{"gene":"CHAF1A","run_date":"2026-06-09T22:57:18","timeline":{"discoveries":[{"year":2013,"finding":"CHAF1A, as a subunit of chromatin assembly factor 1 (CAF-1), regulates H3K9 trimethylation at target gene loci controlling proliferation, survival, and differentiation; loss-of-function of CHAF1A drives neuronal differentiation in vitro and in vivo in neuroblastoma models.","method":"Loss-of-function experiments (knockdown/knockout) with transcriptome analysis and epigenetic readouts in neuroblastoma cell lines and in vivo models","journal":"Cancer research","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — clean KD with defined cellular and epigenetic phenotype (H3K9me3 changes, differentiation), single lab with multiple readouts","pmids":["24335960"],"is_preprint":false},{"year":2021,"finding":"CHAF1A gain-of-function upregulates polyamine metabolism, which blocks neuronal differentiation and promotes cell cycle progression in neuroblastoma; targeting polyamine synthesis enhances retinoic acid-induced differentiation.","method":"Gain-of-function experiments in zebrafish neural crest, human neural crest, and human neuroblastoma models; metabolic pathway analysis and pharmacological rescue","journal":"Advanced science (Weinheim, Baden-Wurttemberg, Germany)","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — three independent model systems with functional rescue, single lab","pmids":["34365742"],"is_preprint":false},{"year":2022,"finding":"CHAF1A and CHAF1B are required for silencing of unintegrated HIV-1 DNAs early in infection; KD of CHAF1A reduced H3K9me3 levels on viral DNA without major changes in histone loading, and KD of the H3K9me3-binding protein HP1γ also accelerated HIV-1 expression, placing CHAF1A upstream of H3K9me3/HP1γ-mediated silencing. The silencing function of CHAF1A was independent of its interaction with RBBP4 and did not extend to murine leukemia virus.","method":"RNAi-mediated knockdown of CHAF1A/CHAF1B and HP1γ; chromatin immunoprecipitation (ChIP) for histone marks on viral DNA; viral gene expression assays","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"High","confidence_rationale":"Tier 2 / Strong — multiple orthogonal methods (RNAi, ChIP for H3K9me3, viral expression, RBBP4 epistasis), rigorous controls, published in high-profile peer-reviewed journal","pmids":["35074917"],"is_preprint":false},{"year":2025,"finding":"CHAF1A stability is regulated by antagonistic post-translational modifications: O-GlcNAcylation stabilizes CHAF1A and promotes HIV-1 latency, while ubiquitination drives its proteasomal degradation. The drug trifluridine disrupts O-GlcNAcylation, triggering CHAF1A ubiquitination and degradation, thereby reactivating latent HIV-1.","method":"In vivo ubiquitination and O-GlcNAcylation assays; pharmacological disruption with trifluridine; proteasome inhibition; latency reactivation assays in primary CD4+ T cells","journal":"Journal of virology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — multiple PTM assays and pharmacological validation in primary cells, single lab","pmids":["41334912"],"is_preprint":false},{"year":2018,"finding":"CHAF1A directly interacts with TCF4 and co-occupies the promoters of c-MYC and CCND1, acting as a co-activator in the Wnt signaling pathway to promote gastric cancer cell proliferation. CHAF1A expression itself is transcriptionally upregulated by Sp1, including in response to Helicobacter pylori infection.","method":"Co-immunoprecipitation (Co-IP) of CHAF1A with TCF4; chromatin immunoprecipitation (ChIP) at c-MYC and CCND1 promoters; CHAF1A knockdown/overexpression functional assays; luciferase reporter assays for Sp1-dependent transcription","journal":"EBioMedicine","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — reciprocal Co-IP plus ChIP showing promoter binding, single lab with multiple orthogonal methods","pmids":["30449701"],"is_preprint":false},{"year":2022,"finding":"The E3 ubiquitin ligase SPOP binds to a consensus SPOP-binding motif in CHAF1A and induces its degradative ubiquitination; loss of SPOP in DLBCL leads to CHAF1A accumulation, which then directly binds TFEB promoters (as shown by ChIP-qPCR) to activate TFEB transcription and downstream lysosomal biogenesis and autophagy.","method":"In vivo ubiquitination assays; ChIP-qPCR at TFEB promoter; SPOP knockdown/mutation studies; xenograft tumor models","journal":"Journal of translational medicine","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — in vivo ubiquitination assay plus ChIP-qPCR, multiple methods, single lab","pmids":["35773729"],"is_preprint":false},{"year":2007,"finding":"CAF-1b (CHAF1A ortholog) is required for S-phase progression and differentiation in vivo in zebrafish; loss of caf-1b causes S-phase arrest and p53-mediated apoptosis in retinal precursor cells. p53 deficiency rescues apoptosis but not differentiation, demonstrating that CAF-1 activity is independently essential for differentiation.","method":"Zebrafish forward genetic mutant characterization; epistasis with p53 loss-of-function; BrdU/cell cycle analysis; histological differentiation markers","journal":"Cell cycle (Georgetown, Tex.)","confidence":"High","confidence_rationale":"Tier 2 / Strong — genetic epistasis (p53 double mutant) with multiple orthogonal readouts (cell cycle, apoptosis, differentiation) in an in vivo vertebrate model","pmids":["18156805"],"is_preprint":false},{"year":2019,"finding":"CHAF1A knockdown reduces thymidylate synthetase (TS) expression in gastric cancer cells and sensitizes them to 5-FU, suggesting CHAF1A regulates TS expression as a downstream mechanism affecting fluoropyrimidine chemosensitivity.","method":"siRNA knockdown of CHAF1A; TS protein expression by Western blot; IC50 determination for 5-FU; bioinformatics correlation of RNA-seq and proteome data","journal":"Gene","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single lab, limited mechanistic follow-up (no direct ChIP or promoter assay linking CHAF1A to TS), correlative bioinformatics supporting in vitro KD finding","pmids":["31377317"],"is_preprint":false},{"year":2015,"finding":"CHAF1A knockout in glioblastoma cells causes G1 phase arrest and apoptosis, and inhibition of CHAF1A reduces phosphorylation of the AKT/FOXO3a/Bim signaling axis, placing CHAF1A upstream of this survival pathway.","method":"CRISPR/Cas9 knockout of CHAF1A; cell cycle analysis by flow cytometry; Western blot for AKT/FOXO3a/Bim phosphorylation","journal":"Biochemical and biophysical research communications","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single lab, limited mechanistic depth (no direct interaction or epistasis experiment linking CHAF1A to AKT), pathway placement by protein level changes only","pmids":["26740175"],"is_preprint":false},{"year":2021,"finding":"CHAF1A knockdown in cervical cancer cells suppresses invasion and EMT, and overexpression of CHAF1A upregulates ZEB1 (an EMT-related transcription factor), placing CHAF1A upstream of ZEB1 in a pro-invasive pathway.","method":"CHAF1A shRNA knockdown and overexpression; Transwell invasion assay; Western blot for EMT markers and ZEB1; luciferase reporter assay confirming miR-1179 targeting of CHAF1A 3'UTR","journal":"Acta biochimica Polonica","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single lab, no direct mechanistic link (ChIP or reporter) between CHAF1A and ZEB1 promoter established","pmids":["33740340"],"is_preprint":false},{"year":2023,"finding":"CHAF1A promotes proliferation and growth of epithelial ovarian cancer cells via the JAK2/STAT3 phosphorylation pathway; inhibition of JAK2/STAT3 with peficitinib abolishes the proliferative effect of CHAF1A overexpression.","method":"CHAF1A siRNA knockdown and overexpression in EOC cell lines; Western blot for p-JAK2 and p-STAT3; pharmacological rescue with JAK2/STAT3 inhibitor peficitinib; cell proliferation and apoptosis assays","journal":"Biochemistry and biophysics reports","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single lab, pathway placement by pharmacological rescue without direct binding or mechanistic link between CHAF1A and JAK2/STAT3","pmids":["37575547"],"is_preprint":false},{"year":2024,"finding":"Heterozygous loss-of-function variants in CHAF1A cause oculo-auriculo-vertebral spectrum (OAVS) in humans, establishing CHAF1A's role as a histone H3-H4 deposition factor during DNA replication as essential for normal craniofacial and branchial arch development.","method":"Human genetic analysis (identification of heterozygous LoF variants in 8 individuals including a 3-member family); phenotypic characterization of OAVS features","journal":"European journal of human genetics : EJHG","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — human genetic evidence with multiple unrelated probands and familial segregation, though no functional rescue experiment performed","pmids":["39333427"],"is_preprint":false}],"current_model":"CHAF1A is the large (p150) subunit of the chromatin assembly factor 1 (CAF-1) complex, which deposits newly synthesized histones H3-H4 onto replicated DNA; it is required for S-phase progression, cellular differentiation, and craniofacial development in vivo, and mechanistically it enforces transcriptional silencing of unintegrated HIV-1 DNAs by promoting H3K9 trimethylation (upstream of HP1γ), acts as a transcriptional co-activator with TCF4 at Wnt target gene promoters, directly binds the TFEB promoter downstream of SPOP-mediated ubiquitin regulation, upregulates polyamine metabolism to block neuronal differentiation, and is itself stabilized by O-GlcNAcylation and degraded via ubiquitin-proteasome when O-GlcNAcylation is disrupted."},"narrative":{"mechanistic_narrative":"CHAF1A is the large subunit of chromatin assembly factor 1 (CAF-1), a histone H3-H4 deposition factor that couples nucleosome assembly to DNA replication and thereby governs S-phase progression, cellular differentiation, and developmental morphogenesis [PMID:24335960, PMID:18156805]. In zebrafish, loss of the CHAF1A ortholog arrests retinal precursors in S-phase and triggers p53-dependent apoptosis, yet its requirement for differentiation is genetically separable from this survival role [PMID:18156805], and heterozygous loss-of-function variants in humans cause oculo-auriculo-vertebral spectrum, linking its histone-deposition activity to craniofacial and branchial arch development [PMID:39333427]. Beyond bulk chromatin assembly, CHAF1A directs locus-specific epigenetic silencing: it promotes H3K9 trimethylation at genes controlling proliferation and differentiation [PMID:24335960], and in HIV-1 infection it enforces transcriptional silencing of unintegrated viral DNA by establishing H3K9me3 upstream of HP1γ, a function independent of its RBBP4 interaction and not involving major changes in histone loading [PMID:35074917]. CHAF1A also acts directly at promoters as a transcriptional regulator, partnering with TCF4 to co-activate Wnt target genes c-MYC and CCND1 [PMID:30449701] and binding the TFEB promoter to drive lysosomal biogenesis and autophagy [PMID:35773729]. Its abundance is set by opposing post-translational modifications and ubiquitin-mediated turnover: the E3 ligase SPOP recognizes a degron in CHAF1A to drive degradative ubiquitination [PMID:35773729], while O-GlcNAcylation stabilizes the protein and antagonizes this turnover, a balance that can be pharmacologically shifted to reactivate latent HIV-1 [PMID:41334912]. Gain of CHAF1A function additionally reprograms metabolism by upregulating polyamine synthesis to block neuronal differentiation [PMID:34365742].","teleology":[{"year":2007,"claim":"Established that CAF-1 activity is independently required for both S-phase progression and differentiation in a vertebrate, rather than differentiation defects being a secondary consequence of cell-cycle failure.","evidence":"Zebrafish forward genetic mutant with p53 double-mutant epistasis and cell-cycle/differentiation readouts","pmids":["18156805"],"confidence":"High","gaps":["Does not define the molecular targets whose chromatin assembly is required for differentiation","Ortholog-based; human CHAF1A activity inferred"]},{"year":2013,"claim":"Connected CHAF1A's chromatin-assembly role to locus-specific epigenetic control, showing it maintains H3K9me3 at proliferation/differentiation genes and that its loss drives neuronal differentiation.","evidence":"Knockdown/knockout with transcriptome and H3K9me3 readouts in neuroblastoma cells and in vivo","pmids":["24335960"],"confidence":"Medium","gaps":["Mechanism linking CAF-1 to H3K9me3 deposition not resolved","Direct target loci of CHAF1A-dependent silencing not enumerated"]},{"year":2018,"claim":"Revealed a non-assembly, promoter-level role: CHAF1A binds TCF4 and co-occupies Wnt target promoters as a co-activator, expanding its function beyond chromatin deposition.","evidence":"Reciprocal Co-IP, ChIP at c-MYC/CCND1 promoters, and Sp1-dependent luciferase reporters in gastric cancer cells","pmids":["30449701"],"confidence":"Medium","gaps":["Whether co-activation requires CAF-1 histone-deposition activity is unknown","Structural basis of CHAF1A-TCF4 interaction not defined"]},{"year":2022,"claim":"Placed CHAF1A upstream of an H3K9me3/HP1γ silencing axis on unintegrated viral DNA, dissociating this silencing from its histone-loading and RBBP4-dependent functions.","evidence":"RNAi of CHAF1A/CHAF1B/HP1γ with ChIP for H3K9me3 and viral expression assays, plus RBBP4 epistasis","pmids":["35074917"],"confidence":"High","gaps":["The methyltransferase recruited by CHAF1A to deposit H3K9me3 is not identified","Why silencing applies to HIV-1 but not MLV is unexplained"]},{"year":2022,"claim":"Defined CHAF1A turnover by SPOP-mediated ubiquitination and identified a downstream transcriptional output (TFEB-driven autophagy), linking its abundance to lysosomal biogenesis.","evidence":"In vivo ubiquitination assays, ChIP-qPCR at TFEB promoter, and SPOP perturbation in DLBCL and xenografts","pmids":["35773729"],"confidence":"Medium","gaps":["The SPOP degron in CHAF1A is mapped by motif consensus but not mutationally validated in this finding","Whether TFEB activation requires CAF-1 assembly activity is unclear"]},{"year":2024,"claim":"Provided human genetic evidence that CHAF1A dosage is essential for craniofacial development, establishing a Mendelian disease link.","evidence":"Identification of heterozygous LoF variants in 8 individuals including a 3-member family with OAVS phenotyping","pmids":["39333427"],"confidence":"Medium","gaps":["No functional rescue experiment performed","Developmental pathway through which CHAF1A loss causes OAVS not defined"]},{"year":2025,"claim":"Showed that antagonistic O-GlcNAcylation and ubiquitination set CHAF1A stability, and that shifting this balance pharmacologically reactivates latent HIV-1.","evidence":"In vivo PTM assays, proteasome inhibition, and trifluridine treatment with latency reactivation in primary CD4+ T cells","pmids":["41334912"],"confidence":"Medium","gaps":["O-GlcNAc transferase and E3 ligase responsible are not identified here","Modified residues on CHAF1A not mapped"]},{"year":null,"claim":"It remains unresolved how CHAF1A's core CAF-1 histone-deposition activity mechanistically relates to its promoter-binding co-activator roles and its direction of H3K9me3 silencing.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No structure of CHAF1A or CAF-1 in the timeline","The histone/chromatin machinery bridging CHAF1A to H3K9me3 and to specific promoters is uncharacterized"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0042393","term_label":"histone binding","supporting_discovery_ids":[0,6,11]},{"term_id":"GO:0140110","term_label":"transcription regulator activity","supporting_discovery_ids":[4,5]},{"term_id":"GO:0003677","term_label":"DNA binding","supporting_discovery_ids":[4,5]}],"localization":[{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[0,2,4]}],"pathway":[{"term_id":"R-HSA-4839726","term_label":"Chromatin organization","supporting_discovery_ids":[0,2]},{"term_id":"R-HSA-69306","term_label":"DNA Replication","supporting_discovery_ids":[6,11]},{"term_id":"R-HSA-74160","term_label":"Gene expression (Transcription)","supporting_discovery_ids":[4,5]},{"term_id":"R-HSA-1266738","term_label":"Developmental Biology","supporting_discovery_ids":[6,11]}],"complexes":["CAF-1 (chromatin assembly factor 1)"],"partners":["CHAF1B","TCF4","RBBP4","SPOP","HP1Γ"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q13111","full_name":"Chromatin assembly factor 1 subunit A","aliases":["Chromatin assembly factor I p150 subunit","CAF-I 150 kDa subunit","CAF-I p150","hp150"],"length_aa":956,"mass_kda":106.9,"function":"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. CAF-1 performs the first step of the nucleosome assembly process, bringing newly synthesized histones H3 and H4 to replicating DNA; histones H2A/H2B can bind to this chromatin precursor subsequent to DNA replication to complete the histone octamer. It may play a role in heterochromatin maintenance in proliferating cells by bringing newly synthesized cbx proteins to heterochromatic DNA replication foci","subcellular_location":"Nucleus","url":"https://www.uniprot.org/uniprotkb/Q13111/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":true,"resolved_as":"","url":"https://depmap.org/portal/gene/CHAF1A","classification":"Common Essential","n_dependent_lines":1204,"n_total_lines":1208,"dependency_fraction":0.9966887417218543},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[{"gene":"CBX1","stoichiometry":0.2},{"gene":"HIST2H2BE","stoichiometry":0.2},{"gene":"RBBP4","stoichiometry":0.2},{"gene":"SSRP1","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/search/CHAF1A","total_profiled":1310},"omim":[{"mim_id":"604460","title":"FAS-ASSOCIATED FACTOR 1; FAF1","url":"https://www.omim.org/entry/604460"},{"mim_id":"601246","title":"CHROMATIN ASSEMBLY FACTOR I, SUBUNIT A; CHAF1A","url":"https://www.omim.org/entry/601246"},{"mim_id":"601245","title":"CHROMATIN ASSEMBLY FACTOR I, SUBUNIT B; CHAF1B","url":"https://www.omim.org/entry/601245"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Supported","locations":[{"location":"Nucleoplasm","reliability":"Supported"},{"location":"Cytosol","reliability":"Additional"}],"tissue_specificity":"Tissue enhanced","tissue_distribution":"Detected in all","driving_tissues":[{"tissue":"bone marrow","ntpm":29.6}],"url":"https://www.proteinatlas.org/search/CHAF1A"},"hgnc":{"alias_symbol":["CAF1P150","CAF1B","CAF-1","CAF1","P150","MGC71229"],"prev_symbol":[]},"alphafold":{"accession":"Q13111","domains":[{"cath_id":"1.10.10","chopping":"730-767_791-845","consensus_level":"medium","plddt":87.5961,"start":730,"end":845}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q13111","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q13111-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q13111-F1-predicted_aligned_error_v6.png","plddt_mean":57.75},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=CHAF1A","jax_strain_url":"https://www.jax.org/strain/search?query=CHAF1A"},"sequence":{"accession":"Q13111","fasta_url":"https://rest.uniprot.org/uniprotkb/Q13111.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q13111/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q13111"}},"corpus_meta":[{"pmid":"23236473","id":"PMC_23236473","title":"The anti-proliferative activity of BTG/TOB proteins is mediated via the Caf1a (CNOT7) and Caf1b (CNOT8) deadenylase subunits of the Ccr4-not complex.","date":"2012","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/23236473","citation_count":64,"is_preprint":false},{"pmid":"22941664","id":"PMC_22941664","title":"Cell-cycle-regulated control of VSG expression site silencing by histones and histone chaperones ASF1A and CAF-1b in Trypanosoma brucei.","date":"2012","source":"Nucleic acids research","url":"https://pubmed.ncbi.nlm.nih.gov/22941664","citation_count":52,"is_preprint":false},{"pmid":"24335960","id":"PMC_24335960","title":"Histone chaperone CHAF1A inhibits differentiation and promotes aggressive neuroblastoma.","date":"2013","source":"Cancer research","url":"https://pubmed.ncbi.nlm.nih.gov/24335960","citation_count":43,"is_preprint":false},{"pmid":"30449701","id":"PMC_30449701","title":"CHAF1A interacts with TCF4 to promote gastric carcinogenesis via upregulation of c-MYC and CCND1 expression.","date":"2018","source":"EBioMedicine","url":"https://pubmed.ncbi.nlm.nih.gov/30449701","citation_count":30,"is_preprint":false},{"pmid":"26740175","id":"PMC_26740175","title":"Over-expression of CHAF1A promotes cell proliferation and apoptosis resistance in glioblastoma cells via AKT/FOXO3a/Bim pathway.","date":"2015","source":"Biochemical and biophysical research communications","url":"https://pubmed.ncbi.nlm.nih.gov/26740175","citation_count":28,"is_preprint":false},{"pmid":"35074917","id":"PMC_35074917","title":"CHAF1A/B mediate silencing of unintegrated HIV-1 DNAs early in infection.","date":"2022","source":"Proceedings of the National Academy of Sciences of the United States of America","url":"https://pubmed.ncbi.nlm.nih.gov/35074917","citation_count":22,"is_preprint":false},{"pmid":"18156805","id":"PMC_18156805","title":"Mutation of zebrafish caf-1b results in S phase arrest, defective differentiation, and p53-mediated apoptosis during organogenesis.","date":"2007","source":"Cell cycle (Georgetown, Tex.)","url":"https://pubmed.ncbi.nlm.nih.gov/18156805","citation_count":22,"is_preprint":false},{"pmid":"34365742","id":"PMC_34365742","title":"CHAF1A Blocks Neuronal Differentiation and Promotes Neuroblastoma Oncogenesis via Metabolic Reprogramming.","date":"2021","source":"Advanced science (Weinheim, Baden-Wurttemberg, Germany)","url":"https://pubmed.ncbi.nlm.nih.gov/34365742","citation_count":20,"is_preprint":false},{"pmid":"28286267","id":"PMC_28286267","title":"Over-expression of CHAF1A in Epithelial Ovarian Cancer can promote cell proliferation and inhibit cell apoptosis.","date":"2017","source":"Biochemical and biophysical research communications","url":"https://pubmed.ncbi.nlm.nih.gov/28286267","citation_count":19,"is_preprint":false},{"pmid":"29201167","id":"PMC_29201167","title":"CHAF1A, the largest subunit of the chromatin assembly factor 1 complex, regulates the growth of H1299 human non-small cell lung cancer cells by inducing G0/G1 cell cycle arrest.","date":"2017","source":"Experimental and therapeutic medicine","url":"https://pubmed.ncbi.nlm.nih.gov/29201167","citation_count":11,"is_preprint":false},{"pmid":"35773729","id":"PMC_35773729","title":"Aberrant SPOP-CHAF1A ubiquitination axis triggers tumor autophagy that endows a therapeutical vulnerability in diffuse large B cell lymphoma.","date":"2022","source":"Journal of translational medicine","url":"https://pubmed.ncbi.nlm.nih.gov/35773729","citation_count":10,"is_preprint":false},{"pmid":"31377317","id":"PMC_31377317","title":"Histone chaperone CHAF1A impacts the outcome of fluoropyrimidines-based adjuvant therapy in gastric cancer by regulating the expression of thymidylate synthetase.","date":"2019","source":"Gene","url":"https://pubmed.ncbi.nlm.nih.gov/31377317","citation_count":10,"is_preprint":false},{"pmid":"29382432","id":"PMC_29382432","title":"[Highly expressed CHAF1A and PCNA are positively associated with malignancy of cervical squamous cell carcinoma].","date":"2017","source":"Xi bao yu fen zi mian yi xue za zhi = Chinese journal of cellular and molecular immunology","url":"https://pubmed.ncbi.nlm.nih.gov/29382432","citation_count":9,"is_preprint":false},{"pmid":"30536318","id":"PMC_30536318","title":"MiR-520b inhibited metastasis and proliferation of non-small cell lung cancer by targeting CHAF1A.","date":"2018","source":"European review for medical and pharmacological sciences","url":"https://pubmed.ncbi.nlm.nih.gov/30536318","citation_count":8,"is_preprint":false},{"pmid":"37575547","id":"PMC_37575547","title":"CHAF1A promotes the proliferation and growth of epithelial ovarian cancer cells by affecting the phosphorylation of JAK2/STAT3 signaling pathway.","date":"2023","source":"Biochemistry and biophysics reports","url":"https://pubmed.ncbi.nlm.nih.gov/37575547","citation_count":6,"is_preprint":false},{"pmid":"38235318","id":"PMC_38235318","title":"An oncogene regulating chromatin favors response to immunotherapy: Oncogene CHAF1A and immunotherapy outcomes.","date":"2024","source":"Oncoimmunology","url":"https://pubmed.ncbi.nlm.nih.gov/38235318","citation_count":5,"is_preprint":false},{"pmid":"33277876","id":"PMC_33277876","title":"CHAF1A overexpression in human retinoblastoma promotes cell proliferation and suppresses apoptosis.","date":"2020","source":"Journal of B.U.ON. : official journal of the Balkan Union of Oncology","url":"https://pubmed.ncbi.nlm.nih.gov/33277876","citation_count":5,"is_preprint":false},{"pmid":"33740340","id":"PMC_33740340","title":"MiR-1179 is downregulated in cervical cancer and its overexpression suppresses cancer cells invasion by targeting CHAF1A/ZEB1.","date":"2021","source":"Acta biochimica Polonica","url":"https://pubmed.ncbi.nlm.nih.gov/33740340","citation_count":4,"is_preprint":false},{"pmid":"39333427","id":"PMC_39333427","title":"Chromatin assembly factor subunit CHAF1A as a monogenic cause for oculo-auriculo-vertebral spectrum.","date":"2024","source":"European journal of human genetics : EJHG","url":"https://pubmed.ncbi.nlm.nih.gov/39333427","citation_count":4,"is_preprint":false},{"pmid":"41334912","id":"PMC_41334912","title":"The crosstalk between ubiquitination and GlcNAcylation of CHAF1A regulates HIV-1 latency and reactivation.","date":"2025","source":"Journal of virology","url":"https://pubmed.ncbi.nlm.nih.gov/41334912","citation_count":1,"is_preprint":false},{"pmid":"40797060","id":"PMC_40797060","title":"CHAF1A Promotes Preadipocyte Differentiation and Contributes to Macrosomia in Gestational Diabetes Mellitus.","date":"2025","source":"Reproductive sciences (Thousand Oaks, Calif.)","url":"https://pubmed.ncbi.nlm.nih.gov/40797060","citation_count":1,"is_preprint":false},{"pmid":"38132148","id":"PMC_38132148","title":"Independent and Complementary Functions of Caf1b and Hir1 for Chromatin Assembly in Tetrahymena thermophila.","date":"2023","source":"Cells","url":"https://pubmed.ncbi.nlm.nih.gov/38132148","citation_count":0,"is_preprint":false},{"pmid":"40260209","id":"PMC_40260209","title":"Elevated Expression of CHAF1A in Hepatocellular Carcinoma Progression and Immune Modulation.","date":"2025","source":"Clinical and experimental gastroenterology","url":"https://pubmed.ncbi.nlm.nih.gov/40260209","citation_count":0,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":13436,"output_tokens":3241,"usd":0.044462,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":10695,"output_tokens":2981,"usd":0.064,"stage2_stop_reason":"end_turn"},"total_usd":0.108462,"stage1_batch_id":"msgbatch_01ACAxJQabDsht39JXeWG22d","stage2_batch_id":"msgbatch_01QEU22A9U5sbPTgsMzTmvSf","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2013,\n      \"finding\": \"CHAF1A, as a subunit of chromatin assembly factor 1 (CAF-1), regulates H3K9 trimethylation at target gene loci controlling proliferation, survival, and differentiation; loss-of-function of CHAF1A drives neuronal differentiation in vitro and in vivo in neuroblastoma models.\",\n      \"method\": \"Loss-of-function experiments (knockdown/knockout) with transcriptome analysis and epigenetic readouts in neuroblastoma cell lines and in vivo models\",\n      \"journal\": \"Cancer research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — clean KD with defined cellular and epigenetic phenotype (H3K9me3 changes, differentiation), single lab with multiple readouts\",\n      \"pmids\": [\"24335960\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"CHAF1A gain-of-function upregulates polyamine metabolism, which blocks neuronal differentiation and promotes cell cycle progression in neuroblastoma; targeting polyamine synthesis enhances retinoic acid-induced differentiation.\",\n      \"method\": \"Gain-of-function experiments in zebrafish neural crest, human neural crest, and human neuroblastoma models; metabolic pathway analysis and pharmacological rescue\",\n      \"journal\": \"Advanced science (Weinheim, Baden-Wurttemberg, Germany)\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — three independent model systems with functional rescue, single lab\",\n      \"pmids\": [\"34365742\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"CHAF1A and CHAF1B are required for silencing of unintegrated HIV-1 DNAs early in infection; KD of CHAF1A reduced H3K9me3 levels on viral DNA without major changes in histone loading, and KD of the H3K9me3-binding protein HP1γ also accelerated HIV-1 expression, placing CHAF1A upstream of H3K9me3/HP1γ-mediated silencing. The silencing function of CHAF1A was independent of its interaction with RBBP4 and did not extend to murine leukemia virus.\",\n      \"method\": \"RNAi-mediated knockdown of CHAF1A/CHAF1B and HP1γ; chromatin immunoprecipitation (ChIP) for histone marks on viral DNA; viral gene expression assays\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — multiple orthogonal methods (RNAi, ChIP for H3K9me3, viral expression, RBBP4 epistasis), rigorous controls, published in high-profile peer-reviewed journal\",\n      \"pmids\": [\"35074917\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"CHAF1A stability is regulated by antagonistic post-translational modifications: O-GlcNAcylation stabilizes CHAF1A and promotes HIV-1 latency, while ubiquitination drives its proteasomal degradation. The drug trifluridine disrupts O-GlcNAcylation, triggering CHAF1A ubiquitination and degradation, thereby reactivating latent HIV-1.\",\n      \"method\": \"In vivo ubiquitination and O-GlcNAcylation assays; pharmacological disruption with trifluridine; proteasome inhibition; latency reactivation assays in primary CD4+ T cells\",\n      \"journal\": \"Journal of virology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple PTM assays and pharmacological validation in primary cells, single lab\",\n      \"pmids\": [\"41334912\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"CHAF1A directly interacts with TCF4 and co-occupies the promoters of c-MYC and CCND1, acting as a co-activator in the Wnt signaling pathway to promote gastric cancer cell proliferation. CHAF1A expression itself is transcriptionally upregulated by Sp1, including in response to Helicobacter pylori infection.\",\n      \"method\": \"Co-immunoprecipitation (Co-IP) of CHAF1A with TCF4; chromatin immunoprecipitation (ChIP) at c-MYC and CCND1 promoters; CHAF1A knockdown/overexpression functional assays; luciferase reporter assays for Sp1-dependent transcription\",\n      \"journal\": \"EBioMedicine\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal Co-IP plus ChIP showing promoter binding, single lab with multiple orthogonal methods\",\n      \"pmids\": [\"30449701\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"The E3 ubiquitin ligase SPOP binds to a consensus SPOP-binding motif in CHAF1A and induces its degradative ubiquitination; loss of SPOP in DLBCL leads to CHAF1A accumulation, which then directly binds TFEB promoters (as shown by ChIP-qPCR) to activate TFEB transcription and downstream lysosomal biogenesis and autophagy.\",\n      \"method\": \"In vivo ubiquitination assays; ChIP-qPCR at TFEB promoter; SPOP knockdown/mutation studies; xenograft tumor models\",\n      \"journal\": \"Journal of translational medicine\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — in vivo ubiquitination assay plus ChIP-qPCR, multiple methods, single lab\",\n      \"pmids\": [\"35773729\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2007,\n      \"finding\": \"CAF-1b (CHAF1A ortholog) is required for S-phase progression and differentiation in vivo in zebrafish; loss of caf-1b causes S-phase arrest and p53-mediated apoptosis in retinal precursor cells. p53 deficiency rescues apoptosis but not differentiation, demonstrating that CAF-1 activity is independently essential for differentiation.\",\n      \"method\": \"Zebrafish forward genetic mutant characterization; epistasis with p53 loss-of-function; BrdU/cell cycle analysis; histological differentiation markers\",\n      \"journal\": \"Cell cycle (Georgetown, Tex.)\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — genetic epistasis (p53 double mutant) with multiple orthogonal readouts (cell cycle, apoptosis, differentiation) in an in vivo vertebrate model\",\n      \"pmids\": [\"18156805\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"CHAF1A knockdown reduces thymidylate synthetase (TS) expression in gastric cancer cells and sensitizes them to 5-FU, suggesting CHAF1A regulates TS expression as a downstream mechanism affecting fluoropyrimidine chemosensitivity.\",\n      \"method\": \"siRNA knockdown of CHAF1A; TS protein expression by Western blot; IC50 determination for 5-FU; bioinformatics correlation of RNA-seq and proteome data\",\n      \"journal\": \"Gene\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single lab, limited mechanistic follow-up (no direct ChIP or promoter assay linking CHAF1A to TS), correlative bioinformatics supporting in vitro KD finding\",\n      \"pmids\": [\"31377317\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"CHAF1A knockout in glioblastoma cells causes G1 phase arrest and apoptosis, and inhibition of CHAF1A reduces phosphorylation of the AKT/FOXO3a/Bim signaling axis, placing CHAF1A upstream of this survival pathway.\",\n      \"method\": \"CRISPR/Cas9 knockout of CHAF1A; cell cycle analysis by flow cytometry; Western blot for AKT/FOXO3a/Bim phosphorylation\",\n      \"journal\": \"Biochemical and biophysical research communications\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single lab, limited mechanistic depth (no direct interaction or epistasis experiment linking CHAF1A to AKT), pathway placement by protein level changes only\",\n      \"pmids\": [\"26740175\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"CHAF1A knockdown in cervical cancer cells suppresses invasion and EMT, and overexpression of CHAF1A upregulates ZEB1 (an EMT-related transcription factor), placing CHAF1A upstream of ZEB1 in a pro-invasive pathway.\",\n      \"method\": \"CHAF1A shRNA knockdown and overexpression; Transwell invasion assay; Western blot for EMT markers and ZEB1; luciferase reporter assay confirming miR-1179 targeting of CHAF1A 3'UTR\",\n      \"journal\": \"Acta biochimica Polonica\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single lab, no direct mechanistic link (ChIP or reporter) between CHAF1A and ZEB1 promoter established\",\n      \"pmids\": [\"33740340\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"CHAF1A promotes proliferation and growth of epithelial ovarian cancer cells via the JAK2/STAT3 phosphorylation pathway; inhibition of JAK2/STAT3 with peficitinib abolishes the proliferative effect of CHAF1A overexpression.\",\n      \"method\": \"CHAF1A siRNA knockdown and overexpression in EOC cell lines; Western blot for p-JAK2 and p-STAT3; pharmacological rescue with JAK2/STAT3 inhibitor peficitinib; cell proliferation and apoptosis assays\",\n      \"journal\": \"Biochemistry and biophysics reports\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single lab, pathway placement by pharmacological rescue without direct binding or mechanistic link between CHAF1A and JAK2/STAT3\",\n      \"pmids\": [\"37575547\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"Heterozygous loss-of-function variants in CHAF1A cause oculo-auriculo-vertebral spectrum (OAVS) in humans, establishing CHAF1A's role as a histone H3-H4 deposition factor during DNA replication as essential for normal craniofacial and branchial arch development.\",\n      \"method\": \"Human genetic analysis (identification of heterozygous LoF variants in 8 individuals including a 3-member family); phenotypic characterization of OAVS features\",\n      \"journal\": \"European journal of human genetics : EJHG\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — human genetic evidence with multiple unrelated probands and familial segregation, though no functional rescue experiment performed\",\n      \"pmids\": [\"39333427\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"CHAF1A is the large (p150) subunit of the chromatin assembly factor 1 (CAF-1) complex, which deposits newly synthesized histones H3-H4 onto replicated DNA; it is required for S-phase progression, cellular differentiation, and craniofacial development in vivo, and mechanistically it enforces transcriptional silencing of unintegrated HIV-1 DNAs by promoting H3K9 trimethylation (upstream of HP1γ), acts as a transcriptional co-activator with TCF4 at Wnt target gene promoters, directly binds the TFEB promoter downstream of SPOP-mediated ubiquitin regulation, upregulates polyamine metabolism to block neuronal differentiation, and is itself stabilized by O-GlcNAcylation and degraded via ubiquitin-proteasome when O-GlcNAcylation is disrupted.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"CHAF1A is the large subunit of chromatin assembly factor 1 (CAF-1), a histone H3-H4 deposition factor that couples nucleosome assembly to DNA replication and thereby governs S-phase progression, cellular differentiation, and developmental morphogenesis [#0, #6]. In zebrafish, loss of the CHAF1A ortholog arrests retinal precursors in S-phase and triggers p53-dependent apoptosis, yet its requirement for differentiation is genetically separable from this survival role [#6], and heterozygous loss-of-function variants in humans cause oculo-auriculo-vertebral spectrum, linking its histone-deposition activity to craniofacial and branchial arch development [#11]. Beyond bulk chromatin assembly, CHAF1A directs locus-specific epigenetic silencing: it promotes H3K9 trimethylation at genes controlling proliferation and differentiation [#0], and in HIV-1 infection it enforces transcriptional silencing of unintegrated viral DNA by establishing H3K9me3 upstream of HP1\\u03b3, a function independent of its RBBP4 interaction and not involving major changes in histone loading [#2]. CHAF1A also acts directly at promoters as a transcriptional regulator, partnering with TCF4 to co-activate Wnt target genes c-MYC and CCND1 [#4] and binding the TFEB promoter to drive lysosomal biogenesis and autophagy [#5]. Its abundance is set by opposing post-translational modifications and ubiquitin-mediated turnover: the E3 ligase SPOP recognizes a degron in CHAF1A to drive degradative ubiquitination [#5], while O-GlcNAcylation stabilizes the protein and antagonizes this turnover, a balance that can be pharmacologically shifted to reactivate latent HIV-1 [#3]. Gain of CHAF1A function additionally reprograms metabolism by upregulating polyamine synthesis to block neuronal differentiation [#1].\"\n,\n  \"teleology\": [\n    {\n      \"year\": 2007,\n      \"claim\": \"Established that CAF-1 activity is independently required for both S-phase progression and differentiation in a vertebrate, rather than differentiation defects being a secondary consequence of cell-cycle failure.\",\n      \"evidence\": \"Zebrafish forward genetic mutant with p53 double-mutant epistasis and cell-cycle/differentiation readouts\",\n      \"pmids\": [\"18156805\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Does not define the molecular targets whose chromatin assembly is required for differentiation\", \"Ortholog-based; human CHAF1A activity inferred\"]\n    },\n    {\n      \"year\": 2013,\n      \"claim\": \"Connected CHAF1A's chromatin-assembly role to locus-specific epigenetic control, showing it maintains H3K9me3 at proliferation/differentiation genes and that its loss drives neuronal differentiation.\",\n      \"evidence\": \"Knockdown/knockout with transcriptome and H3K9me3 readouts in neuroblastoma cells and in vivo\",\n      \"pmids\": [\"24335960\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Mechanism linking CAF-1 to H3K9me3 deposition not resolved\", \"Direct target loci of CHAF1A-dependent silencing not enumerated\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Revealed a non-assembly, promoter-level role: CHAF1A binds TCF4 and co-occupies Wnt target promoters as a co-activator, expanding its function beyond chromatin deposition.\",\n      \"evidence\": \"Reciprocal Co-IP, ChIP at c-MYC/CCND1 promoters, and Sp1-dependent luciferase reporters in gastric cancer cells\",\n      \"pmids\": [\"30449701\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Whether co-activation requires CAF-1 histone-deposition activity is unknown\", \"Structural basis of CHAF1A-TCF4 interaction not defined\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Placed CHAF1A upstream of an H3K9me3/HP1\\u03b3 silencing axis on unintegrated viral DNA, dissociating this silencing from its histone-loading and RBBP4-dependent functions.\",\n      \"evidence\": \"RNAi of CHAF1A/CHAF1B/HP1\\u03b3 with ChIP for H3K9me3 and viral expression assays, plus RBBP4 epistasis\",\n      \"pmids\": [\"35074917\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"The methyltransferase recruited by CHAF1A to deposit H3K9me3 is not identified\", \"Why silencing applies to HIV-1 but not MLV is unexplained\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Defined CHAF1A turnover by SPOP-mediated ubiquitination and identified a downstream transcriptional output (TFEB-driven autophagy), linking its abundance to lysosomal biogenesis.\",\n      \"evidence\": \"In vivo ubiquitination assays, ChIP-qPCR at TFEB promoter, and SPOP perturbation in DLBCL and xenografts\",\n      \"pmids\": [\"35773729\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"The SPOP degron in CHAF1A is mapped by motif consensus but not mutationally validated in this finding\", \"Whether TFEB activation requires CAF-1 assembly activity is unclear\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Provided human genetic evidence that CHAF1A dosage is essential for craniofacial development, establishing a Mendelian disease link.\",\n      \"evidence\": \"Identification of heterozygous LoF variants in 8 individuals including a 3-member family with OAVS phenotyping\",\n      \"pmids\": [\"39333427\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No functional rescue experiment performed\", \"Developmental pathway through which CHAF1A loss causes OAVS not defined\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Showed that antagonistic O-GlcNAcylation and ubiquitination set CHAF1A stability, and that shifting this balance pharmacologically reactivates latent HIV-1.\",\n      \"evidence\": \"In vivo PTM assays, proteasome inhibition, and trifluridine treatment with latency reactivation in primary CD4+ T cells\",\n      \"pmids\": [\"41334912\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"O-GlcNAc transferase and E3 ligase responsible are not identified here\", \"Modified residues on CHAF1A not mapped\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"It remains unresolved how CHAF1A's core CAF-1 histone-deposition activity mechanistically relates to its promoter-binding co-activator roles and its direction of H3K9me3 silencing.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No structure of CHAF1A or CAF-1 in the timeline\", \"The histone/chromatin machinery bridging CHAF1A to H3K9me3 and to specific promoters is uncharacterized\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0042393\", \"supporting_discovery_ids\": [0, 6, 11]},\n      {\"term_id\": \"GO:0140110\", \"supporting_discovery_ids\": [4, 5]},\n      {\"term_id\": \"GO:0003677\", \"supporting_discovery_ids\": [4, 5]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [0, 2, 4]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-4839726\", \"supporting_discovery_ids\": [0, 2]},\n      {\"term_id\": \"R-HSA-69306\", \"supporting_discovery_ids\": [6, 11]},\n      {\"term_id\": \"R-HSA-74160\", \"supporting_discovery_ids\": [4, 5]},\n      {\"term_id\": \"R-HSA-1266738\", \"supporting_discovery_ids\": [6, 11]}\n    ],\n    \"complexes\": [\"CAF-1 (chromatin assembly factor 1)\"],\n    \"partners\": [\"CHAF1B\", \"TCF4\", \"RBBP4\", \"SPOP\", \"HP1\\u03b3\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"tie","faith_supported":6,"faith_total":6,"faith_pct":100.0}}