CHAF1A (p150) is the large subunit of Chromatin Assembly Factor 1 (CAF-1), a heterotrimeric histone H3-H4 chaperone composed of CHAF1A, CHAF1B (p60) and RBBP4 (p48). CAF-1 performs the first step of nucleosome assembly, depositing newly synthesized histones H3 and H4 (the replicative variant H3.1) onto DNA during replication-coupled and repair-coupled chromatin assembly; histones H2A/H2B are subsequently added to complete the octamer. CHAF1A binds histones H3-H4 directly and couples assembly to the replication fork by binding the sliding clamp PCNA via its N-terminal region. It also contains a PxVxL motif that binds the chromo shadow domain of HP1 (CBX5), contributing to heterochromatin maintenance by delivering newly synthesized HP1 proteins to heterochromatic replication foci. CHAF1A homodimerizes, an activity required for chromatin assembly, and acts in the nucleus, concentrating at DNA replication foci during S phase.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0005634 nucleus | IBA GO_REF:0000033 | KEEP AS NON CORE | Summary: CHAF1A is a nuclear protein; as the large subunit of CAF-1 it assembles chromatin in the nucleus and concentrates at DNA replication foci during S phase. Nucleus is correct but is a broad localization term. Reason: Nuclear localization is well-supported by direct experimental data and by the phylogenetic inference, but is a general cellular component term rather than the core histone chaperone function. More specific localization (chromatin, nucleoplasm) is captured by other annotations. Supporting Evidence: PMID:9614144 During S phase, p150 and p60 are concentrated at sites of intranuclear DNA replication. file:human/CHAF1A/CHAF1A-uniprot.txt SUBCELLULAR LOCATION; Nucleus. Note=DNA replication foci. |
| GO:0005634 nucleus | IEA GO_REF:0000044 | KEEP AS NON CORE | Summary: Nuclear localization assigned by UniProt subcellular location keyword mapping. Consistent with experimental data but a broad term. Reason: Correct localization but general; duplicates the IBA nucleus annotation and is less specific than the chromatin/nucleoplasm annotations. Supporting Evidence: file:human/CHAF1A/CHAF1A-uniprot.txt SUBCELLULAR LOCATION; Nucleus. |
| GO:0005515 protein binding | IPI PMID:15805117 Proliferating cell nuclear antigen (PCNA) may function as a ... | MARK AS OVER ANNOTATED | Summary: This IPI annotation (WITH PCNA, P12004) reflects the biologically important CHAF1A-PCNA interaction that couples chromatin assembly to the replication fork, but is captured only by the uninformative generic term protein binding. Reason: The bare protein binding term conveys no specific molecular function. The underlying PCNA interaction is biologically meaningful and is represented more informatively by a proposed PCNA binding annotation; the generic term should not be retained as a core function. Supporting Evidence: PMID:15805117 PCNA may function as a double homotrimer complex in the mammalian cell. |
| GO:0005515 protein binding | IPI PMID:16826239 The replication kinase Cdc7-Dbf4 promotes the interaction of... | MARK AS OVER ANNOTATED | Summary: IPI annotation (WITH PCNA, P12004) from the study showing Cdc7-Dbf4 phosphorylation of p150 promotes PCNA binding. Biologically meaningful but captured only by the generic protein binding term. Reason: Bare protein binding is uninformative. The specific p150-PCNA interaction is better represented by a dedicated PCNA binding annotation. Supporting Evidence: PMID:16826239 its targeting to sites of DNA synthesis involves a physical interaction between its largest subunit, p150, and the homotrimeric sliding clamp, proliferating cell nuclear antigen (PCNA). |
| GO:0005515 protein binding | IPI PMID:17474147 Systematic identification of SH3 domain-mediated human prote... | MARK AS OVER ANNOTATED | Summary: Bare protein binding from a high-throughput SH3 domain peptide array screen (WITH NCK1, PIK3R1). No specific function conveyed. Reason: Generic protein binding from a large-scale interaction screen does not represent a specific molecular function and these interactions are not part of the core histone chaperone activity. Supporting Evidence: PMID:17474147 Systematic identification of SH3 domain-mediated human protein-protein interactions by peptide array target screening. |
| GO:0005515 protein binding | IPI PMID:19498464 The HP1alpha-CAF1-SetDB1-containing complex provides H3K9me1... | MARK AS OVER ANNOTATED | Summary: IPI annotation (WITH CBX5/HP1alpha, P45973) from the HP1alpha-CAF1-SetDB1 study. Reflects the HP1 interaction but only via the generic protein binding term. Reason: Bare protein binding is uninformative. The CHAF1A-HP1 (CBX5) interaction is captured more specifically by the chromo shadow domain binding annotation. Supporting Evidence: PMID:19498464 the histone H3K9 methyltransferase SetDB1 associates with the specific heterochromatin protein 1alpha (HP1alpha)-chromatin assembly factor 1 (CAF1) chaperone complex. |
| GO:0005515 protein binding | IPI PMID:20562864 Human POGZ modulates dissociation of HP1alpha from mitotic c... | MARK AS OVER ANNOTATED | Summary: IPI annotation (WITH CBX5, P45973) from the POGZ/HP1alpha study, which also mapped the V240/L242 PxVxL residues required for CBX5 binding. Captured only by generic protein binding. Reason: Bare protein binding is uninformative. The CHAF1A-CBX5 interaction is represented specifically by the chromo shadow domain binding annotation. Supporting Evidence: PMID:20562864 Human POGZ modulates dissociation of HP1alpha from mitotic chromosome arms through Aurora B activation. |
| GO:0005515 protein binding | IPI PMID:20936779 A human MAP kinase interactome. | MARK AS OVER ANNOTATED | Summary: Bare protein binding from a large-scale MAP kinase interactome screen (WITH YWHAE/14-3-3 epsilon). No specific function conveyed. Reason: Generic protein binding from a high-throughput interactome map; not a specific molecular function and not part of the core activity. Supporting Evidence: PMID:20936779 A human MAP kinase interactome. |
| GO:0005515 protein binding | IPI PMID:21570500 The p150 subunit of the histone chaperone Caf-1 interacts wi... | MARK AS OVER ANNOTATED | Summary: IPI annotation (WITH GFI1, Q99684) showing p150 is part of the Gfi1 transcriptional repression complex; the same study confirms p150 binds histones H3 and H4 directly. The Gfi1 interaction itself is captured only by generic protein binding. Reason: The bare protein binding term for the Gfi1 interaction is uninformative. The biologically core histone H3/H4 binding demonstrated in this paper is captured by a proposed histone binding annotation rather than this generic term. Supporting Evidence: PMID:21570500 Since p150 binds directly to histones H3 and H4, our findings suggest that p150 may link the DNA-bound Gfi1 repressor complex to histones enabling modifications required for transcriptional silencing. |
| GO:0005515 protein binding | IPI PMID:23075851 DAXX envelops a histone H3.3-H4 dimer for H3.3-specific reco... | MARK AS OVER ANNOTATED | Summary: IPI annotation (WITH histones H3-3B/H3C15) from a DAXX-H3.3 structural study. Although histone partners are involved, this is a DAXX-focused study and the annotation is captured only by generic protein binding. Reason: Bare protein binding is uninformative. CHAF1A histone H3-H4 binding is better represented by a dedicated histone binding annotation supported by direct CAF-1 studies. Supporting Evidence: PMID:23075851 DAXX envelops a histone H3.3-H4 dimer for H3.3-specific recognition. |
| GO:0005515 protein binding | IPI PMID:24981860 Human-chromatin-related protein interactions identify a deme... | MARK AS OVER ANNOTATED | Summary: IPI annotation (WITH CBX5, P45973) from a chromatin-protein interaction study. Reflects the HP1 interaction but only via generic protein binding. Reason: Bare protein binding is uninformative; the CHAF1A-CBX5 interaction is captured specifically by chromo shadow domain binding. Supporting Evidence: PMID:24981860 Human-chromatin-related protein interactions identify a demethylase complex required for chromosome segregation. |
| GO:0005515 protein binding | IPI PMID:25416956 A proteome-scale map of the human interactome network. | MARK AS OVER ANNOTATED | Summary: Bare protein binding from a proteome-scale binary interactome map. No specific function conveyed. Reason: Generic protein binding from a high-throughput interactome study; not a specific molecular function. Supporting Evidence: PMID:25416956 A proteome-scale map of the human interactome network. |
| GO:0005515 protein binding | IPI PMID:26496610 A human interactome in three quantitative dimensions organiz... | MARK AS OVER ANNOTATED | Summary: Bare protein binding from a quantitative interactome study (WITH PCNA, PIK3R1). No specific function conveyed by the generic term. Reason: Generic protein binding from a high-throughput interactome map; the PCNA interaction is better captured by a dedicated PCNA binding annotation. Supporting Evidence: PMID:26496610 A human interactome in three quantitative dimensions organized by stoichiometries and abundances. |
| GO:0005515 protein binding | IPI PMID:27705803 A High-Density Map for Navigating the Human Polycomb Complex... | MARK AS OVER ANNOTATED | Summary: Bare protein binding from a Polycomb complexome map (WITH CBX5). No specific function conveyed. Reason: Generic protein binding from a high-throughput complexome study; not a specific molecular function. Supporting Evidence: PMID:27705803 A High-Density Map for Navigating the Human Polycomb Complexome. |
| GO:0005515 protein binding | IPI PMID:31980649 Extensive rewiring of the EGFR network in colorectal cancer ... | MARK AS OVER ANNOTATED | Summary: Bare protein binding from an EGFR/KRAS network rewiring study (WITH YWHAE). No specific function conveyed. Reason: Generic protein binding from a large-scale network study; not a specific molecular function and not part of the core activity. Supporting Evidence: PMID:31980649 Extensive rewiring of the EGFR network in colorectal cancer cells expressing transforming levels of KRAS(G13D). |
| GO:0005515 protein binding | IPI PMID:32296183 A reference map of the human binary protein interactome. | MARK AS OVER ANNOTATED | Summary: Bare protein binding from a reference binary interactome map (multiple partners). No specific function conveyed. Reason: Generic protein binding from a high-throughput binary interactome study; not a specific molecular function. Supporting Evidence: PMID:32296183 A reference map of the human binary protein interactome. |
| GO:0005515 protein binding | IPI PMID:33961781 Dual proteome-scale networks reveal cell-specific remodeling... | MARK AS OVER ANNOTATED | Summary: Bare protein binding from a proteome-scale interactome study (WITH histone H3-3B). No specific function conveyed by the generic term. Reason: Generic protein binding from a high-throughput interactome map; histone binding is better captured by a dedicated annotation. Supporting Evidence: PMID:33961781 Dual proteome-scale networks reveal cell-specific remodeling of the human interactome. |
| GO:0005515 protein binding | IPI PMID:35271311 OpenCell: Endogenous tagging for the cartography of human ce... | MARK AS OVER ANNOTATED | Summary: Bare protein binding from the OpenCell endogenous-tagging interactome (WITH YWHAE). No specific function conveyed. Reason: Generic protein binding from a high-throughput cartography study; not a specific molecular function. Supporting Evidence: PMID:35271311 OpenCell: Endogenous tagging for the cartography of human cellular organization. |
| GO:0042802 identical protein binding | IPI PMID:16826239 The replication kinase Cdc7-Dbf4 promotes the interaction of... | ACCEPT | Summary: IPI annotation (WITH CHAF1A, Q13111) capturing the homodimerization of p150. CHAF1A is a homodimer, and dimerization is required for competence for chromatin assembly. Reason: Identical protein binding accurately represents the well-documented p150 homodimerization, which is functionally important for chromatin assembly. Supporting Evidence: file:human/CHAF1A/CHAF1A-uniprot.txt SUBUNIT; Homodimer. REGION 642..678; Necessary for homodimerization and competence for chromatin assembly. |
| GO:0006335 DNA replication-dependent chromatin assembly | IDA PMID:14718166 Histone H3.1 and H3.3 complexes mediate nucleosome assembly ... | ACCEPT | Summary: CAF-1 (with the replicative histone variant H3.1) mediates DNA-synthesis-dependent nucleosome assembly. This is the core biological process for CHAF1A. Reason: Directly supported by experimental data distinguishing CAF-1/H3.1 (replication-coupled) from HIRA/H3.3 (replication-independent) assembly; represents the core function. Supporting Evidence: PMID:14718166 The H3.1 and H3.3 complexes contain distinct histone chaperones, CAF-1 and HIRA, that we show are necessary to mediate DNA-synthesis-dependent and -independent nucleosome assembly, respectively. |
| GO:0005654 nucleoplasm | IDA GO_REF:0000052 | KEEP AS NON CORE | Summary: Immunofluorescence (HPA) localizes CHAF1A to the nucleoplasm, consistent with its nuclear histone chaperone role. Reason: Accurate subcellular localization but a general component term, not the core molecular function. Supporting Evidence: file:human/CHAF1A/CHAF1A-uniprot.txt SUBCELLULAR LOCATION; Nucleus. Note=DNA replication foci. |
| GO:0000785 chromatin | IDA PMID:9614144 Nucleosome assembly activity and intracellular localization ... | ACCEPT | Summary: CHAF1A localizes to chromatin, concentrating at intranuclear DNA replication foci during S phase, consistent with deposition of histones onto replicating DNA. Reason: Direct experimental localization to chromatin/replication sites is well-supported and biologically appropriate for a histone chaperone acting at the replication fork. Supporting Evidence: PMID:9614144 During S phase, p150 and p60 are concentrated at sites of intranuclear DNA replication. |
| GO:0006335 DNA replication-dependent chromatin assembly | IDA PMID:9614144 Nucleosome assembly activity and intracellular localization ... | ACCEPT | Summary: CAF-1 nucleosome assembly activity is cell-cycle regulated, and active CAF-1 (isolated as a 6.5S complex) deposits histones at S-phase replication foci. Core biological process for CHAF1A. Reason: Directly supported experimental evidence for replication-coupled chromatin assembly; represents the core function. Supporting Evidence: PMID:9614144 Active CAF-1 can be isolated as a 6.5 S complex from G1, S, and G2 phase nuclei. |
| GO:0033186 CAF-1 complex | IPI PMID:9614144 Nucleosome assembly activity and intracellular localization ... | ACCEPT | Summary: CHAF1A (p150) is a constitutive subunit of the CAF-1 complex together with CHAF1B (p60) and RBBP4 (p48). Core complex membership. Reason: Well-established as the large subunit of the heterotrimeric CAF-1 complex; directly supported. Supporting Evidence: PMID:9614144 Active CAF-1 can be isolated as a 6.5 S complex from G1, S, and G2 phase nuclei. file:human/CHAF1A/CHAF1A-uniprot.txt SUBUNIT; Part of the CAF-1 complex that contains RBBP4, CHAF1B and CHAF1A. |
| GO:0006335 DNA replication-dependent chromatin assembly | IDA PMID:8858152 Nucleosome assembly by a complex of CAF-1 and acetylated his... | ACCEPT | Summary: A complex of CAF-1 and acetylated histones H3/H4 carries out nucleosome assembly. Core biological process. Reason: Direct experimental demonstration of CAF-1-mediated nucleosome assembly with newly synthesized acetylated histones; core function. Supporting Evidence: PMID:8858152 Nucleosome assembly by a complex of CAF-1 and acetylated histones H3/H4. |
| GO:0032991 protein-containing complex | IDA PMID:14718166 Histone H3.1 and H3.3 complexes mediate nucleosome assembly ... | MARK AS OVER ANNOTATED | Summary: CHAF1A is part of a protein complex (the H3.1-CAF-1 histone chaperone complex). This is a very general complex term. Reason: The generic protein-containing complex term is uninformative; the specific CAF-1 complex membership is captured by the GO:0033186 annotations. Supporting Evidence: PMID:14718166 Histone H3.1 and H3.3 complexes mediate nucleosome assembly pathways dependent or independent of DNA synthesis. |
| GO:0000785 chromatin | IDA PMID:14718166 Histone H3.1 and H3.3 complexes mediate nucleosome assembly ... | ACCEPT | Summary: CHAF1A/CAF-1 associates with chromatin in the context of H3.1 deposition onto replicating DNA. Reason: Direct experimental localization to chromatin is appropriate for a histone chaperone depositing histones onto DNA. Supporting Evidence: PMID:14718166 The H3.1 and H3.3 complexes contain distinct histone chaperones, CAF-1 and HIRA. |
| GO:0033186 CAF-1 complex | IDA PMID:8858152 Nucleosome assembly by a complex of CAF-1 and acetylated his... | ACCEPT | Summary: CHAF1A is part of the CAF-1 chromatin assembly complex (CAC) containing p150, p60 and p48. Core complex membership. Reason: Directly supported membership in the heterotrimeric CAF-1 complex; core. Supporting Evidence: PMID:8858152 a chromatin assembly complex (CAC), which contains the three subunits of CAF-1 (p150, p60, p48). |
| GO:0070087 chromo shadow domain binding | IPI PMID:15882967 The mammalian heterochromatin protein 1 binds diverse nuclea... | ACCEPT | Summary: CHAF1A p150 carries a PxVxL motif that binds directly and with high affinity to the chromo shadow domain of HP1 (CBX5), mediating recruitment of HP1 to heterochromatic replication foci. Reason: Specific, experimentally supported molecular function (PxVxL-chromo shadow domain binding) underlying CHAF1A's role in heterochromatin maintenance. Supporting Evidence: PMID:15882967 KAP-1, CAF-1 p150, and NIPBL carry a canonical amino acid motif, PxVxL, which binds directly to the CSD with high affinity. |
| GO:0003682 chromatin binding | TAS PMID:7600578 The p150 and p60 subunits of chromatin assembly factor I: a ... | ACCEPT | Summary: CHAF1A binds chromatin, consistent with its function depositing histones onto replicating DNA as the large subunit of CAF-1. Reason: Supported molecular function; CHAF1A engages chromatin/DNA during nucleosome assembly. Supporting Evidence: PMID:7600578 The p150 and p60 subunits of chromatin assembly factor I; a molecular link between newly synthesized histones and DNA replication. |
| GO:0042393 histone binding | IC PMID:21570500 The p150 subunit of the histone chaperone Caf-1 interacts wi... | NEW | Summary: Proposed annotation not present in the current GOA for CHAF1A. Reason: CHAF1A p150 binds directly to histones H3 and H4 (including the replicative variants H3.1, H3.2 and H3.1t), the core substrate-recognition activity of its histone chaperone function, yet there is no histone binding MF annotation; the histone interactions are currently captured only by generic protein binding. Supporting Evidence: PMID:21570500 p150 binds directly to histones H3 and H4. file:human/CHAF1A/CHAF1A-uniprot.txt Interacts with histones H3.1, H3.2 and H3.1t (PubMed:33857403). |
| GO:0140713 histone chaperone activity | IC PMID:8858152 Nucleosome assembly by a complex of CAF-1 and acetylated his... | NEW | Summary: Proposed annotation not present in the current GOA for CHAF1A. Reason: As the large subunit of CAF-1, CHAF1A directly mediates histone chaperone activity (escorting and depositing H3-H4), which is its core molecular function but is not currently annotated as a molecular function term. Supporting Evidence: PMID:8858152 Nucleosome assembly by a complex of CAF-1 and acetylated histones H3/H4. PMID:14718166 The H3.1 and H3.3 complexes contain distinct histone chaperones, CAF-1 and HIRA. |
| GO:0006334 nucleosome assembly | IC file:human/CHAF1A/CHAF1A-uniprot.txt | NEW | Summary: Proposed annotation not present in the current GOA for CHAF1A. Reason: CHAF1A drives nucleosome assembly; this BP is asserted by UniProt GO refs (IDA, GO_Central) but is absent from the current GOA set and complements the more specific DNA replication-dependent chromatin assembly term. Supporting Evidence: file:human/CHAF1A/CHAF1A-uniprot.txt GO:0006334; P:nucleosome assembly; IDA:GO_Central. |
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Download this section (compressed HTML)Q: How is CHAF1A-mediated histone deposition coordinated with the upstream histone supply chaperones (ASF1A/ASF1B) and the downstream H2A/H2B deposition machinery during a single round of replication?
Q: To what extent is the heterochromatin-maintenance role of CHAF1A (via HP1/CBX5 delivery) separable from its bulk replication-coupled nucleosome assembly function?
Experiment: Acute degron-mediated depletion of CHAF1A in synchronized cells followed by nascent-chromatin (NCC/iPOND) proteomics and MNase-seq to quantify the kinetics of replication-coupled H3.1-H4 deposition and nucleosome maturation genome-wide.
Experiment: Structure-guided separation-of-function mutants disrupting the PCNA-binding region (1-49), the PxVxL/HP1 motif (V240/L242), or the homodimerization region (642-678), assayed for in vitro nucleosome assembly and for heterochromatin re-establishment after replication.
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