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.
| 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. Proposed replacements: negative regulation of canonical Wnt signaling pathway 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/EBPΞ± 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. Proposed replacements: promoter-specific chromatin binding 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. Proposed replacements: promoter-specific chromatin binding 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. Proposed replacements: promoter-specific chromatin binding 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. Proposed replacements: promoter-specific chromatin binding 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. Proposed replacements: promoter-specific chromatin binding 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. Proposed replacements: promoter-specific chromatin binding 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. Proposed replacements: promoter-specific chromatin binding 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. Proposed replacements: promoter-specific chromatin binding 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. |
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