{"gene":"BRPF3","run_date":"2026-06-09T22:02:45","timeline":{"discoveries":[{"year":2015,"finding":"BRPF3 forms a tetrameric complex specifically with HBO1 (KAT7/MYST2) and two other subunits, but not with related acetyltransferases MOZ, MORF, TIP60, or MOF, and this complex preferentially acetylates histone H3K14.","method":"Co-immunoprecipitation of endogenous proteins, biochemical complex characterization","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal Co-IP of endogenous proteins replicated across multiple studies (PMID:26677226 and PMID:26620551), with consistent H3K14ac functional readout","pmids":["26677226","26620551"],"is_preprint":false},{"year":2015,"finding":"BRPF3-HBO1 complex specifically acetylates histone H3K14 (not H4 marks) and is highly enriched at ORC1-binding sites and replication origins near transcription start sites (TSSs); BRPF3 depletion reduces H3K14ac at selected origins.","method":"RNAi knockdown, genome-wide ChIP-seq for BRPF3, HBO1, and H3K14ac, co-immunoprecipitation","journal":"The EMBO journal","confidence":"High","confidence_rationale":"Tier 2 / Strong — multiple orthogonal methods (RNAi, ChIP-seq, Co-IP) in a single rigorous study establishing both complex composition and genome-wide functional localization","pmids":["26620551"],"is_preprint":false},{"year":2015,"finding":"BRPF3 is required for efficient replication origin activation: BRPF3 depletion impairs CDC45 recruitment to origins but does not affect MCM2-7 loading, placing BRPF3-HBO1 function specifically at the origin activation step.","method":"RNAi knockdown with RPA accumulation assay (replication stress screen), CDC45 and MCM2-7 chromatin recruitment assays","journal":"The EMBO journal","confidence":"High","confidence_rationale":"Tier 2 / Strong — genetic epistasis via depletion combined with orthogonal chromatin recruitment assays precisely positioning BRPF3 in the replication pathway","pmids":["26620551"],"is_preprint":false},{"year":2020,"finding":"BRPF3 protects HBO1 (MYST2) from ubiquitin-mediated proteasomal degradation by the E3 ligase HUWE1: protein-protein interaction between BRPF3 and MYST2 antagonizes HUWE1-mediated ubiquitination, stabilizing MYST2 protein levels.","method":"Co-immunoprecipitation, overexpression and knockdown of BRPF3 and HUWE1, ubiquitination assays in mouse ESCs","journal":"Cell death and differentiation","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP and functional rescue experiments in single lab; HUWE1 identified as E3 ligase for MYST2 with BRPF3 antagonism demonstrated by overexpression/knockdown","pmids":["32555450"],"is_preprint":false},{"year":2020,"finding":"BRPF3 overexpression causes aberrant upregulation of MYST2 protein levels, leading to dysregulated cell-cycle progression and delay of embryoid-body formation and lineage commitment in mouse ESCs; these phenotypes are rescued by HUWE1 overexpression.","method":"BRPF3 and HUWE1 overexpression in mouse ESCs, embryoid body formation assays, cell-cycle analysis","journal":"Cell death and differentiation","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — defined cellular phenotypes with genetic rescue by HUWE1, single lab","pmids":["32555450"],"is_preprint":false},{"year":2021,"finding":"The BRPF3 bromodomain recognizes mono-acetylated H4K5ac and di-acetylated H4K5acK12ac histone peptides; pull-down assays on purified histones from human cells confirmed binding to acetylated histone H4.","method":"Histone peptide binding assays, pull-down from purified human histones, MD simulation of bromodomain-histone complexes","journal":"Chemistry, an Asian journal","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — in vitro binding assays with purified components plus MD simulation, single lab, two orthogonal methods","pmids":["34448544"],"is_preprint":false},{"year":2015,"finding":"Brpf3 shows dynamic spatiotemporal expression during mouse embryogenesis (highest in adult brain and testis), but Brpf3 disruption results in no gross developmental phenotype, distinguishing it from paralogs Brpf1 and Brpf2 whose loss causes lethality.","method":"LacZ reporter knock-in at Brpf3 locus, β-galactosidase staining, Brpf3 knockout mouse analysis","journal":"The Journal of biological chemistry","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — clean knockout mouse with systematic phenotypic analysis; negative result (no gross phenotype) is itself mechanistically informative for functional distinction from paralogs","pmids":["26677226"],"is_preprint":false},{"year":2023,"finding":"Knockdown and pharmacologic inhibition of BRPF3 reduces PARP inhibitor (olaparib) resistance in high-grade serous ovarian carcinoma cells, while HBO1 inhibition (which depletes H3K14ac) does not affect PARPi response, indicating BRPF3's role in PARPi resistance is through its bromodomain reader function rather than solely via H3K14 acetylation.","method":"siRNA knockdown and pharmacologic inhibition of BRPF3 and HBO1 in isogenic PARPi-sensitive/resistant HGSOC cell lines, mass spectrometry histone modification profiling","journal":"Molecular carcinogenesis","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — knockdown and inhibitor experiments with isogenic cell lines; single lab, two orthogonal perturbation methods","pmids":["37493106"],"is_preprint":false},{"year":2025,"finding":"In cardiac fibroblasts, circ-CELF1 reduces the ubiquitination-degradation rate of BRPF3, elevating BRPF3 protein levels; elevated BRPF3 then acts as a scaffold to recruit KAT7 histone acetyltransferase to the Celf1 gene promoter, facilitating H3K14 acetylation and Celf1 transcriptional activation, thereby promoting cardiac fibrosis.","method":"CircRNA knockdown/overexpression, ubiquitination assays, ChIP for H3K14ac at Celf1 promoter, protein interaction assays in cardiac fibroblasts","journal":"Acta pharmaceutica Sinica. B","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — multiple orthogonal methods (ubiquitination assay, ChIP, Co-IP) in single lab; mechanistically defines BRPF3 as scaffold recruiting KAT7 to specific promoter","pmids":["41132846"],"is_preprint":false}],"current_model":"BRPF3 is a multidomain chromatin scaffold protein (containing PHD fingers, a bromodomain, and a PWWP domain) that preferentially assembles a tetrameric complex with the HBO1/KAT7 histone acetyltransferase; this complex acetylates histone H3K14 at replication origins and gene promoters, with BRPF3 directing CDC45 recruitment for origin activation; the BRPF3 bromodomain reads H4K5ac and H4K5acK12ac marks to recruit the complex to chromatin; BRPF3 additionally stabilizes HBO1/MYST2 by antagonizing HUWE1-mediated ubiquitin degradation; and BRPF3 acts as a scaffold recruiting KAT7 to specific promoters (e.g., Celf1) to drive H3K14 acetylation and transcriptional activation in contexts such as cardiac fibrosis."},"narrative":{"mechanistic_narrative":"BRPF3 is a chromatin scaffold protein that assembles a dedicated tetrameric complex with the HBO1/KAT7 (MYST2) histone acetyltransferase, distinguishing it from other MYST-family enzymes, and directs this complex to acetylate histone H3K14 [PMID:26677226, PMID:26620551]. Genome-wide, the BRPF3-HBO1 complex is enriched at ORC1-binding replication origins near transcription start sites, where it deposits H3K14ac, and BRPF3 is required for efficient origin activation by promoting CDC45 recruitment downstream of MCM2-7 loading [PMID:26620551]. Beyond its catalytic targeting role, BRPF3 stabilizes its partner enzyme by binding MYST2 and antagonizing HUWE1-mediated ubiquitination and proteasomal degradation, so that BRPF3 levels set MYST2 abundance and thereby influence cell-cycle progression and stem-cell differentiation [PMID:32555450]. The BRPF3 bromodomain functions as an acetyl-lysine reader, recognizing H4K5ac and H4K5acK12ac marks [PMID:34448544]. This reader-scaffold activity is functionally separable from H3K14 acetylation: BRPF3 supports PARP-inhibitor resistance in ovarian carcinoma cells through its bromodomain function rather than through HBO1-dependent H3K14ac [PMID:37493106], and in cardiac fibroblasts stabilized BRPF3 recruits KAT7 to the Celf1 promoter to drive H3K14ac and transcriptional activation, promoting fibrosis [PMID:41132846].","teleology":[{"year":2015,"claim":"Establishing which acetyltransferase BRPF3 partners with answered whether it has a dedicated enzymatic complex; it forms a specific tetramer with HBO1/KAT7 that acetylates H3K14, excluding other MYST enzymes.","evidence":"reciprocal Co-IP of endogenous proteins and biochemical complex characterization, replicated across two studies","pmids":["26677226","26620551"],"confidence":"High","gaps":["Identity and contribution of the other two tetramer subunits not resolved","Structural basis of complex assembly not defined"]},{"year":2015,"claim":"Mapping where the complex acts and what it does there showed BRPF3-HBO1 is enriched at replication origins near TSSs and is required for origin activation via CDC45 recruitment, placing it precisely in the replication pathway.","evidence":"RNAi knockdown with genome-wide ChIP-seq for BRPF3/HBO1/H3K14ac and CDC45 vs MCM2-7 chromatin recruitment assays","pmids":["26620551"],"confidence":"High","gaps":["Mechanism linking H3K14ac to CDC45 loading not defined","Relative contribution of origin vs promoter functions unresolved"]},{"year":2015,"claim":"Knockout analysis tested whether BRPF3 is developmentally essential; unlike paralogs Brpf1/Brpf2, Brpf3 loss produces no gross phenotype despite dynamic embryonic expression, functionally distinguishing the paralogs.","evidence":"LacZ reporter knock-in and knockout mouse phenotypic analysis","pmids":["26677226"],"confidence":"Medium","gaps":["Possible redundancy with paralogs not directly tested","Subtle or stress-conditional phenotypes not assessed"]},{"year":2020,"claim":"Identifying how BRPF3 controls its partner's abundance showed it binds MYST2 and antagonizes HUWE1-mediated ubiquitination, revealing a stabilizing rather than purely catalytic-targeting role.","evidence":"Co-IP, overexpression/knockdown of BRPF3 and HUWE1, and ubiquitination assays in mouse ESCs","pmids":["32555450"],"confidence":"Medium","gaps":["Single lab without reciprocal validation in other cell types","Whether stabilization requires complex assembly or is direct competition with HUWE1 unclear"]},{"year":2020,"claim":"Testing the consequence of excess BRPF3 demonstrated that overexpression elevates MYST2, dysregulating cell cycle and delaying lineage commitment, with HUWE1 rescue confirming the stabilization axis is causal.","evidence":"BRPF3/HUWE1 overexpression, embryoid body formation and cell-cycle assays in mouse ESCs","pmids":["32555450"],"confidence":"Medium","gaps":["Phenotype from overexpression rather than physiological levels","Downstream targets driving differentiation delay not identified"]},{"year":2021,"claim":"Defining the histone-mark specificity of the BRPF3 bromodomain established it as an acetyl-lysine reader recognizing H4K5ac and H4K5acK12ac, providing a chromatin-recruitment mechanism distinct from its H3K14ac deposition.","evidence":"histone peptide binding and pull-down assays from purified human histones with MD simulation","pmids":["34448544"],"confidence":"Medium","gaps":["In vitro binding not validated by genome-wide reader occupancy in cells","Affinity and selectivity relative to other bromodomain readers not benchmarked"]},{"year":2023,"claim":"Separating reader from catalytic function in cancer showed BRPF3 loss reduces PARPi resistance whereas HBO1 inhibition does not, implicating the bromodomain reader function independently of H3K14ac.","evidence":"siRNA and pharmacologic inhibition of BRPF3 vs HBO1 in isogenic PARPi-sensitive/resistant HGSOC lines with histone MS","pmids":["37493106"],"confidence":"Medium","gaps":["Molecular pathway connecting BRPF3 reader function to PARPi resistance not defined","Single tumor type and cell-line model"]},{"year":2025,"claim":"Linking BRPF3 to a disease pathway showed circ-CELF1 stabilizes BRPF3, which scaffolds KAT7 to the Celf1 promoter to drive H3K14ac and transcription, demonstrating gene-specific scaffolding in cardiac fibrosis.","evidence":"circRNA knockdown/overexpression, ubiquitination assays, ChIP for H3K14ac and protein interaction assays in cardiac fibroblasts","pmids":["41132846"],"confidence":"Medium","gaps":["Single lab and model system","Generalizability of promoter-specific scaffolding beyond Celf1 not established"]},{"year":null,"claim":"How BRPF3's reader (bromodomain/PWWP/PHD) and catalytic-targeting activities are integrated to select between replication origins, specific promoters, and partner stabilization in different cell contexts remains unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No structural model of the full BRPF3-HBO1 tetramer","Determinants of locus selectivity unknown","Endogenous loss-of-function phenotype in mammals remains mild and largely uncharacterized mechanistically"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0042393","term_label":"histone binding","supporting_discovery_ids":[5]},{"term_id":"GO:0140096","term_label":"catalytic activity, acting on a protein","supporting_discovery_ids":[0,1,8]},{"term_id":"GO:0060090","term_label":"molecular adaptor activity","supporting_discovery_ids":[8]},{"term_id":"GO:0098772","term_label":"molecular function regulator activity","supporting_discovery_ids":[3]}],"localization":[{"term_id":"GO:0000228","term_label":"nuclear chromosome","supporting_discovery_ids":[1,2]},{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[1,8]}],"pathway":[{"term_id":"R-HSA-69306","term_label":"DNA Replication","supporting_discovery_ids":[1,2]},{"term_id":"R-HSA-4839726","term_label":"Chromatin organization","supporting_discovery_ids":[0,1,8]},{"term_id":"R-HSA-74160","term_label":"Gene expression (Transcription)","supporting_discovery_ids":[8]}],"complexes":["BRPF3-HBO1/KAT7 tetrameric acetyltransferase complex"],"partners":["KAT7","HUWE1"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q9ULD4","full_name":"Bromodomain and PHD finger-containing protein 3","aliases":[],"length_aa":1205,"mass_kda":135.7,"function":"Scaffold subunit of various histone acetyltransferase (HAT) complexes, such as the MOZ/MORF and HBO1 complexes, which have a histone H3 acetyltransferase activity (PubMed:16387653, PubMed:26620551, PubMed:26677226). Plays a role in DNA replication initiation by directing KAT7/HBO1 specificity towards histone H3 'Lys-14' acetylation (H3K14ac), thereby facilitating the activation of replication origins (PubMed:26620551). Component of the MOZ/MORF complex which has a histone H3 acetyltransferase activity (PubMed:16387653)","subcellular_location":"Nucleus","url":"https://www.uniprot.org/uniprotkb/Q9ULD4/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/BRPF3","classification":"Not Classified","n_dependent_lines":1,"n_total_lines":1208,"dependency_fraction":0.0008278145695364238},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[{"gene":"CAPZB","stoichiometry":0.2},{"gene":"HIST2H2BE","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/search/BRPF3","total_profiled":1310},"omim":[{"mim_id":"616856","title":"BROMODOMAIN- AND PHD FINGER-CONTAINING PROTEIN 3; BRPF3","url":"https://www.omim.org/entry/616856"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Approved","locations":[{"location":"Nucleoplasm","reliability":"Approved"},{"location":"Mitochondria","reliability":"Additional"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/BRPF3"},"hgnc":{"alias_symbol":["KIAA1286"],"prev_symbol":[]},"alphafold":{"accession":"Q9ULD4","domains":[{"cath_id":"-","chopping":"27-61","consensus_level":"medium","plddt":72.9031,"start":27,"end":61},{"cath_id":"-","chopping":"160-172_179-203_497-520","consensus_level":"medium","plddt":87.3732,"start":160,"end":520},{"cath_id":"-","chopping":"230-383","consensus_level":"medium","plddt":90.0995,"start":230,"end":383},{"cath_id":"1.20.920.10","chopping":"592-783","consensus_level":"medium","plddt":91.6051,"start":592,"end":783},{"cath_id":"2.30.30.140","chopping":"1079-1195","consensus_level":"high","plddt":89.6117,"start":1079,"end":1195}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9ULD4","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q9ULD4-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q9ULD4-F1-predicted_aligned_error_v6.png","plddt_mean":67.06},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=BRPF3","jax_strain_url":"https://www.jax.org/strain/search?query=BRPF3"},"sequence":{"accession":"Q9ULD4","fasta_url":"https://rest.uniprot.org/uniprotkb/Q9ULD4.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q9ULD4/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9ULD4"}},"corpus_meta":[{"pmid":"21753189","id":"PMC_21753189","title":"The Hbo1-Brd1/Brpf2 complex is responsible for global acetylation of H3K14 and required for fetal liver erythropoiesis.","date":"2011","source":"Blood","url":"https://pubmed.ncbi.nlm.nih.gov/21753189","citation_count":173,"is_preprint":false},{"pmid":"26620551","id":"PMC_26620551","title":"BRPF3-HBO1 regulates replication origin activation and histone H3K14 acetylation.","date":"2015","source":"The EMBO journal","url":"https://pubmed.ncbi.nlm.nih.gov/26620551","citation_count":115,"is_preprint":false},{"pmid":"25920810","id":"PMC_25920810","title":"MOZ and MORF acetyltransferases: Molecular interaction, animal development and human disease.","date":"2015","source":"Biochimica et biophysica acta","url":"https://pubmed.ncbi.nlm.nih.gov/25920810","citation_count":107,"is_preprint":false},{"pmid":"25408830","id":"PMC_25408830","title":"1,3-Dimethyl Benzimidazolones Are Potent, Selective Inhibitors of the BRPF1 Bromodomain.","date":"2014","source":"ACS medicinal chemistry letters","url":"https://pubmed.ncbi.nlm.nih.gov/25408830","citation_count":71,"is_preprint":false},{"pmid":"28500727","id":"PMC_28500727","title":"Biological function and histone recognition of family IV bromodomain-containing proteins.","date":"2017","source":"Journal of cellular physiology","url":"https://pubmed.ncbi.nlm.nih.gov/28500727","citation_count":66,"is_preprint":false},{"pmid":"27326325","id":"PMC_27326325","title":"GSK6853, a Chemical Probe for Inhibition of the BRPF1 Bromodomain.","date":"2016","source":"ACS medicinal chemistry letters","url":"https://pubmed.ncbi.nlm.nih.gov/27326325","citation_count":58,"is_preprint":false},{"pmid":"28402630","id":"PMC_28402630","title":"Benzoisoquinolinediones as Potent and Selective Inhibitors of BRPF2 and TAF1/TAF1L Bromodomains.","date":"2017","source":"Journal of medicinal chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/28402630","citation_count":48,"is_preprint":false},{"pmid":"26677226","id":"PMC_26677226","title":"The Chromatin Regulator BRPF3 Preferentially Activates the HBO1 Acetyltransferase but Is Dispensable for Mouse Development and Survival.","date":"2015","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/26677226","citation_count":34,"is_preprint":false},{"pmid":"38867170","id":"PMC_38867170","title":"Identifying therapeutic target genes for migraine by systematic druggable genome-wide Mendelian randomization.","date":"2024","source":"The journal of headache and pain","url":"https://pubmed.ncbi.nlm.nih.gov/38867170","citation_count":25,"is_preprint":false},{"pmid":"32555450","id":"PMC_32555450","title":"BRPF3-HUWE1-mediated regulation of MYST2 is required for differentiation and cell-cycle progression in embryonic stem cells.","date":"2020","source":"Cell death and differentiation","url":"https://pubmed.ncbi.nlm.nih.gov/32555450","citation_count":13,"is_preprint":false},{"pmid":"34448544","id":"PMC_34448544","title":"Insights into the Molecular Mechanisms of Histone Code Recognition by the BRPF3 Bromodomain.","date":"2021","source":"Chemistry, an Asian journal","url":"https://pubmed.ncbi.nlm.nih.gov/34448544","citation_count":12,"is_preprint":false},{"pmid":"32664413","id":"PMC_32664413","title":"Genetic Markers for Later Remission in Response to Early Improvement of Antidepressants.","date":"2020","source":"International journal of molecular sciences","url":"https://pubmed.ncbi.nlm.nih.gov/32664413","citation_count":12,"is_preprint":false},{"pmid":"37493106","id":"PMC_37493106","title":"Targeting BRPF3 moderately reverses olaparib resistance in high grade serous ovarian carcinoma.","date":"2023","source":"Molecular carcinogenesis","url":"https://pubmed.ncbi.nlm.nih.gov/37493106","citation_count":4,"is_preprint":false},{"pmid":"41132846","id":"PMC_41132846","title":"A novel feedback loop: CELF1/circ-CELF1/BRPF3/KAT7 in cardiac fibrosis.","date":"2025","source":"Acta pharmaceutica Sinica. 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BRPF3 depletion reduces H3K14ac at selected origins.\",\n      \"method\": \"RNAi knockdown, genome-wide ChIP-seq for BRPF3, HBO1, and H3K14ac, co-immunoprecipitation\",\n      \"journal\": \"The EMBO journal\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — multiple orthogonal methods (RNAi, ChIP-seq, Co-IP) in a single rigorous study establishing both complex composition and genome-wide functional localization\",\n      \"pmids\": [\"26620551\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"BRPF3 is required for efficient replication origin activation: BRPF3 depletion impairs CDC45 recruitment to origins but does not affect MCM2-7 loading, placing BRPF3-HBO1 function specifically at the origin activation step.\",\n      \"method\": \"RNAi knockdown with RPA accumulation assay (replication stress screen), CDC45 and MCM2-7 chromatin recruitment assays\",\n      \"journal\": \"The EMBO journal\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — genetic epistasis via depletion combined with orthogonal chromatin recruitment assays precisely positioning BRPF3 in the replication pathway\",\n      \"pmids\": [\"26620551\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"BRPF3 protects HBO1 (MYST2) from ubiquitin-mediated proteasomal degradation by the E3 ligase HUWE1: protein-protein interaction between BRPF3 and MYST2 antagonizes HUWE1-mediated ubiquitination, stabilizing MYST2 protein levels.\",\n      \"method\": \"Co-immunoprecipitation, overexpression and knockdown of BRPF3 and HUWE1, ubiquitination assays in mouse ESCs\",\n      \"journal\": \"Cell death and differentiation\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP and functional rescue experiments in single lab; HUWE1 identified as E3 ligase for MYST2 with BRPF3 antagonism demonstrated by overexpression/knockdown\",\n      \"pmids\": [\"32555450\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"BRPF3 overexpression causes aberrant upregulation of MYST2 protein levels, leading to dysregulated cell-cycle progression and delay of embryoid-body formation and lineage commitment in mouse ESCs; these phenotypes are rescued by HUWE1 overexpression.\",\n      \"method\": \"BRPF3 and HUWE1 overexpression in mouse ESCs, embryoid body formation assays, cell-cycle analysis\",\n      \"journal\": \"Cell death and differentiation\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — defined cellular phenotypes with genetic rescue by HUWE1, single lab\",\n      \"pmids\": [\"32555450\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"The BRPF3 bromodomain recognizes mono-acetylated H4K5ac and di-acetylated H4K5acK12ac histone peptides; pull-down assays on purified histones from human cells confirmed binding to acetylated histone H4.\",\n      \"method\": \"Histone peptide binding assays, pull-down from purified human histones, MD simulation of bromodomain-histone complexes\",\n      \"journal\": \"Chemistry, an Asian journal\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — in vitro binding assays with purified components plus MD simulation, single lab, two orthogonal methods\",\n      \"pmids\": [\"34448544\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"Brpf3 shows dynamic spatiotemporal expression during mouse embryogenesis (highest in adult brain and testis), but Brpf3 disruption results in no gross developmental phenotype, distinguishing it from paralogs Brpf1 and Brpf2 whose loss causes lethality.\",\n      \"method\": \"LacZ reporter knock-in at Brpf3 locus, β-galactosidase staining, Brpf3 knockout mouse analysis\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — clean knockout mouse with systematic phenotypic analysis; negative result (no gross phenotype) is itself mechanistically informative for functional distinction from paralogs\",\n      \"pmids\": [\"26677226\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"Knockdown and pharmacologic inhibition of BRPF3 reduces PARP inhibitor (olaparib) resistance in high-grade serous ovarian carcinoma cells, while HBO1 inhibition (which depletes H3K14ac) does not affect PARPi response, indicating BRPF3's role in PARPi resistance is through its bromodomain reader function rather than solely via H3K14 acetylation.\",\n      \"method\": \"siRNA knockdown and pharmacologic inhibition of BRPF3 and HBO1 in isogenic PARPi-sensitive/resistant HGSOC cell lines, mass spectrometry histone modification profiling\",\n      \"journal\": \"Molecular carcinogenesis\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — knockdown and inhibitor experiments with isogenic cell lines; single lab, two orthogonal perturbation methods\",\n      \"pmids\": [\"37493106\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"In cardiac fibroblasts, circ-CELF1 reduces the ubiquitination-degradation rate of BRPF3, elevating BRPF3 protein levels; elevated BRPF3 then acts as a scaffold to recruit KAT7 histone acetyltransferase to the Celf1 gene promoter, facilitating H3K14 acetylation and Celf1 transcriptional activation, thereby promoting cardiac fibrosis.\",\n      \"method\": \"CircRNA knockdown/overexpression, ubiquitination assays, ChIP for H3K14ac at Celf1 promoter, protein interaction assays in cardiac fibroblasts\",\n      \"journal\": \"Acta pharmaceutica Sinica. B\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple orthogonal methods (ubiquitination assay, ChIP, Co-IP) in single lab; mechanistically defines BRPF3 as scaffold recruiting KAT7 to specific promoter\",\n      \"pmids\": [\"41132846\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"BRPF3 is a multidomain chromatin scaffold protein (containing PHD fingers, a bromodomain, and a PWWP domain) that preferentially assembles a tetrameric complex with the HBO1/KAT7 histone acetyltransferase; this complex acetylates histone H3K14 at replication origins and gene promoters, with BRPF3 directing CDC45 recruitment for origin activation; the BRPF3 bromodomain reads H4K5ac and H4K5acK12ac marks to recruit the complex to chromatin; BRPF3 additionally stabilizes HBO1/MYST2 by antagonizing HUWE1-mediated ubiquitin degradation; and BRPF3 acts as a scaffold recruiting KAT7 to specific promoters (e.g., Celf1) to drive H3K14 acetylation and transcriptional activation in contexts such as cardiac fibrosis.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"BRPF3 is a chromatin scaffold protein that assembles a dedicated tetrameric complex with the HBO1/KAT7 (MYST2) histone acetyltransferase, distinguishing it from other MYST-family enzymes, and directs this complex to acetylate histone H3K14 [#0]. Genome-wide, the BRPF3-HBO1 complex is enriched at ORC1-binding replication origins near transcription start sites, where it deposits H3K14ac, and BRPF3 is required for efficient origin activation by promoting CDC45 recruitment downstream of MCM2-7 loading [#1, #2]. Beyond its catalytic targeting role, BRPF3 stabilizes its partner enzyme by binding MYST2 and antagonizing HUWE1-mediated ubiquitination and proteasomal degradation, so that BRPF3 levels set MYST2 abundance and thereby influence cell-cycle progression and stem-cell differentiation [#3, #4]. The BRPF3 bromodomain functions as an acetyl-lysine reader, recognizing H4K5ac and H4K5acK12ac marks [#5]. This reader-scaffold activity is functionally separable from H3K14 acetylation: BRPF3 supports PARP-inhibitor resistance in ovarian carcinoma cells through its bromodomain function rather than through HBO1-dependent H3K14ac [#7], and in cardiac fibroblasts stabilized BRPF3 recruits KAT7 to the Celf1 promoter to drive H3K14ac and transcriptional activation, promoting fibrosis [#8].\",\n  \"teleology\": [\n    {\n      \"year\": 2015,\n      \"claim\": \"Establishing which acetyltransferase BRPF3 partners with answered whether it has a dedicated enzymatic complex; it forms a specific tetramer with HBO1/KAT7 that acetylates H3K14, excluding other MYST enzymes.\",\n      \"evidence\": \"reciprocal Co-IP of endogenous proteins and biochemical complex characterization, replicated across two studies\",\n      \"pmids\": [\"26677226\", \"26620551\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Identity and contribution of the other two tetramer subunits not resolved\", \"Structural basis of complex assembly not defined\"]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"Mapping where the complex acts and what it does there showed BRPF3-HBO1 is enriched at replication origins near TSSs and is required for origin activation via CDC45 recruitment, placing it precisely in the replication pathway.\",\n      \"evidence\": \"RNAi knockdown with genome-wide ChIP-seq for BRPF3/HBO1/H3K14ac and CDC45 vs MCM2-7 chromatin recruitment assays\",\n      \"pmids\": [\"26620551\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Mechanism linking H3K14ac to CDC45 loading not defined\", \"Relative contribution of origin vs promoter functions unresolved\"]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"Knockout analysis tested whether BRPF3 is developmentally essential; unlike paralogs Brpf1/Brpf2, Brpf3 loss produces no gross phenotype despite dynamic embryonic expression, functionally distinguishing the paralogs.\",\n      \"evidence\": \"LacZ reporter knock-in and knockout mouse phenotypic analysis\",\n      \"pmids\": [\"26677226\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Possible redundancy with paralogs not directly tested\", \"Subtle or stress-conditional phenotypes not assessed\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Identifying how BRPF3 controls its partner's abundance showed it binds MYST2 and antagonizes HUWE1-mediated ubiquitination, revealing a stabilizing rather than purely catalytic-targeting role.\",\n      \"evidence\": \"Co-IP, overexpression/knockdown of BRPF3 and HUWE1, and ubiquitination assays in mouse ESCs\",\n      \"pmids\": [\"32555450\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Single lab without reciprocal validation in other cell types\", \"Whether stabilization requires complex assembly or is direct competition with HUWE1 unclear\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Testing the consequence of excess BRPF3 demonstrated that overexpression elevates MYST2, dysregulating cell cycle and delaying lineage commitment, with HUWE1 rescue confirming the stabilization axis is causal.\",\n      \"evidence\": \"BRPF3/HUWE1 overexpression, embryoid body formation and cell-cycle assays in mouse ESCs\",\n      \"pmids\": [\"32555450\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Phenotype from overexpression rather than physiological levels\", \"Downstream targets driving differentiation delay not identified\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Defining the histone-mark specificity of the BRPF3 bromodomain established it as an acetyl-lysine reader recognizing H4K5ac and H4K5acK12ac, providing a chromatin-recruitment mechanism distinct from its H3K14ac deposition.\",\n      \"evidence\": \"histone peptide binding and pull-down assays from purified human histones with MD simulation\",\n      \"pmids\": [\"34448544\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"In vitro binding not validated by genome-wide reader occupancy in cells\", \"Affinity and selectivity relative to other bromodomain readers not benchmarked\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Separating reader from catalytic function in cancer showed BRPF3 loss reduces PARPi resistance whereas HBO1 inhibition does not, implicating the bromodomain reader function independently of H3K14ac.\",\n      \"evidence\": \"siRNA and pharmacologic inhibition of BRPF3 vs HBO1 in isogenic PARPi-sensitive/resistant HGSOC lines with histone MS\",\n      \"pmids\": [\"37493106\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Molecular pathway connecting BRPF3 reader function to PARPi resistance not defined\", \"Single tumor type and cell-line model\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Linking BRPF3 to a disease pathway showed circ-CELF1 stabilizes BRPF3, which scaffolds KAT7 to the Celf1 promoter to drive H3K14ac and transcription, demonstrating gene-specific scaffolding in cardiac fibrosis.\",\n      \"evidence\": \"circRNA knockdown/overexpression, ubiquitination assays, ChIP for H3K14ac and protein interaction assays in cardiac fibroblasts\",\n      \"pmids\": [\"41132846\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Single lab and model system\", \"Generalizability of promoter-specific scaffolding beyond Celf1 not established\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How BRPF3's reader (bromodomain/PWWP/PHD) and catalytic-targeting activities are integrated to select between replication origins, specific promoters, and partner stabilization in different cell contexts remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No structural model of the full BRPF3-HBO1 tetramer\", \"Determinants of locus selectivity unknown\", \"Endogenous loss-of-function phenotype in mammals remains mild and largely uncharacterized mechanistically\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0042393\", \"supporting_discovery_ids\": [5]},\n      {\"term_id\": \"GO:0140096\", \"supporting_discovery_ids\": [0, 1, 8]},\n      {\"term_id\": \"GO:0060090\", \"supporting_discovery_ids\": [8]},\n      {\"term_id\": \"GO:0098772\", \"supporting_discovery_ids\": [3]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0000228\", \"supporting_discovery_ids\": [1, 2]},\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [1, 8]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-69306\", \"supporting_discovery_ids\": [1, 2]},\n      {\"term_id\": \"R-HSA-4839726\", \"supporting_discovery_ids\": [0, 1, 8]},\n      {\"term_id\": \"R-HSA-74160\", \"supporting_discovery_ids\": [8]}\n    ],\n    \"complexes\": [\"BRPF3-HBO1/KAT7 tetrameric acetyltransferase complex\"],\n    \"partners\": [\"KAT7\", \"HUWE1\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":5,"faith_total":5,"faith_pct":100.0}}