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CHAF1B (gene symbol: CHAF1B, UniProt: Q13112) encodes the p60 subunit of the human chromatin assembly factor 1 (CAF-1) complex. The protein is also known as CAF-1 subunit B, CAF-I p60, or M-phase phosphoprotein 7 (liu2023structuralinsightsinto pages 1-3, wen2022dynamicactivityof pages 1-2). CHAF1B belongs to the WD repeat HIR1 family and contains characteristic WD40-repeat domains that form a seven-bladed β-propeller structure (liu2023structuralinsightsinto pages 1-3, liu2023structuralinsightsinto pages 3-4). The human CAF-1 complex is heterotrimeric, consisting of CHAF1A (p150), CHAF1B (p60), and RBBP4 (p48) subunits (liu2023structuralinsightsinto pages 1-3, wen2022dynamicactivityof pages 1-2).
The primary molecular function of CHAF1B is to serve as the principal histone H3-H4 binding subunit within the CAF-1 complex. Groundbreaking structural studies using cryo-electron microscopy have revealed the molecular details of CHAF1B's histone binding mechanism (liu2023structuralinsightsinto pages 1-3, liu2023structuralinsightsinto pages 3-4). The p60 subunit binds one histone H3-H4 heterodimer mainly through its ventral surface area, which is enriched with negatively charged residues along with several tyrosine and phenylalanine residues (liu2023structuralinsightsinto pages 6-8).
The structural analysis shows that histone H4 interacts extensively with the central area of p60's ventral surface through residues located at the C-terminal end of α2, the entire α3 helix, and the following C-terminal tail (liu2023structuralinsightsinto pages 6-8). Notably, H4 residues Tyr88 and Lys91 insert into the central basin of the p60 ventral surface, with Tyr88 surrounded by hydrophobic residues (Tyr133, Tyr173, and Phe236) and Lys91 positioned within bonding distances from Asp86 and Asp131 of p60 (liu2023structuralinsightsinto pages 6-8). Additionally, a partially unfolded αN region of histone H3 wraps around the perimeter of the p60 β-propeller (liu2023structuralinsightsinto pages 1-3, liu2023structuralinsightsinto pages 4-6).
CHAF1B directly binds H3-H4 and is absolutely required for CAF-1's nucleosome assembly activity (liu2023structuralinsightsinto pages 1-3). The p60 subunit plays a critical role in preventing premature H3-H4 tetramer formation through steric constraints—the binding mode ensures that only one H3-H4 heterodimer can bind to one CAF-1 complex, as joining a second H3-H4 dimer in the configuration of a tetramer would be sterically prohibited by p60 (liu2023structuralinsightsinto pages 6-8).
CHAF1B contains a C-terminal ASF1-interacting motif (B domain) that facilitates the transfer of newly synthesized H3-H4 from the upstream histone chaperone ASF1 to CAF-1 (liu2023structuralinsightsinto pages 1-3). This interaction is crucial for the coordinated handoff of histones during the chromatin assembly pathway. Conformational changes in the CAF-1 complex allow the delivery of H3-H4 dimers from ASF1 to CAF-1, providing direct evidence for coordination between histone chaperones (zhang2020thereplisomeguides pages 1-2).
While the CHAF1A subunit contains the primary DNA-binding domains (WHD and KER), structural and biochemical analyses indicate that CHAF1B also contacts DNA in assembled intermediates (liu2023structuralinsightsinto pages 8-9). The p60 subunit contains a DNA-binding surface adjacent to its H4-binding region and stabilizes histone-DNA intermediates during chromatin assembly (liu2023structuralinsightsinto pages 8-9). Electrophoretic mobility shift assays confirmed p60's DNA-binding capability (liu2023structuralinsightsinto pages 8-9).
CHAF1B is a nuclear protein that carries out its functions within the nucleus (ma2021histonechaperonecaf‐1 pages 1-2, saleiro2023targetingchaf1benhances pages 1-2). The protein localizes to several distinct nuclear compartments and structures:
Replication Forks: CHAF1B is enriched at DNA replication forks during S-phase, where it functions as part of the CAF-1 complex to deposit newly synthesized histones (zhang2020thereplisomeguides pages 1-2, nair2022unorthodoxpcnabinding pages 1-3).
Nuclear Bodies: Recent studies have revealed that CAF-1, including CHAF1B, forms phase-separated nuclear bodies with liquid-liquid phase separation (LLPS) properties (ma2021histonechaperonecaf‐1 pages 1-2). These CAF-1 nuclear bodies are enriched on specific chromatin regions and recruit epigenetic modifiers and histone chaperones (ma2021histonechaperonecaf‐1 pages 1-2).
Chromatin: CHAF1B is enriched on chromatin, particularly at sites undergoing DNA replication or repair (zhang2020histoneloaderscaf1 pages 1-2).
Nuclear Compartment Interactions: CHAF1B has been identified as a ULK1-interactive protein in the nuclear compartment of myeloproliferative neoplasm cells (saleiro2023targetingchaf1benhances pages 1-2).
The primary pathway in which CHAF1B functions is replication-coupled (RC) nucleosome assembly during S-phase of the cell cycle (liu2023structuralinsightsinto pages 1-3, wen2022dynamicactivityof pages 1-2, zhang2020thereplisomeguides pages 1-2). CAF-1 is recruited to replication forks through interaction with PCNA (proliferating cell nuclear antigen), the replication processivity factor (zhang2020thereplisomeguides pages 1-2, nair2022unorthodoxpcnabinding pages 1-3). Although the direct PCNA-binding determinants map mainly to the CHAF1A/p150 subunit, CHAF1B functions within the PCNA-recruited CAF-1 complex to execute H3-H4 deposition (nair2022unorthodoxpcnabinding pages 1-3).
The mechanism of nucleosome assembly proceeds through several steps (liu2023structuralinsightsinto pages 1-3, zhang2020thereplisomeguides pages 1-2, liu2023structuralinsightsinto pages 8-9):
Histone Delivery: Newly synthesized histone H3.1-H4 dimers are acetylated (H4K5,12ac in mammals, H3K56ac in yeast) and delivered to CAF-1 from ASF1 (zhang2020thereplisomeguides pages 1-2).
H3-H4 Deposition: CAF-1 deposits two H3-H4 dimers onto newly replicated DNA to form the tetrasome, the central core of the nucleosome (liu2023structuralinsightsinto pages 1-3, zhang2020thereplisomeguides pages 1-2).
Tetramer Assembly: Structural studies suggest that DNA promotes dimerization of CAF-1-H3-H4 complexes, positioning two H3-H4 heterodimers for tetramer assembly (liu2023structuralinsightsinto pages 1-3, liu2023structuralinsightsinto pages 8-9). Remarkably, CAF-1 can facilitate the assembly of a right-handed nucleosome precursor or di-tetrasome intermediate, distinct from the left-handed DNA wrapping in mature nucleosomes (liu2023structuralinsightsinto pages 1-3, liu2023structuralinsightsinto pages 8-9).
H2A-H2B Addition: Following H3-H4 tetrasome formation, two H2A-H2B dimers are added to complete nucleosome assembly (zhang2020thereplisomeguides pages 1-2).
CAF-1, including CHAF1B, plays important roles in chromatin assembly following DNA damage repair (liu2023structuralinsightsinto pages 1-3, rosas2023anovelsingle pages 1-2). The complex is involved in chromatin repair after UV-induced DNA damage and contributes to DNA damage survival (rosas2023anovelsingle pages 1-2). The KER domain of CHAF1A cooperates with CHAF1B-mediated histone binding to overcome DNA damage sensitivity in vivo (rosas2023anovelsingle pages 1-2).
CHAF1B contributes significantly to heterochromatin integrity and the establishment of repressive chromatin states (franklin2022regulationofchromatin pages 1-2, ma2021histonechaperonecaf‐1 pages 1-2, zhang2020histoneloaderscaf1 pages 1-2). CAF-1 promotes the deposition and maintenance of repressive histone modifications, particularly H3K9me3 and H3K27me3 (ma2021histonechaperonecaf‐1 pages 1-2, zhang2020histoneloaderscaf1 pages 1-2). Studies in viral latency models demonstrate that CAF-1 depletion diminishes occupancy of histones 3.1 and 3.3 and reduces repressive H3K9me3 and H3K27me3 marks at viral genome lytic cycle regulatory elements (zhang2020histoneloaderscaf1 pages 1-2).
The mechanism involves CAF-1 recruiting epigenetic modifiers to newly assembled chromatin. In HIV-1 latency, CAF-1 forms nuclear bodies that recruit epigenetic modifiers and histone chaperones to establish and maintain suppressive chromatin modifications (ma2021histonechaperonecaf‐1 pages 1-2). Similarly, in EBV latency, CAF-1 is essential for maintaining the epigenetic silencing of lytic cycle genes (zhang2020histoneloaderscaf1 pages 1-2).
CHAF1B influences gene transcription primarily through chromatin assembly and accessibility control rather than sequence-specific DNA binding (franklin2022regulationofchromatin pages 1-2, franklin2025histonechaperonescoupled pages 1-2, dean2023repressionoftrim13 pages 1-2). Recent studies in hematopoietic systems have revealed that CHAF1B plays a critical role in maintaining cell identity and preventing premature differentiation (franklin2022regulationofchromatin pages 1-2, franklin2025histonechaperonescoupled pages 1-2).
In myeloid stem and progenitor cells, CAF-1 suppression triggers rapid differentiation into a mixed lineage state (franklin2022regulationofchromatin pages 1-2). CAF-1 sustains lineage fidelity by controlling chromatin accessibility at specific loci and limiting the binding of transcription factors such as ELF1 at newly accessible diverging regulatory elements (franklin2022regulationofchromatin pages 1-2). Loss of CAF-1 leads to increased chromatin accessibility, particularly at heterochromatic regions (H3K27me3 sites), and aberrant multilineage gene expression (franklin2025histonechaperonescoupled pages 1-2).
In acute myeloid leukemia (AML), CHAF1B is upregulated and promotes leukemic development by repressing differentiation genes and tumor suppressors (dean2023repressionoftrim13 pages 1-2). CHAF1B binds to promoters and enhancers, resulting in transcriptional repression through displacement of transcription factors such as C/EBPα (dean2023repressionoftrim13 pages 1-2). One specific target is TRIM13, an E3 ubiquitin ligase whose repression by CHAF1B is critical for maintaining AML cell self-renewal (dean2023repressionoftrim13 pages 1-2).
A recently discovered function of CHAF1B is preventing the mislocalization of the centromeric histone H3 variant CENP-A to non-centromeric regions (shrestha2023thehistoneh3h4 pages 1-2). CHAF1B-depleted cells exhibit CENP-A mislocalization, chromosomal instability (CIN) phenotypes, and increased enrichment of CENP-A in chromatin fractions (shrestha2023thehistoneh3h4 pages 1-2). The mechanism appears to involve an interplay with DAXX, a histone H3.3 chaperone—depletion of DAXX suppresses CENP-A mislocalization and CIN in CHAF1B-depleted cells, suggesting that DAXX promotes mislocalization of overexpressed CENP-A in the absence of CHAF1B (shrestha2023thehistoneh3h4 pages 1-2).
CHAF1B functions primarily during S-phase of the cell cycle, when DNA replication occurs (liu2023structuralinsightsinto pages 1-3, wen2022dynamicactivityof pages 1-2, zhang2020thereplisomeguides pages 1-2). The protein is essential for replication-coupled nucleosome assembly, ensuring that newly replicated DNA is properly packaged into chromatin (zhang2020thereplisomeguides pages 1-2). CAF-1 depletion leads to defects in nascent nucleosome assembly, altered cell cycle progression, and S-phase accumulation (franklin2025histonechaperonescoupled pages 1-2).
Multiple recent studies have established CHAF1B as a key regulator of cell fate and stem cell identity (franklin2022regulationofchromatin pages 1-2, franklin2025histonechaperonescoupled pages 1-2). In hematopoietic stem and progenitor cells, CHAF1B is required to maintain the self-renewal state and prevent differentiation (franklin2022regulationofchromatin pages 1-2, franklin2025histonechaperonescoupled pages 1-2). A comprehensive screen of histone chaperones in hematopoietic cells revealed that perturbation of CHAF1B (and the broader CAF-1 complex) triggers differentiation, with effects that require cell division but have distinct chromatin and transcriptional consequences compared to other histone chaperones (franklin2025histonechaperonescoupled pages 1-2).
CHAF1B plays important roles in establishing and maintaining viral latency for multiple viruses (ma2021histonechaperonecaf‐1 pages 1-2, zhang2020histoneloaderscaf1 pages 1-2). In Epstein-Barr virus (EBV) infection, CAF-1 is strongly upregulated in newly infected primary human B-cells prior to the first mitosis, and histones 3.1 and 3.3 are loaded onto the EBV genome by this early time point (zhang2020histoneloaderscaf1 pages 1-2). CAF-1 depletion triggers lytic reactivation and virion secretion from latently infected cells (zhang2020histoneloaderscaf1 pages 1-2). Similarly, in HIV-1 infection, CAF-1 forms phase-separated nuclear bodies enriched on the HIV-1 long terminal repeat (LTR) and recruits epigenetic modifiers to establish and maintain HIV-1 latency (ma2021histonechaperonecaf‐1 pages 1-2).
CHAF1B is overexpressed in a wide variety of cancers, and enhanced expression correlates with poor prognosis (wen2022dynamicactivityof pages 1-2, dean2023repressionoftrim13 pages 1-2). The protein is upregulated in almost all AML samples and promotes leukemic progression by repressing transcription of differentiation factors and tumor suppressors (dean2023repressionoftrim13 pages 1-2). CHAF1B expression is also elevated in high-grade glioma, melanomas, prostatic, renal, cervical, endometrial, hepatocellular, and squamous cell carcinomas, among others (wen2022dynamicactivityof pages 1-2). As a proliferation marker, CAF-1 expression strongly correlates with Ki-67 and other proliferation markers, and overexpression is associated with advanced tumor stage, recurrence, metastasis, and decreased patient survival (wen2022dynamicactivityof pages 1-2).
CHAF1B encodes the p60/middle subunit of the chromatin assembly factor 1 (CAF-1) complex, which serves as the primary histone H3-H4 chaperone for replication-coupled nucleosome assembly. The protein functions in the nucleus, where it binds histone H3-H4 heterodimers through its WD40-repeat β-propeller structure and deposits them onto newly replicated DNA during S-phase. CHAF1B is essential for CAF-1's nucleosome assembly activity, interacts with ASF1 to facilitate histone transfer, and contributes to DNA binding during chromatin assembly.
Beyond its core role in replication-coupled chromatin assembly, CHAF1B participates in diverse biological processes including DNA repair, heterochromatin formation, transcriptional regulation, cell fate maintenance, and viral latency establishment. The protein's dysregulation is implicated in multiple cancers, where overexpression promotes proliferation and prevents differentiation. Recent structural and functional studies have provided unprecedented molecular detail into CHAF1B's mechanisms of action, revealing how it prevents premature histone tetramer formation, promotes specific DNA-histone intermediate structures, and integrates chromatin assembly with broader cellular programs controlling genome stability and cell identity.
| Molecular Function/Activity | Mechanism/Molecular Details | Binding Partners/Interactions | Key References |
|---|---|---|---|
| Histone binding | CHAF1B (CAF-1 p60) is a WD40-repeat subunit and the principal H3-H4-binding component of human CAF-1. Structural work showed one CAF-1 complex binds one H3-H4 heterodimer, with p60 contacting H4 through its ventral β-propeller surface and engaging a partially unfolded H3 region; this configuration helps prevent premature H3-H4 tetramerization. CHAF1B is required for CAF-1 histone binding and nucleosome assembly activity. | Histones H3.1/H4; CAF-1 subunits CHAF1A/p150 and RBBP4/p48 (liu2023structuralinsightsinto pages 1-3, liu2023structuralinsightsinto pages 3-4, liu2023structuralinsightsinto pages 4-6, liu2023structuralinsightsinto pages 6-8) | (liu2023structuralinsightsinto pages 1-3, liu2023structuralinsightsinto pages 3-4, liu2023structuralinsightsinto pages 4-6, liu2023structuralinsightsinto pages 6-8) |
| Nucleosome assembly | CHAF1B functions in replication-coupled chromatin assembly by helping CAF-1 deposit newly synthesized H3-H4 onto nascent DNA. CAF-1-H3-H4 complexes can dimerize on DNA, positioning two H3-H4 dimers for tetramer formation; structural data further suggest CAF-1 can promote a right-handed nucleosome precursor/di-tetrasome intermediate. | CAF-1 complex; nascent DNA; histone H3-H4 dimers; replication machinery (liu2023structuralinsightsinto pages 1-3, zhang2020thereplisomeguides pages 1-2, liu2023structuralinsightsinto pages 8-9, rosas2023anovelsingle pages 1-2) | (liu2023structuralinsightsinto pages 1-3, zhang2020thereplisomeguides pages 1-2, liu2023structuralinsightsinto pages 8-9, rosas2023anovelsingle pages 1-2) |
| DNA binding | Direct DNA-binding by CAF-1 is primarily assigned to CHAF1A domains, but structural and biochemical analyses indicate CHAF1B/p60 also contacts DNA in assembled intermediates and contains a DNA-binding surface adjacent to its H4-binding region. In the deposited complex, p60 appears to stabilize histone-DNA intermediates during chromatin assembly rather than acting as the main DNA-recruitment module. | DNA; histone-DNA assembly intermediates; CHAF1A KER/WHD domains cooperate at the complex level (liu2023structuralinsightsinto pages 8-9, rosas2023anovelsingle pages 1-2) | (liu2023structuralinsightsinto pages 8-9, rosas2023anovelsingle pages 1-2) |
| PCNA interaction | CAF-1 is targeted to replication forks through PCNA, enabling DNA synthesis-coupled chromatin assembly. The direct canonical PCNA-binding determinants map mainly to CHAF1A/p150, but CHAF1B acts within the PCNA-recruited CAF-1 complex at forks to execute H3-H4 deposition in S phase. | PCNA indirectly via CAF-1 complex architecture; replisome; nascent DNA (zhang2020thereplisomeguides pages 1-2, nair2022unorthodoxpcnabinding pages 1-3, wen2022dynamicactivityof pages 1-2) | (zhang2020thereplisomeguides pages 1-2, nair2022unorthodoxpcnabinding pages 1-3, wen2022dynamicactivityof pages 1-2) |
| ASF1 interaction | CHAF1B contains a C-terminal ASF1-interacting B domain that helps transfer newly synthesized H3-H4 from ASF1 to CAF-1. This positions CHAF1B as the handoff subunit linking upstream histone chaperoning to downstream nucleosome assembly. | ASF1; newly synthesized H3-H4; CAF-1 complex (liu2023structuralinsightsinto pages 1-3, wen2022dynamicactivityof pages 1-2) | (liu2023structuralinsightsinto pages 1-3, wen2022dynamicactivityof pages 1-2) |
| Heterochromatin formation | CAF-1, including CHAF1B, contributes to heterochromatin integrity and gene silencing by promoting nucleosome reassembly and supporting repressive chromatin states. Loss of CAF-1 function derepresses many genes, reduces proper silencing, and in viral systems diminishes repressive marks such as H3K9me3/H3K27me3 at latent genomes. | Repressive chromatin factors and marks including H3K9me3, H3K27me3, HP1-associated pathways; viral episomal chromatin (liu2023structuralinsightsinto pages 6-8, ma2021histonechaperonecaf‐1 pages 1-2, zhang2020histoneloaderscaf1 pages 1-2) | (liu2023structuralinsightsinto pages 6-8, ma2021histonechaperonecaf‐1 pages 1-2, zhang2020histoneloaderscaf1 pages 1-2) |
| Transcriptional regulation | CHAF1B influences transcription chiefly through chromatin assembly and accessibility control rather than sequence-specific DNA recognition. In hematopoietic and leukemia models, elevated CHAF1B helps maintain self-renewal and an undifferentiated state by repressing differentiation/tumor suppressor genes; depletion increases accessibility at selected loci and permits transcription factor binding. CHAF1B also restrains aberrant CENP-A chromatin incorporation, linking chromatin regulation to genome stability. | Chromatin at promoters/enhancers; lineage TFs such as ELF1 and C/EBPα (context-dependent at CAF-1-regulated loci); CENP-A/DAXX pathway in chromosomal stability assays (franklin2022regulationofchromatin pages 1-2, shrestha2023thehistoneh3h4 pages 1-2, franklin2025histonechaperonescoupled pages 1-2, dean2023repressionoftrim13 pages 1-2, saleiro2023targetingchaf1benhances pages 1-2) | (franklin2022regulationofchromatin pages 1-2, shrestha2023thehistoneh3h4 pages 1-2, franklin2025histonechaperonescoupled pages 1-2, dean2023repressionoftrim13 pages 1-2, saleiro2023targetingchaf1benhances pages 1-2) |
Table: This table summarizes the core molecular activities attributed to human CHAF1B/CAF-1 p60, emphasizing what is direct versus complex-mediated. It is useful for distinguishing CHAF1B’s primary histone-chaperone role from broader CAF-1 functions in replication, heterochromatin, and transcriptional control.
References
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