CHAF1B (p60, CAF-1 subunit B) is the WD40-repeat medium subunit of Chromatin Assembly Factor 1 (CAF-1), a heterotrimeric histone H3-H4 chaperone composed of CHAF1A (p150), CHAF1B (p60), and RBBP4 (p48). Within CAF-1, p60 bridges the large subunit CHAF1A and the histone-binding subunit RBBP4, and the direct p150-p60 interaction is required for CAF-1-mediated nucleosome assembly. CAF-1 performs the first step of nucleosome assembly by depositing newly synthesized histones H3.1-H4 onto DNA in a replication-coupled (DNA-synthesis-dependent) manner, and it is also recruited to chromatin undergoing DNA repair. CHAF1B is built from an N-terminal seven-bladed WD40 beta-propeller and a C-terminal disordered region that is heavily phosphorylated in a cell-cycle-dependent fashion. The active complex resides in the nucleus, where it concentrates at DNA replication foci during S phase; during mitosis the p60 subunit is hyperphosphorylated, CAF-1 is inactivated, and p60 is displaced into the cytoplasm. The gene maps to chromosome 21q22.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0005634 nucleus | IBA GO_REF:0000033 | ACCEPT | Summary: Phylogenetically-inferred nuclear localization. The active CAF-1 complex, including CHAF1B, is nuclear and concentrates at DNA replication foci during S phase, so this is the correct primary site of action. Reason: Nuclear localization is well supported experimentally for human CAF-1 in interphase, where p150 and p60 are bound to the nucleus and concentrate at sites of intranuclear DNA replication during S phase. Supporting Evidence: PMID:9614144 In interphase, p150 and p60 are bound to the nucleus, but they predominantly dissociate from chromatin during mitosis. During S phase, p150 and p60 are concentrated at sites of intranuclear DNA replication. |
| GO:0005634 nucleus | IEA GO_REF:0000044 | KEEP AS NON CORE | Summary: Electronic transfer of nuclear localization from the UniProt subcellular location vocabulary. Redundant with the IBA/NAS nucleus annotations but correct; retained as non-core duplicate of the primary nuclear assignment. Reason: Correct localization but a redundant electronic duplicate of the experimentally supported nucleus annotation. Supporting Evidence: file:human/CHAF1B/CHAF1B-uniprot.txt SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:9614144}. |
| GO:0005737 cytoplasm | IEA GO_REF:0000044 | KEEP AS NON CORE | Summary: Electronic transfer of cytoplasmic localization. CHAF1B is cytoplasmic only as the inactive, hyperphosphorylated M-phase form displaced from chromatin; this is a secondary, regulated location, not the site of CAF-1 activity. Reason: Cytoplasmic localization is real but corresponds to the inactive M-phase pool of p60 displaced into the cytosol, not the active nuclear function. Supporting Evidence: file:human/CHAF1B/CHAF1B-uniprot.txt Cytoplasm {ECO:0000269|PubMed:9614144}. Note=DNA replication foci. Cytoplasmic in M phase. |
| GO:0006335 DNA replication-dependent chromatin assembly | IEA GO_REF:0000002 | KEEP AS NON CORE | Summary: InterPro2GO electronic transfer of the core CAF-1 process. Correct and consistent with the direct experimental annotations of the same term, but redundant with them. Reason: Electronic InterPro2GO duplicate of the experimentally supported core process term; correct but redundant. Supporting Evidence: PMID:8858152 copurifies with a chromatin assembly complex (CAC), which contains the three subunits of CAF-1 (p150, p60, p48) and H3 and H4, and promotes DNA replication-dependent chromatin assembly. |
| GO:0005515 protein binding | IPI PMID:16980972 Structure of a human ASF1a-HIRA complex and insights into sp... | MARK AS OVER ANNOTATED | Summary: Bare protein binding capturing the CAF-1 p60 interaction with ASF1a/ASF1b. Although this is a biologically meaningful histone-chaperone hand-off, the GO term itself is uninformative as a molecular function. Reason: Per curation guidelines, bare 'protein binding' is uninformative. The underlying ASF1-p60 interaction is better represented by histone chaperone activity and complex membership terms. Supporting Evidence: PMID:16980972 CAF-1 p60 also uses B domain-like motifs for binding to ASF1a, thereby competing with HIRA. |
| GO:0005515 protein binding | IPI PMID:24981860 Human-chromatin-related protein interactions identify a deme... | MARK AS OVER ANNOTATED | Summary: Bare protein binding from a high-throughput chromatin-related interactome study (interactor ASF1A). Uninformative as a molecular function. Reason: Generic 'protein binding' from a large-scale interaction map; provides no specific molecular function information. Supporting Evidence: PMID:24981860 Human-chromatin-related protein interactions identify a demethylase complex required for chromosome segregation. |
| 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 high-throughput Polycomb complexome AP-MS map (interactor ASF1B). Uninformative as a molecular function. Reason: Generic 'protein binding' from a large-scale interaction map; provides no specific molecular function information. Supporting Evidence: PMID:27705803 A High-Density Map for Navigating the Human Polycomb Complexome. |
| GO:0005515 protein binding | IPI PMID:28514442 Architecture of the human interactome defines protein commun... | MARK AS OVER ANNOTATED | Summary: Bare protein binding from the BioPlex high-throughput AP-MS interactome (interactor ASF1B). Uninformative as a molecular function. Reason: Generic 'protein binding' from a large-scale interaction map; provides no specific molecular function information. Supporting Evidence: PMID:28514442 Architecture of the human interactome defines protein communities and disease networks. |
| GO:0005515 protein binding | IPI PMID:33961781 Dual proteome-scale networks reveal cell-specific remodeling... | MARK AS OVER ANNOTATED | Summary: Bare protein binding from the BioPlex dual proteome-scale interactome (interactor ASF1B). Uninformative as a molecular function. Reason: Generic 'protein binding' from a large-scale interaction map; provides no specific molecular function information. Supporting Evidence: PMID:33961781 Dual proteome-scale networks reveal cell-specific remodeling of the human interactome. |
| GO:0005515 protein binding | IPI PMID:40205054 Multimodal cell maps as a foundation for structural and func... | MARK AS OVER ANNOTATED | Summary: Bare protein binding from a high-throughput multimodal cell-map study (interactor ASF1B). Uninformative as a molecular function. Reason: Generic 'protein binding' from a large-scale interaction map; provides no specific molecular function information. Supporting Evidence: PMID:40205054 Multimodal cell maps as a foundation for structural and functional genomics. |
| GO:0006335 DNA replication-dependent chromatin assembly | IDA PMID:14718166 Histone H3.1 and H3.3 complexes mediate nucleosome assembly ... | ACCEPT | Summary: Direct evidence that CAF-1 (containing CHAF1B) mediates the DNA-synthesis-dependent nucleosome assembly pathway via histone H3.1-H4 deposition. This is the core biological process of the gene. Reason: CHAF1B is an essential subunit of the CAF-1 complex that mediates replication-coupled (DNA-synthesis-dependent) nucleosome assembly, the gene's defining process. 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) nucleoplasmic localization, consistent with the nuclear site of CAF-1 action. Retained as a non-core refinement of the primary nucleus annotation. Reason: Consistent nuclear/nucleoplasmic localization; a more granular but non-core refinement of the core nucleus assignment. Supporting Evidence: PMID:9614144 In interphase, p150 and p60 are bound to the nucleus. |
| GO:0000785 chromatin | IDA PMID:9614144 Nucleosome assembly activity and intracellular localization ... | ACCEPT | Summary: CAF-1 binds chromatin and concentrates at replication foci during S phase, dissociating during mitosis. Chromatin localization is consistent with the gene's role in chromatin assembly on replicating DNA. Reason: CHAF1B/CAF-1 acts directly on chromatin at sites of DNA replication; chromatin localization is well supported and integral to its function. Supporting Evidence: PMID:9614144 In interphase, p150 and p60 are bound to the nucleus, but they predominantly dissociate from chromatin during mitosis. 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: Direct evidence that human CAF-1 (including p60) mediates nucleosome assembly coupled to DNA synthesis. Core process of the gene. Reason: Replication-coupled nucleosome assembly is the defining function of CAF-1 and its CHAF1B subunit. Supporting Evidence: PMID:9614144 Human CAF-1 efficiently mediates nucleosome assembly during complementary DNA strand synthesis in G1, S, and G2 phase cytosolic extracts. |
| GO:0033186 CAF-1 complex | IPI PMID:9614144 Nucleosome assembly activity and intracellular localization ... | ACCEPT | Summary: CHAF1B (p60) is a core subunit of the CAF-1 complex together with CHAF1A (p150) and RBBP4 (p48). This is the defining complex membership of the gene. Reason: CHAF1B is one of the three constitutive subunits of CAF-1; complex membership is central to its identity and function. Supporting Evidence: PMID:9614144 All three subunits of human CAF-1 (p150, p60, and p48) are present during the entire cell cycle. |
| GO:0006335 DNA replication-dependent chromatin assembly | IDA PMID:8858152 Nucleosome assembly by a complex of CAF-1 and acetylated his... | ACCEPT | Summary: The chromatin assembly complex containing the three CAF-1 subunits and histones H3/H4 promotes DNA replication-dependent chromatin assembly. Core process. Reason: Direct biochemical evidence that the CAF-1-containing complex promotes replication-dependent chromatin assembly, the gene's core process. Supporting Evidence: PMID:8858152 copurifies with a chromatin assembly complex (CAC), which contains the three subunits of CAF-1 (p150, p60, p48) and H3 and H4, and promotes DNA replication-dependent chromatin assembly. |
| GO:0032991 protein-containing complex | IDA PMID:14718166 Histone H3.1 and H3.3 complexes mediate nucleosome assembly ... | MARK AS OVER ANNOTATED | Summary: Generic complex membership. CHAF1B is part of the specific CAF-1 complex (GO:0033186), so the root-level protein-containing complex term is an over-general annotation. Reason: The specific CAF-1 complex term is annotated and is far more informative; the generic protein-containing complex term adds no information. Supporting Evidence: PMID:14718166 these complexes possess one molecule each of H3.1/H3.3 and H4, suggesting that histones H3 and H4 exist as dimeric units that are important intermediates in nucleosome formation. |
| GO:0000785 chromatin | IDA PMID:14718166 Histone H3.1 and H3.3 complexes mediate nucleosome assembly ... | ACCEPT | Summary: CAF-1 acts on chromatin during replication-coupled H3.1-H4 deposition; chromatin localization is consistent with the gene's nucleosome assembly role. Reason: Chromatin is the direct substrate location for CAF-1-mediated nucleosome assembly; well supported and functionally integral. 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:0033186 CAF-1 complex | IDA PMID:8858152 Nucleosome assembly by a complex of CAF-1 and acetylated his... | ACCEPT | Summary: CHAF1B is a constitutive subunit of the CAF-1 complex (with CHAF1A and RBBP4). Defining complex membership. Reason: Core CAF-1 complex membership, biochemically demonstrated in the chromatin assembly complex containing all three subunits. Supporting Evidence: PMID:8858152 a chromatin assembly complex (CAC), which contains the three subunits of CAF-1 (p150, p60, p48) and H3 and H4. |
| GO:0005829 cytosol | HDA PMID:16780588 Cell array-based intracellular localization screening reveal... | KEEP AS NON CORE | Summary: High-throughput colocalization with the cytosol. CHAF1B is cytosolic only as the inactive M-phase form translocated out of the nucleus during cell division; this is a regulated secondary location, not the site of activity. Reason: The cytosolic pool corresponds to the inactive M-phase form of p60; it is a genuine but non-core, cell-cycle-restricted location. Supporting Evidence: PMID:16780588 The chromatin assembly factor I p60 subunit (CHAF1B) protein translocated from the nucleus into the cytoplasm during cell division. |
| GO:0005654 nucleoplasm | HDA PMID:16780588 Cell array-based intracellular localization screening reveal... | KEEP AS NON CORE | Summary: High-throughput colocalization with the nucleoplasm, consistent with the nuclear site of CAF-1 action at interphase. Reason: Nucleoplasmic localization is consistent with the core nuclear function but is a non-core refinement supported by high-throughput data. Supporting Evidence: PMID:16780588 most of the CHAF1B protein localizing in the nucleus at interphase, where it is involved in chromatin assembly and DNA replication. |
| GO:0005634 nucleus | NAS PMID:9614144 Nucleosome assembly activity and intracellular localization ... | ACCEPT | Summary: Nuclear localization of CAF-1/p60 in interphase, where the complex performs replication-coupled chromatin assembly. Core localization. Reason: The active CAF-1 complex including CHAF1B is nuclear; this is the primary site of its function. Supporting Evidence: PMID:9614144 In interphase, p150 and p60 are bound to the nucleus. |
| GO:0005737 cytoplasm | NAS PMID:9614144 Nucleosome assembly activity and intracellular localization ... | KEEP AS NON CORE | Summary: Cytoplasmic localization corresponds to the inactive, hyperphosphorylated M-phase form of p60 displaced from chromatin; a regulated secondary location. Reason: Real but non-core; reflects the inactive mitotic pool rather than the active nuclear function. Supporting Evidence: PMID:9614144 In mitosis, the p60 subunit of inactive CAF-1 is hyperphosphorylated. |
| GO:0042393 histone binding | NAS PMID:7600578 The p150 and p60 subunits of chromatin assembly factor I: a ... | ACCEPT | Summary: CAF-1 p150/p60 form complexes with newly synthesized histones H3 and acetylated H4, and p60 binds histones H3.1/H3.2/H3.1t. Histone binding is a core molecular function of this histone chaperone subunit. Cryo-EM structural work (Liu et al. 2023, Science) specifically identifies p60/CHAF1B as the principal H3-H4-binding subunit of human CAF-1, contacting H4 through its ventral beta-propeller surface and engaging a partially unfolded H3 region; this is direct, subunit-specific structural support for histone binding by CHAF1B itself rather than only by the holo-complex. Reason: CHAF1B directly contacts histones in the CAF-1 complex (newly synthesized H3-H4; H3.1/H3.2/H3.1t), supporting histone binding as a core MF. The falcon deep-research report (summarizing Liu et al. 2023 cryo-EM) adds subunit-resolved structural evidence that p60 is the principal H3-H4-binding component and is required for CAF-1 histone binding, reinforcing this as a direct molecular function of CHAF1B. Supporting Evidence: PMID:7600578 p150 and p60 form complexes with newly synthesized histones H3 and acetylated H4 in human cell extracts. file:human/CHAF1B/CHAF1B-uniprot.txt Interacts with histones H3.1, H3.2 and H3.1t (PubMed:33857403). file:human/CHAF1B/CHAF1B-deep-research-falcon.md The primary molecular function of CHAF1B is to serve as the principal histone H3-H4 binding subunit within the CAF-1 complex. |
| GO:0003682 chromatin binding | TAS PMID:7600578 The p150 and p60 subunits of chromatin assembly factor I: a ... | KEEP AS NON CORE | Summary: Chromatin binding is consistent with CAF-1 acting on replicating chromatin, but it is a generic molecular function relative to the more informative histone chaperone / histone binding activities of CHAF1B. Reason: Supported but generic; histone binding and histone chaperone activity are more informative descriptors of the molecular function. Supporting Evidence: PMID:9614144 During S phase, p150 and p60 are concentrated at sites of intranuclear DNA replication. |
| GO:0140713 histone chaperone activity | IC file:human/CHAF1B/CHAF1B-uniprot.txt | NEW | Summary: Proposed annotation not present in the current GOA for CHAF1B. Reason: CHAF1B is a subunit of the CAF-1 histone H3-H4 chaperone and directly binds newly synthesized histones H3-H4 (and H3.1/H3.2/H3.1t). The molecular function of the complex is histone chaperone activity, which is not currently captured in the CHAF1B GOA and would be more informative than the existing bare protein binding annotations. Cryo-EM structural work (Liu et al. 2023) shows p60 is not merely a passive scaffold but is required for CAF-1 histone binding and nucleosome assembly activity, supporting a subunit-level histone chaperone activity annotation. Supporting Evidence: file:human/CHAF1B/CHAF1B-uniprot.txt Acts as a component of the histone chaperone complex chromatin assembly factor 1 (CAF-1), which assembles histone octamers onto DNA during replication and repair. file:human/CHAF1B/CHAF1B-deep-research-falcon.md CHAF1B directly binds H3-H4 and is absolutely required for CAF-1's nucleosome assembly activity |
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Download this section (compressed HTML)Q: Is CHAF1B's histone-chaperone activity exerted only as part of the CAF-1 complex, or does the isolated p60 subunit have an autonomous histone-binding / chaperone role that warrants a gene-level molecular-function annotation?
Suggested experts: Kaufman PD, Almouzni G
Q: Does cell-cycle-dependent phosphorylation of the C-terminal disordered region of CHAF1B directly regulate CAF-1 assembly activity and its nuclear-cytoplasmic partitioning?
Suggested experts: Marheineke K, Krude T
Experiment: Acute degradation (e.g., auxin-inducible degron) of CHAF1B in human cells followed by SCAR-seq / nascent-chromatin capture to measure replication-coupled new-histone deposition and parental-histone recycling.
Hypothesis: CHAF1B is required for replication-coupled H3.1-H4 deposition and its loss impairs nucleosome assembly genome-wide during S phase.
Type: replication-coupled nucleosome assembly assay
Experiment: Generate phospho-null and phospho-mimetic mutants of the mapped CHAF1B phosphosites and assay CAF-1 nucleosome assembly activity, complex integrity, and subcellular localization across the cell cycle.
Hypothesis: Mitotic hyperphosphorylation of the CHAF1B C-terminal tail inactivates CAF-1 and drives its cytoplasmic relocalization.
Type: phosphomutant functional and localization assay
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