279482).
    supported_by:
    - reference_id: PMID:30279482
      supporting_text: Genetic deletion of HDAC1/2 in ES cells increases global levels of histone
        crotonylation and causes an 85% reduction in total decrotonylase activity
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD,
        Sin3, CoREST, and related chromatin-repressor complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein
        corepressor complexes, especially SIN3, NuRD, and CoREST.
- term:
    id: GO:0160216
    label: protein lysine delactylase activity
  evidence_type: ISO
  original_reference_id: GO_REF:0000119
  review:
    summary: UniProt/GOA includes protein lysine delactylase activity for HDAC1, but this row is
      similarity-based; the accessible experimental paper supports HDAC1/2 decrotonylase activity,
      not direct mouse delactylase activity.
    action: KEEP_AS_NON_CORE
    reason: Do not treat delactylase activity as a direct/core Hdac1 function here. The stronger
      experimental support is for histone deacetylase and decrotonylase activity.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: 'GO; GO:0160216; F:protein lysine delactylase activity; ISS:UniProtKB.'
    - reference_id: PMID:30279482
      supporting_text: A ternary complex of HDAC1/CoREST1/LSD1 is able to hydrolyse both histone H3
        Lys18-acetyl (H3K18ac) and H3 Lys18-crotonyl (H3K18cr) peptide substrates
- term:
    id: GO:0000122
    label: negative regulation of transcription by RNA polymerase II
  evidence_type: NAS
  original_reference_id: PMID:22865885
  review:
    summary: HDAC1 negatively regulates transcription by RNA polymerase II through histone
      deacetylation at target gene promoters. This is a core biological process annotation for
      HDAC1.
    action: ACCEPT
    reason: Negative regulation of pol II transcription is a primary biological function of HDAC1.
      Supported by multiple lines of evidence (PMID:8917507, PMID:9271381, PMID:21093383).
    supported_by:
    - reference_id: PMID:22865885
      supporting_text: The SIN3A-HDAC complex deacetylates histones thereby repressing gene
        transcription
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD,
        Sin3, CoREST, and related chromatin-repressor complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein
        corepressor complexes, especially SIN3, NuRD, and CoREST.
- term:
    id: GO:0000122
    label: negative regulation of transcription by RNA polymerase II
  evidence_type: NAS
  original_reference_id: PMID:9651585
  review:
    summary: HDAC1 negatively regulates transcription by RNA polymerase II through histone
      deacetylation at target gene promoters. This is a core biological process annotation for
      HDAC1.
    action: ACCEPT
    reason: Negative regulation of pol II transcription is a primary biological function of HDAC1.
      Supported by multiple lines of evidence (PMID:8917507, PMID:9271381, PMID:21093383).
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD,
        Sin3, CoREST, and related chromatin-repressor complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylase that catalyzes the deacetylation of lysine residues on
        the N-terminal part of the core histones.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein
        corepressor complexes, especially SIN3, NuRD, and CoREST.
- term:
    id: GO:0005634
    label: nucleus
  evidence_type: NAS
  original_reference_id: PMID:28554894
  review:
    summary: HDAC1 is predominantly nuclear, consistent with its function in chromatin modification
      and transcriptional regulation. Nuclear localization confirmed by multiple methods including
      immunofluorescence (PMID:11115394).
    action: ACCEPT
    reason: Nuclear localization is a well-established core feature of HDAC1. It is a Class I HDAC
      that is predominantly nuclear.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD,
        Sin3, CoREST, and related chromatin-repressor complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylase that catalyzes the deacetylation of lysine residues on
        the N-terminal part of the core histones.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: Class I HDACs, including HDAC1, are predominantly or exclusively nuclear,
        consistent with chromatin accessibility and transcriptional control roles.
- term:
    id: GO:0030336
    label: negative regulation of cell migration
  evidence_type: NAS
  original_reference_id: PMID:22984288
  review:
    summary: HDAC1 negatively regulates cell migration (PMID:22984288).
    action: KEEP_AS_NON_CORE
    reason: Downstream pleiotropic effect.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 has many developmental and signaling consequences through chromatin
        deacetylation; these are non-core outputs of the core enzymatic function.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylation gives a tag for epigenetic repression and plays an
        important role in transcriptional regulation, cell cycle progression and developmental
        events.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: The report supports HDAC1 as a chromatin deacetylase whose developmental,
        signaling, cell-cycle, DNA-damage, and pathway phenotypes are context-specific downstream
        outputs.
- term:
    id: GO:0030512
    label: negative regulation of transforming growth factor beta receptor signaling pathway
  evidence_type: NAS
  original_reference_id: PMID:22984288
  review:
    summary: HDAC1 negatively regulates TGF-beta receptor signaling (PMID:22984288).
    action: KEEP_AS_NON_CORE
    reason: Specific signaling context.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 has many developmental and signaling consequences through chromatin
        deacetylation; these are non-core outputs of the core enzymatic function.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylation gives a tag for epigenetic repression and plays an
        important role in transcriptional regulation, cell cycle progression and developmental
        events.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: The report supports HDAC1 as a chromatin deacetylase whose developmental,
        signaling, cell-cycle, DNA-damage, and pathway phenotypes are context-specific downstream
        outputs.
- term:
    id: GO:0042659
    label: regulation of cell fate specification
  evidence_type: NAS
  original_reference_id: PMID:22560079
  review:
    summary: HDAC1 participates in regulation of cell fate specification through epigenetic gene
      regulation.
    action: KEEP_AS_NON_CORE
    reason: Broad developmental process. Pleiotropic downstream effect.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 has many developmental and signaling consequences through chromatin
        deacetylation; these are non-core outputs of the core enzymatic function.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylation gives a tag for epigenetic repression and plays an
        important role in transcriptional regulation, cell cycle progression and developmental
        events.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: The report supports HDAC1 as a chromatin deacetylase whose developmental,
        signaling, cell-cycle, DNA-damage, and pathway phenotypes are context-specific downstream
        outputs.
- term:
    id: GO:0045892
    label: negative regulation of DNA-templated transcription
  evidence_type: NAS
  original_reference_id: PMID:22560079
  review:
    summary: HDAC1 negatively regulates DNA-templated transcription through its histone deacetylase
      activity as part of co-repressor complexes.
    action: ACCEPT
    reason: Transcriptional repression is a core function of HDAC1. Well supported by extensive
      literature.
    supported_by:
    - reference_id: PMID:22560079
      supporting_text: the action of NuRD is sufficient to silence transcription of these
        pluripotency genes, allowing cells to exit self-renewal
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD,
        Sin3, CoREST, and related chromatin-repressor complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein
        corepressor complexes, especially SIN3, NuRD, and CoREST.
- term:
    id: GO:0045893
    label: positive regulation of DNA-templated transcription
  evidence_type: NAS
  original_reference_id: PMID:19927129
  review:
    summary: Although HDAC1 is primarily a transcriptional repressor, it can indirectly promote
      transcription of certain genes in specific contexts.
    action: KEEP_AS_NON_CORE
    reason: HDAC1 is primarily a repressor, but there is evidence that it can positively regulate
      transcription indirectly. This is a secondary, context-dependent function.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 has many developmental and signaling consequences through chromatin
        deacetylation; these are non-core outputs of the core enzymatic function.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylation gives a tag for epigenetic repression and plays an
        important role in transcriptional regulation, cell cycle progression and developmental
        events.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: The report supports HDAC1 as a chromatin deacetylase whose developmental,
        signaling, cell-cycle, DNA-damage, and pathway phenotypes are context-specific downstream
        outputs.
- term:
    id: GO:1902455
    label: negative regulation of stem cell population maintenance
  evidence_type: NAS
  original_reference_id: PMID:28554894
  review:
    summary: HDAC1 negatively regulates stem cell maintenance in certain contexts (PMID:28554894).
    action: KEEP_AS_NON_CORE
    reason: Context-specific downstream effect.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 has many developmental and signaling consequences through chromatin
        deacetylation; these are non-core outputs of the core enzymatic function.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylation gives a tag for epigenetic repression and plays an
        important role in transcriptional regulation, cell cycle progression and developmental
        events.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: The report supports HDAC1 as a chromatin deacetylase whose developmental,
        signaling, cell-cycle, DNA-damage, and pathway phenotypes are context-specific downstream
        outputs.
- term:
    id: GO:1902459
    label: positive regulation of stem cell population maintenance
  evidence_type: NAS
  original_reference_id: PMID:28554894
  review:
    summary: HDAC1 positively regulates stem cell maintenance as part of the variant Sin3a-Hdac
      complex in ESCs (PMID:28554894).
    action: KEEP_AS_NON_CORE
    reason: Context-specific downstream effect.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 has many developmental and signaling consequences through chromatin
        deacetylation; these are non-core outputs of the core enzymatic function.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylation gives a tag for epigenetic repression and plays an
        important role in transcriptional regulation, cell cycle progression and developmental
        events.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: The report supports HDAC1 as a chromatin deacetylase whose developmental,
        signaling, cell-cycle, DNA-damage, and pathway phenotypes are context-specific downstream
        outputs.
- term:
    id: GO:2000736
    label: regulation of stem cell differentiation
  evidence_type: NAS
  original_reference_id: PMID:22560079
  review:
    summary: HDAC1 participates in regulation of stem cell differentiation (PMID:28554894).
    action: KEEP_AS_NON_CORE
    reason: Downstream biological process affected by HDAC1 activity.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 has many developmental and signaling consequences through chromatin
        deacetylation; these are non-core outputs of the core enzymatic function.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylation gives a tag for epigenetic repression and plays an
        important role in transcriptional regulation, cell cycle progression and developmental
        events.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: The report supports HDAC1 as a chromatin deacetylase whose developmental,
        signaling, cell-cycle, DNA-damage, and pathway phenotypes are context-specific downstream
        outputs.
- term:
    id: GO:0004407
    label: histone deacetylase activity
  evidence_type: TAS
  original_reference_id: Reactome:R-MMU-573376
  review:
    summary: HDAC1 is a zinc-dependent histone deacetylase (EC 3.5.1.98) that catalyzes removal of
      acetyl groups from N-acetyl-lysine residues on histones H2A, H2B, H3, and H4. This is the core
      enzymatic function of HDAC1, well established by direct biochemical assays (PMID:10615135,
      PMID:21960634, PMID:30279482).
    action: ACCEPT
    reason: Histone deacetylase activity is the primary enzymatic function of HDAC1, supported by
      multiple direct experimental studies demonstrating catalytic activity on histone substrates.
    supported_by:
    - reference_id: PMID:10615135
      supporting_text: Here we show that Dnmt1 is itself associated with histone deacetylase
        activity in vivo
    - reference_id: PMID:30279482
      supporting_text: A ternary complex of HDAC1/CoREST1/LSD1 is able to hydrolyse both histone H3
        Lys18-acetyl (H3K18ac) and H3 Lys18-crotonyl (H3K18cr) peptide substrates
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD,
        Sin3, CoREST, and related chromatin-repressor complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: HDAC1 is a class I Zn2+-dependent histone/protein deacetylase that removes
        acetyl groups from lysine residues on histone tails and non-histone proteins.
- term:
    id: GO:0160216
    label: protein lysine delactylase activity
  evidence_type: ISS
  original_reference_id: GO_REF:0000024
  review:
    summary: UniProt/GOA includes protein lysine delactylase activity for HDAC1, but this row is
      similarity-based; the accessible experimental paper supports HDAC1/2 decrotonylase activity,
      not direct mouse delactylase activity.
    action: KEEP_AS_NON_CORE
    reason: Do not treat delactylase activity as a direct/core Hdac1 function here. The stronger
      experimental support is for histone deacetylase and decrotonylase activity.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: 'GO; GO:0160216; F:protein lysine delactylase activity; ISS:UniProtKB.'
    - reference_id: PMID:30279482
      supporting_text: A ternary complex of HDAC1/CoREST1/LSD1 is able to hydrolyse both histone H3
        Lys18-acetyl (H3K18ac) and H3 Lys18-crotonyl (H3K18cr) peptide substrates
- term:
    id: GO:0005634
    label: nucleus
  evidence_type: IDA
  original_reference_id: PMID:11115394
  review:
    summary: HDAC1 is predominantly nuclear, consistent with its function in chromatin modification
      and transcriptional regulation. Nuclear localization confirmed by multiple methods including
      immunofluorescence (PMID:11115394).
    action: ACCEPT
    reason: Nuclear localization is a well-established core feature of HDAC1. It is a Class I HDAC
      that is predominantly nuclear.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD,
        Sin3, CoREST, and related chromatin-repressor complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylase that catalyzes the deacetylation of lysine residues on
        the N-terminal part of the core histones.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: Class I HDACs, including HDAC1, are predominantly or exclusively nuclear,
        consistent with chromatin accessibility and transcriptional control roles.
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:33831416
  review:
    summary: Protein binding annotation based on physical interaction evidence from PMID:33831416.
      HDAC1 is known to interact with a very large number of proteins as it functions within
      multiple co-repressor complexes (NuRD, SIN3, CoREST) and binds many transcription factors.
    action: REMOVE
    reason: Per curation guidelines, protein binding (GO:0005515) is uninformative and should be
      replaced with more specific molecular function terms. HDAC1 physically interacts with many
      proteins, but this generic term does not convey functional information. More specific
      annotations such as histone deacetylase binding, transcription corepressor binding, NF-kappaB
      binding, and DNA-binding transcription factor binding are already present.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: Generic protein binding and weakly mechanistic interaction annotations are
        less informative than HDAC1 deacetylase activity and defined corepressor-complex membership.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylases act via the formation of large multiprotein complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: The report supports specific enzymatic and chromatin-complex annotations for
        HDAC1 rather than generic binding or weakly localized annotations.
- term:
    id: GO:0004407
    label: histone deacetylase activity
  evidence_type: IDA
  original_reference_id: PMID:30279482
  review:
    summary: HDAC1 is a zinc-dependent histone deacetylase (EC 3.5.1.98) that catalyzes removal of
      acetyl groups from N-acetyl-lysine residues on histones H2A, H2B, H3, and H4. This is the core
      enzymatic function of HDAC1, well established by direct biochemical assays (PMID:10615135,
      PMID:21960634, PMID:30279482).
    action: ACCEPT
    reason: Histone deacetylase activity is the primary enzymatic function of HDAC1, supported by
      multiple direct experimental studies demonstrating catalytic activity on histone substrates.
    supported_by:
    - reference_id: PMID:10615135
      supporting_text: Here we show that Dnmt1 is itself associated with histone deacetylase
        activity in vivo
    - reference_id: PMID:30279482
      supporting_text: A ternary complex of HDAC1/CoREST1/LSD1 is able to hydrolyse both histone H3
        Lys18-acetyl (H3K18ac) and H3 Lys18-crotonyl (H3K18cr) peptide substrates
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD,
        Sin3, CoREST, and related chromatin-repressor complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: HDAC1 is a class I Zn2+-dependent histone/protein deacetylase that removes
        acetyl groups from lysine residues on histone tails and non-histone proteins.
- term:
    id: GO:0160009
    label: histone decrotonylase activity
  evidence_type: IDA
  original_reference_id: PMID:30279482
  review:
    summary: HDAC1 can remove crotonyl modifications from histone lysine residues. Directly
      demonstrated by Kelly et al. (PMID:30279482) showing HDAC1/2 complexes are important histone
      decrotonylases in vivo.
    action: ACCEPT
    reason: Directly supported by experimental evidence. Genetic deletion of HDAC1/2 in ES cells
      increases global histone crotonylation and causes an 85% reduction in total decrotonylase
      activity (PMID:30279482).
    supported_by:
    - reference_id: PMID:30279482
      supporting_text: Genetic deletion of HDAC1/2 in ES cells increases global levels of histone
        crotonylation and causes an 85% reduction in total decrotonylase activity
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD,
        Sin3, CoREST, and related chromatin-repressor complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein
        corepressor complexes, especially SIN3, NuRD, and CoREST.
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:30228260
  review:
    summary: Protein binding annotation based on physical interaction evidence from PMID:30228260.
      HDAC1 is known to interact with a very large number of proteins as it functions within
      multiple co-repressor complexes (NuRD, SIN3, CoREST) and binds many transcription factors.
    action: REMOVE
    reason: Per curation guidelines, protein binding (GO:0005515) is uninformative and should be
      replaced with more specific molecular function terms. HDAC1 physically interacts with many
      proteins, but this generic term does not convey functional information. More specific
      annotations such as histone deacetylase binding, transcription corepressor binding, NF-kappaB
      binding, and DNA-binding transcription factor binding are already present.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: Generic protein binding and weakly mechanistic interaction annotations are
        less informative than HDAC1 deacetylase activity and defined corepressor-complex membership.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylases act via the formation of large multiprotein complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: The report supports specific enzymatic and chromatin-complex annotations for
        HDAC1 rather than generic binding or weakly localized annotations.
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:34180153
  review:
    summary: Protein binding annotation based on physical interaction evidence from PMID:34180153.
      HDAC1 is known to interact with a very large number of proteins as it functions within
      multiple co-repressor complexes (NuRD, SIN3, CoREST) and binds many transcription factors.
    action: REMOVE
    reason: Per curation guidelines, protein binding (GO:0005515) is uninformative and should be
      replaced with more specific molecular function terms. HDAC1 physically interacts with many
      proteins, but this generic term does not convey functional information. More specific
      annotations such as histone deacetylase binding, transcription corepressor binding, NF-kappaB
      binding, and DNA-binding transcription factor binding are already present.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: Generic protein binding and weakly mechanistic interaction annotations are
        less informative than HDAC1 deacetylase activity and defined corepressor-complex membership.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylases act via the formation of large multiprotein complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: The report supports specific enzymatic and chromatin-complex annotations for
        HDAC1 rather than generic binding or weakly localized annotations.
- term:
    id: GO:0004407
    label: histone deacetylase activity
  evidence_type: IDA
  original_reference_id: PMID:10615135
  review:
    summary: HDAC1 is a zinc-dependent histone deacetylase (EC 3.5.1.98) that catalyzes removal of
      acetyl groups from N-acetyl-lysine residues on histones H2A, H2B, H3, and H4. This is the core
      enzymatic function of HDAC1, well established by direct biochemical assays (PMID:10615135,
      PMID:21960634, PMID:30279482).
    action: ACCEPT
    reason: Histone deacetylase activity is the primary enzymatic function of HDAC1, supported by
      multiple direct experimental studies demonstrating catalytic activity on histone substrates.
    supported_by:
    - reference_id: PMID:10615135
      supporting_text: Here we show that Dnmt1 is itself associated with histone deacetylase
        activity in vivo
    - reference_id: PMID:30279482
      supporting_text: A ternary complex of HDAC1/CoREST1/LSD1 is able to hydrolyse both histone H3
        Lys18-acetyl (H3K18ac) and H3 Lys18-crotonyl (H3K18cr) peptide substrates
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD,
        Sin3, CoREST, and related chromatin-repressor complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: HDAC1 is a class I Zn2+-dependent histone/protein deacetylase that removes
        acetyl groups from lysine residues on histone tails and non-histone proteins.
- term:
    id: GO:0140297
    label: DNA-binding transcription factor binding
  evidence_type: IPI
  original_reference_id: PMID:33795231
  review:
    summary: HDAC1 binds numerous DNA-binding transcription factors as part of its recruitment to
      target genes. Documented interactions include MyoD, YY1, KLF1, NR4A2, INSM1, and many others.
    action: ACCEPT
    reason: HDAC1 interaction with DNA-binding transcription factors is central to its biological
      function - this is how it is recruited to specific genomic loci.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD,
        Sin3, CoREST, and related chromatin-repressor complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylase that catalyzes the deacetylation of lysine residues on
        the N-terminal part of the core histones.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein
        corepressor complexes, especially SIN3, NuRD, and CoREST.
- term:
    id: GO:0140297
    label: DNA-binding transcription factor binding
  evidence_type: IPI
  original_reference_id: PMID:18486321
  review:
    summary: HDAC1 binds numerous DNA-binding transcription factors as part of its recruitment to
      target genes. Documented interactions include MyoD, YY1, KLF1, NR4A2, INSM1, and many others.
    action: ACCEPT
    reason: HDAC1 interaction with DNA-binding transcription factors is central to its biological
      function - this is how it is recruited to specific genomic loci.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD,
        Sin3, CoREST, and related chromatin-repressor complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylase that catalyzes the deacetylation of lysine residues on
        the N-terminal part of the core histones.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein
        corepressor complexes, especially SIN3, NuRD, and CoREST.
- term:
    id: GO:0140297
    label: DNA-binding transcription factor binding
  evidence_type: TAS
  original_reference_id: PMID:12711221
  review:
    summary: HDAC1 binds numerous DNA-binding transcription factors as part of its recruitment to
      target genes. Documented interactions include MyoD, YY1, KLF1, NR4A2, INSM1, and many others.
    action: ACCEPT
    reason: HDAC1 interaction with DNA-binding transcription factors is central to its biological
      function - this is how it is recruited to specific genomic loci.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD,
        Sin3, CoREST, and related chromatin-repressor complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylase that catalyzes the deacetylation of lysine residues on
        the N-terminal part of the core histones.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein
        corepressor complexes, especially SIN3, NuRD, and CoREST.
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:30911105
  review:
    summary: Protein binding annotation based on physical interaction evidence from PMID:30911105.
      HDAC1 is known to interact with a very large number of proteins as it functions within
      multiple co-repressor complexes (NuRD, SIN3, CoREST) and binds many transcription factors.
    action: REMOVE
    reason: Per curation guidelines, protein binding (GO:0005515) is uninformative and should be
      replaced with more specific molecular function terms. HDAC1 physically interacts with many
      proteins, but this generic term does not convey functional information. More specific
      annotations such as histone deacetylase binding, transcription corepressor binding, NF-kappaB
      binding, and DNA-binding transcription factor binding are already present.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: Generic protein binding and weakly mechanistic interaction annotations are
        less informative than HDAC1 deacetylase activity and defined corepressor-complex membership.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylases act via the formation of large multiprotein complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: The report supports specific enzymatic and chromatin-complex annotations for
        HDAC1 rather than generic binding or weakly localized annotations.
- term:
    id: GO:0003682
    label: chromatin binding
  evidence_type: IDA
  original_reference_id: PMID:15608638
  review:
    summary: HDAC1 binds chromatin as part of its function in co-repressor complexes. ChIP
      experiments have confirmed HDAC1 occupancy at promoters and other regulatory regions.
    action: ACCEPT
    reason: Chromatin binding is well supported by extensive ChIP-seq and ChIP-qPCR data showing
      HDAC1 occupancy at promoters, enhancers, and heterochromatic regions.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD,
        Sin3, CoREST, and related chromatin-repressor complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylase that catalyzes the deacetylation of lysine residues on
        the N-terminal part of the core histones.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein
        corepressor complexes, especially SIN3, NuRD, and CoREST.
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:12900441
  review:
    summary: Protein binding annotation based on physical interaction evidence from PMID:12900441.
      HDAC1 is known to interact with a very large number of proteins as it functions within
      multiple co-repressor complexes (NuRD, SIN3, CoREST) and binds many transcription factors.
    action: REMOVE
    reason: Per curation guidelines, protein binding (GO:0005515) is uninformative and should be
      replaced with more specific molecular function terms. HDAC1 physically interacts with many
      proteins, but this generic term does not convey functional information. More specific
      annotations such as histone deacetylase binding, transcription corepressor binding, NF-kappaB
      binding, and DNA-binding transcription factor binding are already present.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: Generic protein binding and weakly mechanistic interaction annotations are
        less informative than HDAC1 deacetylase activity and defined corepressor-complex membership.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylases act via the formation of large multiprotein complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: The report supports specific enzymatic and chromatin-complex annotations for
        HDAC1 rather than generic binding or weakly localized annotations.
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:19796622
  review:
    summary: Protein binding annotation based on physical interaction evidence from PMID:19796622.
      HDAC1 is known to interact with a very large number of proteins as it functions within
      multiple co-repressor complexes (NuRD, SIN3, CoREST) and binds many transcription factors.
    action: REMOVE
    reason: Per curation guidelines, protein binding (GO:0005515) is uninformative and should be
      replaced with more specific molecular function terms. HDAC1 physically interacts with many
      proteins, but this generic term does not convey functional information. More specific
      annotations such as histone deacetylase binding, transcription corepressor binding, NF-kappaB
      binding, and DNA-binding transcription factor binding are already present.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: Generic protein binding and weakly mechanistic interaction annotations are
        less informative than HDAC1 deacetylase activity and defined corepressor-complex membership.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylases act via the formation of large multiprotein complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: The report supports specific enzymatic and chromatin-complex annotations for
        HDAC1 rather than generic binding or weakly localized annotations.
- term:
    id: GO:0003682
    label: chromatin binding
  evidence_type: IDA
  original_reference_id: PMID:17392792
  review:
    summary: HDAC1 binds chromatin as part of its function in co-repressor complexes. ChIP
      experiments have confirmed HDAC1 occupancy at promoters and other regulatory regions.
    action: ACCEPT
    reason: Chromatin binding is well supported by extensive ChIP-seq and ChIP-qPCR data showing
      HDAC1 occupancy at promoters, enhancers, and heterochromatic regions.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD,
        Sin3, CoREST, and related chromatin-repressor complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylase that catalyzes the deacetylation of lysine residues on
        the N-terminal part of the core histones.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein
        corepressor complexes, especially SIN3, NuRD, and CoREST.
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:15907476
  review:
    summary: Protein binding annotation based on physical interaction evidence from PMID:15907476.
      HDAC1 is known to interact with a very large number of proteins as it functions within
      multiple co-repressor complexes (NuRD, SIN3, CoREST) and binds many transcription factors.
    action: REMOVE
    reason: Per curation guidelines, protein binding (GO:0005515) is uninformative and should be
      replaced with more specific molecular function terms. HDAC1 physically interacts with many
      proteins, but this generic term does not convey functional information. More specific
      annotations such as histone deacetylase binding, transcription corepressor binding, NF-kappaB
      binding, and DNA-binding transcription factor binding are already present.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: Generic protein binding and weakly mechanistic interaction annotations are
        less informative than HDAC1 deacetylase activity and defined corepressor-complex membership.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylases act via the formation of large multiprotein complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: The report supports specific enzymatic and chromatin-complex annotations for
        HDAC1 rather than generic binding or weakly localized annotations.
- term:
    id: GO:0070888
    label: E-box binding
  evidence_type: IDA
  original_reference_id: PMID:24736997
  review:
    summary: HDAC1 is recruited to E-box-containing circadian gene promoters, but the evidence is
      chromatin occupancy/repressor-complex recruitment rather than direct sequence-specific E-box
      motif binding by HDAC1.
    action: MODIFY
    reason: Replace direct E-box binding with promoter-specific chromatin binding, which matches the
      ChIP/recruitment evidence.
    proposed_replacement_terms:
    - id: GO:1990841
      label: promoter-specific chromatin binding
    supported_by:
    - reference_id: PMID:24736997
      supporting_text: The HDAC1 occupancies at the endogenous E-box of the Per2 promoter were
        detected in the WT MEF cells at 28, 36, 44, and 52 h after induction with dexamethasone
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein
        corepressor complexes, especially SIN3, NuRD, and CoREST.
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:17442941
  review:
    summary: Protein binding annotation based on physical interaction evidence from PMID:17442941.
      HDAC1 is known to interact with a very large number of proteins as it functions within
      multiple co-repressor complexes (NuRD, SIN3, CoREST) and binds many transcription factors.
    action: REMOVE
    reason: Per curation guidelines, protein binding (GO:0005515) is uninformative and should be
      replaced with more specific molecular function terms. HDAC1 physically interacts with many
      proteins, but this generic term does not convey functional information. More specific
      annotations such as histone deacetylase binding, transcription corepressor binding, NF-kappaB
      binding, and DNA-binding transcription factor binding are already present.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: Generic protein binding and weakly mechanistic interaction annotations are
        less informative than HDAC1 deacetylase activity and defined corepressor-complex membership.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylases act via the formation of large multiprotein complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: The report supports specific enzymatic and chromatin-complex annotations for
        HDAC1 rather than generic binding or weakly localized annotations.
- term:
    id: GO:0032991
    label: protein-containing complex
  evidence_type: IDA
  original_reference_id: PMID:19796622
  review:
    summary: HDAC1 is found in protein-containing complexes (NuRD, SIN3, CoREST). Very general
      cellular component annotation.
    action: ACCEPT
    reason: HDAC1 is found in protein-containing complexes. Correct as a root-level CC annotation
      alongside more specific complex terms.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: approximately 92% of cellular HDAC1 in ESCs was found in just three
        complexes, about 49% in the NuRD complex, 28% in CoREST, and 15% in SIN3A
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein
        corepressor complexes, especially SIN3, NuRD, and CoREST.
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:28554894
  review:
    summary: Protein binding annotation based on physical interaction evidence from PMID:28554894.
      HDAC1 is known to interact with a very large number of proteins as it functions within
      multiple co-repressor complexes (NuRD, SIN3, CoREST) and binds many transcription factors.
    action: REMOVE
    reason: Per curation guidelines, protein binding (GO:0005515) is uninformative and should be
      replaced with more specific molecular function terms. HDAC1 physically interacts with many
      proteins, but this generic term does not convey functional information. More specific
      annotations such as histone deacetylase binding, transcription corepressor binding, NF-kappaB
      binding, and DNA-binding transcription factor binding are already present.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: Generic protein binding and weakly mechanistic interaction annotations are
        less informative than HDAC1 deacetylase activity and defined corepressor-complex membership.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylases act via the formation of large multiprotein complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: The report supports specific enzymatic and chromatin-complex annotations for
        HDAC1 rather than generic binding or weakly localized annotations.
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:22770845
  review:
    summary: Protein binding annotation based on physical interaction evidence from PMID:22770845.
      HDAC1 is known to interact with a very large number of proteins as it functions within
      multiple co-repressor complexes (NuRD, SIN3, CoREST) and binds many transcription factors.
    action: REMOVE
    reason: Per curation guidelines, protein binding (GO:0005515) is uninformative and should be
      replaced with more specific molecular function terms. HDAC1 physically interacts with many
      proteins, but this generic term does not convey functional information. More specific
      annotations such as histone deacetylase binding, transcription corepressor binding, NF-kappaB
      binding, and DNA-binding transcription factor binding are already present.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: Generic protein binding and weakly mechanistic interaction annotations are
        less informative than HDAC1 deacetylase activity and defined corepressor-complex membership.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylases act via the formation of large multiprotein complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: The report supports specific enzymatic and chromatin-complex annotations for
        HDAC1 rather than generic binding or weakly localized annotations.
- term:
    id: GO:0005634
    label: nucleus
  evidence_type: IDA
  original_reference_id: PMID:22770845
  review:
    summary: HDAC1 is predominantly nuclear, consistent with its function in chromatin modification
      and transcriptional regulation. Nuclear localization confirmed by multiple methods including
      immunofluorescence (PMID:11115394).
    action: ACCEPT
    reason: Nuclear localization is a well-established core feature of HDAC1. It is a Class I HDAC
      that is predominantly nuclear.
    supported_by:
    - reference_id: PMID:22770845
      supporting_text: key interactions (Ring1b, Mbd3, Hdac1, and Oct4) are not the result of
        proximity at promoters, as they were stable in the presence of ethidium bromide
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD,
        Sin3, CoREST, and related chromatin-repressor complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: Class I HDACs, including HDAC1, are predominantly or exclusively nuclear,
        consistent with chromatin accessibility and transcriptional control roles.
- term:
    id: GO:1990841
    label: promoter-specific chromatin binding
  evidence_type: IDA
  original_reference_id: PMID:22770845
  review:
    summary: HDAC1 binds to specific promoter regions as shown by ChIP experiments. HDAC1 occupancy
      has been demonstrated at the Per2 promoter E-box (PMID:21960634) and other gene promoters.
    action: ACCEPT
    reason: Directly supported by ChIP experiments showing HDAC1 at specific promoters.
    supported_by:
    - reference_id: PMID:21960634
      supporting_text: Chromatin immunoprecipitation followed by quantitative PCR (ChIP-QPCR)
        analysis from mouse liver chromatin showed a nearly constant HDAC1 occupancy at the Per2
        E-box
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD,
        Sin3, CoREST, and related chromatin-repressor complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein
        corepressor complexes, especially SIN3, NuRD, and CoREST.
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:21454521
  review:
    summary: Protein binding annotation based on physical interaction evidence from PMID:21454521.
      HDAC1 is known to interact with a very large number of proteins as it functions within
      multiple co-repressor complexes (NuRD, SIN3, CoREST) and binds many transcription factors.
    action: REMOVE
    reason: Per curation guidelines, protein binding (GO:0005515) is uninformative and should be
      replaced with more specific molecular function terms. HDAC1 physically interacts with many
      proteins, but this generic term does not convey functional information. More specific
      annotations such as histone deacetylase binding, transcription corepressor binding, NF-kappaB
      binding, and DNA-binding transcription factor binding are already present.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: Generic protein binding and weakly mechanistic interaction annotations are
        less informative than HDAC1 deacetylase activity and defined corepressor-complex membership.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylases act via the formation of large multiprotein complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: The report supports specific enzymatic and chromatin-complex annotations for
        HDAC1 rather than generic binding or weakly localized annotations.
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:24335282
  review:
    summary: Protein binding annotation based on physical interaction evidence from PMID:24335282.
      HDAC1 is known to interact with a very large number of proteins as it functions within
      multiple co-repressor complexes (NuRD, SIN3, CoREST) and binds many transcription factors.
    action: REMOVE
    reason: Per curation guidelines, protein binding (GO:0005515) is uninformative and should be
      replaced with more specific molecular function terms. HDAC1 physically interacts with many
      proteins, but this generic term does not convey functional information. More specific
      annotations such as histone deacetylase binding, transcription corepressor binding, NF-kappaB
      binding, and DNA-binding transcription factor binding are already present.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: Generic protein binding and weakly mechanistic interaction annotations are
        less informative than HDAC1 deacetylase activity and defined corepressor-complex membership.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylases act via the formation of large multiprotein complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: The report supports specific enzymatic and chromatin-complex annotations for
        HDAC1 rather than generic binding or weakly localized annotations.
- term:
    id: GO:0004407
    label: histone deacetylase activity
  evidence_type: IDA
  original_reference_id: PMID:21960634
  review:
    summary: HDAC1 is a zinc-dependent histone deacetylase (EC 3.5.1.98) that catalyzes removal of
      acetyl groups from N-acetyl-lysine residues on histones H2A, H2B, H3, and H4. This is the core
      enzymatic function of HDAC1, well established by direct biochemical assays (PMID:10615135,
      PMID:21960634, PMID:30279482).
    action: ACCEPT
    reason: Histone deacetylase activity is the primary enzymatic function of HDAC1, supported by
      multiple direct experimental studies demonstrating catalytic activity on histone substrates.
    supported_by:
    - reference_id: PMID:10615135
      supporting_text: Here we show that Dnmt1 is itself associated with histone deacetylase
        activity in vivo
    - reference_id: PMID:30279482
      supporting_text: A ternary complex of HDAC1/CoREST1/LSD1 is able to hydrolyse both histone H3
        Lys18-acetyl (H3K18ac) and H3 Lys18-crotonyl (H3K18cr) peptide substrates
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD,
        Sin3, CoREST, and related chromatin-repressor complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: HDAC1 is a class I Zn2+-dependent histone/protein deacetylase that removes
        acetyl groups from lysine residues on histone tails and non-histone proteins.
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:21960634
  review:
    summary: Protein binding annotation based on physical interaction evidence from PMID:21960634.
      HDAC1 is known to interact with a very large number of proteins as it functions within
      multiple co-repressor complexes (NuRD, SIN3, CoREST) and binds many transcription factors.
    action: REMOVE
    reason: Per curation guidelines, protein binding (GO:0005515) is uninformative and should be
      replaced with more specific molecular function terms. HDAC1 physically interacts with many
      proteins, but this generic term does not convey functional information. More specific
      annotations such as histone deacetylase binding, transcription corepressor binding, NF-kappaB
      binding, and DNA-binding transcription factor binding are already present.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: Generic protein binding and weakly mechanistic interaction annotations are
        less informative than HDAC1 deacetylase activity and defined corepressor-complex membership.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylases act via the formation of large multiprotein complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: The report supports specific enzymatic and chromatin-complex annotations for
        HDAC1 rather than generic binding or weakly localized annotations.
- term:
    id: GO:0045892
    label: negative regulation of DNA-templated transcription
  evidence_type: IDA
  original_reference_id: PMID:21960634
  review:
    summary: HDAC1 negatively regulates DNA-templated transcription through its histone deacetylase
      activity as part of co-repressor complexes.
    action: ACCEPT
    reason: Transcriptional repression is a core function of HDAC1. Well supported by extensive
      literature.
    supported_by:
    - reference_id: PMID:21960634
      supporting_text: JARID1a increased histone acetylation by inhibiting histone deacetylase 1
        function and enhanced transcription by CLOCK-BMAL1 in a demethylase-independent manner
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD,
        Sin3, CoREST, and related chromatin-repressor complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein
        corepressor complexes, especially SIN3, NuRD, and CoREST.
- term:
    id: GO:0043124
    label: negative regulation of canonical NF-kappaB signal transduction
  evidence_type: IGI
  original_reference_id: PMID:19805123
  review:
    summary: HDAC1 negatively regulates NF-kappaB signaling by deacetylating RelA/p65 at Lys-310.
    action: KEEP_AS_NON_CORE
    reason: Well-characterized regulatory mechanism but represents one of many signaling pathways
      where HDAC1 functions.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 has many developmental and signaling consequences through chromatin
        deacetylation; these are non-core outputs of the core enzymatic function.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylation gives a tag for epigenetic repression and plays an
        important role in transcriptional regulation, cell cycle progression and developmental
        events.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: The report supports HDAC1 as a chromatin deacetylase whose developmental,
        signaling, cell-cycle, DNA-damage, and pathway phenotypes are context-specific downstream
        outputs.
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:15226430
  review:
    summary: Protein binding annotation based on physical interaction evidence from PMID:15226430.
      HDAC1 is known to interact with a very large number of proteins as it functions within
      multiple co-repressor complexes (NuRD, SIN3, CoREST) and binds many transcription factors.
    action: REMOVE
    reason: Per curation guidelines, protein binding (GO:0005515) is uninformative and should be
      replaced with more specific molecular function terms. HDAC1 physically interacts with many
      proteins, but this generic term does not convey functional information. More specific
      annotations such as histone deacetylase binding, transcription corepressor binding, NF-kappaB
      binding, and DNA-binding transcription factor binding are already present.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: Generic protein binding and weakly mechanistic interaction annotations are
        less informative than HDAC1 deacetylase activity and defined corepressor-complex membership.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylases act via the formation of large multiprotein complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: The report supports specific enzymatic and chromatin-complex annotations for
        HDAC1 rather than generic binding or weakly localized annotations.
- term:
    id: GO:0032922
    label: circadian regulation of gene expression
  evidence_type: IDA
  original_reference_id: PMID:15226430
  review:
    summary: HDAC1 participates in circadian gene regulation. Recruited to E-box elements at
      Per1/Per2 promoters by CRY1 and CIART/CHRONO (PMID:15226430, PMID:24736997).
    action: KEEP_AS_NON_CORE
    reason: HDAC1 has a documented role in circadian gene regulation but this is one of many
      biological contexts where it functions as a corepressor.
    supported_by:
    - reference_id: PMID:15226430
      supporting_text: Mouse CRY1 (mCRY1) repressed transcription with HDACs and mSin3B, which was
        relieved by the HDAC inhibitor trichostatin A (TSA)
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 has many developmental and signaling consequences through chromatin
        deacetylation; these are non-core outputs of the core enzymatic function.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: The report supports HDAC1 as a chromatin deacetylase whose developmental,
        signaling, cell-cycle, DNA-damage, and pathway phenotypes are context-specific downstream
        outputs.
- term:
    id: GO:0007623
    label: circadian rhythm
  evidence_type: IDA
  original_reference_id: PMID:24736997
  review:
    summary: HDAC1 is involved in circadian rhythm regulation by mediating histone deacetylation at
      circadian gene promoters.
    action: KEEP_AS_NON_CORE
    reason: HDAC1 participates in circadian clock regulation but this is one of many biological
      contexts where it serves as a corepressor.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 has many developmental and signaling consequences through chromatin
        deacetylation; these are non-core outputs of the core enzymatic function.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylation gives a tag for epigenetic repression and plays an
        important role in transcriptional regulation, cell cycle progression and developmental
        events.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: The report supports HDAC1 as a chromatin deacetylase whose developmental,
        signaling, cell-cycle, DNA-damage, and pathway phenotypes are context-specific downstream
        outputs.
- term:
    id: GO:0000976
    label: transcription cis-regulatory region binding
  evidence_type: IDA
  original_reference_id: PMID:24413057
  review:
    summary: HDAC1 is recruited to E-box-containing circadian promoters as part of PER-associated
      repressor complexes, but the evidence shows promoter occupancy/recruitment rather than direct
      cis-regulatory DNA binding by HDAC1.
    action: MODIFY
    reason: Replace the direct DNA-binding term with promoter-specific chromatin binding, which
      better matches the ChIP/recruitment evidence.
    proposed_replacement_terms:
    - id: GO:1990841
      label: promoter-specific chromatin binding
    supported_by:
    - reference_id: PMID:24413057
      supporting_text: PER complexes containing HDAC1 or HP1gamma-Suv39h appeared to be physically
        separable. Circadian clock negative feedback by the PER complex thus involves dynamic,
        ordered recruitment of repressive chromatin modifiers to DNA-bound Clock-Bmal1.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein
        corepressor complexes, especially SIN3, NuRD, and CoREST.
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:24413057
  review:
    summary: Protein binding annotation based on physical interaction evidence from PMID:24413057.
      HDAC1 is known to interact with a very large number of proteins as it functions within
      multiple co-repressor complexes (NuRD, SIN3, CoREST) and binds many transcription factors.
    action: REMOVE
    reason: Per curation guidelines, protein binding (GO:0005515) is uninformative and should be
      replaced with more specific molecular function terms. HDAC1 physically interacts with many
      proteins, but this generic term does not convey functional information. More specific
      annotations such as histone deacetylase binding, transcription corepressor binding, NF-kappaB
      binding, and DNA-binding transcription factor binding are already present.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: Generic protein binding and weakly mechanistic interaction annotations are
        less informative than HDAC1 deacetylase activity and defined corepressor-complex membership.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylases act via the formation of large multiprotein complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: The report supports specific enzymatic and chromatin-complex annotations for
        HDAC1 rather than generic binding or weakly localized annotations.
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:21931736
  review:
    summary: Protein binding annotation based on physical interaction evidence from PMID:21931736.
      HDAC1 is known to interact with a very large number of proteins as it functions within
      multiple co-repressor complexes (NuRD, SIN3, CoREST) and binds many transcription factors.
    action: REMOVE
    reason: Per curation guidelines, protein binding (GO:0005515) is uninformative and should be
      replaced with more specific molecular function terms. HDAC1 physically interacts with many
      proteins, but this generic term does not convey functional information. More specific
      annotations such as histone deacetylase binding, transcription corepressor binding, NF-kappaB
      binding, and DNA-binding transcription factor binding are already present.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: Generic protein binding and weakly mechanistic interaction annotations are
        less informative than HDAC1 deacetylase activity and defined corepressor-complex membership.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylases act via the formation of large multiprotein complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: The report supports specific enzymatic and chromatin-complex annotations for
        HDAC1 rather than generic binding or weakly localized annotations.
- term:
    id: GO:0035851
    label: Krueppel-associated box domain binding
  evidence_type: IPI
  original_reference_id: PMID:21177534
  review:
    summary: HDAC1 binds to KRAB domain-containing zinc finger proteins. Demonstrated for ZNF431
      (PMID:21177534), which recruits HDAC1 via its KRAB domain to repress target genes.
    action: ACCEPT
    reason: KRAB-ZFP interaction with HDAC1 is directly demonstrated by co-immunoprecipitation
      (PMID:21177534).
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD,
        Sin3, CoREST, and related chromatin-repressor complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylase that catalyzes the deacetylation of lysine residues on
        the N-terminal part of the core histones.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein
        corepressor complexes, especially SIN3, NuRD, and CoREST.
- term:
    id: GO:0005654
    label: nucleoplasm
  evidence_type: TAS
  original_reference_id: Reactome:R-MMU-573336
  review:
    summary: HDAC1 is localized to the nucleoplasm where it functions as part of chromatin-modifying
      complexes.
    action: ACCEPT
    reason: Nucleoplasm localization is consistent with HDAC1 function in chromatin modification.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD,
        Sin3, CoREST, and related chromatin-repressor complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylase that catalyzes the deacetylation of lysine residues on
        the N-terminal part of the core histones.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: Class I HDACs, including HDAC1, are predominantly or exclusively nuclear,
        consistent with chromatin accessibility and transcriptional control roles.
- term:
    id: GO:0005654
    label: nucleoplasm
  evidence_type: TAS
  original_reference_id: Reactome:R-MMU-573376
  review:
    summary: HDAC1 is localized to the nucleoplasm where it functions as part of chromatin-modifying
      complexes.
    action: ACCEPT
    reason: Nucleoplasm localization is consistent with HDAC1 function in chromatin modification.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD,
        Sin3, CoREST, and related chromatin-repressor complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylase that catalyzes the deacetylation of lysine residues on
        the N-terminal part of the core histones.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: Class I HDACs, including HDAC1, are predominantly or exclusively nuclear,
        consistent with chromatin accessibility and transcriptional control roles.
- term:
    id: GO:0005654
    label: nucleoplasm
  evidence_type: TAS
  original_reference_id: Reactome:R-MMU-573383
  review:
    summary: HDAC1 is localized to the nucleoplasm where it functions as part of chromatin-modifying
      complexes.
    action: ACCEPT
    reason: Nucleoplasm localization is consistent with HDAC1 function in chromatin modification.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD,
        Sin3, CoREST, and related chromatin-repressor complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylase that catalyzes the deacetylation of lysine residues on
        the N-terminal part of the core histones.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: Class I HDACs, including HDAC1, are predominantly or exclusively nuclear,
        consistent with chromatin accessibility and transcriptional control roles.
- term:
    id: GO:0005654
    label: nucleoplasm
  evidence_type: TAS
  original_reference_id: Reactome:R-MMU-8978954
  review:
    summary: HDAC1 is localized to the nucleoplasm where it functions as part of chromatin-modifying
      complexes.
    action: ACCEPT
    reason: Nucleoplasm localization is consistent with HDAC1 function in chromatin modification.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD,
        Sin3, CoREST, and related chromatin-repressor complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylase that catalyzes the deacetylation of lysine residues on
        the N-terminal part of the core histones.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: Class I HDACs, including HDAC1, are predominantly or exclusively nuclear,
        consistent with chromatin accessibility and transcriptional control roles.
- term:
    id: GO:0005654
    label: nucleoplasm
  evidence_type: TAS
  original_reference_id: Reactome:R-MMU-8978970
  review:
    summary: HDAC1 is localized to the nucleoplasm where it functions as part of chromatin-modifying
      complexes.
    action: ACCEPT
    reason: Nucleoplasm localization is consistent with HDAC1 function in chromatin modification.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD,
        Sin3, CoREST, and related chromatin-repressor complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylase that catalyzes the deacetylation of lysine residues on
        the N-terminal part of the core histones.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: Class I HDACs, including HDAC1, are predominantly or exclusively nuclear,
        consistent with chromatin accessibility and transcriptional control roles.
- term:
    id: GO:0005654
    label: nucleoplasm
  evidence_type: TAS
  original_reference_id: Reactome:R-MMU-8978980
  review:
    summary: HDAC1 is localized to the nucleoplasm where it functions as part of chromatin-modifying
      complexes.
    action: ACCEPT
    reason: Nucleoplasm localization is consistent with HDAC1 function in chromatin modification.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD,
        Sin3, CoREST, and related chromatin-repressor complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylase that catalyzes the deacetylation of lysine residues on
        the N-terminal part of the core histones.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: Class I HDACs, including HDAC1, are predominantly or exclusively nuclear,
        consistent with chromatin accessibility and transcriptional control roles.
- term:
    id: GO:0005654
    label: nucleoplasm
  evidence_type: TAS
  original_reference_id: Reactome:R-MMU-8978989
  review:
    summary: HDAC1 is localized to the nucleoplasm where it functions as part of chromatin-modifying
      complexes.
    action: ACCEPT
    reason: Nucleoplasm localization is consistent with HDAC1 function in chromatin modification.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD,
        Sin3, CoREST, and related chromatin-repressor complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylase that catalyzes the deacetylation of lysine residues on
        the N-terminal part of the core histones.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: Class I HDACs, including HDAC1, are predominantly or exclusively nuclear,
        consistent with chromatin accessibility and transcriptional control roles.
- term:
    id: GO:0005654
    label: nucleoplasm
  evidence_type: TAS
  original_reference_id: Reactome:R-MMU-9006133
  review:
    summary: HDAC1 is localized to the nucleoplasm where it functions as part of chromatin-modifying
      complexes.
    action: ACCEPT
    reason: Nucleoplasm localization is consistent with HDAC1 function in chromatin modification.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD,
        Sin3, CoREST, and related chromatin-repressor complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylase that catalyzes the deacetylation of lysine residues on
        the N-terminal part of the core histones.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: Class I HDACs, including HDAC1, are predominantly or exclusively nuclear,
        consistent with chromatin accessibility and transcriptional control roles.
- term:
    id: GO:0005654
    label: nucleoplasm
  evidence_type: TAS
  original_reference_id: Reactome:R-MMU-9017958
  review:
    summary: HDAC1 is localized to the nucleoplasm where it functions as part of chromatin-modifying
      complexes.
    action: ACCEPT
    reason: Nucleoplasm localization is consistent with HDAC1 function in chromatin modification.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD,
        Sin3, CoREST, and related chromatin-repressor complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylase that catalyzes the deacetylation of lysine residues on
        the N-terminal part of the core histones.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: Class I HDACs, including HDAC1, are predominantly or exclusively nuclear,
        consistent with chromatin accessibility and transcriptional control roles.
- term:
    id: GO:0005654
    label: nucleoplasm
  evidence_type: TAS
  original_reference_id: Reactome:R-MMU-9625109
  review:
    summary: HDAC1 is localized to the nucleoplasm where it functions as part of chromatin-modifying
      complexes.
    action: ACCEPT
    reason: Nucleoplasm localization is consistent with HDAC1 function in chromatin modification.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD,
        Sin3, CoREST, and related chromatin-repressor complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylase that catalyzes the deacetylation of lysine residues on
        the N-terminal part of the core histones.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: Class I HDACs, including HDAC1, are predominantly or exclusively nuclear,
        consistent with chromatin accessibility and transcriptional control roles.
- term:
    id: GO:0005654
    label: nucleoplasm
  evidence_type: TAS
  original_reference_id: Reactome:R-MMU-9727502
  review:
    summary: HDAC1 is localized to the nucleoplasm where it functions as part of chromatin-modifying
      complexes.
    action: ACCEPT
    reason: Nucleoplasm localization is consistent with HDAC1 function in chromatin modification.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD,
        Sin3, CoREST, and related chromatin-repressor complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylase that catalyzes the deacetylation of lysine residues on
        the N-terminal part of the core histones.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: Class I HDACs, including HDAC1, are predominantly or exclusively nuclear,
        consistent with chromatin accessibility and transcriptional control roles.
- term:
    id: GO:0005654
    label: nucleoplasm
  evidence_type: TAS
  original_reference_id: Reactome:R-MMU-9844527
  review:
    summary: HDAC1 is localized to the nucleoplasm where it functions as part of chromatin-modifying
      complexes.
    action: ACCEPT
    reason: Nucleoplasm localization is consistent with HDAC1 function in chromatin modification.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD,
        Sin3, CoREST, and related chromatin-repressor complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylase that catalyzes the deacetylation of lysine residues on
        the N-terminal part of the core histones.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: Class I HDACs, including HDAC1, are predominantly or exclusively nuclear,
        consistent with chromatin accessibility and transcriptional control roles.
- term:
    id: GO:0005654
    label: nucleoplasm
  evidence_type: TAS
  original_reference_id: Reactome:R-MMU-9845305
  review:
    summary: HDAC1 is localized to the nucleoplasm where it functions as part of chromatin-modifying
      complexes.
    action: ACCEPT
    reason: Nucleoplasm localization is consistent with HDAC1 function in chromatin modification.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD,
        Sin3, CoREST, and related chromatin-repressor complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylase that catalyzes the deacetylation of lysine residues on
        the N-terminal part of the core histones.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: Class I HDACs, including HDAC1, are predominantly or exclusively nuclear,
        consistent with chromatin accessibility and transcriptional control roles.
- term:
    id: GO:0005654
    label: nucleoplasm
  evidence_type: TAS
  original_reference_id: Reactome:R-NUL-573373
  review:
    summary: HDAC1 is localized to the nucleoplasm where it functions as part of chromatin-modifying
      complexes.
    action: ACCEPT
    reason: Nucleoplasm localization is consistent with HDAC1 function in chromatin modification.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD,
        Sin3, CoREST, and related chromatin-repressor complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylase that catalyzes the deacetylation of lysine residues on
        the N-terminal part of the core histones.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: Class I HDACs, including HDAC1, are predominantly or exclusively nuclear,
        consistent with chromatin accessibility and transcriptional control roles.
- term:
    id: GO:0005654
    label: nucleoplasm
  evidence_type: TAS
  original_reference_id: Reactome:R-NUL-573385
  review:
    summary: HDAC1 is localized to the nucleoplasm where it functions as part of chromatin-modifying
      complexes.
    action: ACCEPT
    reason: Nucleoplasm localization is consistent with HDAC1 function in chromatin modification.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD,
        Sin3, CoREST, and related chromatin-repressor complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylase that catalyzes the deacetylation of lysine residues on
        the N-terminal part of the core histones.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: Class I HDACs, including HDAC1, are predominantly or exclusively nuclear,
        consistent with chromatin accessibility and transcriptional control roles.
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:11923873
  review:
    summary: Protein binding annotation based on physical interaction evidence from PMID:11923873.
      HDAC1 is known to interact with a very large number of proteins as it functions within
      multiple co-repressor complexes (NuRD, SIN3, CoREST) and binds many transcription factors.
    action: REMOVE
    reason: Per curation guidelines, protein binding (GO:0005515) is uninformative and should be
      replaced with more specific molecular function terms. HDAC1 physically interacts with many
      proteins, but this generic term does not convey functional information. More specific
      annotations such as histone deacetylase binding, transcription corepressor binding, NF-kappaB
      binding, and DNA-binding transcription factor binding are already present.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: Generic protein binding and weakly mechanistic interaction annotations are
        less informative than HDAC1 deacetylase activity and defined corepressor-complex membership.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylases act via the formation of large multiprotein complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: The report supports specific enzymatic and chromatin-complex annotations for
        HDAC1 rather than generic binding or weakly localized annotations.
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:11115394
  review:
    summary: Protein binding annotation based on physical interaction evidence from PMID:11115394.
      HDAC1 is known to interact with a very large number of proteins as it functions within
      multiple co-repressor complexes (NuRD, SIN3, CoREST) and binds many transcription factors.
    action: REMOVE
    reason: Per curation guidelines, protein binding (GO:0005515) is uninformative and should be
      replaced with more specific molecular function terms. HDAC1 physically interacts with many
      proteins, but this generic term does not convey functional information. More specific
      annotations such as histone deacetylase binding, transcription corepressor binding, NF-kappaB
      binding, and DNA-binding transcription factor binding are already present.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: Generic protein binding and weakly mechanistic interaction annotations are
        less informative than HDAC1 deacetylase activity and defined corepressor-complex membership.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylases act via the formation of large multiprotein complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: The report supports specific enzymatic and chromatin-complex annotations for
        HDAC1 rather than generic binding or weakly localized annotations.
- term:
    id: GO:2001243
    label: negative regulation of intrinsic apoptotic signaling pathway
  evidence_type: IGI
  original_reference_id: PMID:21093383
  review:
    summary: HDAC1 negatively regulates the intrinsic apoptotic signaling pathway. HDAC1/2 double
      knockout in epidermis leads to increased apoptosis (PMID:21093383).
    action: ACCEPT
    reason: PMID:21093383 directly links HDAC1/2 chromatin repression to suppression of p53
      activity in epidermal progenitors; this supports negative regulation of intrinsic
      apoptotic signaling as a direct output of HDAC1-containing repressor complexes.
    supported_by:
    - reference_id: PMID:21093383
      supporting_text: Mutant embryos display increased levels of acetylated p53, which opposes p63 functions
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 can deacetylate p53, reducing p53 activity and thereby modulating
        apoptosis and DNA damage responses.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylation gives a tag for epigenetic repression and plays an
        important role in transcriptional regulation, cell cycle progression and developmental
        events.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein
        corepressor complexes.
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:21937600
  review:
    summary: Protein binding annotation based on physical interaction evidence from PMID:21937600.
      HDAC1 is known to interact with a very large number of proteins as it functions within
      multiple co-repressor complexes (NuRD, SIN3, CoREST) and binds many transcription factors.
    action: REMOVE
    reason: Per curation guidelines, protein binding (GO:0005515) is uninformative and should be
      replaced with more specific molecular function terms. HDAC1 physically interacts with many
      proteins, but this generic term does not convey functional information. More specific
      annotations such as histone deacetylase binding, transcription corepressor binding, NF-kappaB
      binding, and DNA-binding transcription factor binding are already present.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: Generic protein binding and weakly mechanistic interaction annotations are
        less informative than HDAC1 deacetylase activity and defined corepressor-complex membership.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylases act via the formation of large multiprotein complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: The report supports specific enzymatic and chromatin-complex annotations for
        HDAC1 rather than generic binding or weakly localized annotations.
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:19501046
  review:
    summary: Protein binding annotation based on physical interaction evidence from PMID:19501046.
      HDAC1 is known to interact with a very large number of proteins as it functions within
      multiple co-repressor complexes (NuRD, SIN3, CoREST) and binds many transcription factors.
    action: REMOVE
    reason: Per curation guidelines, protein binding (GO:0005515) is uninformative and should be
      replaced with more specific molecular function terms. HDAC1 physically interacts with many
      proteins, but this generic term does not convey functional information. More specific
      annotations such as histone deacetylase binding, transcription corepressor binding, NF-kappaB
      binding, and DNA-binding transcription factor binding are already present.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: Generic protein binding and weakly mechanistic interaction annotations are
        less informative than HDAC1 deacetylase activity and defined corepressor-complex membership.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylases act via the formation of large multiprotein complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: The report supports specific enzymatic and chromatin-complex annotations for
        HDAC1 rather than generic binding or weakly localized annotations.
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:11836251
  review:
    summary: Protein binding annotation based on physical interaction evidence from PMID:11836251.
      HDAC1 is known to interact with a very large number of proteins as it functions within
      multiple co-repressor complexes (NuRD, SIN3, CoREST) and binds many transcription factors.
    action: REMOVE
    reason: Per curation guidelines, protein binding (GO:0005515) is uninformative and should be
      replaced with more specific molecular function terms. HDAC1 physically interacts with many
      proteins, but this generic term does not convey functional information. More specific
      annotations such as histone deacetylase binding, transcription corepressor binding, NF-kappaB
      binding, and DNA-binding transcription factor binding are already present.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: Generic protein binding and weakly mechanistic interaction annotations are
        less informative than HDAC1 deacetylase activity and defined corepressor-complex membership.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylases act via the formation of large multiprotein complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: The report supports specific enzymatic and chromatin-complex annotations for
        HDAC1 rather than generic binding or weakly localized annotations.
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:22242125
  review:
    summary: Protein binding annotation based on physical interaction evidence from PMID:22242125.
      HDAC1 is known to interact with a very large number of proteins as it functions within
      multiple co-repressor complexes (NuRD, SIN3, CoREST) and binds many transcription factors.
    action: REMOVE
    reason: Per curation guidelines, protein binding (GO:0005515) is uninformative and should be
      replaced with more specific molecular function terms. HDAC1 physically interacts with many
      proteins, but this generic term does not convey functional information. More specific
      annotations such as histone deacetylase binding, transcription corepressor binding, NF-kappaB
      binding, and DNA-binding transcription factor binding are already present.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: Generic protein binding and weakly mechanistic interaction annotations are
        less informative than HDAC1 deacetylase activity and defined corepressor-complex membership.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylases act via the formation of large multiprotein complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: The report supports specific enzymatic and chromatin-complex annotations for
        HDAC1 rather than generic binding or weakly localized annotations.
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:22075476
  review:
    summary: Protein binding annotation based on physical interaction evidence from PMID:22075476.
      HDAC1 is known to interact with a very large number of proteins as it functions within
      multiple co-repressor complexes (NuRD, SIN3, CoREST) and binds many transcription factors.
    action: REMOVE
    reason: Per curation guidelines, protein binding (GO:0005515) is uninformative and should be
      replaced with more specific molecular function terms. HDAC1 physically interacts with many
      proteins, but this generic term does not convey functional information. More specific
      annotations such as histone deacetylase binding, transcription corepressor binding, NF-kappaB
      binding, and DNA-binding transcription factor binding are already present.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: Generic protein binding and weakly mechanistic interaction annotations are
        less informative than HDAC1 deacetylase activity and defined corepressor-complex membership.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylases act via the formation of large multiprotein complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: The report supports specific enzymatic and chromatin-complex annotations for
        HDAC1 rather than generic binding or weakly localized annotations.
- term:
    id: GO:0016581
    label: NuRD complex
  evidence_type: IDA
  original_reference_id: PMID:22075476
  review:
    summary: HDAC1 is a core catalytic subunit of the NuRD (nucleosome remodeling and deacetylase)
      complex. Proteomic studies show approximately 49% of cellular HDAC1 in ESCs is in the NuRD
      complex (deep research review). Well supported by mass spectrometry identification
      (PMID:27806305) and multiple interaction studies.
    action: ACCEPT
    reason: NuRD complex membership is a core aspect of HDAC1 function. HDAC1 serves as the
      catalytic deacetylase subunit within NuRD. Extensively validated by proteomics and
      co-immunoprecipitation studies.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD,
        Sin3, CoREST, and related chromatin-repressor complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylase that catalyzes the deacetylation of lysine residues on
        the N-terminal part of the core histones.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein
        corepressor complexes, especially SIN3, NuRD, and CoREST.
- term:
    id: GO:0005634
    label: nucleus
  evidence_type: IDA
  original_reference_id: PMID:20720167
  review:
    summary: HDAC1 is predominantly nuclear, consistent with its function in chromatin modification
      and transcriptional regulation. Nuclear localization confirmed by multiple methods including
      immunofluorescence (PMID:11115394).
    action: ACCEPT
    reason: Nuclear localization is a well-established core feature of HDAC1. It is a Class I HDAC
      that is predominantly nuclear.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD,
        Sin3, CoREST, and related chromatin-repressor complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylase that catalyzes the deacetylation of lysine residues on
        the N-terminal part of the core histones.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: Class I HDACs, including HDAC1, are predominantly or exclusively nuclear,
        consistent with chromatin accessibility and transcriptional control roles.
- term:
    id: GO:0005634
    label: nucleus
  evidence_type: IDA
  original_reference_id: PMID:21874024
  review:
    summary: HDAC1 is predominantly nuclear, consistent with its function in chromatin modification
      and transcriptional regulation. Nuclear localization confirmed by multiple methods including
      immunofluorescence (PMID:11115394).
    action: ACCEPT
    reason: Nuclear localization is a well-established core feature of HDAC1. It is a Class I HDAC
      that is predominantly nuclear.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 is predominantly a nuclear protein, consistent with its role in
        modifying chromatin
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: Class I HDACs, including HDAC1, are predominantly or exclusively nuclear,
        consistent with chromatin accessibility and transcriptional control roles.
- term:
    id: GO:0061629
    label: RNA polymerase II-specific DNA-binding transcription factor binding
  evidence_type: IPI
  original_reference_id: PMID:19235719
  review:
    summary: HDAC1 binds RNA polymerase II-specific transcription factors that recruit it to target
      genes for transcriptional repression.
    action: ACCEPT
    reason: This is a more specific version of DNA-binding transcription factor binding, appropriate
      given that HDAC1 primarily regulates RNA pol II-transcribed genes through interactions with
      pol II-specific TFs.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD,
        Sin3, CoREST, and related chromatin-repressor complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylase that catalyzes the deacetylation of lysine residues on
        the N-terminal part of the core histones.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein
        corepressor complexes, especially SIN3, NuRD, and CoREST.
- term:
    id: GO:0005667
    label: transcription regulator complex
  evidence_type: IDA
  original_reference_id: PMID:17707228
  review:
    summary: HDAC1 is a component of transcription regulator complexes. This is a broad parent term
      for the more specific NuRD, SIN3, and CoREST complexes.
    action: ACCEPT
    reason: Correct but very general. HDAC1 does function in transcription regulator complexes. More
      specific complex annotations (NuRD, SIN3) are also present.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD,
        Sin3, CoREST, and related chromatin-repressor complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylase that catalyzes the deacetylation of lysine residues on
        the N-terminal part of the core histones.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein
        corepressor complexes, especially SIN3, NuRD, and CoREST.
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:20599664
  review:
    summary: Protein binding annotation based on physical interaction evidence from PMID:20599664.
      HDAC1 is known to interact with a very large number of proteins as it functions within
      multiple co-repressor complexes (NuRD, SIN3, CoREST) and binds many transcription factors.
    action: REMOVE
    reason: Per curation guidelines, protein binding (GO:0005515) is uninformative and should be
      replaced with more specific molecular function terms. HDAC1 physically interacts with many
      proteins, but this generic term does not convey functional information. More specific
      annotations such as histone deacetylase binding, transcription corepressor binding, NF-kappaB
      binding, and DNA-binding transcription factor binding are already present.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: Generic protein binding and weakly mechanistic interaction annotations are
        less informative than HDAC1 deacetylase activity and defined corepressor-complex membership.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylases act via the formation of large multiprotein complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: The report supports specific enzymatic and chromatin-complex annotations for
        HDAC1 rather than generic binding or weakly localized annotations.
- term:
    id: GO:0003682
    label: chromatin binding
  evidence_type: IDA
  original_reference_id: PMID:17905753
  review:
    summary: HDAC1 binds chromatin as part of its function in co-repressor complexes. ChIP
      experiments have confirmed HDAC1 occupancy at promoters and other regulatory regions.
    action: ACCEPT
    reason: Chromatin binding is well supported by extensive ChIP-seq and ChIP-qPCR data showing
      HDAC1 occupancy at promoters, enhancers, and heterochromatic regions.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD,
        Sin3, CoREST, and related chromatin-repressor complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylase that catalyzes the deacetylation of lysine residues on
        the N-terminal part of the core histones.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein
        corepressor complexes, especially SIN3, NuRD, and CoREST.
- term:
    id: GO:0045892
    label: negative regulation of DNA-templated transcription
  evidence_type: IDA
  original_reference_id: PMID:9271381
  review:
    summary: HDAC1 negatively regulates DNA-templated transcription through its histone deacetylase
      activity as part of co-repressor complexes.
    action: ACCEPT
    reason: Transcriptional repression is a core function of HDAC1. Well supported by extensive
      literature.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD,
        Sin3, CoREST, and related chromatin-repressor complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylase that catalyzes the deacetylation of lysine residues on
        the N-terminal part of the core histones.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein
        corepressor complexes, especially SIN3, NuRD, and CoREST.
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:19503085
  review:
    summary: Protein binding annotation based on physical interaction evidence from PMID:19503085.
      HDAC1 is known to interact with a very large number of proteins as it functions within
      multiple co-repressor complexes (NuRD, SIN3, CoREST) and binds many transcription factors.
    action: REMOVE
    reason: Per curation guidelines, protein binding (GO:0005515) is uninformative and should be
      replaced with more specific molecular function terms. HDAC1 physically interacts with many
      proteins, but this generic term does not convey functional information. More specific
      annotations such as histone deacetylase binding, transcription corepressor binding, NF-kappaB
      binding, and DNA-binding transcription factor binding are already present.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: Generic protein binding and weakly mechanistic interaction annotations are
        less informative than HDAC1 deacetylase activity and defined corepressor-complex membership.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylases act via the formation of large multiprotein complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: The report supports specific enzymatic and chromatin-complex annotations for
        HDAC1 rather than generic binding or weakly localized annotations.
- term:
    id: GO:0048714
    label: positive regulation of oligodendrocyte differentiation
  evidence_type: IGI
  original_reference_id: PMID:19503085
  review:
    summary: HDAC1/2 positively regulate oligodendrocyte differentiation, likely by repressing
      inhibitors of myelination (PMID:19503085).
    action: KEEP_AS_NON_CORE
    reason: Cell-type-specific developmental process rather than a core function.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 has many developmental and signaling consequences through chromatin
        deacetylation; these are non-core outputs of the core enzymatic function.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylation gives a tag for epigenetic repression and plays an
        important role in transcriptional regulation, cell cycle progression and developmental
        events.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: The report supports HDAC1 as a chromatin deacetylase whose developmental,
        signaling, cell-cycle, DNA-damage, and pathway phenotypes are context-specific downstream
        outputs.
- term:
    id: GO:0090090
    label: negative regulation of canonical Wnt signaling pathway
  evidence_type: IGI
  original_reference_id: PMID:19503085
  review:
    summary: HDAC1/2 negatively regulate canonical Wnt signaling by deacetylating histones at Wnt
      target gene promoters. Demonstrated in neural development.
    action: KEEP_AS_NON_CORE
    reason: Well-supported role in neural development but represents a downstream biological
      consequence rather than a core molecular function.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 has many developmental and signaling consequences through chromatin
        deacetylation; these are non-core outputs of the core enzymatic function.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylation gives a tag for epigenetic repression and plays an
        important role in transcriptional regulation, cell cycle progression and developmental
        events.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: The report supports HDAC1 as a chromatin deacetylase whose developmental,
        signaling, cell-cycle, DNA-damage, and pathway phenotypes are context-specific downstream
        outputs.
- term:
    id: GO:0016581
    label: NuRD complex
  evidence_type: IDA
  original_reference_id: PMID:11836251
  review:
    summary: HDAC1 is a core catalytic subunit of the NuRD (nucleosome remodeling and deacetylase)
      complex. Proteomic studies show approximately 49% of cellular HDAC1 in ESCs is in the NuRD
      complex (deep research review). Well supported by mass spectrometry identification
      (PMID:27806305) and multiple interaction studies.
    action: ACCEPT
    reason: NuRD complex membership is a core aspect of HDAC1 function. HDAC1 serves as the
      catalytic deacetylase subunit within NuRD. Extensively validated by proteomics and
      co-immunoprecipitation studies.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD,
        Sin3, CoREST, and related chromatin-repressor complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylase that catalyzes the deacetylation of lysine residues on
        the N-terminal part of the core histones.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein
        corepressor complexes, especially SIN3, NuRD, and CoREST.
- term:
    id: GO:0000122
    label: negative regulation of transcription by RNA polymerase II
  evidence_type: IGI
  original_reference_id: PMID:21093383
  review:
    summary: HDAC1 negatively regulates transcription by RNA polymerase II through histone
      deacetylation at target gene promoters. This is a core biological process annotation for
      HDAC1.
    action: ACCEPT
    reason: Negative regulation of pol II transcription is a primary biological function of HDAC1.
      Supported by multiple lines of evidence (PMID:8917507, PMID:9271381, PMID:21093383).
    supported_by:
    - reference_id: PMID:21093383
      supporting_text: HDAC1/2 directly mediate repressive functions of p63 and suppress p53
        activity
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD,
        Sin3, CoREST, and related chromatin-repressor complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein
        corepressor complexes, especially SIN3, NuRD, and CoREST.
- term:
    id: GO:0000785
    label: chromatin
  evidence_type: IDA
  original_reference_id: PMID:21093383
  review:
    summary: HDAC1 is a chromatin-associated protein that modifies histone tails as part of
      co-repressor complexes.
    action: ACCEPT
    reason: HDAC1 is a histone-modifying enzyme that directly acts on chromatin. Association with
      chromatin is inherent to its function.
    supported_by:
    - reference_id: PMID:21093383
      supporting_text: HDACs bind and are active at their promoter regions in normal
        undifferentiated keratinocytes
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD,
        Sin3, CoREST, and related chromatin-repressor complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein
        corepressor complexes, especially SIN3, NuRD, and CoREST.
- term:
    id: GO:0008284
    label: positive regulation of cell population proliferation
  evidence_type: IGI
  original_reference_id: PMID:21093383
  review:
    summary: HDAC1 promotes cell proliferation by repressing cell cycle inhibitors through the
      Rb-HDAC1 complex.
    action: KEEP_AS_NON_CORE
    reason: Well-documented pro-proliferative role but downstream biological consequence of
      deacetylase activity.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 has many developmental and signaling consequences through chromatin
        deacetylation; these are non-core outputs of the core enzymatic function.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylation gives a tag for epigenetic repression and plays an
        important role in transcriptional regulation, cell cycle progression and developmental
        events.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: The report supports HDAC1 as a chromatin deacetylase whose developmental,
        signaling, cell-cycle, DNA-damage, and pathway phenotypes are context-specific downstream
        outputs.
- term:
    id: GO:0009913
    label: epidermal cell differentiation
  evidence_type: IGI
  original_reference_id: PMID:21093383
  review:
    summary: HDAC1/2 are required for proper epidermal cell differentiation (PMID:21093383).
    action: KEEP_AS_NON_CORE
    reason: Tissue-specific developmental process affected by HDAC1.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 has many developmental and signaling consequences through chromatin
        deacetylation; these are non-core outputs of the core enzymatic function.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylation gives a tag for epigenetic repression and plays an
        important role in transcriptional regulation, cell cycle progression and developmental
        events.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: The report supports HDAC1 as a chromatin deacetylase whose developmental,
        signaling, cell-cycle, DNA-damage, and pathway phenotypes are context-specific downstream
        outputs.
- term:
    id: GO:0042475
    label: odontogenesis of dentin-containing tooth
  evidence_type: IGI
  original_reference_id: PMID:21093383
  review:
    summary: HDAC1/2 conditional knockout affects tooth development (PMID:21093383).
    action: KEEP_AS_NON_CORE
    reason: Highly specific downstream developmental phenotype.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 has many developmental and signaling consequences through chromatin
        deacetylation; these are non-core outputs of the core enzymatic function.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylation gives a tag for epigenetic repression and plays an
        important role in transcriptional regulation, cell cycle progression and developmental
        events.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: The report supports HDAC1 as a chromatin deacetylase whose developmental,
        signaling, cell-cycle, DNA-damage, and pathway phenotypes are context-specific downstream
        outputs.
- term:
    id: GO:0042733
    label: embryonic digit morphogenesis
  evidence_type: IGI
  original_reference_id: PMID:21093383
  review:
    summary: HDAC1/2 conditional loss affects digit morphogenesis (PMID:21093383).
    action: KEEP_AS_NON_CORE
    reason: Pleiotropic downstream developmental effect.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 has many developmental and signaling consequences through chromatin
        deacetylation; these are non-core outputs of the core enzymatic function.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylation gives a tag for epigenetic repression and plays an
        important role in transcriptional regulation, cell cycle progression and developmental
        events.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: The report supports HDAC1 as a chromatin deacetylase whose developmental,
        signaling, cell-cycle, DNA-damage, and pathway phenotypes are context-specific downstream
        outputs.
- term:
    id: GO:0043066
    label: negative regulation of apoptotic process
  evidence_type: IGI
  original_reference_id: PMID:21093383
  review:
    summary: HDAC1 negatively regulates apoptosis, in part through deacetylation and inactivation of
      p53.
    action: KEEP_AS_NON_CORE
    reason: Anti-apoptotic effects are a downstream consequence of HDAC1 activity.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 has many developmental and signaling consequences through chromatin
        deacetylation; these are non-core outputs of the core enzymatic function.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylation gives a tag for epigenetic repression and plays an
        important role in transcriptional regulation, cell cycle progression and developmental
        events.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: The report supports HDAC1 as a chromatin deacetylase whose developmental,
        signaling, cell-cycle, DNA-damage, and pathway phenotypes are context-specific downstream
        outputs.
- term:
    id: GO:0060789
    label: hair follicle placode formation
  evidence_type: IGI
  original_reference_id: PMID:21093383
  review:
    summary: HDAC1/2 are required for hair follicle placode formation (PMID:21093383).
    action: KEEP_AS_NON_CORE
    reason: Specific epidermal phenotype. Pleiotropic downstream effect.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 has many developmental and signaling consequences through chromatin
        deacetylation; these are non-core outputs of the core enzymatic function.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylation gives a tag for epigenetic repression and plays an
        important role in transcriptional regulation, cell cycle progression and developmental
        events.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: The report supports HDAC1 as a chromatin deacetylase whose developmental,
        signaling, cell-cycle, DNA-damage, and pathway phenotypes are context-specific downstream
        outputs.
- term:
    id: GO:0061029
    label: eyelid development in camera-type eye
  evidence_type: IGI
  original_reference_id: PMID:21093383
  review:
    summary: HDAC1/2 conditional knockout in epidermis affects eyelid development (PMID:21093383).
    action: KEEP_AS_NON_CORE
    reason: Specific developmental phenotype. Pleiotropic downstream effect.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 has many developmental and signaling consequences through chromatin
        deacetylation; these are non-core outputs of the core enzymatic function.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylation gives a tag for epigenetic repression and plays an
        important role in transcriptional regulation, cell cycle progression and developmental
        events.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: The report supports HDAC1 as a chromatin deacetylase whose developmental,
        signaling, cell-cycle, DNA-damage, and pathway phenotypes are context-specific downstream
        outputs.
- term:
    id: GO:0061198
    label: fungiform papilla formation
  evidence_type: IGI
  original_reference_id: PMID:21093383
  review:
    summary: HDAC1/2 conditional loss in epidermis affects fungiform papilla formation
      (PMID:21093383).
    action: KEEP_AS_NON_CORE
    reason: Specific developmental phenotype. Pleiotropic downstream effect.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 has many developmental and signaling consequences through chromatin
        deacetylation; these are non-core outputs of the core enzymatic function.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylation gives a tag for epigenetic repression and plays an
        important role in transcriptional regulation, cell cycle progression and developmental
        events.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: The report supports HDAC1 as a chromatin deacetylase whose developmental,
        signaling, cell-cycle, DNA-damage, and pathway phenotypes are context-specific downstream
        outputs.
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:16805913
  review:
    summary: Protein binding annotation based on physical interaction evidence from PMID:16805913.
      HDAC1 is known to interact with a very large number of proteins as it functions within
      multiple co-repressor complexes (NuRD, SIN3, CoREST) and binds many transcription factors.
    action: REMOVE
    reason: Per curation guidelines, protein binding (GO:0005515) is uninformative and should be
      replaced with more specific molecular function terms. HDAC1 physically interacts with many
      proteins, but this generic term does not convey functional information. More specific
      annotations such as histone deacetylase binding, transcription corepressor binding, NF-kappaB
      binding, and DNA-binding transcription factor binding are already present.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: Generic protein binding and weakly mechanistic interaction annotations are
        less informative than HDAC1 deacetylase activity and defined corepressor-complex membership.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylases act via the formation of large multiprotein complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: The report supports specific enzymatic and chromatin-complex annotations for
        HDAC1 rather than generic binding or weakly localized annotations.
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:19144721
  review:
    summary: Protein binding annotation based on physical interaction evidence from PMID:19144721.
      HDAC1 is known to interact with a very large number of proteins as it functions within
      multiple co-repressor complexes (NuRD, SIN3, CoREST) and binds many transcription factors.
    action: REMOVE
    reason: Per curation guidelines, protein binding (GO:0005515) is uninformative and should be
      replaced with more specific molecular function terms. HDAC1 physically interacts with many
      proteins, but this generic term does not convey functional information. More specific
      annotations such as histone deacetylase binding, transcription corepressor binding, NF-kappaB
      binding, and DNA-binding transcription factor binding are already present.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: Generic protein binding and weakly mechanistic interaction annotations are
        less informative than HDAC1 deacetylase activity and defined corepressor-complex membership.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylases act via the formation of large multiprotein complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: The report supports specific enzymatic and chromatin-complex annotations for
        HDAC1 rather than generic binding or weakly localized annotations.
- term:
    id: GO:0005667
    label: transcription regulator complex
  evidence_type: IPI
  original_reference_id: PMID:17182846
  review:
    summary: HDAC1 is a component of transcription regulator complexes. This is a broad parent term
      for the more specific NuRD, SIN3, and CoREST complexes.
    action: ACCEPT
    reason: Correct but very general. HDAC1 does function in transcription regulator complexes. More
      specific complex annotations (NuRD, SIN3) are also present.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD,
        Sin3, CoREST, and related chromatin-repressor complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylase that catalyzes the deacetylation of lysine residues on
        the N-terminal part of the core histones.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein
        corepressor complexes, especially SIN3, NuRD, and CoREST.
- term:
    id: GO:0017053
    label: transcription repressor complex
  evidence_type: IPI
  original_reference_id: PMID:17182846
  review:
    summary: HDAC1 functions within transcription repressor complexes including NuRD, SIN3, and
      CoREST, which mediate transcriptional repression through histone deacetylation.
    action: ACCEPT
    reason: HDAC1 is a core catalytic subunit of several transcription repressor complexes. This is
      a correct and informative annotation.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD,
        Sin3, CoREST, and related chromatin-repressor complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylase that catalyzes the deacetylation of lysine residues on
        the N-terminal part of the core histones.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein
        corepressor complexes, especially SIN3, NuRD, and CoREST.
- term:
    id: GO:0003682
    label: chromatin binding
  evidence_type: IDA
  original_reference_id: PMID:16109736
  review:
    summary: HDAC1 binds chromatin as part of its function in co-repressor complexes. ChIP
      experiments have confirmed HDAC1 occupancy at promoters and other regulatory regions.
    action: ACCEPT
    reason: Chromatin binding is well supported by extensive ChIP-seq and ChIP-qPCR data showing
      HDAC1 occupancy at promoters, enhancers, and heterochromatic regions.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD,
        Sin3, CoREST, and related chromatin-repressor complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylase that catalyzes the deacetylation of lysine residues on
        the N-terminal part of the core histones.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein
        corepressor complexes, especially SIN3, NuRD, and CoREST.
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:16109736
  review:
    summary: Protein binding annotation based on physical interaction evidence from PMID:16109736.
      HDAC1 is known to interact with a very large number of proteins as it functions within
      multiple co-repressor complexes (NuRD, SIN3, CoREST) and binds many transcription factors.
    action: REMOVE
    reason: Per curation guidelines, protein binding (GO:0005515) is uninformative and should be
      replaced with more specific molecular function terms. HDAC1 physically interacts with many
      proteins, but this generic term does not convey functional information. More specific
      annotations such as histone deacetylase binding, transcription corepressor binding, NF-kappaB
      binding, and DNA-binding transcription factor binding are already present.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: Generic protein binding and weakly mechanistic interaction annotations are
        less informative than HDAC1 deacetylase activity and defined corepressor-complex membership.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylases act via the formation of large multiprotein complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: The report supports specific enzymatic and chromatin-complex annotations for
        HDAC1 rather than generic binding or weakly localized annotations.
- term:
    id: GO:0000122
    label: negative regulation of transcription by RNA polymerase II
  evidence_type: IDA
  original_reference_id: PMID:8917507
  review:
    summary: HDAC1 negatively regulates transcription by RNA polymerase II through histone
      deacetylation at target gene promoters. This is a core biological process annotation for
      HDAC1.
    action: ACCEPT
    reason: Negative regulation of pol II transcription is a primary biological function of HDAC1.
      Supported by multiple lines of evidence (PMID:8917507, PMID:9271381, PMID:21093383).
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD,
        Sin3, CoREST, and related chromatin-repressor complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylase that catalyzes the deacetylation of lysine residues on
        the N-terminal part of the core histones.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein
        corepressor complexes, especially SIN3, NuRD, and CoREST.
- term:
    id: GO:0000122
    label: negative regulation of transcription by RNA polymerase II
  evidence_type: IDA
  original_reference_id: PMID:9271381
  review:
    summary: HDAC1 negatively regulates transcription by RNA polymerase II through histone
      deacetylation at target gene promoters. This is a core biological process annotation for
      HDAC1.
    action: ACCEPT
    reason: Negative regulation of pol II transcription is a primary biological function of HDAC1.
      Supported by multiple lines of evidence (PMID:8917507, PMID:9271381, PMID:21093383).
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD,
        Sin3, CoREST, and related chromatin-repressor complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylase that catalyzes the deacetylation of lysine residues on
        the N-terminal part of the core histones.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein
        corepressor complexes, especially SIN3, NuRD, and CoREST.
- term:
    id: GO:0003714
    label: transcription corepressor activity
  evidence_type: IDA
  original_reference_id: PMID:8917507
  review:
    summary: HDAC1 functions as a transcription corepressor by deacetylating histones at target gene
      promoters, leading to chromatin compaction and transcriptional silencing.
    action: ACCEPT
    reason: Transcription corepressor activity is a core function of HDAC1. It mediates
      transcriptional repression through histone deacetylation when recruited to target promoters by
      sequence-specific repressors.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD,
        Sin3, CoREST, and related chromatin-repressor complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylase that catalyzes the deacetylation of lysine residues on
        the N-terminal part of the core histones.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein
        corepressor complexes, especially SIN3, NuRD, and CoREST.
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:8917507
  review:
    summary: Protein binding annotation based on physical interaction evidence from PMID:8917507.
      HDAC1 is known to interact with a very large number of proteins as it functions within
      multiple co-repressor complexes (NuRD, SIN3, CoREST) and binds many transcription factors.
    action: REMOVE
    reason: Per curation guidelines, protein binding (GO:0005515) is uninformative and should be
      replaced with more specific molecular function terms. HDAC1 physically interacts with many
      proteins, but this generic term does not convey functional information. More specific
      annotations such as histone deacetylase binding, transcription corepressor binding, NF-kappaB
      binding, and DNA-binding transcription factor binding are already present.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: Generic protein binding and weakly mechanistic interaction annotations are
        less informative than HDAC1 deacetylase activity and defined corepressor-complex membership.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylases act via the formation of large multiprotein complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: The report supports specific enzymatic and chromatin-complex annotations for
        HDAC1 rather than generic binding or weakly localized annotations.
- term:
    id: GO:0021766
    label: hippocampus development
  evidence_type: IGI
  original_reference_id: PMID:19380719
  review:
    summary: HDAC1 contributes to hippocampus development (PMID:19380719).
    action: KEEP_AS_NON_CORE
    reason: Specific developmental process affected by HDAC1 loss. Pleiotropic downstream effect.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 has many developmental and signaling consequences through chromatin
        deacetylation; these are non-core outputs of the core enzymatic function.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylation gives a tag for epigenetic repression and plays an
        important role in transcriptional regulation, cell cycle progression and developmental
        events.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: The report supports HDAC1 as a chromatin deacetylase whose developmental,
        signaling, cell-cycle, DNA-damage, and pathway phenotypes are context-specific downstream
        outputs.
- term:
    id: GO:0030182
    label: neuron differentiation
  evidence_type: IGI
  original_reference_id: PMID:19380719
  review:
    summary: HDAC1 is involved in neuron differentiation (PMID:19380719).
    action: KEEP_AS_NON_CORE
    reason: Downstream pleiotropic developmental effect.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 has many developmental and signaling consequences through chromatin
        deacetylation; these are non-core outputs of the core enzymatic function.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylation gives a tag for epigenetic repression and plays an
        important role in transcriptional regulation, cell cycle progression and developmental
        events.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: The report supports HDAC1 as a chromatin deacetylase whose developmental,
        signaling, cell-cycle, DNA-damage, and pathway phenotypes are context-specific downstream
        outputs.
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:12198165
  review:
    summary: Protein binding annotation based on physical interaction evidence from PMID:12198165.
      HDAC1 is known to interact with a very large number of proteins as it functions within
      multiple co-repressor complexes (NuRD, SIN3, CoREST) and binds many transcription factors.
    action: REMOVE
    reason: Per curation guidelines, protein binding (GO:0005515) is uninformative and should be
      replaced with more specific molecular function terms. HDAC1 physically interacts with many
      proteins, but this generic term does not convey functional information. More specific
      annotations such as histone deacetylase binding, transcription corepressor binding, NF-kappaB
      binding, and DNA-binding transcription factor binding are already present.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: Generic protein binding and weakly mechanistic interaction annotations are
        less informative than HDAC1 deacetylase activity and defined corepressor-complex membership.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylases act via the formation of large multiprotein complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: The report supports specific enzymatic and chromatin-complex annotations for
        HDAC1 rather than generic binding or weakly localized annotations.
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:16085498
  review:
    summary: Protein binding annotation based on physical interaction evidence from PMID:16085498.
      HDAC1 is known to interact with a very large number of proteins as it functions within
      multiple co-repressor complexes (NuRD, SIN3, CoREST) and binds many transcription factors.
    action: REMOVE
    reason: Per curation guidelines, protein binding (GO:0005515) is uninformative and should be
      replaced with more specific molecular function terms. HDAC1 physically interacts with many
      proteins, but this generic term does not convey functional information. More specific
      annotations such as histone deacetylase binding, transcription corepressor binding, NF-kappaB
      binding, and DNA-binding transcription factor binding are already present.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: Generic protein binding and weakly mechanistic interaction annotations are
        less informative than HDAC1 deacetylase activity and defined corepressor-complex membership.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylases act via the formation of large multiprotein complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: The report supports specific enzymatic and chromatin-complex annotations for
        HDAC1 rather than generic binding or weakly localized annotations.
- term:
    id: GO:0043025
    label: neuronal cell body
  evidence_type: IDA
  original_reference_id: PMID:18651664
  review:
    summary: HDAC1 has been localized to neuronal cell bodies (PMID:18651664).
    action: ACCEPT
    reason: Neuronal cell body localization supported by IDA evidence.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD,
        Sin3, CoREST, and related chromatin-repressor complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylase that catalyzes the deacetylation of lysine residues on
        the N-terminal part of the core histones.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein
        corepressor complexes, especially SIN3, NuRD, and CoREST.
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:16103876
  review:
    summary: Protein binding annotation based on physical interaction evidence from PMID:16103876.
      HDAC1 is known to interact with a very large number of proteins as it functions within
      multiple co-repressor complexes (NuRD, SIN3, CoREST) and binds many transcription factors.
    action: REMOVE
    reason: Per curation guidelines, protein binding (GO:0005515) is uninformative and should be
      replaced with more specific molecular function terms. HDAC1 physically interacts with many
      proteins, but this generic term does not convey functional information. More specific
      annotations such as histone deacetylase binding, transcription corepressor binding, NF-kappaB
      binding, and DNA-binding transcription factor binding are already present.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: Generic protein binding and weakly mechanistic interaction annotations are
        less informative than HDAC1 deacetylase activity and defined corepressor-complex membership.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylases act via the formation of large multiprotein complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: The report supports specific enzymatic and chromatin-complex annotations for
        HDAC1 rather than generic binding or weakly localized annotations.
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:9139821
  review:
    summary: Protein binding annotation based on physical interaction evidence from PMID:9139821.
      HDAC1 is known to interact with a very large number of proteins as it functions within
      multiple co-repressor complexes (NuRD, SIN3, CoREST) and binds many transcription factors.
    action: REMOVE
    reason: Per curation guidelines, protein binding (GO:0005515) is uninformative and should be
      replaced with more specific molecular function terms. HDAC1 physically interacts with many
      proteins, but this generic term does not convey functional information. More specific
      annotations such as histone deacetylase binding, transcription corepressor binding, NF-kappaB
      binding, and DNA-binding transcription factor binding are already present.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: Generic protein binding and weakly mechanistic interaction annotations are
        less informative than HDAC1 deacetylase activity and defined corepressor-complex membership.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylases act via the formation of large multiprotein complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: The report supports specific enzymatic and chromatin-complex annotations for
        HDAC1 rather than generic binding or weakly localized annotations.
- term:
    id: GO:0003677
    label: DNA binding
  evidence_type: IDA
  original_reference_id: PMID:14593184
  review:
    summary: General DNA binding annotation. HDAC1 associates with DNA through chromatin complexes
      rather than having intrinsic sequence-specific DNA binding.
    action: MARK_AS_OVER_ANNOTATED
    reason: HDAC1 does not have intrinsic DNA binding activity in the classical sense. It associates
      with DNA indirectly through chromatin complexes and recruitment by DNA-binding transcription
      factors. More appropriate terms like chromatin binding (GO:0003682) are already annotated.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 is recruited to chromatin by DNA-binding factors but is not itself a
        sequence-specific DNA-binding transcription factor.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylase that catalyzes the deacetylation of lysine residues on
        core histones.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: The report supports HDAC1 as a chromatin deacetylase whose developmental,
        signaling, cell-cycle, DNA-damage, and pathway phenotypes are context-specific downstream
        outputs.
- term:
    id: GO:0003682
    label: chromatin binding
  evidence_type: IDA
  original_reference_id: PMID:16678101
  review:
    summary: HDAC1 binds chromatin as part of its function in co-repressor complexes. ChIP
      experiments have confirmed HDAC1 occupancy at promoters and other regulatory regions.
    action: ACCEPT
    reason: Chromatin binding is well supported by extensive ChIP-seq and ChIP-qPCR data showing
      HDAC1 occupancy at promoters, enhancers, and heterochromatic regions.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD,
        Sin3, CoREST, and related chromatin-repressor complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylase that catalyzes the deacetylation of lysine residues on
        the N-terminal part of the core histones.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein
        corepressor complexes, especially SIN3, NuRD, and CoREST.
- term:
    id: GO:0003714
    label: transcription corepressor activity
  evidence_type: IDA
  original_reference_id: PMID:15509593
  review:
    summary: HDAC1 functions as a transcription corepressor by deacetylating histones at target gene
      promoters, leading to chromatin compaction and transcriptional silencing.
    action: ACCEPT
    reason: Transcription corepressor activity is a core function of HDAC1. It mediates
      transcriptional repression through histone deacetylation when recruited to target promoters by
      sequence-specific repressors.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD,
        Sin3, CoREST, and related chromatin-repressor complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylase that catalyzes the deacetylation of lysine residues on
        the N-terminal part of the core histones.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein
        corepressor complexes, especially SIN3, NuRD, and CoREST.
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:15509593
  review:
    summary: Protein binding annotation based on physical interaction evidence from PMID:15509593.
      HDAC1 is known to interact with a very large number of proteins as it functions within
      multiple co-repressor complexes (NuRD, SIN3, CoREST) and binds many transcription factors.
    action: REMOVE
    reason: Per curation guidelines, protein binding (GO:0005515) is uninformative and should be
      replaced with more specific molecular function terms. HDAC1 physically interacts with many
      proteins, but this generic term does not convey functional information. More specific
      annotations such as histone deacetylase binding, transcription corepressor binding, NF-kappaB
      binding, and DNA-binding transcription factor binding are already present.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: Generic protein binding and weakly mechanistic interaction annotations are
        less informative than HDAC1 deacetylase activity and defined corepressor-complex membership.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylases act via the formation of large multiprotein complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: The report supports specific enzymatic and chromatin-complex annotations for
        HDAC1 rather than generic binding or weakly localized annotations.
- term:
    id: GO:0000792
    label: heterochromatin
  evidence_type: IDA
  original_reference_id: PMID:14643676
  review:
    summary: HDAC1 has been localized to heterochromatin regions by immunofluorescence/ChIP studies,
      consistent with its role in histone deacetylation and chromatin compaction.
    action: ACCEPT
    reason: HDAC1 localization to heterochromatin is experimentally validated and consistent with
      its function in promoting chromatin condensation through deacetylation.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD,
        Sin3, CoREST, and related chromatin-repressor complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylase that catalyzes the deacetylation of lysine residues on
        the N-terminal part of the core histones.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein
        corepressor complexes, especially SIN3, NuRD, and CoREST.
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:16462733
  review:
    summary: Protein binding annotation based on physical interaction evidence from PMID:16462733.
      HDAC1 is known to interact with a very large number of proteins as it functions within
      multiple co-repressor complexes (NuRD, SIN3, CoREST) and binds many transcription factors.
    action: REMOVE
    reason: Per curation guidelines, protein binding (GO:0005515) is uninformative and should be
      replaced with more specific molecular function terms. HDAC1 physically interacts with many
      proteins, but this generic term does not convey functional information. More specific
      annotations such as histone deacetylase binding, transcription corepressor binding, NF-kappaB
      binding, and DNA-binding transcription factor binding are already present.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: Generic protein binding and weakly mechanistic interaction annotations are
        less informative than HDAC1 deacetylase activity and defined corepressor-complex membership.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylases act via the formation of large multiprotein complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: The report supports specific enzymatic and chromatin-complex annotations for
        HDAC1 rather than generic binding or weakly localized annotations.
- term:
    id: GO:0016581
    label: NuRD complex
  evidence_type: IPI
  original_reference_id: PMID:16462733
  review:
    summary: HDAC1 is a core catalytic subunit of the NuRD (nucleosome remodeling and deacetylase)
      complex. Proteomic studies show approximately 49% of cellular HDAC1 in ESCs is in the NuRD
      complex (deep research review). Well supported by mass spectrometry identification
      (PMID:27806305) and multiple interaction studies.
    action: ACCEPT
    reason: NuRD complex membership is a core aspect of HDAC1 function. HDAC1 serves as the
      catalytic deacetylase subunit within NuRD. Extensively validated by proteomics and
      co-immunoprecipitation studies.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD,
        Sin3, CoREST, and related chromatin-repressor complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylase that catalyzes the deacetylation of lysine residues on
        the N-terminal part of the core histones.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein
        corepressor complexes, especially SIN3, NuRD, and CoREST.
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:11641275
  review:
    summary: Protein binding annotation based on physical interaction evidence from PMID:11641275.
      HDAC1 is known to interact with a very large number of proteins as it functions within
      multiple co-repressor complexes (NuRD, SIN3, CoREST) and binds many transcription factors.
    action: REMOVE
    reason: Per curation guidelines, protein binding (GO:0005515) is uninformative and should be
      replaced with more specific molecular function terms. HDAC1 physically interacts with many
      proteins, but this generic term does not convey functional information. More specific
      annotations such as histone deacetylase binding, transcription corepressor binding, NF-kappaB
      binding, and DNA-binding transcription factor binding are already present.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: Generic protein binding and weakly mechanistic interaction annotations are
        less informative than HDAC1 deacetylase activity and defined corepressor-complex membership.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylases act via the formation of large multiprotein complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: The report supports specific enzymatic and chromatin-complex annotations for
        HDAC1 rather than generic binding or weakly localized annotations.
- term:
    id: GO:0016581
    label: NuRD complex
  evidence_type: IPI
  original_reference_id: PMID:14645126
  review:
    summary: HDAC1 is a core catalytic subunit of the NuRD (nucleosome remodeling and deacetylase)
      complex. Proteomic studies show approximately 49% of cellular HDAC1 in ESCs is in the NuRD
      complex (deep research review). Well supported by mass spectrometry identification
      (PMID:27806305) and multiple interaction studies.
    action: ACCEPT
    reason: NuRD complex membership is a core aspect of HDAC1 function. HDAC1 serves as the
      catalytic deacetylase subunit within NuRD. Extensively validated by proteomics and
      co-immunoprecipitation studies.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD,
        Sin3, CoREST, and related chromatin-repressor complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylase that catalyzes the deacetylation of lysine residues on
        the N-terminal part of the core histones.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein
        corepressor complexes, especially SIN3, NuRD, and CoREST.
- term:
    id: GO:0007492
    label: endoderm development
  evidence_type: IDA
  original_reference_id: PMID:15060137
  review:
    summary: HDAC1 plays a role in endoderm development (PMID:15060137).
    action: KEEP_AS_NON_CORE
    reason: Specific developmental process affected by HDAC1. Pleiotropic downstream effect.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 has many developmental and signaling consequences through chromatin
        deacetylation; these are non-core outputs of the core enzymatic function.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylation gives a tag for epigenetic repression and plays an
        important role in transcriptional regulation, cell cycle progression and developmental
        events.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: The report supports HDAC1 as a chromatin deacetylase whose developmental,
        signaling, cell-cycle, DNA-damage, and pathway phenotypes are context-specific downstream
        outputs.
- term:
    id: GO:0007492
    label: endoderm development
  evidence_type: IMP
  original_reference_id: PMID:15060137
  review:
    summary: HDAC1 plays a role in endoderm development (PMID:15060137).
    action: KEEP_AS_NON_CORE
    reason: Specific developmental process affected by HDAC1. Pleiotropic downstream effect.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 has many developmental and signaling consequences through chromatin
        deacetylation; these are non-core outputs of the core enzymatic function.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylation gives a tag for epigenetic repression and plays an
        important role in transcriptional regulation, cell cycle progression and developmental
        events.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: The report supports HDAC1 as a chromatin deacetylase whose developmental,
        signaling, cell-cycle, DNA-damage, and pathway phenotypes are context-specific downstream
        outputs.
- term:
    id: GO:0000792
    label: heterochromatin
  evidence_type: IDA
  original_reference_id: PMID:14519686
  review:
    summary: HDAC1 has been localized to heterochromatin regions by immunofluorescence/ChIP studies,
      consistent with its role in histone deacetylation and chromatin compaction.
    action: ACCEPT
    reason: HDAC1 localization to heterochromatin is experimentally validated and consistent with
      its function in promoting chromatin condensation through deacetylation.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD,
        Sin3, CoREST, and related chromatin-repressor complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylase that catalyzes the deacetylation of lysine residues on
        the N-terminal part of the core histones.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein
        corepressor complexes, especially SIN3, NuRD, and CoREST.
- term:
    id: GO:0000118
    label: histone deacetylase complex
  evidence_type: IPI
  original_reference_id: PMID:14645126
  review:
    summary: HDAC1 is a core component of multiple histone deacetylase complexes including NuRD,
      SIN3, and CoREST. This is a general parent term encompassing all such complexes.
    action: ACCEPT
    reason: HDAC1 is the defining catalytic subunit of multiple HDAC complexes. This broader term is
      appropriate as a parent annotation alongside the more specific NuRD and SIN3 complex terms.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD,
        Sin3, CoREST, and related chromatin-repressor complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylase that catalyzes the deacetylation of lysine residues on
        the N-terminal part of the core histones.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: HDAC1 is a class I Zn2+-dependent histone/protein deacetylase that removes
        acetyl groups from lysine residues on histone tails and non-histone proteins.
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:14645126
  review:
    summary: Protein binding annotation based on physical interaction evidence from PMID:14645126.
      HDAC1 is known to interact with a very large number of proteins as it functions within
      multiple co-repressor complexes (NuRD, SIN3, CoREST) and binds many transcription factors.
    action: REMOVE
    reason: Per curation guidelines, protein binding (GO:0005515) is uninformative and should be
      replaced with more specific molecular function terms. HDAC1 physically interacts with many
      proteins, but this generic term does not convey functional information. More specific
      annotations such as histone deacetylase binding, transcription corepressor binding, NF-kappaB
      binding, and DNA-binding transcription factor binding are already present.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: Generic protein binding and weakly mechanistic interaction annotations are
        less informative than HDAC1 deacetylase activity and defined corepressor-complex membership.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylases act via the formation of large multiprotein complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: The report supports specific enzymatic and chromatin-complex annotations for
        HDAC1 rather than generic binding or weakly localized annotations.
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:12529400
  review:
    summary: Protein binding annotation based on physical interaction evidence from PMID:12529400.
      HDAC1 is known to interact with a very large number of proteins as it functions within
      multiple co-repressor complexes (NuRD, SIN3, CoREST) and binds many transcription factors.
    action: REMOVE
    reason: Per curation guidelines, protein binding (GO:0005515) is uninformative and should be
      replaced with more specific molecular function terms. HDAC1 physically interacts with many
      proteins, but this generic term does not convey functional information. More specific
      annotations such as histone deacetylase binding, transcription corepressor binding, NF-kappaB
      binding, and DNA-binding transcription factor binding are already present.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: Generic protein binding and weakly mechanistic interaction annotations are
        less informative than HDAC1 deacetylase activity and defined corepressor-complex membership.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylases act via the formation of large multiprotein complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: The report supports specific enzymatic and chromatin-complex annotations for
        HDAC1 rather than generic binding or weakly localized annotations.
- term:
    id: GO:0000118
    label: histone deacetylase complex
  evidence_type: TAS
  original_reference_id: PMID:12711221
  review:
    summary: HDAC1 is a core component of multiple histone deacetylase complexes including NuRD,
      SIN3, and CoREST. This is a general parent term encompassing all such complexes.
    action: ACCEPT
    reason: HDAC1 is the defining catalytic subunit of multiple HDAC complexes. This broader term is
      appropriate as a parent annotation alongside the more specific NuRD and SIN3 complex terms.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD,
        Sin3, CoREST, and related chromatin-repressor complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylase that catalyzes the deacetylation of lysine residues on
        the N-terminal part of the core histones.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: HDAC1 is a class I Zn2+-dependent histone/protein deacetylase that removes
        acetyl groups from lysine residues on histone tails and non-histone proteins.
- term:
    id: GO:0005737
    label: cytoplasm
  evidence_type: TAS
  original_reference_id: PMID:12711221
  review:
    summary: HDAC1 has some cytoplasmic localization in addition to its predominant nuclear
      localization.
    action: KEEP_AS_NON_CORE
    reason: Cytoplasm is a minor localization relative to HDAC1's predominant nuclear
      chromatin/corepressor role and should not be treated as a core cellular-component call.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: 'GO; GO:0005737; C:cytoplasm; TAS:UniProtKB.'
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: Class I HDACs, including HDAC1, are predominantly or exclusively nuclear,
        consistent with chromatin accessibility and transcriptional control roles.
- term:
    id: GO:0006325
    label: chromatin organization
  evidence_type: TAS
  original_reference_id: PMID:12711221
  review:
    summary: HDAC1 plays a role in chromatin organization through histone deacetylation, which
      promotes nucleosome compaction.
    action: ACCEPT
    reason: Chromatin organization is a direct consequence of HDAC1 enzymatic activity.
    supported_by:
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
      supporting_text: HDAC1 is a zinc-dependent histone/protein deacetylase and deacylase in NuRD,
        Sin3, CoREST, and related chromatin-repressor complexes.
    - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
      supporting_text: Histone deacetylase that catalyzes the deacetylation of lysine residues on
        the N-terminal part of the core histones.
    - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
      supporting_text: HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein
        corepressor complexes, especially SIN3, NuRD, and CoREST.
core_functions:
- description: Catalyzes zinc-dependent hydrolytic removal of acetyl groups from lysine residues on
    histones H2A, H2B, H3, and H4 as the catalytic subunit of the NuRD corepressor complex,
    mediating transcriptional repression through chromatin compaction. Approximately 49% of cellular
    HDAC1 resides in the NuRD complex in embryonic stem cells.
  molecular_function:
    id: GO:0004407
    label: histone deacetylase activity
  directly_involved_in:
  - id: GO:0000122
    label: negative regulation of transcription by RNA polymerase II
  - id: GO:0006325
    label: chromatin organization
  locations:
  - id: GO:0000785
    label: chromatin
  - id: GO:0005634
    label: nucleus
  in_complex:
    id: GO:0016581
    label: NuRD complex
  supported_by:
  - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
    supporting_text: Histone deacetylase that catalyzes the deacetylation of lysine residues on the
      N-terminal part of the core histones.
  - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
    supporting_text: HDAC1 is a catalytic subunit of NuRD, Sin3, CoREST and related repressor
      complexes.
  - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
    supporting_text: HDAC1 is a class I Zn2+-dependent histone/protein deacetylase that removes
      acetyl groups from lysine residues on histone tails and non-histone proteins.
- description: Catalyzes histone deacetylation as the catalytic subunit of the Sin3 corepressor
    complex, which is recruited to target gene promoters by sequence-specific transcription factors
    and scaffold proteins SIN3A/SIN3B. Approximately 15% of cellular HDAC1 resides in the SIN3
    complex.
  molecular_function:
    id: GO:0004407
    label: histone deacetylase activity
  directly_involved_in:
  - id: GO:0000122
    label: negative regulation of transcription by RNA polymerase II
  locations:
  - id: GO:0000785
    label: chromatin
  - id: GO:0005634
    label: nucleus
  in_complex:
    id: GO:0070822
    label: Sin3-type complex
  supported_by:
  - reference_id: file:mouse/Hdac1/Hdac1-uniprot.txt
    supporting_text: Histone deacetylase that catalyzes the deacetylation of lysine residues on the
      N-terminal part of the core histones.
  - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
    supporting_text: HDAC1 is a catalytic subunit of NuRD, Sin3, CoREST and related repressor
      complexes.
  - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
    supporting_text: HDAC1 is a class I Zn2+-dependent histone/protein deacetylase that removes
      acetyl groups from lysine residues on histone tails and non-histone proteins.
- description: Catalyzes histone deacetylation as part of CoREST repressor complexes,
    including the HDAC1/CoREST1/LSD1 ternary complex that represses transcription
    through chromatin deacetylation and demethylase-associated corepression.
  molecular_function:
    id: GO:0004407
    label: histone deacetylase activity
  directly_involved_in:
  - id: GO:0000122
    label: negative regulation of transcription by RNA polymerase II
  locations:
  - id: GO:0000785
    label: chromatin
  - id: GO:0005634
    label: nucleus
  in_complex:
    id: GO:0000118
    label: histone deacetylase complex
  supported_by:
  - reference_id: PMID:30279482
    supporting_text: A ternary complex of HDAC1/CoREST1/LSD1 is able to hydrolyse both histone H3
      Lys18-acetyl (H3K18ac) and H3 Lys18-crotonyl (H3K18cr) peptide substrates
  - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
    supporting_text: HDAC1 is a catalytic subunit of NuRD, Sin3, CoREST and related repressor
      complexes.
  - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
    supporting_text: HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein
      corepressor complexes, especially SIN3, NuRD, and CoREST.
- description: Removes crotonyl groups from histone lysine residues in vivo. Genetic deletion of
    HDAC1/2 in ES cells causes an 85% reduction in total decrotonylase activity and increased global
    histone crotonylation.
  molecular_function:
    id: GO:0160009
    label: histone decrotonylase activity
  locations:
  - id: GO:0005634
    label: nucleus
  supported_by:
  - reference_id: PMID:30279482
    supporting_text: Genetic deletion of HDAC1/2 in ES cells increases global levels of histone
      crotonylation and causes an 85% reduction in total decrotonylase activity
  - reference_id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
    supporting_text: HDAC1 is a catalytic subunit of chromatin corepressor complexes and mediates
      histone deacetylation-dependent transcriptional repression.
  - reference_id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
    supporting_text: HDAC1 functions predominantly as a catalytic subunit of nuclear multiprotein
      corepressor complexes, especially SIN3, NuRD, and CoREST.
references:
- id: GO_REF:0000024
  title: Method for ISS annotations
  findings: []
- id: GO_REF:0000033
  title: Phylogenetic Annotation (IBA)
  findings: []
- id: GO_REF:0000096
  title: UniProt-GOA annotation (ISO)
  findings: []
- id: GO_REF:0000107
  title: Automatic transfer of experimentally verified manual GO annotation data to orthologs using
    Ensembl Compara
  findings: []
- id: GO_REF:0000116
  title: Rhea-based UniProt to GO mapping
  findings: []
- id: GO_REF:0000117
  title: Automatic Gene Ontology annotation by MGI
  findings: []
- id: GO_REF:0000119
  title: Manual transfer of experimentally verified GO annotation data to orthologs by UniProt
  findings: []
- id: GO_REF:0000120
  title: UniProt-based electronic GO annotation (UniRule/ARBA/InterPro)
  findings: []
- id: PMID:10615135
  title: DNA methyltransferase Dnmt1 associates with histone deacetylase activity.
  findings: []
- id: PMID:11115394
  title: Msx3 protein recruits histone deacetylase to down-regulate the Msx1 promoter.
  findings: []
- id: PMID:11641275
  title: The hairless gene mutated in congenital hair loss disorders encodes a novel nuclear
    receptor corepressor.
  findings: []
- id: PMID:11836251
  title: Murine Sall1 represses transcription by recruiting a histone deacetylase complex.
  findings: []
- id: PMID:11923873
  title: Bop encodes a muscle-restricted protein containing MYND and SET domains and is essential
    for cardiac differentiation and morphogenesis.
  findings: []
- id: PMID:11931769
  title: The phosphorylation status of nuclear NF-kappa B determines its association with CBP/p300
    or HDAC-1.
  findings: []
- id: PMID:12198165
  title: The chromatin remodeling complex NoRC targets HDAC1 to the ribosomal gene promoter and
    represses RNA polymerase I transcription.
  findings: []
- id: PMID:12529400
  title: Homeodomain-interacting protein kinase 1 modulates Daxx localization, phosphorylation, and
    transcriptional activity.
  findings: []
- id: PMID:12711221
  title: 'Class II histone deacetylases: versatile regulators.'
  findings: []
- id: PMID:12900441
  title: Consequences of the depletion of zygotic and embryonic enhancer of zeste 2 during
    preimplantation mouse development.
  findings: []
- id: PMID:14519686
  title: Analysis of mammalian proteins involved in chromatin modification reveals new metaphase
    centromeric proteins and distinct chromosomal distribution patterns.
  findings: []
- id: PMID:14593184
  title: DNA methylation-related chromatin remodeling in activity-dependent BDNF gene regulation.
  findings: []
- id: PMID:14643676
  title: Expression and localization of components of the histone deacetylases multiprotein
    repressory complexes in the mouse preimplantation embryo.
  findings: []
- id: PMID:14645126
  title: Atrophin 2 recruits histone deacetylase and is required for the function of multiple
    signaling centers during mouse embryogenesis.
  findings: []
- id: PMID:15060137
  title: Regulation of mammalian epithelial differentiation and intestine development by class I
    histone deacetylases.
  findings: []
- id: PMID:15226430
  title: Circadian and light-induced transcription of clock gene Per1 depends on histone acetylation
    and deacetylation.
  findings: []
- id: PMID:15337766
  title: Leukemia/lymphoma-related factor, a POZ domain-containing transcriptional repressor,
    interacts with histone deacetylase-1 and inhibits cartilage oligomeric matrix protein gene
    expression and chondrogenesis.
  findings: []
- id: PMID:15509593
  title: HNF1beta/TCF2 mutations impair transactivation potential through altered co-regulator
    recruitment.
  findings: []
- id: PMID:15608638
  title: Loss of silent-chromatin looping and impaired imprinting of DLX5 in Rett syndrome.
  findings: []
- id: PMID:15907476
  title: REST and its corepressors mediate plasticity of neuronal gene chromatin throughout
    neurogenesis.
  findings: []
- id: PMID:16085498
  title: The PHD finger/bromodomain of NoRC interacts with acetylated histone H4K16 and is
    sufficient for rDNA silencing.
  findings: []
- id: PMID:16103876
  title: Mnt transcriptional repressor is functionally regulated during cell cycle progression.
  findings: []
- id: PMID:16109736
  title: Adrenocorticotropic hormone-mediated signaling cascades coordinate a cyclic pattern of
    steroidogenic factor 1-dependent transcriptional activation.
  findings: []
- id: PMID:16407974
  title: ETO2 coordinates cellular proliferation and differentiation during erythropoiesis.
  findings: []
- id: PMID:16462733
  title: The NuRD component Mbd3 is required for pluripotency of embryonic stem cells.
  findings: []
- id: PMID:16678101
  title: Homeodomain-mediated beta-catenin-dependent switching events dictate cell-lineage
    determination.
  findings: []
- id: PMID:16805913
  title: 'Identification and characterization of Smyd2: a split SET/MYND domain-containing histone H3
    lysine 36-specific methyltransferase that interacts with the Sin3 histone deacetylase complex.'
  findings: []
- id: PMID:17056544
  title: The transcriptional repressor cAMP response element modulator alpha interacts with histone
    deacetylase 1 to repress promoter activity.
  findings: []
- id: PMID:17182846
  title: Cell fate determination factor DACH1 inhibits c-Jun-induced contact-independent growth.
  findings: []
- id: PMID:17392792
  title: Opposing LSD1 complexes function in developmental gene activation and repression
    programmes.
  findings: []
- id: PMID:17442941
  title: Protein inhibitor of activated STAT 3 modulates osteoclastogenesis by down-regulation of
    NFATc1 and osteoclast-associated receptor.
  findings: []
- id: PMID:17568773
  title: Foxh1 recruits Gsc to negatively regulate Mixl1 expression during early mouse development.
  findings: []
- id: PMID:17707228
  title: Epigenetic regulation of hematopoietic differentiation by Gfi-1 and Gfi-1b is mediated by
    the cofactors CoREST and LSD1.
  findings: []
- id: PMID:17905753
  title: Adipose tissue mass is modulated by SLUG (SNAI2).
  findings: []
- id: PMID:18486321
  title: Acetylation and deacetylation regulate CCAAT/enhancer binding protein beta at K39 in
    mediating gene transcription.
  findings: []
- id: PMID:18651664
  title: Histone deacetylases 1 and 2 are expressed at distinct stages of neuro-glial development.
  findings: []
- id: PMID:19144721
  title: Pitx3 potentiates Nurr1 in dopamine neuron terminal differentiation through release of
    SMRT-mediated repression.
  findings: []
- id: PMID:19235719
  title: The homeobox gene Mohawk represses transcription by recruiting the sin3A/HDAC co-repressor
    complex.
  findings: []
- id: PMID:19380719
  title: Histone deacetylases 1 and 2 control the progression of neural precursors to neurons during
    brain development.
  findings: []
- id: PMID:19424149
  title: HDAC2 negatively regulates memory formation and synaptic plasticity.
  findings: []
- id: PMID:19497860
  title: LSD1-mediated epigenetic modification is required for TAL1 function and hematopoiesis.
  findings: []
- id: PMID:19501046
  title: Znhit1 causes cell cycle arrest and down-regulates CDK6 expression.
  findings: []
- id: PMID:19503085
  title: HDAC1 and HDAC2 regulate oligodendrocyte differentiation by disrupting the beta-catenin-TCF
    interaction.
  findings: []
- id: PMID:19796622
  title: Uncovering early response of gene regulatory networks in ESCs by systematic induction of
    transcription factors.
  findings: []
- id: PMID:19805123
  title: NF-kappaB activity is constitutively elevated in c-Abl null fibroblasts.
  findings: []
- id: PMID:19927129
  title: NuRD mediates activating and repressive functions of GATA-1 and FOG-1 during blood
    development.
  findings: []
- id: PMID:20404188
  title: Histone deacetylase 1 (HDAC1), but not HDAC2, controls embryonic stem cell differentiation.
  findings: []
- id: PMID:20596014
  title: Chromatin regulation by Brg1 underlies heart muscle development and disease.
  findings: []
- id: PMID:20599664
  title: A novel role for cardiac ankyrin repeat protein Ankrd1/CARP as a co-activator of the p53
    tumor suppressor protein.
  findings: []
- id: PMID:20720167
  title: Metastasis tumor antigen 2 (MTA2) is involved in proper imprinted expression of H19 and
    Peg3 during mouse preimplantation development.
  findings: []
- id: PMID:21093383
  title: Hdac1 and Hdac2 act redundantly to control p63 and p53 functions in epidermal progenitor
    cells.
  findings: []
- id: PMID:21177534
  title: A novel KRAB domain-containing zinc finger transcription factor ZNF431 directly represses
    Patched1 transcription.
  findings: []
- id: PMID:21448134
  title: KDM5B regulates embryonic stem cell self-renewal and represses cryptic intragenic
    transcription.
  findings: []
- id: PMID:21454521
  title: The developmental regulator protein Gon4l associates with protein YY1, co-repressor Sin3a,
    and histone deacetylase 1 and mediates transcriptional repression.
  findings: []
- id: PMID:21874018
  title: lincRNAs act in the circuitry controlling pluripotency and differentiation.
  findings: []
- id: PMID:21874024
  title: The ubiquitin ligase Peli1 negatively regulates T cell activation and prevents
    autoimmunity.
  findings: []
- id: PMID:21931736
  title: CHD5, a brain-specific paralog of Mi2 chromatin remodeling enzymes, regulates expression of
    neuronal genes.
  findings: []
- id: PMID:21937600
  title: Transposon mutagenesis with coat color genotyping identifies an essential role for Skor2 in
    sonic hedgehog signaling and cerebellum development.
  findings: []
- id: PMID:21960634
  title: Histone lysine demethylase JARID1a activates CLOCK-BMAL1 and influences the circadian
    clock.
  findings: []
- id: PMID:22075476
  title: Metastasis-associated protein 3 (MTA3) regulates G2/M progression in proliferating mouse
    granulosa cells.
  findings: []
- id: PMID:22242125
  title: Stress-induced C/EBP homology protein (CHOP) represses MyoD transcription to delay myoblast
    differentiation.
  findings: []
- id: PMID:22297846
  title: Enhancer decommissioning by LSD1 during embryonic stem cell differentiation.
  findings: []
- id: PMID:22334647
  title: Protooncogene Ski cooperates with the chromatin-remodeling factor Satb2 in specifying
    callosal neurons.
  findings: []
- id: PMID:22560079
  title: NuRD suppresses pluripotency gene expression to promote transcriptional heterogeneity and
    lineage commitment.
  findings: []
- id: PMID:22770845
  title: The polycomb group protein L3mbtl2 assembles an atypical PRC1-family complex that is
    essential in pluripotent stem cells and early development.
  findings: []
- id: PMID:22865885
  title: Family with sequence similarity 60A (FAM60A) protein is a cell cycle-fluctuating regulator
    of the SIN3-HDAC1 histone deacetylase complex.
  findings: []
- id: PMID:22918830
  title: Histone deacetylase-1 (HDAC1) is a molecular switch between neuronal survival and death.
  findings: []
- id: PMID:22984288
  title: 'Human family with sequence similarity 60 member A (FAM60A) protein: a new subunit of the Sin3
    deacetylase complex.'
  findings: []
- id: PMID:24240174
  title: Divergent roles of HDAC1 and HDAC2 in the regulation of epidermal development and
    tumorigenesis.
  findings: []
- id: PMID:24335282
  title: Analysis of the SWI/SNF chromatin-remodeling complex during early heart development and
    BAF250a repression cardiac gene transcription during P19 cell differentiation.
  findings: []
- id: PMID:24413057
  title: Temporal orchestration of repressive chromatin modifiers by circadian clock Period
    complexes.
  findings: []
- id: PMID:24736997
  title: A novel protein, CHRONO, functions as a core component of the mammalian circadian clock.
  findings: []
- id: PMID:26816381
  title: Transcription factors LRF and BCL11A independently repress expression of fetal hemoglobin.
  findings: []
- id: PMID:26974661
  title: "C/EBPα creates elite cells for iPSC reprogramming by upregulating Klf4 and increasing the levels
    of Lsd1 and Brd4."
  findings: []
- id: PMID:28554894
  title: Fam60a defines a variant Sin3a-Hdac complex in embryonic stem cells required for
    self-renewal.
  findings: []
- id: PMID:30228260
  title: A variant NuRD complex containing PWWP2A/B excludes MBD2/3 to regulate transcription at
    active genes.
  findings: []
- id: PMID:30279482
  title: Histone deacetylase (HDAC) 1 and 2 complexes regulate both histone acetylation and
    crotonylation in vivo.
  findings: []
- id: PMID:30726206
  title: Genes encoding SATB2-interacting proteins in adult cerebral cortex contribute to human
    cognitive ability.
  findings: []
- id: PMID:30911105
  title: Safeguard function of PU.1 shapes the inflammatory epigenome of neutrophils.
  findings: []
- id: PMID:33795231
  title: Regulation of otocyst patterning by Tbx2 and Tbx3 is required for inner ear morphogenesis
    in the mouse.
  findings: []
- id: PMID:33831416
  title: The uncharacterized SANT and BTB domain-containing protein SANBR inhibits class switch
    recombination.
  findings: []
- id: PMID:34180153
  title: PWWP2B Fine-Tunes Adipose Thermogenesis by Stabilizing HDACs in a NuRD Subcomplex.
  findings: []
- id: PMID:8917507
  title: Transcriptional repression by YY1 is mediated by interaction with a mammalian homolog of
    the yeast global regulator RPD3.
  findings: []
- id: PMID:9139821
  title: Role for N-CoR and histone deacetylase in Sin3-mediated transcriptional repression.
  findings: []
- id: PMID:9271381
  title: Identification of mouse histone deacetylase 1 as a growth factor-inducible gene.
  findings: []
- id: PMID:9651585
  title: SAP30, a novel protein conserved between human and yeast, is a component of a histone
    deacetylase complex.
  findings: []
- id: Reactome:R-MMU-573336
  title: Reactome pathway annotation
  findings: []
- id: Reactome:R-MMU-573376
  title: Reactome pathway annotation
  findings: []
- id: Reactome:R-MMU-573383
  title: Reactome pathway annotation
  findings: []
- id: Reactome:R-MMU-8978954
  title: Reactome pathway annotation
  findings: []
- id: Reactome:R-MMU-8978970
  title: Reactome pathway annotation
  findings: []
- id: Reactome:R-MMU-8978980
  title: Reactome pathway annotation
  findings: []
- id: Reactome:R-MMU-8978989
  title: Reactome pathway annotation
  findings: []
- id: Reactome:R-MMU-9006133
  title: Reactome pathway annotation
  findings: []
- id: Reactome:R-MMU-9017958
  title: Reactome pathway annotation
  findings: []
- id: Reactome:R-MMU-9625109
  title: Reactome pathway annotation
  findings: []
- id: Reactome:R-MMU-9727502
  title: Reactome pathway annotation
  findings: []
- id: Reactome:R-MMU-9844527
  title: Reactome pathway annotation
  findings: []
- id: Reactome:R-MMU-9845305
  title: Reactome pathway annotation
  findings: []
- id: Reactome:R-NUL-573373
  title: Reactome pathway annotation
  findings: []
- id: Reactome:R-NUL-573385
  title: Reactome pathway annotation
  findings: []
- id: file:mouse/Hdac1/Hdac1-uniprot.txt
  title: UniProt record for mouse Hdac1
  findings:
  - statement: Hdac1 is a histone/protein deacetylase and deacylase in corepressor complexes.
    supporting_text: Histone deacetylase that catalyzes the deacetylation of lysine residues on the
      N-terminal part of the core histones.
- id: file:mouse/Hdac1/Hdac1-deep-research-openai.md
  title: OpenAI deep research report on mouse Hdac1
  findings:
  - statement: HDAC1 is a catalytic subunit of NuRD, Sin3, CoREST and related chromatin-repressor
      complexes.
- id: file:mouse/Hdac1/Hdac1-deep-research-falcon.md
  title: Falcon deep research report on mouse Hdac1
  findings:
  - statement: HDAC1 is a complex-integrated nuclear lysine deacetylase in SIN3, NuRD, CoREST, and
      related chromatin regulatory complexes.
    supporting_text: HDAC1 is best annotated as a complex-integrated nuclear lysine deacetylase;
      modern evidence supports that most HDAC1 is embedded in corepressor complexes that specify
      function and genomic binding.