CHRAC1

Existing Annotations Review

GO Term	Evidence	Action	Reason
GO:0005634 nucleus	IBA GO_REF:0000033	ACCEPT	Summary: CHRAC1 is a nuclear protein that functions in chromatin remodeling. The Human Protein Atlas confirms nuclear/nucleoplasm localization. UniProt states "Nucleus" for subcellular location. This is well-supported by its role as a subunit of the nuclear CHRAC chromatin remodeling complex [PMID:10880450]. Reason: Nuclear localization is strongly supported by CHRAC1's established role as a subunit of the CHRAC complex, which functions in the nucleus on chromatin. IBA inference is consistent with experimental data showing CHRAC1 is a chromatin-associated nuclear protein. Supporting Evidence: file:human/CHRAC1/CHRAC1-deep-research-openai.md CHRAC1 is an intracellular, nuclear protein. It lacks any signal peptides or transmembrane domains, and consistent with its role in chromatin dynamics, it localizes to the cell nucleus, predominantly in the nucleoplasm
GO:0006261 DNA-templated DNA replication	IBA GO_REF:0000033	MODIFY	Summary: CHRAC1 is part of the CHRAC complex which facilitates DNA replication through heterochromatin by remodeling nucleosomes. The ACF1-ISWI complex (part of CHRAC) is required for DNA replication through pericentromeric heterochromatin [PMID:12434153]. However, CHRAC1 does not directly participate in DNA synthesis; it facilitates chromatin accessibility for the replication machinery. Reason: While CHRAC1's complex facilitates DNA replication through chromatin, the term "DNA-templated DNA replication" implies direct involvement in DNA synthesis. CHRAC1 functions in chromatin remodeling to support replication, not in replication itself. A more accurate term would be "regulation of DNA replication" or chromatin remodeling during replication. Proposed replacements: regulation of DNA replication Supporting Evidence: PMID:12434153 an ACF1-ISWI chromatin-remodeling complex is required for replication through heterochromatin in mammalian cells
GO:0006338 chromatin remodeling	IBA GO_REF:0000033	ACCEPT	Summary: CHRAC1 is a core subunit of the CHRAC chromatin remodeling complex. The CHRAC1-POLE3 heterodimer enhances ATP-dependent nucleosome sliding and chromatin assembly mediated by ACF [PMID:14759371]. This is a primary function of CHRAC1. Reason: Chromatin remodeling is the core function of the CHRAC complex of which CHRAC1 is an essential structural subunit. Multiple publications confirm CHRAC1's role in facilitating nucleosome sliding and chromatin reorganization. Supporting Evidence: PMID:14759371 these histone-fold proteins facilitate ATP-dependent nucleosome sliding by ACF
GO:0008623 CHRAC	IBA GO_REF:0000033	ACCEPT	Summary: CHRAC1 is a defining component of the CHRAC (Chromatin Accessibility Complex). It was identified as part of HuCHRAC along with SMARCA5, BAZ1A, and POLE3 [PMID:10880450]. This is the eponymous complex for CHRAC1. Reason: CHRAC1 is one of the four subunits that compose the CHRAC complex (along with SMARCA5/SNF2H, BAZ1A/ACF1, and POLE3). This cellular component annotation is directly supported by the original publication describing human CHRAC. Supporting Evidence: PMID:10880450 the human homologues of two novel putative histone-fold proteins in Drosophila CHRAC are present in HuCHRAC
GO:0003677 DNA binding	IEA GO_REF:0000043	ACCEPT	Summary: CHRAC1 forms a heterodimer with POLE3 that binds naked double-stranded DNA. This is experimentally demonstrated in the original HuCHRAC characterization [PMID:10880450]. The annotation is correct but could be more specific. Reason: While DNA binding is accurate, CHRAC1-POLE3 specifically binds double-stranded DNA, not nucleosomal DNA. A more specific term would be more informative, but this annotation is not incorrect. Supporting Evidence: PMID:10880450 two human histone-fold proteins form a stable complex that binds naked DNA but not nucleosomes
GO:0003887 DNA-directed DNA polymerase activity	IEA GO_REF:0000043	REMOVE	Summary: CHRAC1 does NOT have DNA polymerase activity. This annotation is based on UniProt keyword mapping that is incorrect. CHRAC1 is a histone-fold structural protein with no catalytic activity. Its partner POLE3 is shared with DNA polymerase epsilon, but CHRAC1 itself is not a polymerase component. Reason: This is an erroneous annotation. CHRAC1 has no enzymatic activity and is not a DNA polymerase. The confusion likely arises because POLE3 (CHRAC1's binding partner) is also a subunit of DNA polymerase epsilon, but CHRAC1 is specific to the CHRAC complex and is not part of Pol epsilon. Supporting Evidence: PMID:14759371 CHRAC-17 interacts with another histone-fold protein, p12, in DNA polymerase epsilon, but CHRAC-15 is essential for interaction with ACF
GO:0005634 nucleus	IEA GO_REF:0000044	ACCEPT	Summary: Duplicate annotation of nuclear localization via UniProt subcellular location mapping. Correct annotation but redundant with the IBA annotation. Reason: Nuclear localization is accurate for CHRAC1. The duplicate evidence codes (IBA and IEA) both correctly identify the nuclear localization. Supporting Evidence: file:human/CHRAC1/CHRAC1-deep-research-openai.md CHRAC1 is an intracellular, nuclear protein
GO:0016740 transferase activity	IEA GO_REF:0000043	REMOVE	Summary: CHRAC1 does NOT have transferase activity. This is an erroneous annotation derived from incorrect UniProt keyword mapping. CHRAC1 is a non-enzymatic histone-fold protein that serves as a structural adapter in chromatin remodeling complexes. Reason: CHRAC1 has no catalytic activity whatsoever. It is a structural subunit that binds DNA and enhances the activity of the CHRAC complex's ATPase (SMARCA5), but has no enzymatic function itself. This annotation is completely incorrect.
GO:0016779 nucleotidyltransferase activity	IEA GO_REF:0000043	REMOVE	Summary: CHRAC1 does NOT have nucleotidyltransferase activity. This annotation is erroneous, likely derived from the same incorrect keyword mapping that generated the DNA polymerase and transferase annotations. Reason: CHRAC1 is a non-enzymatic structural protein. It has no nucleotidyltransferase or any other enzymatic activity. This annotation should be removed as it misrepresents the function of CHRAC1.
GO:0046982 protein heterodimerization activity	IEA GO_REF:0000002	ACCEPT	Summary: CHRAC1 forms a stable heterodimer with POLE3 (CHRAC-17) via their histone-fold domains. This interaction is well-documented and essential for CHRAC1 function [PMID:10880450, PMID:14759371]. The annotation is accurate. Reason: Heterodimerization with POLE3 is a core biochemical property of CHRAC1. The CHRAC1-POLE3 heterodimer is analogous to the H2A-H2B histone dimer and is essential for DNA binding and interaction with the ACF complex. Supporting Evidence: PMID:14759371 CHRAC-17 interacts with another histone-fold protein, p12, in DNA polymerase epsilon, but CHRAC-15 is essential for interaction with ACF
GO:0071897 DNA biosynthetic process	IEA GO_REF:0000108	REMOVE	Summary: CHRAC1 is not directly involved in DNA biosynthesis. This annotation appears to be derived from logical inference that is not accurate for CHRAC1's actual function. CHRAC1 facilitates chromatin remodeling during replication but does not participate in DNA synthesis. Reason: CHRAC1 does not synthesize DNA. While the CHRAC complex facilitates DNA replication by remodeling chromatin, CHRAC1 itself does not have any role in the actual biosynthesis of DNA. This annotation conflates the complex's role in supporting replication with direct participation in DNA synthesis.
GO:0005515 protein binding	IPI PMID:21516116 Next-generation sequencing to generate interactome datasets.	REMOVE	Summary: This annotation is from a large-scale interactome study. While CHRAC1 does bind proteins (POLE3, SMARCA5, BAZ1A), "protein binding" is too vague and uninformative for curation purposes. Reason: GO:0005515 (protein binding) is considered uninformative per GO curation guidelines. CHRAC1's specific protein interactions (heterodimerization with POLE3, interaction with ACF1/BAZ1A) are captured by more specific terms. Supporting Evidence: PMID:21516116 Next-generation sequencing to generate interactome datasets.
GO:0005515 protein binding	IPI PMID:25416956 A proteome-scale map of the human interactome network.	REMOVE	Summary: Large-scale proteome interactome study. The "protein binding" term is uninformative and should not be used for annotation. Reason: GO:0005515 (protein binding) is considered too vague per GO guidelines. High-throughput interactome studies do not provide sufficient specificity for meaningful functional annotation. Supporting Evidence: PMID:25416956 A proteome-scale map of the human interactome network.
GO:0005515 protein binding	IPI PMID:31515488 Extensive disruption of protein interactions by genetic vari...	REMOVE	Summary: Interactome study on genetic variants. The generic "protein binding" annotation is uninformative. Reason: GO:0005515 (protein binding) should be avoided as it provides no specific functional information. CHRAC1's important protein interactions are better captured by heterodimerization activity and complex membership annotations. Supporting Evidence: PMID:31515488 Extensive disruption of protein interactions by genetic variants across the allele frequency spectrum in human populations.
GO:0005515 protein binding	IPI PMID:32296183 A reference map of the human binary protein interactome.	REMOVE	Summary: Binary protein interactome reference map study. Generic protein binding annotation is uninformative. Reason: GO:0005515 should not be used for annotation. CHRAC1's specific binding partners and functions are already captured by more informative terms. Supporting Evidence: PMID:32296183 Apr 8. A reference map of the human binary protein interactome.
GO:0005515 protein binding	IPI PMID:33961781 Dual proteome-scale networks reveal cell-specific remodeling...	REMOVE	Summary: Dual proteome-scale interactome network study. Protein binding is uninformative as a molecular function annotation. Reason: GO:0005515 (protein binding) provides no specific functional insight. This generic term should be replaced by more specific molecular function terms that describe CHRAC1's actual interactions. Supporting Evidence: PMID:33961781 2021 May 6. Dual proteome-scale networks reveal cell-specific remodeling of the human interactome.
GO:0005721 pericentric heterochromatin	IEA GO_REF:0000107	ACCEPT	Summary: The CHRAC complex (containing CHRAC1) localizes to pericentric heterochromatin during late S phase when this region is replicated. ACF1 and SNF2H colocalize with heterochromatin and BrdU during S phase [PMID:12434153]. Reason: CHRAC1 is part of the CHRAC complex which is specifically recruited to pericentromeric heterochromatin during DNA replication. This localization is functionally relevant for CHRAC's role in facilitating replication through condensed chromatin. Supporting Evidence: PMID:12434153 ACF1 (ATP-utilizing chromatin assembly and remodeling factor 1) and an ISWI isoform, SNF2H (sucrose nonfermenting-2 homolog), become specifically enriched in replicating pericentromeric heterochromatin
GO:0005721 pericentric heterochromatin	ISO GO_REF:0000114	ACCEPT	Summary: Manual transfer of heterochromatin localization from homologous complexes. This is consistent with CHRAC's established role in heterochromatin replication. Reason: Pericentric heterochromatin localization is supported by experimental data for the CHRAC complex, making this ISO annotation well-justified. The complex is enriched at heterochromatin during late S-phase replication. Supporting Evidence: PMID:12434153 RNAi-mediated depletion of ACF1 specifically impairs the replication of pericentromeric heterochromatin
GO:0006275 regulation of DNA replication	IMP PMID:12434153 An ACF1-ISWI chromatin-remodeling complex is required for DN...	ACCEPT	Summary: This annotation is based on the study showing that depletion of ACF1 (CHRAC component) impairs replication of pericentromeric heterochromatin and delays cell cycle progression through late S phase [PMID:12434153]. CHRAC1 is part of this complex. Reason: The CHRAC complex, of which CHRAC1 is a subunit, regulates DNA replication by facilitating replication through heterochromatin. Loss of complex components leads to replication defects, demonstrating a regulatory role. Supporting Evidence: PMID:12434153 depletion of ACF1 causes a delay in cell-cycle progression through the late stages of S phase
GO:0006334 nucleosome assembly	IDA PMID:14759371 The histone-fold protein complex CHRAC-15/17 enhances nucleo...	ACCEPT	Summary: CHRAC1 (as part of the CHRAC1-POLE3 complex) facilitates chromatin assembly mediated by ACF. The study shows that CHRAC-15/17, p12/CHRAC-17, and NC2 complexes facilitate ACF-mediated chromatin assembly [PMID:14759371]. Reason: Nucleosome assembly is a core function of the CHRAC complex. The CHRAC1-POLE3 heterodimer enhances the chromatin assembly activity of ACF, making this a valid molecular function of CHRAC1. Supporting Evidence: PMID:14759371 CHRAC-15/17, p12/CHRAC-17, and NC2 complexes facilitate ACF-mediated chromatin assembly by a mechanism different from nucleosome sliding enhancement
GO:0006338 chromatin remodeling	IDA PMID:10880450 HuCHRAC, a human ISWI chromatin remodelling complex contains...	ACCEPT	Summary: The original publication identifying HuCHRAC demonstrates that this complex has ATP-dependent chromatin remodeling activity. CHRAC1 is an essential subunit of this complex [PMID:10880450]. Reason: Chromatin remodeling is the defining function of the CHRAC complex. This IDA annotation from the original characterization paper is well-supported. Supporting Evidence: PMID:10880450 HuCHRAC, a human ISWI chromatin remodelling complex contains hACF1 and two novel histone-fold proteins
GO:0008623 CHRAC	NAS PMID:10880450 HuCHRAC, a human ISWI chromatin remodelling complex contains...	ACCEPT	Summary: This NAS annotation for CHRAC complex membership is from the same publication that identified HuCHRAC. While NAS is a weaker evidence code, the data clearly supports CHRAC1 as a CHRAC subunit. Reason: CHRAC1 is definitionally a component of the CHRAC complex - it is named for this complex (CHRAC-15). The original publication provides direct evidence for this complex membership. Supporting Evidence: PMID:10880450 the human homologues of two novel putative histone-fold proteins in Drosophila CHRAC are present in HuCHRAC
GO:0003887 DNA-directed DNA polymerase activity	NAS PMID:10880450 HuCHRAC, a human ISWI chromatin remodelling complex contains...	REMOVE	Summary: This NAS annotation is INCORRECT. PMID:10880450 does not claim that CHRAC1 has DNA polymerase activity. The publication describes CHRAC1 as a histone-fold protein in a chromatin remodeling complex, not as an enzyme. Reason: This annotation is erroneous. CHRAC1 has no DNA polymerase activity. The original publication (PMID:10880450) describes CHRAC1 as a structural histone-fold protein, not an enzyme. The confusion may arise from POLE3's dual role in Pol epsilon, but CHRAC1 is not part of the polymerase complex. Supporting Evidence: PMID:14759371 CHRAC-17 interacts with another histone-fold protein, p12, in DNA polymerase epsilon, but CHRAC-15 is essential for interaction with ACF PMID:10880450 HuCHRAC, a human ISWI chromatin remodelling complex contains hACF1 and two novel histone-fold proteins.
GO:0008622 epsilon DNA polymerase complex	NAS PMID:10880450 HuCHRAC, a human ISWI chromatin remodelling complex contains...	REMOVE	Summary: This annotation is INCORRECT. CHRAC1 is NOT a component of DNA polymerase epsilon. POLE3 (CHRAC1's binding partner) is shared between CHRAC and Pol epsilon, but CHRAC1 itself is specific to the CHRAC complex [PMID:14759371]. Reason: CHRAC1 is not a subunit of DNA polymerase epsilon. While POLE3 (p17) is shared between CHRAC and Pol epsilon, CHRAC1 (p15) is unique to CHRAC. The original literature clearly distinguishes CHRAC1 from Pol epsilon components. Supporting Evidence: PMID:14759371 CHRAC-17 interacts with another histone-fold protein, p12, in DNA polymerase epsilon, but CHRAC-15 is essential for interaction with ACF PMID:10880450 HuCHRAC, a human ISWI chromatin remodelling complex contains hACF1 and two novel histone-fold proteins.
GO:0003677 DNA binding	NAS PMID:10880450 HuCHRAC, a human ISWI chromatin remodelling complex contains...	ACCEPT	Summary: DNA binding is demonstrated for the CHRAC1-POLE3 heterodimer in the original publication. The complex binds naked DNA but not nucleosomes [PMID:10880450]. Reason: DNA binding is experimentally demonstrated for the CHRAC1-containing heterodimer. While a more specific term (double-stranded DNA binding) would be preferable, the NAS annotation accurately reflects CHRAC1's DNA-binding capability. Supporting Evidence: PMID:10880450 two human histone-fold proteins form a stable complex that binds naked DNA but not nucleosomes
GO:0006338 chromatin remodeling	NAS PMID:10880450 HuCHRAC, a human ISWI chromatin remodelling complex contains...	ACCEPT	Summary: Duplicate annotation of chromatin remodeling with NAS evidence. Already covered by IBA and IDA annotations for the same term. Reason: While redundant with other evidence codes, this annotation correctly reflects CHRAC1's role in chromatin remodeling as a CHRAC complex subunit. Supporting Evidence: PMID:10880450 HuCHRAC, a human ISWI chromatin remodelling complex contains hACF1 and two novel histone-fold proteins

Gene Description

Existing Annotations Review

Core Functions

CHRAC1 forms a stable heterodimer with POLE3 via their histone-fold domains. This dimerization is analogous to H2A-H2B and is essential for DNA binding and interaction with the ACF complex [PMID:10880450, PMID:14759371].

The CHRAC1-POLE3 heterodimer binds naked double-stranded DNA but not nucleosomes. This DNA-binding capability is essential for tethering the remodeling complex to chromatin [PMID:10880450].

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