CAC2 encodes Cac2, the middle (p60-like) WD40-repeat subunit of chromatin assembly factor 1 (CAF-1), the heterotrimeric H3-H4 histone chaperone (Cac1-Cac2-Cac3/Msi1) that deposits newly synthesized H3-H4 onto DNA during DNA replication and repair synthesis. Cac2 binds the large subunit Cac1 and, together with the Cac1 acidic region, forms the composite H3-H4 binding interface; it is indispensable for productive histone binding and nucleosome assembly by CAF-1. A C-terminal B-domain mediates interaction with the upstream H3-H4 chaperone Asf1, which hands off histone dimers to CAF-1. Cac2 is nuclear; it is not essential for growth, but cac2 deletion, like loss of the other CAF-1 subunits, reduces telomeric and HM-locus silencing and increases UV sensitivity.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0000775 chromosome, centromeric region | IDA PMID:11782447 Chromatin assembly factor I and Hir proteins contribute to b... | KEEP AS NON CORE | Summary: CAC2/CAF-I is enriched at centromeres (ChIP). Reason: Sharp et al. report that CAF-I subunits are enriched at centromeres and, redundantly with Hir proteins, contribute to functional kinetochore chromatin. The localization is credible (abstract states it directly; full text not cached) but reflects one of several genomic sites where CAF-1 assembles chromatin rather than a dedicated centromeric role. Supporting Evidence: PMID:11782447 CAF-I subunits and Hir1 are enriched at centromeres, indicating that these proteins make a direct contribution to centromeric chromatin structures |
| GO:0000786 nucleosome | IDA PMID:30239791 Mechanistic insights into histone deposition and nucleosome ... | REMOVE | Summary: Complex Portal annotation placing CAC2 (a CAF-1 subunit) as part_of the nucleosome, citing a review of CAF-1 mechanism (PMID:30239791). Reason: CAF-1 is a histone H3-H4 chaperone that deposits H3-H4 onto DNA to build the tetrasome; it is not a structural component of the nucleosome core particle, which consists of the histone octamer and DNA. The cited paper (full text cached; a review) describes CAF-1 binding a single H3-H4 dimer and depositing (H3-H4)2 tetramers onto nucleosome-free DNA, i.e. a transient assembly intermediate, not stable membership of the nucleosome. The part_of nucleosome claim is contradicted by the very source cited, so it is removed; the chaperone role is captured by GO:0006335 and CAF-1 complex membership (GO:0033186). Supporting Evidence: PMID:30239791 The Histone chaperone Chromatin Assembly Factor-1 (CAF-1) interacts with the replisome and deposits H3-H4 directly onto newly synthesized DNA. PMID:30239791 Two CAF-1•H3-H4 complexes co-associate on nucleosome-free DNA depositing (H3-H4)2 tetramers in the first step of nucleosome assembly. |
| GO:0005515 protein binding | IPI PMID:16429126 Proteome survey reveals modularity of the yeast cell machine... | REMOVE | Summary: Generic protein binding (IPI) between CAC2 and Msi1/Cac3. Reason: GO:0005515 protein binding is uninformative about molecular function. Removal does not mean the reported interaction is false. This is an interaction between subunits of the CAF-1 heterotrimer, which is captured informatively by part_of CAF-1 complex (GO:0033186). |
| GO:0005515 protein binding | IPI PMID:21256037 Structure of the Rtt109-AcCoA/Vps75 complex and implications... | REMOVE | Summary: Generic protein binding (IPI) between CAC2 and Msi1/Cac3. Reason: GO:0005515 protein binding is uninformative about molecular function. Removal does not mean the reported interaction is false. This is an interaction between subunits of the CAF-1 heterotrimer, which is captured informatively by part_of CAF-1 complex (GO:0033186). |
| GO:0005515 protein binding | IPI PMID:37968396 The social and structural architecture of the yeast protein ... | REMOVE | Summary: Generic protein binding (IPI) between CAC2 and Msi1/Cac3. Reason: GO:0005515 protein binding is uninformative about molecular function. Removal does not mean the reported interaction is false. This is an interaction between subunits of the CAF-1 heterotrimer, which is captured informatively by part_of CAF-1 complex (GO:0033186). |
| GO:0005634 nucleus | IBA GO_REF:0000033 | ACCEPT | Summary: Phylogenetic inference that CAC2 is active in the nucleus. Reason: CAF-1 acts on nuclear chromatin at replication forks; consistent with direct localization data. Supporting Evidence: PMID:30239791 It localizes to sites of ongoing DNA synthesis by binding to the processivity factor for DNA polymerases known as Proliferating cell nuclear antigen (PCNA) |
| GO:0005634 nucleus | IDA PMID:22932476 The nuclear localization of SWI/SNF proteins is subjected to... | ACCEPT | Summary: Cac2-GFP is nuclear under normoxia in a genome-scale localization/relocalization study. Reason: Nuclear localization is consistent with CAF-1 function; the study lists Cac2 among nuclear proteins that relocalize under hypoxia. Supporting Evidence: PMID:22932476 Nuclear proteins that relocalized to the cytosol in response to hypoxia in a shorter time period |
| GO:0005634 nucleus | IEA GO_REF:0000044 | ACCEPT | Summary: UniProt subcellular-location mapping places CAC2 in the nucleus. Reason: Consistent with direct localization evidence and with CAF-1 function on nuclear chromatin. |
| GO:0005829 cytosol | IDA PMID:22932476 The nuclear localization of SWI/SNF proteins is subjected to... | KEEP AS NON CORE | Summary: Cac2-GFP relocalizes from nucleus to cytosol in response to hypoxia. Reason: The cytosolic signal is a condition-specific relocalization observed in a GFP screen for hypoxia-responsive proteins; it is not where CAF-1 acts and no cytosolic function of Cac2 is known. Retained as a non-core, condition-dependent localization. Supporting Evidence: PMID:22932476 Nuclear proteins that relocalized to the cytosol in response to hypoxia in a shorter time period |
| GO:0006260 DNA replication | NAS PMID:30239791 Mechanistic insights into histone deposition and nucleosome ... | MARK AS OVER ANNOTATED | Summary: Complex Portal NAS annotation of CAC2/CAF-1 to the broad process DNA replication. Reason: CAF-1 does not synthesize or duplicate DNA; it couples nucleosome assembly to replication fork progression through PCNA binding. The replication-coupled role is precisely described by GO:0006335 (DNA replication-dependent chromatin assembly), which is annotated with direct evidence. CAC genes are not essential for viability, and no DNA synthesis defect is reported for cac mutants, so the parent process DNA replication overstates the contribution. Supporting Evidence: PMID:30239791 The Histone chaperone Chromatin Assembly Factor-1 (CAF-1) interacts with the replisome and deposits H3-H4 directly onto newly synthesized DNA. PMID:9030687 Genes encoding the CAF-I subunits (collectively referred to as CAC genes) are not essential for cell viability |
| GO:0006281 DNA repair | NAS PMID:30239791 Mechanistic insights into histone deposition and nucleosome ... | KEEP AS NON CORE | Summary: Complex Portal NAS annotation of CAC2/CAF-1 to DNA repair. Reason: Deletion of any CAC gene causes UV sensitivity, and cac1 deletion increases the UV sensitivity of mutants in every major repair epistasis group, consistent with CAF-1 restoring chromatin on repaired DNA (it assembles nucleosomes on templates undergoing nucleotide excision repair in vitro). CAF-1 is also required for resistance to double-strand-break agents, but it is not required for repair of the DNA per se. The contribution is chromatin restoration coupled to repair rather than a repair activity, so this is kept as a non-core, pleiotropic process. Supporting Evidence: PMID:9030687 deletion of any CAC gene causes an increase in sensitivity to ultraviolet radiation, without significantly increasing sensitivity to gamma rays PMID:9927445 these data suggest that CAF-I has a role in error-free postreplicative damage repair and may also have an auxiliary role in other repair mechanisms PMID:16143623 CAF-1 is not required for repair of the DNA per se or for DNA damage checkpoint function. |
| GO:0006325 chromatin organization | IDA PMID:30239791 Mechanistic insights into histone deposition and nucleosome ... | MODIFY | Summary: Complex Portal annotation of CAC2/CAF-1 to the general process chromatin organization. Reason: Correct but uninformative. CAF-1 organizes chromatin specifically by depositing newly synthesized H3-H4 onto replicating DNA; the specific child term GO:0006335 DNA replication-dependent chromatin assembly is the appropriate term and is already supported by direct evidence for this subunit. Proposed replacements: DNA replication-dependent chromatin assembly Supporting Evidence: PMID:30239791 The Histone chaperone Chromatin Assembly Factor-1 (CAF-1) interacts with the replisome and deposits H3-H4 directly onto newly synthesized DNA. |
| GO:0006334 nucleosome assembly | IBA GO_REF:0000033 | ACCEPT | Summary: Phylogenetic inference that CAC2 is involved in nucleosome assembly. Reason: Correct: Cac2 is required for productive H3-H4 association with CAF-1 and hence for nucleosome assembly; GO:0006335 is the more specific term and is also annotated. Supporting Evidence: PMID:30239791 In addition to binding to ASF1, the middle subunit is also required for productive association with H3–H4, and thus for nucleosome assembly |
| GO:0006335 DNA replication-dependent chromatin assembly | IDA PMID:30239791 Mechanistic insights into histone deposition and nucleosome ... | ACCEPT | Summary: Complex Portal annotation of CAC2/CAF-1 to DNA replication-dependent chromatin assembly. Reason: This is the defining function of CAF-1: the complex is recruited to replication forks via PCNA and deposits H3-H4 onto newly synthesized DNA. The cited paper (full text) summarizes the structural and biochemical work on the yeast complex. Supporting Evidence: PMID:30239791 The Histone chaperone Chromatin Assembly Factor-1 (CAF-1) interacts with the replisome and deposits H3-H4 directly onto newly synthesized DNA. PMID:30239791 Two CAF-1•H3-H4 complexes co-associate on nucleosome-free DNA depositing (H3-H4)2 tetramers in the first step of nucleosome assembly. |
| GO:0006335 DNA replication-dependent chromatin assembly | IDA PMID:9030687 Ultraviolet radiation sensitivity and reduction of telomeric... | ACCEPT | Summary: CAC2 is a subunit of yeast CAF-I purified by Kaufman et al. using an in vitro replication-coupled nucleosome assembly assay. Reason: Kaufman et al. purified yeast CAF-I as the activity that assembles nucleosomes onto DNA undergoing replication in vitro, and identified CAC1/RLF2, CAC2 and CAC3/MSI1 as the genes for its three subunits. This is the founding biochemical evidence for the core function. Supporting Evidence: PMID:9030687 we now report the purification of CAF-I from the budding yeast Saccharomyces cerevisiae PMID:9030687 The CAC1 and CAC2 (chromatin assembly complex) genes encode proteins similar to the p150 and p60 subunits of human CAF-I, respectively PMID:9030687 The gene encoding the p50 subunit of yeast CAF-I (CAC3) is similar to the human p48 CAF-I subunit and was identified previously as MSI1 |
| GO:0006335 DNA replication-dependent chromatin assembly | IEA GO_REF:0000002 | ACCEPT | Summary: InterPro2GO mapping (IPR045145, CAF-1 p60 family) to DNA replication-dependent chromatin assembly. Reason: Family-level mapping agrees with direct experimental evidence for Cac2. |
| GO:0006335 DNA replication-dependent chromatin assembly | IMP PMID:9030687 Ultraviolet radiation sensitivity and reduction of telomeric... | ACCEPT | Summary: cac2 deletion phenocopies loss of CAF-I (UV sensitivity, loss of telomeric silencing). Reason: Kaufman et al. show that deletion of any CAC gene, including CAC2, gives UV sensitivity and reduced telomeric silencing, the in vivo signature of CAF-I loss; combined with biochemistry showing Cac2 is needed for productive H3-H4 binding, this supports the process annotation. Supporting Evidence: PMID:9030687 deletion of any CAC gene causes an increase in sensitivity to ultraviolet radiation, without significantly increasing sensitivity to gamma rays PMID:9030687 Deletion of CAC genes also strongly reduces silencing of genes adjacent to telomeric DNA PMID:30239791 In addition to binding to ASF1, the middle subunit is also required for productive association with H3–H4, and thus for nucleosome assembly |
| GO:0033186 CAF-1 complex | IBA GO_REF:0000033 | ACCEPT | Summary: Phylogenetic inference that CAC2 is a CAF-1 complex subunit. Reason: The IBA agrees with direct biochemical evidence for the yeast protein (it appears among the IBA sources, as expected when the target carries its own experimental annotation). CAF-1 subunit composition is conserved from yeast to human. Supporting Evidence: PMID:9030687 The CAC1 and CAC2 (chromatin assembly complex) genes encode proteins similar to the p150 and p60 subunits of human CAF-I, respectively |
| GO:0033186 CAF-1 complex | IDA PMID:9030687 Ultraviolet radiation sensitivity and reduction of telomeric... | ACCEPT | Summary: CAC2 identified as a subunit of purified yeast CAF-I. Reason: Direct purification and peptide sequencing of yeast CAF-I identified the three subunits encoded by CAC1 (RLF2), CAC2 and CAC3 (MSI1). The recombinant heterotrimer has since been reconstituted and characterized structurally. Supporting Evidence: PMID:9030687 we now report the purification of CAF-I from the budding yeast Saccharomyces cerevisiae PMID:9030687 The CAC1 and CAC2 (chromatin assembly complex) genes encode proteins similar to the p150 and p60 subunits of human CAF-I, respectively PMID:9030687 The gene encoding the p50 subunit of yeast CAF-I (CAC3) is similar to the human p48 CAF-I subunit and was identified previously as MSI1 PMID:28315525 Budding yeast CAF1 (yCAF1) is a heterotrimeric complex containing the Cac1, Cac2 and Cac3 subunits (Kaufman et al., 1997). |
| GO:0033186 CAF-1 complex | IPI PMID:30239791 Mechanistic insights into histone deposition and nucleosome ... | ACCEPT | Summary: Complex Portal annotation of CAC2 as a CAF-1 complex subunit. Reason: Consistent with the purification of yeast CAF-I and the reconstitution of the Cac1-Cac2-Cac3 heterotrimer. Supporting Evidence: PMID:28315525 Budding yeast CAF1 (yCAF1) is a heterotrimeric complex containing the Cac1, Cac2 and Cac3 subunits (Kaufman et al., 1997). |
| GO:0042393 histone binding | IDA PMID:16503640 Chromatin assembly factor 1 interacts with histone H3 methyl... | ACCEPT | Summary: CAC2 contributes to H3-H4 binding by CAF-1; CAF-1 was co-purified with H3 and H4 from yeast cells. Reason: Yeast CAF-1 was isolated from cells in complex with H3 and H4 carrying newly-synthesized histone marks (H4K5/K12ac, H3K56ac). Structural work shows the H3-H4 binding site is formed by the acidic region of Cac1 in conjunction with Cac2, so contributes_to histone binding is appropriate for CAC2. The more specific activity, H3-H4 histone complex chaperone activity, is captured in core_functions. Supporting Evidence: PMID:16503640 we have purified a complex containing CAF-1 and H3 and H4 from yeast cells PMID:28315523 On CAF-1, the H3-H4 binding site is formed by the acidic region of Cac1 (Liu et al., 2016), in conjunction with Cac1-bound Cac2 (Mattiroli et al., 2017). |
| GO:0000510 H3-H4 histone complex chaperone activity | IDA PMID:28418026 The Cac2 subunit is essential for productive histone binding... | NEW | Summary: Proposed: Cac2 contributes to the H3-H4 histone complex chaperone activity of CAF-1. Reason: HX-MS and mutagenesis of reconstituted yeast CAF-1 show that H3-H4 is bound by a composite interface formed by Cac1-bound Cac2 and the Cac1 acidic region, and that Cac2 is indispensable for productive histone binding and nucleosome assembly. Cac2 also receives H3-H4 from Asf1 through its B-domain. Isolated Cac2 is not a high-affinity chaperone, so the contributes_to qualifier is appropriate. The large subunit (RLF2) already carries GO:0000510 by IBA; CAC2 carries only contributes_to histone binding, which is less specific. Supporting Evidence: PMID:28418026 Strikingly, H3-H4 binding is mediated by a composite interface, shaped by Cac1-bound Cac2 and the Cac1 acidic region. PMID:28418026 Cac2 is indispensable for productive histone binding, while deletion of Cac3 has only moderate effects on H3-H4 binding and nucleosome assembly. PMID:28315525 Free monomeric yCAF1 (step 1) is loaded with dimeric H3-H4 through association of yAsf1 with the Cac2 subunit. file:yeast/CAC2/CAC2-deep-research-falcon.md Cac2 is therefore indispensable for productive H3–H4 configuration and deposition |
| GO:0031509 subtelomeric heterochromatin formation | IMP PMID:9030687 Ultraviolet radiation sensitivity and reduction of telomeric... | NEW | Summary: Proposed: CAC2, as a CAF-1 subunit, is involved in subtelomeric heterochromatin formation. Reason: Deletion of any CAC gene strongly reduces silencing of telomere-adjacent reporters, and loss of CAF-I subunits destabilizes HML repression. Participation test: CAF-1 performs a step of the process itself, depositing H3-H4 into the chromatin that Sir proteins then compact (Enomoto et al. propose Rlf2p facilitates timely assembly of histones into telomeric chromatin); it is not merely a substrate or upstream requirement. Comparator check: the partner H3-H4 chaperone ASF1 (P32447) already carries GO:0031509 and GO:0030466 by IGI (PMID:15840725), as does SIR3 by IMP, so the term is used for chromatin-assembly factors in yeast; the CAF-1 subunits currently carry no heterochromatin-formation annotation at all in GOA. This is proposed as non-core relative to the general replication-coupled assembly function. Supporting Evidence: PMID:9030687 Deletion of CAC genes also strongly reduces silencing of genes adjacent to telomeric DNA PMID:9030688 We propose that Rlf2p facilitates the efficient and timely assembly of histones into telomeric chromatin PMID:9436982 Loss of the other CAF-I subunits (Cac2p and Cac3p/Msi1p) also results in the shmoo cluster phenotype, implying that loss of CAF-I activity gives rise to this unstable repression of HML. |
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Download this section (compressed HTML)Q: What is the structural basis for Cac2 shaping the H3-H4 binding interface, and does the Asf1 B-domain interaction directly transfer histones to the Cac1-Cac2 composite site?
Q: Is the hypoxia-induced relocalization of Cac2 to the cytosol functionally meaningful for chromatin assembly under low oxygen?
Experiment: Determine a structure of yeast CAF-1 bound to H3-H4 and Asf1, and test B-domain mutants for histone handoff kinetics in vitro and silencing in vivo.
Hypothesis: The Cac2 B-domain docks Asf1 adjacent to the Cac1-Cac2 histone site, enabling direct transfer of H3-H4.
Type: structural biology
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