{"gene":"RBBP5","run_date":"2026-06-10T06:43:36","timeline":{"discoveries":[{"year":2010,"finding":"A novel interaction site on WDR5 recruits RbBP5 through a conserved motif; X-ray crystallography characterized this WDR5–RbBP5 interface as fundamental to WRAD complex assembly and to stimulation of MLL1 histone H3K4 methyltransferase activity. WDR5 and RbBP5 act cooperatively to activate MLL1.","method":"X-ray crystallography; biochemical binding assays; in vitro methyltransferase activity assays","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1 / Strong — crystal structure plus in vitro activity assays with mutagenesis in a dedicated mechanistic study","pmids":["20716525"],"is_preprint":false},{"year":2014,"finding":"A non-active-site surface of the MLL1 SET domain (the Kabuki interaction surface, KIS) is required for interaction with the RbBP5/Ash2L heterodimer; disease-associated missense mutations at this surface abolish H3K4 dimethylation by the MLL1 core complex and disrupt binding to WRAD or the RbBP5/Ash2L heterodimer.","method":"In vitro methyltransferase assays; Co-immunoprecipitation/pulldown; structure-guided mutagenesis","journal":"Journal of molecular biology","confidence":"High","confidence_rationale":"Tier 1–2 / Moderate — in vitro reconstitution with mutagenesis and binding assays, single lab but multiple orthogonal methods","pmids":["24680668"],"is_preprint":false},{"year":2015,"finding":"Crystal structure of the WRAD complex reveals that the Ash2L SPRY domain binds a cluster of acidic residues (D/E box) in RbBP5; a phosphorylation switch on RbBP5 stimulates WRAD complex formation and significantly increases KMT2 methylation rates. Residues at the Ash2L/RbBP5 interface are required for heterodimer formation and stimulation of MLL1 catalytic activity.","method":"X-ray crystallography; mutational analysis; in vitro methyltransferase activity assays; erythroid differentiation assays","journal":"Genes & development","confidence":"High","confidence_rationale":"Tier 1 / Strong — crystal structure, mutagenesis, in vitro activity assays, and cell-based functional validation in one study","pmids":["25593305"],"is_preprint":false},{"year":2018,"finding":"The RbBP5 β-propeller (WD40) domain has a feature-rich surface dominated by clusters of arginine residues; NMR binding data indicate this domain directly interacts with nucleic acids, suggesting a role for RbBP5 in targeting MLL complexes to chromatin through its β-propeller domain.","method":"X-ray crystallography (β-propeller structure); NMR binding assays with nucleic acids","journal":"Nucleic acids research","confidence":"Medium","confidence_rationale":"Tier 1–2 / Weak — structure determined and NMR binding shown, but functional consequence of nucleic-acid binding not fully validated; single lab","pmids":["29897600"],"is_preprint":false},{"year":2019,"finding":"The structure of full-length human RBBP5 reveals an internal interaction between its WD40 propeller and C-terminal distal region that maintains the compact conformation of the MLL1 complex. A vertebrate-specific motif in the C-terminal distal region of RBBP5 contributes to nucleosome recognition and methylation of nucleosomes by the MLL1 complex.","method":"X-ray/cryo structure determination; biochemical assembly assays; nucleosome methylation assays; mutagenesis","journal":"Nucleic acids research","confidence":"High","confidence_rationale":"Tier 1 / Moderate — crystal structure of full-length RBBP5 combined with in vitro nucleosome methylation and assembly assays, single lab","pmids":["31544921"],"is_preprint":false},{"year":2016,"finding":"siRNA-mediated knockdown of RBBP5 or WDR5 suppressed DNA re-replication and chromosomal polyploidy induced by Geminin or CRL4CDT2 depletion. RBBP5 and WDR5 co-localize with the origin recognition complex (ORC) and MCM2-7 at replication origins, and their knockdown reduced H3K4 methylation at origins and suppressed MCM2-7 recruitment, indicating the MLL-WDR5-RBBP5 complex promotes DNA replication licensing.","method":"siRNA knockdown; ChIP at replication origins; flow cytometry (polyploidy); co-localization by immunofluorescence","journal":"Biology open","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — ChIP and co-localization with functional knockdown readout, single lab, multiple methods","pmids":["27744293"],"is_preprint":false},{"year":2016,"finding":"During TGF-β1-induced EMT in prostate cancer cells, RbBP5 is recruited to the Snail (SNAI1) transcription start site in a manner dependent on SMAD2/3 and CBP binding, leading to increased H3K4me3 at the Snail TSS. Knockdown of RbBP5 decreased Snail expression and suppressed EMT.","method":"ChIP assay; siRNA knockdown; Western blot; qRT-PCR; immunofluorescence","journal":"Oncotarget","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — ChIP and knockdown with defined molecular readouts, single lab","pmids":["27566588"],"is_preprint":false},{"year":2014,"finding":"Depletion of RBBP5 (as part of the WAR subcomplex with WDR5 and ASH2L) impairs efficient splicing/processing of FOS pre-mRNA transcripts, a function that is independent of changes in H3K4me3 levels at the FOS promoter.","method":"siRNA knockdown; RT-PCR detection of unspliced transcripts; ChIP for H3K4me3","journal":"Cellular & molecular biology letters","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — functional knockdown with multiple orthogonal readouts (splicing and H3K4me3), single lab","pmids":["24715476"],"is_preprint":false},{"year":2021,"finding":"In C. elegans, RBBP-5 (ortholog of RBBP5, member of Set1/MLL complex) functions as a germ cell reprogramming barrier; double RNAi knockdown of lin-53 and rbbp-5 allowed reprogramming, identifying RBBP-5 as a barrier to germ cell fate conversion.","method":"Double RNAi (CONJUDOR); cell reprogramming phenotype assay in C. elegans","journal":"Nucleic acids research","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — genetic epistasis via double RNAi in model organism, single study","pmids":["33290523"],"is_preprint":false},{"year":2021,"finding":"In budding yeast, Swd1 (ortholog of RBBP5, COMPASS subunit) is required for progression through early meiosis and for both homologous recombination and chromosome segregation (established by checkpoint suppression analyses), distinct from the role of Swd3 in late meiosis.","method":"Genetic deletion/meiotic phenotype analysis; checkpoint suppression epistasis; H3K4 methylation assays in yeast","journal":"G3 (Bethesda, Md.)","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — genetic epistasis with defined meiotic phenotypes in yeast ortholog, single lab","pmids":["34849786"],"is_preprint":false},{"year":2024,"finding":"De novo missense variants of RBBP5 (p.T232I and p.E296D) affect conserved residues at the RBBP5–nucleosome interface. In Drosophila, loss of Rbbp5 reduces brain size (microcephaly), and both missense variants fail to rescue this loss-of-function phenotype, confirming they are partial loss-of-function alleles that impair RBBP5's role at the nucleosome interface.","method":"Protein structural analysis; transgenic Drosophila overexpression/rescue assays; Rbbp5 null background complementation","journal":"Genetics in medicine","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — structural analysis combined with Drosophila in vivo rescue assays, multiple variants tested","pmids":["39036895"],"is_preprint":false},{"year":2025,"finding":"Nuclear HKDC1 acts as a protein kinase that phosphorylates RBBP5 at Ser497, which is required for MLL1 complex assembly and subsequent H3K4me3 deposition, leading to transcriptional activation of mitosis-related genes and cell cycle progression in hepatocellular carcinoma cells.","method":"Co-immunoprecipitation; in vitro kinase assay; site-directed mutagenesis (Ser497); ChIP for H3K4me3; HKDC1 inhibition/knockout functional assays","journal":"Cell reports","confidence":"High","confidence_rationale":"Tier 1–2 / Moderate — in vitro kinase assay identifying phosphorylation site, mutagenesis, and ChIP with functional readout, single lab with multiple orthogonal methods","pmids":["39891906"],"is_preprint":false},{"year":2025,"finding":"RBBP5 (as core subunit of SET1/COMPASS) co-activates XBP1s to facilitate dynamic proteostasis gene expression by marking promoter-proximal H3K4me3, which further recruits the Integrator Complex and SWI/SNF chromatin remodelers. RBBP5 ablation in mice causes increased susceptibility to proteotoxic stress, chronic inflammation, and hepatic steatosis, and impairs autophagy and cell survival in vitro.","method":"RBBP5 knockout in mice; ChIP-seq for H3K4me3; co-activator interaction assays; in vitro stress assays","journal":"bioRxiv","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — preprint, in vivo knockout plus ChIP-seq, single lab","pmids":["39314427"],"is_preprint":true},{"year":2025,"finding":"lncRNA HClnc1 recruits an RBBP5/KAT2B epigenetic complex to the ODC1 promoter; RBBP5 directly binds the ODC1 promoter region and its knockdown reduces ODC1 expression and blocks HClnc1-induced upregulation of ODC1 in liver cancer cells.","method":"RNA pulldown; mass spectrometry; ChIP assay; RNAi knockdown; dual luciferase reporter","journal":"Nan fang yi ke da xue xue bao","confidence":"Medium","confidence_rationale":"Tier 2–3 / Weak — ChIP and pulldown identify promoter binding and complex, single lab","pmids":["41022601"],"is_preprint":false},{"year":2024,"finding":"The WRAD core (WDR5/RBBP5/ASH2L/DPY30) interacts with the replisome complex; disruption of DPY30 (a WRAD component) results in DNA re-replication, DNA damage, and chromosomal instability without affecting cancer cell proliferation, indicating the WRAD complex sustains replication fidelity.","method":"Co-immunoprecipitation (WRAD–replisome interaction); DPY30 genetic disruption; DNA damage and CIN assays in PDAC models","journal":"bioRxiv","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — preprint, Co-IP and genetic disruption with defined molecular phenotypes, single lab","pmids":["bio_10.1101_2024.10.21.619543"],"is_preprint":true}],"current_model":"RBBP5 is a scaffold subunit of the WRAD (WDR5–RBBP5–Ash2L–DPY30) complex that is essential for the assembly and allosteric activation of SET1/KMT2-family histone H3K4 methyltransferases: it bridges WDR5 (via a conserved RbBP5 motif binding a dedicated WDR5 site) and Ash2L (via its D/E box), its internal WD40–C-terminal interaction maintains complex compactness, a vertebrate-specific C-terminal motif enables nucleosome recognition, its WD40 β-propeller directly contacts nucleic acids to help target complexes to chromatin, and its activity is regulated post-translationally by phosphorylation (a phospho-switch that stimulates WRAD assembly and methylation rates, and phosphorylation at Ser497 by nuclear HKDC1 that drives MLL1 complex assembly and H3K4me3 deposition); beyond H3K4 methylation, RBBP5 is required for DNA replication licensing, efficient pre-mRNA processing, regulation of proteostasis gene expression via XBP1s co-activation, and in vivo brain development, with loss-of-function causing microcephaly in flies and a syndromic neurodevelopmental disorder in humans."},"narrative":{"mechanistic_narrative":"RBBP5 is a scaffold subunit of the WRAD module that assembles and allosterically activates SET1/KMT2-family histone H3K4 methyltransferases on chromatin [PMID:20716525, PMID:25593305]. It bridges the complex through defined interfaces: a conserved RbBP5 motif binds a dedicated surface on WDR5, and these two proteins act cooperatively to stimulate MLL1 catalytic activity [PMID:20716525], while an acidic D/E box in RBBP5 is engaged by the Ash2L SPRY domain to form the catalytically stimulatory RbBP5/Ash2L heterodimer [PMID:25593305]. This heterodimer in turn docks onto a non-active-site surface of the MLL1 SET domain, and disease-associated mutations at this interface abolish H3K4 dimethylation [PMID:24680668]. Within RBBP5 itself, an internal interaction between the WD40 β-propeller and a C-terminal distal region maintains the compact conformation of the complex, and a vertebrate-specific C-terminal motif mediates nucleosome recognition and methylation [PMID:31544921], with the β-propeller surface additionally contacting nucleic acids to help target the complex to chromatin [PMID:29897600]. RBBP5 activity is tuned post-translationally: a phospho-switch stimulates WRAD assembly and methylation rates [PMID:25593305], and phosphorylation at Ser497 by nuclear HKDC1 drives MLL1 complex assembly and H3K4me3 deposition at mitotic genes [PMID:39891906]. Through these activities RBBP5 deposits promoter H3K4me3 at specific target genes during EMT and proteostasis responses [PMID:27566588, PMID:39314427] and supports DNA replication licensing at origins [PMID:27744293]. RBBP5 is also required for in vivo brain development, and de novo missense variants at its nucleosome interface cause a syndromic neurodevelopmental disorder, with the variants acting as partial loss-of-function alleles that fail to rescue microcephaly in flies [PMID:39036895].","teleology":[{"year":2010,"claim":"Established the molecular basis by which RBBP5 is recruited into the H3K4 methyltransferase complex and why this matters for enzyme activation, defining a dedicated WDR5–RbBP5 interface.","evidence":"X-ray crystallography with biochemical binding and in vitro methyltransferase assays of the WDR5–RbBP5 interface","pmids":["20716525"],"confidence":"High","gaps":["Did not resolve how the assembled module engages nucleosomes","Stoichiometry and dynamics within full WRAD not addressed"]},{"year":2014,"claim":"Identified the MLL1 SET-domain surface that the RbBP5/Ash2L heterodimer engages and linked it to disease, showing this contact is required for H3K4 dimethylation.","evidence":"In vitro methyltransferase assays, Co-IP/pulldown, and structure-guided mutagenesis of the MLL1 KIS surface","pmids":["24680668"],"confidence":"High","gaps":["Did not define the RBBP5 residues contacting this surface","Restricted to MLL1 among KMT2 paralogs"]},{"year":2014,"claim":"Revealed a methylation-independent role for RBBP5 in RNA processing, separating its chromatin-mark function from a direct contribution to pre-mRNA splicing.","evidence":"siRNA knockdown with RT-PCR of unspliced FOS transcripts and ChIP for H3K4me3","pmids":["24715476"],"confidence":"Medium","gaps":["Mechanism connecting WAR subcomplex to the splicing machinery unknown","Tested only on FOS pre-mRNA"]},{"year":2015,"claim":"Defined the Ash2L–RbBP5 (D/E box) interface and a phospho-switch on RBBP5, explaining how heterodimer formation and phosphorylation stimulate KMT2 methylation rates.","evidence":"X-ray crystallography, mutational analysis, in vitro methyltransferase assays, and erythroid differentiation assays","pmids":["25593305"],"confidence":"High","gaps":["Kinase responsible for the phospho-switch not identified here","In vivo relevance of the switch not established"]},{"year":2016,"claim":"Connected RBBP5/WDR5-dependent H3K4 methylation to DNA replication licensing, extending its role beyond transcription.","evidence":"siRNA knockdown, ChIP at replication origins, flow cytometry for polyploidy, and immunofluorescence co-localization with ORC/MCM2-7","pmids":["27744293"],"confidence":"Medium","gaps":["Direct versus indirect contribution of RBBP5 to MCM2-7 loading unresolved","No structural basis for origin targeting"]},{"year":2016,"claim":"Showed signal-dependent recruitment of RBBP5 to a specific target promoter, demonstrating it acts in defined transcriptional programs (EMT) rather than only globally.","evidence":"ChIP, siRNA knockdown, Western blot, and qRT-PCR of the Snail/SNAI1 locus in TGF-β1-treated prostate cancer cells","pmids":["27566588"],"confidence":"Medium","gaps":["Direct RBBP5–SMAD2/3/CBP contacts not biochemically mapped","Generalizability beyond Snail not tested"]},{"year":2018,"claim":"Demonstrated that the RBBP5 β-propeller directly binds nucleic acids, proposing a chromatin-targeting function for this domain.","evidence":"X-ray crystallography of the β-propeller and NMR nucleic-acid binding assays","pmids":["29897600"],"confidence":"Medium","gaps":["Functional consequence of nucleic-acid binding not validated in cells","Sequence specificity of binding undefined"]},{"year":2019,"claim":"Resolved full-length RBBP5 architecture, showing an intramolecular WD40–C-terminal contact maintains complex compactness and a vertebrate-specific motif mediates nucleosome recognition.","evidence":"Structure determination with biochemical assembly and nucleosome methylation assays plus mutagenesis","pmids":["31544921"],"confidence":"High","gaps":["Dynamics of the compact-to-active transition not captured","Role of the vertebrate motif in vivo not tested here"]},{"year":2021,"claim":"Genetic studies in model organisms established conserved roles for RBBP5 orthologs in restricting cell-fate plasticity and in meiotic recombination/segregation.","evidence":"Double RNAi reprogramming assay in C. elegans (rbbp-5) and meiotic deletion/checkpoint epistasis with H3K4 methylation assays in budding yeast (Swd1)","pmids":["33290523","34849786"],"confidence":"Medium","gaps":["Whether these roles depend on H3K4 methylation versus methylation-independent functions not fully separated","Human ortholog equivalence inferred, not directly tested"]},{"year":2024,"claim":"Linked RBBP5 to human disease by showing de novo nucleosome-interface variants are partial loss-of-function alleles and that Rbbp5 loss causes microcephaly in vivo.","evidence":"Protein structural analysis and transgenic Drosophila rescue/complementation in an Rbbp5 null background for p.T232I and p.E296D","pmids":["39036895"],"confidence":"Medium","gaps":["Molecular consequence of variants on methyltransferase output not quantified","Mammalian neurodevelopmental mechanism not established"]},{"year":2025,"claim":"Identified a specific upstream kinase (nuclear HKDC1) and phosphosite (Ser497) controlling MLL1 complex assembly, providing a defined signaling input to RBBP5 function.","evidence":"Co-IP, in vitro kinase assay, Ser497 mutagenesis, and ChIP for H3K4me3 with HKDC1 inhibition/knockout in hepatocellular carcinoma cells","pmids":["39891906"],"confidence":"High","gaps":["Whether Ser497 phosphorylation is the same phospho-switch seen structurally not resolved","Generality across non-HCC contexts unknown"]},{"year":2025,"claim":"Extended RBBP5 to stress-responsive gene programs, showing it co-activates XBP1s to mark proteostasis genes and that its loss sensitizes mice to proteotoxic stress.","evidence":"RBBP5 knockout mice, H3K4me3 ChIP-seq, co-activator interaction assays, and in vitro stress assays (preprint)","pmids":["39314427"],"confidence":"Medium","gaps":["Preprint, not peer-reviewed","Direct RBBP5–XBP1s contact and recruitment order not biochemically defined"]},{"year":2025,"claim":"Showed lncRNA-directed recruitment of RBBP5 to a specific oncogenic promoter, illustrating RNA-guided targeting of RBBP5-containing complexes.","evidence":"RNA pulldown, mass spectrometry, ChIP, RNAi knockdown, and dual luciferase reporter at the ODC1 promoter in liver cancer cells","pmids":["41022601"],"confidence":"Medium","gaps":["Whether RBBP5 binds the lncRNA directly or via partners unclear","KAT2B/RBBP5 functional cooperation not dissected"]},{"year":null,"claim":"How RBBP5's methylation-independent functions (replication licensing, pre-mRNA processing, XBP1s co-activation) are mechanistically separated from its WRAD scaffolding role remains unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No structural model distinguishing methylation-dependent from methylation-independent complexes","Phosphorylation- and RNA-guided targeting mechanisms not integrated into a unified regulatory model"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0140096","term_label":"catalytic activity, acting on a protein","supporting_discovery_ids":[0,2,4]},{"term_id":"GO:0060090","term_label":"molecular adaptor activity","supporting_discovery_ids":[0,2,4]},{"term_id":"GO:0003677","term_label":"DNA binding","supporting_discovery_ids":[3,13]},{"term_id":"GO:0042393","term_label":"histone binding","supporting_discovery_ids":[4]}],"localization":[{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[6,11]},{"term_id":"GO:0000228","term_label":"nuclear chromosome","supporting_discovery_ids":[4,5]}],"pathway":[{"term_id":"R-HSA-4839726","term_label":"Chromatin organization","supporting_discovery_ids":[0,2,4]},{"term_id":"R-HSA-74160","term_label":"Gene expression (Transcription)","supporting_discovery_ids":[6,11,12]},{"term_id":"R-HSA-69306","term_label":"DNA Replication","supporting_discovery_ids":[5]}],"complexes":["WRAD (WDR5–RBBP5–ASH2L–DPY30)","MLL1/SET1 (COMPASS) H3K4 methyltransferase complex"],"partners":["WDR5","ASH2L","DPY30","KMT2A","HKDC1","KAT2B"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q15291","full_name":"Retinoblastoma-binding protein 5","aliases":["Retinoblastoma-binding protein RBQ-3"],"length_aa":538,"mass_kda":59.2,"function":"In embryonic stem (ES) cells, plays a crucial role in the differentiation potential, particularly along the neural lineage, regulating gene induction and H3 'Lys-4' methylation at key developmental loci, including that mediated by retinoic acid (By similarity). Does not affect ES cell self-renewal (By similarity). Component or associated component of some histone methyltransferase complexes which regulates transcription through recruitment of those complexes to gene promoters (PubMed:19131338). As part of the MLL1/MLL complex, involved in mono-, di- and trimethylation at 'Lys-4' of histone H3 (PubMed:19556245). Histone H3 'Lys-4' methylation represents a specific tag for epigenetic transcriptional activation (PubMed:19556245). In association with ASH2L and WDR5, stimulates the histone methyltransferase activities of KMT2A, KMT2B, KMT2C, KMT2D, SETD1A and SETD1B (PubMed:21220120, PubMed:22266653)","subcellular_location":"Nucleus","url":"https://www.uniprot.org/uniprotkb/Q15291/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":true,"resolved_as":"","url":"https://depmap.org/portal/gene/RBBP5","classification":"Common Essential","n_dependent_lines":1180,"n_total_lines":1208,"dependency_fraction":0.9768211920529801},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[{"gene":"H1F0","stoichiometry":0.2},{"gene":"H2AFZ","stoichiometry":0.2},{"gene":"HIST2H2BE","stoichiometry":0.2},{"gene":"HMGA1","stoichiometry":0.2},{"gene":"HMGN5","stoichiometry":0.2},{"gene":"NUCKS1","stoichiometry":0.2},{"gene":"NUMA1","stoichiometry":0.2},{"gene":"RBM15B","stoichiometry":0.2},{"gene":"SSRP1","stoichiometry":0.2},{"gene":"TOP1","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/search/RBBP5","total_profiled":1310},"omim":[{"mim_id":"612033","title":"PAXIP1-ASSOCIATED GLUTAMATE-RICH PROTEIN 1; PAGR1","url":"https://www.omim.org/entry/612033"},{"mim_id":"612032","title":"DPY30 HISTONE METHYLTRANSFERASE COMPLEX REGULATORY SUBUNIT; DPY30","url":"https://www.omim.org/entry/612032"},{"mim_id":"611055","title":"SET DOMAIN-CONTAINING PROTEIN 1B; SETD1B","url":"https://www.omim.org/entry/611055"},{"mim_id":"611052","title":"SET DOMAIN-CONTAINING PROTEIN 1A; SETD1A","url":"https://www.omim.org/entry/611052"},{"mim_id":"608254","title":"PAX TRANSCRIPTION ACTIVATION DOMAIN-INTERACTING PROTEIN 1; PAXIP1","url":"https://www.omim.org/entry/608254"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Supported","locations":[{"location":"Nucleoplasm","reliability":"Supported"},{"location":"Nucleoli","reliability":"Supported"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/RBBP5"},"hgnc":{"alias_symbol":["RBQ3","SWD1"],"prev_symbol":[]},"alphafold":{"accession":"Q15291","domains":[{"cath_id":"2.130.10.10","chopping":"12-321","consensus_level":"medium","plddt":94.2877,"start":12,"end":321}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q15291","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q15291-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q15291-F1-predicted_aligned_error_v6.png","plddt_mean":77.75},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=RBBP5","jax_strain_url":"https://www.jax.org/strain/search?query=RBBP5"},"sequence":{"accession":"Q15291","fasta_url":"https://rest.uniprot.org/uniprotkb/Q15291.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q15291/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q15291"}},"corpus_meta":[{"pmid":"20716525","id":"PMC_20716525","title":"Characterization of a novel WDR5-binding site that recruits RbBP5 through a conserved motif to enhance methylation of histone H3 lysine 4 by mixed lineage leukemia protein-1.","date":"2010","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/20716525","citation_count":95,"is_preprint":false},{"pmid":"25593305","id":"PMC_25593305","title":"A phosphorylation switch on RbBP5 regulates histone H3 Lys4 methylation.","date":"2015","source":"Genes & development","url":"https://pubmed.ncbi.nlm.nih.gov/25593305","citation_count":42,"is_preprint":false},{"pmid":"24680668","id":"PMC_24680668","title":"A non-active-site SET domain surface crucial for the interaction of MLL1 and the RbBP5/Ash2L heterodimer within MLL family core complexes.","date":"2014","source":"Journal of molecular biology","url":"https://pubmed.ncbi.nlm.nih.gov/24680668","citation_count":39,"is_preprint":false},{"pmid":"28229975","id":"PMC_28229975","title":"Diverse roles of WDR5-RbBP5-ASH2L-DPY30 (WRAD) complex in the functions of the SET1 histone methyltransferase family.","date":"2017","source":"Journal of biosciences","url":"https://pubmed.ncbi.nlm.nih.gov/28229975","citation_count":35,"is_preprint":false},{"pmid":"31544921","id":"PMC_31544921","title":"The internal interaction in RBBP5 regulates assembly and activity of MLL1 methyltransferase complex.","date":"2019","source":"Nucleic acids research","url":"https://pubmed.ncbi.nlm.nih.gov/31544921","citation_count":20,"is_preprint":false},{"pmid":"33416179","id":"PMC_33416179","title":"Long non‑coding RNA AC245100.4 promotes prostate cancer tumorigenesis via the microRNA‑145‑5p/RBBP5 axis.","date":"2020","source":"Oncology reports","url":"https://pubmed.ncbi.nlm.nih.gov/33416179","citation_count":17,"is_preprint":false},{"pmid":"27566588","id":"PMC_27566588","title":"Role of RbBP5 and H3K4me3 in the vicinity of Snail transcription start site during epithelial-mesenchymal transition in prostate cancer cell.","date":"2016","source":"Oncotarget","url":"https://pubmed.ncbi.nlm.nih.gov/27566588","citation_count":16,"is_preprint":false},{"pmid":"28182322","id":"PMC_28182322","title":"Somatic cancer mutations in the MLL1 histone methyltransferase modulate its enzymatic activity and dependence on the WDR5/RBBP5/ASH2L complex.","date":"2017","source":"Molecular oncology","url":"https://pubmed.ncbi.nlm.nih.gov/28182322","citation_count":14,"is_preprint":false},{"pmid":"29897600","id":"PMC_29897600","title":"The structure of the RbBP5 β-propeller domain reveals a surface with potential nucleic acid binding sites.","date":"2018","source":"Nucleic acids research","url":"https://pubmed.ncbi.nlm.nih.gov/29897600","citation_count":13,"is_preprint":false},{"pmid":"27744293","id":"PMC_27744293","title":"Regulation of DNA replication and chromosomal polyploidy by the MLL-WDR5-RBBP5 methyltransferases.","date":"2016","source":"Biology 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Md.)","url":"https://pubmed.ncbi.nlm.nih.gov/34849786","citation_count":7,"is_preprint":false},{"pmid":"39036895","id":"PMC_39036895","title":"Loss-of-function in RBBP5 results in a syndromic neurodevelopmental disorder associated with microcephaly.","date":"2024","source":"Genetics in medicine : official journal of the American College of Medical Genetics","url":"https://pubmed.ncbi.nlm.nih.gov/39036895","citation_count":6,"is_preprint":false},{"pmid":"27189701","id":"PMC_27189701","title":"RBQ3 participates in multiple myeloma cell proliferation, adhesion and chemoresistance.","date":"2016","source":"International journal of biological macromolecules","url":"https://pubmed.ncbi.nlm.nih.gov/27189701","citation_count":5,"is_preprint":false},{"pmid":"39891906","id":"PMC_39891906","title":"Nuclear-localized HKDC1 promotes hepatocellular carcinoma through phosphorylating RBBP5 to upregulate H3K4me3.","date":"2025","source":"Cell reports","url":"https://pubmed.ncbi.nlm.nih.gov/39891906","citation_count":5,"is_preprint":false},{"pmid":"37051916","id":"PMC_37051916","title":"Genome-wide in silico analysis leads to identification of deleterious L290V mutation in RBBP5 gene in Bos indicus.","date":"2023","source":"Animal biotechnology","url":"https://pubmed.ncbi.nlm.nih.gov/37051916","citation_count":4,"is_preprint":false},{"pmid":"33290523","id":"PMC_33290523","title":"The CONJUDOR pipeline for multiplexed knockdown of gene pairs identifies RBBP-5 as a germ cell reprogramming barrier in C. elegans.","date":"2021","source":"Nucleic acids research","url":"https://pubmed.ncbi.nlm.nih.gov/33290523","citation_count":4,"is_preprint":false},{"pmid":"39314427","id":"PMC_39314427","title":"The SET1/COMPASS subunit RBBP5 orchestrates epigenetic control of global proteostasis and the 12h oscillator to safeguard metabolic and cellular homeostasis.","date":"2025","source":"bioRxiv : the preprint server for biology","url":"https://pubmed.ncbi.nlm.nih.gov/39314427","citation_count":2,"is_preprint":false},{"pmid":"36799194","id":"PMC_36799194","title":"[Corrigendum] Long non‑coding RNA AC245100.4 promotes prostate cancer tumorigenesis via the microRNA‑145‑5p/RBBP5 axis.","date":"2023","source":"Oncology reports","url":"https://pubmed.ncbi.nlm.nih.gov/36799194","citation_count":1,"is_preprint":false},{"pmid":"41022601","id":"PMC_41022601","title":"[Long noncoding RNA HClnc1 promotes proliferation and migration of liver cancer cells by targeting RBBP5/KAT2B complex to enhance ODC1 transcription].","date":"2025","source":"Nan fang yi ke da xue xue bao = Journal of Southern Medical University","url":"https://pubmed.ncbi.nlm.nih.gov/41022601","citation_count":0,"is_preprint":false},{"pmid":null,"id":"bio_10.1101_2024.10.21.619543","title":"WRAD core perturbation impairs DNA replication fidelity promoting immunoediting in pancreatic cancer","date":"2024-10-24","source":"bioRxiv","url":"https://doi.org/10.1101/2024.10.21.619543","citation_count":0,"is_preprint":true}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":12171,"output_tokens":3843,"usd":0.047079,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":11468,"output_tokens":4339,"usd":0.082907,"stage2_stop_reason":"end_turn"},"total_usd":0.129986,"stage1_batch_id":"msgbatch_01CNoDbkChHEkgrJnL7BwtGJ","stage2_batch_id":"msgbatch_016Y4x9E9Wg5VQDANj9quSQD","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2010,\n      \"finding\": \"A novel interaction site on WDR5 recruits RbBP5 through a conserved motif; X-ray crystallography characterized this WDR5–RbBP5 interface as fundamental to WRAD complex assembly and to stimulation of MLL1 histone H3K4 methyltransferase activity. WDR5 and RbBP5 act cooperatively to activate MLL1.\",\n      \"method\": \"X-ray crystallography; biochemical binding assays; in vitro methyltransferase activity assays\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — crystal structure plus in vitro activity assays with mutagenesis in a dedicated mechanistic study\",\n      \"pmids\": [\"20716525\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"A non-active-site surface of the MLL1 SET domain (the Kabuki interaction surface, KIS) is required for interaction with the RbBP5/Ash2L heterodimer; disease-associated missense mutations at this surface abolish H3K4 dimethylation by the MLL1 core complex and disrupt binding to WRAD or the RbBP5/Ash2L heterodimer.\",\n      \"method\": \"In vitro methyltransferase assays; Co-immunoprecipitation/pulldown; structure-guided mutagenesis\",\n      \"journal\": \"Journal of molecular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Moderate — in vitro reconstitution with mutagenesis and binding assays, single lab but multiple orthogonal methods\",\n      \"pmids\": [\"24680668\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"Crystal structure of the WRAD complex reveals that the Ash2L SPRY domain binds a cluster of acidic residues (D/E box) in RbBP5; a phosphorylation switch on RbBP5 stimulates WRAD complex formation and significantly increases KMT2 methylation rates. Residues at the Ash2L/RbBP5 interface are required for heterodimer formation and stimulation of MLL1 catalytic activity.\",\n      \"method\": \"X-ray crystallography; mutational analysis; in vitro methyltransferase activity assays; erythroid differentiation assays\",\n      \"journal\": \"Genes & development\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — crystal structure, mutagenesis, in vitro activity assays, and cell-based functional validation in one study\",\n      \"pmids\": [\"25593305\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"The RbBP5 β-propeller (WD40) domain has a feature-rich surface dominated by clusters of arginine residues; NMR binding data indicate this domain directly interacts with nucleic acids, suggesting a role for RbBP5 in targeting MLL complexes to chromatin through its β-propeller domain.\",\n      \"method\": \"X-ray crystallography (β-propeller structure); NMR binding assays with nucleic acids\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1–2 / Weak — structure determined and NMR binding shown, but functional consequence of nucleic-acid binding not fully validated; single lab\",\n      \"pmids\": [\"29897600\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"The structure of full-length human RBBP5 reveals an internal interaction between its WD40 propeller and C-terminal distal region that maintains the compact conformation of the MLL1 complex. A vertebrate-specific motif in the C-terminal distal region of RBBP5 contributes to nucleosome recognition and methylation of nucleosomes by the MLL1 complex.\",\n      \"method\": \"X-ray/cryo structure determination; biochemical assembly assays; nucleosome methylation assays; mutagenesis\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — crystal structure of full-length RBBP5 combined with in vitro nucleosome methylation and assembly assays, single lab\",\n      \"pmids\": [\"31544921\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"siRNA-mediated knockdown of RBBP5 or WDR5 suppressed DNA re-replication and chromosomal polyploidy induced by Geminin or CRL4CDT2 depletion. RBBP5 and WDR5 co-localize with the origin recognition complex (ORC) and MCM2-7 at replication origins, and their knockdown reduced H3K4 methylation at origins and suppressed MCM2-7 recruitment, indicating the MLL-WDR5-RBBP5 complex promotes DNA replication licensing.\",\n      \"method\": \"siRNA knockdown; ChIP at replication origins; flow cytometry (polyploidy); co-localization by immunofluorescence\",\n      \"journal\": \"Biology open\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — ChIP and co-localization with functional knockdown readout, single lab, multiple methods\",\n      \"pmids\": [\"27744293\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"During TGF-β1-induced EMT in prostate cancer cells, RbBP5 is recruited to the Snail (SNAI1) transcription start site in a manner dependent on SMAD2/3 and CBP binding, leading to increased H3K4me3 at the Snail TSS. Knockdown of RbBP5 decreased Snail expression and suppressed EMT.\",\n      \"method\": \"ChIP assay; siRNA knockdown; Western blot; qRT-PCR; immunofluorescence\",\n      \"journal\": \"Oncotarget\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — ChIP and knockdown with defined molecular readouts, single lab\",\n      \"pmids\": [\"27566588\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"Depletion of RBBP5 (as part of the WAR subcomplex with WDR5 and ASH2L) impairs efficient splicing/processing of FOS pre-mRNA transcripts, a function that is independent of changes in H3K4me3 levels at the FOS promoter.\",\n      \"method\": \"siRNA knockdown; RT-PCR detection of unspliced transcripts; ChIP for H3K4me3\",\n      \"journal\": \"Cellular & molecular biology letters\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — functional knockdown with multiple orthogonal readouts (splicing and H3K4me3), single lab\",\n      \"pmids\": [\"24715476\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"In C. elegans, RBBP-5 (ortholog of RBBP5, member of Set1/MLL complex) functions as a germ cell reprogramming barrier; double RNAi knockdown of lin-53 and rbbp-5 allowed reprogramming, identifying RBBP-5 as a barrier to germ cell fate conversion.\",\n      \"method\": \"Double RNAi (CONJUDOR); cell reprogramming phenotype assay in C. elegans\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — genetic epistasis via double RNAi in model organism, single study\",\n      \"pmids\": [\"33290523\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"In budding yeast, Swd1 (ortholog of RBBP5, COMPASS subunit) is required for progression through early meiosis and for both homologous recombination and chromosome segregation (established by checkpoint suppression analyses), distinct from the role of Swd3 in late meiosis.\",\n      \"method\": \"Genetic deletion/meiotic phenotype analysis; checkpoint suppression epistasis; H3K4 methylation assays in yeast\",\n      \"journal\": \"G3 (Bethesda, Md.)\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — genetic epistasis with defined meiotic phenotypes in yeast ortholog, single lab\",\n      \"pmids\": [\"34849786\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"De novo missense variants of RBBP5 (p.T232I and p.E296D) affect conserved residues at the RBBP5–nucleosome interface. In Drosophila, loss of Rbbp5 reduces brain size (microcephaly), and both missense variants fail to rescue this loss-of-function phenotype, confirming they are partial loss-of-function alleles that impair RBBP5's role at the nucleosome interface.\",\n      \"method\": \"Protein structural analysis; transgenic Drosophila overexpression/rescue assays; Rbbp5 null background complementation\",\n      \"journal\": \"Genetics in medicine\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — structural analysis combined with Drosophila in vivo rescue assays, multiple variants tested\",\n      \"pmids\": [\"39036895\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"Nuclear HKDC1 acts as a protein kinase that phosphorylates RBBP5 at Ser497, which is required for MLL1 complex assembly and subsequent H3K4me3 deposition, leading to transcriptional activation of mitosis-related genes and cell cycle progression in hepatocellular carcinoma cells.\",\n      \"method\": \"Co-immunoprecipitation; in vitro kinase assay; site-directed mutagenesis (Ser497); ChIP for H3K4me3; HKDC1 inhibition/knockout functional assays\",\n      \"journal\": \"Cell reports\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Moderate — in vitro kinase assay identifying phosphorylation site, mutagenesis, and ChIP with functional readout, single lab with multiple orthogonal methods\",\n      \"pmids\": [\"39891906\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"RBBP5 (as core subunit of SET1/COMPASS) co-activates XBP1s to facilitate dynamic proteostasis gene expression by marking promoter-proximal H3K4me3, which further recruits the Integrator Complex and SWI/SNF chromatin remodelers. RBBP5 ablation in mice causes increased susceptibility to proteotoxic stress, chronic inflammation, and hepatic steatosis, and impairs autophagy and cell survival in vitro.\",\n      \"method\": \"RBBP5 knockout in mice; ChIP-seq for H3K4me3; co-activator interaction assays; in vitro stress assays\",\n      \"journal\": \"bioRxiv\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — preprint, in vivo knockout plus ChIP-seq, single lab\",\n      \"pmids\": [\"39314427\"],\n      \"is_preprint\": true\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"lncRNA HClnc1 recruits an RBBP5/KAT2B epigenetic complex to the ODC1 promoter; RBBP5 directly binds the ODC1 promoter region and its knockdown reduces ODC1 expression and blocks HClnc1-induced upregulation of ODC1 in liver cancer cells.\",\n      \"method\": \"RNA pulldown; mass spectrometry; ChIP assay; RNAi knockdown; dual luciferase reporter\",\n      \"journal\": \"Nan fang yi ke da xue xue bao\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2–3 / Weak — ChIP and pulldown identify promoter binding and complex, single lab\",\n      \"pmids\": [\"41022601\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"The WRAD core (WDR5/RBBP5/ASH2L/DPY30) interacts with the replisome complex; disruption of DPY30 (a WRAD component) results in DNA re-replication, DNA damage, and chromosomal instability without affecting cancer cell proliferation, indicating the WRAD complex sustains replication fidelity.\",\n      \"method\": \"Co-immunoprecipitation (WRAD–replisome interaction); DPY30 genetic disruption; DNA damage and CIN assays in PDAC models\",\n      \"journal\": \"bioRxiv\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — preprint, Co-IP and genetic disruption with defined molecular phenotypes, single lab\",\n      \"pmids\": [\"bio_10.1101_2024.10.21.619543\"],\n      \"is_preprint\": true\n    }\n  ],\n  \"current_model\": \"RBBP5 is a scaffold subunit of the WRAD (WDR5–RBBP5–Ash2L–DPY30) complex that is essential for the assembly and allosteric activation of SET1/KMT2-family histone H3K4 methyltransferases: it bridges WDR5 (via a conserved RbBP5 motif binding a dedicated WDR5 site) and Ash2L (via its D/E box), its internal WD40–C-terminal interaction maintains complex compactness, a vertebrate-specific C-terminal motif enables nucleosome recognition, its WD40 β-propeller directly contacts nucleic acids to help target complexes to chromatin, and its activity is regulated post-translationally by phosphorylation (a phospho-switch that stimulates WRAD assembly and methylation rates, and phosphorylation at Ser497 by nuclear HKDC1 that drives MLL1 complex assembly and H3K4me3 deposition); beyond H3K4 methylation, RBBP5 is required for DNA replication licensing, efficient pre-mRNA processing, regulation of proteostasis gene expression via XBP1s co-activation, and in vivo brain development, with loss-of-function causing microcephaly in flies and a syndromic neurodevelopmental disorder in humans.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"RBBP5 is a scaffold subunit of the WRAD module that assembles and allosterically activates SET1/KMT2-family histone H3K4 methyltransferases on chromatin [#0, #2]. It bridges the complex through defined interfaces: a conserved RbBP5 motif binds a dedicated surface on WDR5, and these two proteins act cooperatively to stimulate MLL1 catalytic activity [#0], while an acidic D/E box in RBBP5 is engaged by the Ash2L SPRY domain to form the catalytically stimulatory RbBP5/Ash2L heterodimer [#2]. This heterodimer in turn docks onto a non-active-site surface of the MLL1 SET domain, and disease-associated mutations at this interface abolish H3K4 dimethylation [#1]. Within RBBP5 itself, an internal interaction between the WD40 \\u03b2-propeller and a C-terminal distal region maintains the compact conformation of the complex, and a vertebrate-specific C-terminal motif mediates nucleosome recognition and methylation [#4], with the \\u03b2-propeller surface additionally contacting nucleic acids to help target the complex to chromatin [#3]. RBBP5 activity is tuned post-translationally: a phospho-switch stimulates WRAD assembly and methylation rates [#2], and phosphorylation at Ser497 by nuclear HKDC1 drives MLL1 complex assembly and H3K4me3 deposition at mitotic genes [#11]. Through these activities RBBP5 deposits promoter H3K4me3 at specific target genes during EMT and proteostasis responses [#6, #12] and supports DNA replication licensing at origins [#5]. RBBP5 is also required for in vivo brain development, and de novo missense variants at its nucleosome interface cause a syndromic neurodevelopmental disorder, with the variants acting as partial loss-of-function alleles that fail to rescue microcephaly in flies [#10].\",\n  \"teleology\": [\n    {\n      \"year\": 2010,\n      \"claim\": \"Established the molecular basis by which RBBP5 is recruited into the H3K4 methyltransferase complex and why this matters for enzyme activation, defining a dedicated WDR5\\u2013RbBP5 interface.\",\n      \"evidence\": \"X-ray crystallography with biochemical binding and in vitro methyltransferase assays of the WDR5\\u2013RbBP5 interface\",\n      \"pmids\": [\"20716525\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not resolve how the assembled module engages nucleosomes\", \"Stoichiometry and dynamics within full WRAD not addressed\"]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"Identified the MLL1 SET-domain surface that the RbBP5/Ash2L heterodimer engages and linked it to disease, showing this contact is required for H3K4 dimethylation.\",\n      \"evidence\": \"In vitro methyltransferase assays, Co-IP/pulldown, and structure-guided mutagenesis of the MLL1 KIS surface\",\n      \"pmids\": [\"24680668\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not define the RBBP5 residues contacting this surface\", \"Restricted to MLL1 among KMT2 paralogs\"]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"Revealed a methylation-independent role for RBBP5 in RNA processing, separating its chromatin-mark function from a direct contribution to pre-mRNA splicing.\",\n      \"evidence\": \"siRNA knockdown with RT-PCR of unspliced FOS transcripts and ChIP for H3K4me3\",\n      \"pmids\": [\"24715476\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Mechanism connecting WAR subcomplex to the splicing machinery unknown\", \"Tested only on FOS pre-mRNA\"]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"Defined the Ash2L\\u2013RbBP5 (D/E box) interface and a phospho-switch on RBBP5, explaining how heterodimer formation and phosphorylation stimulate KMT2 methylation rates.\",\n      \"evidence\": \"X-ray crystallography, mutational analysis, in vitro methyltransferase assays, and erythroid differentiation assays\",\n      \"pmids\": [\"25593305\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Kinase responsible for the phospho-switch not identified here\", \"In vivo relevance of the switch not established\"]\n    },\n    {\n      \"year\": 2016,\n      \"claim\": \"Connected RBBP5/WDR5-dependent H3K4 methylation to DNA replication licensing, extending its role beyond transcription.\",\n      \"evidence\": \"siRNA knockdown, ChIP at replication origins, flow cytometry for polyploidy, and immunofluorescence co-localization with ORC/MCM2-7\",\n      \"pmids\": [\"27744293\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct versus indirect contribution of RBBP5 to MCM2-7 loading unresolved\", \"No structural basis for origin targeting\"]\n    },\n    {\n      \"year\": 2016,\n      \"claim\": \"Showed signal-dependent recruitment of RBBP5 to a specific target promoter, demonstrating it acts in defined transcriptional programs (EMT) rather than only globally.\",\n      \"evidence\": \"ChIP, siRNA knockdown, Western blot, and qRT-PCR of the Snail/SNAI1 locus in TGF-\\u03b21-treated prostate cancer cells\",\n      \"pmids\": [\"27566588\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct RBBP5\\u2013SMAD2/3/CBP contacts not biochemically mapped\", \"Generalizability beyond Snail not tested\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Demonstrated that the RBBP5 \\u03b2-propeller directly binds nucleic acids, proposing a chromatin-targeting function for this domain.\",\n      \"evidence\": \"X-ray crystallography of the \\u03b2-propeller and NMR nucleic-acid binding assays\",\n      \"pmids\": [\"29897600\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Functional consequence of nucleic-acid binding not validated in cells\", \"Sequence specificity of binding undefined\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Resolved full-length RBBP5 architecture, showing an intramolecular WD40\\u2013C-terminal contact maintains complex compactness and a vertebrate-specific motif mediates nucleosome recognition.\",\n      \"evidence\": \"Structure determination with biochemical assembly and nucleosome methylation assays plus mutagenesis\",\n      \"pmids\": [\"31544921\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Dynamics of the compact-to-active transition not captured\", \"Role of the vertebrate motif in vivo not tested here\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Genetic studies in model organisms established conserved roles for RBBP5 orthologs in restricting cell-fate plasticity and in meiotic recombination/segregation.\",\n      \"evidence\": \"Double RNAi reprogramming assay in C. elegans (rbbp-5) and meiotic deletion/checkpoint epistasis with H3K4 methylation assays in budding yeast (Swd1)\",\n      \"pmids\": [\"33290523\", \"34849786\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Whether these roles depend on H3K4 methylation versus methylation-independent functions not fully separated\", \"Human ortholog equivalence inferred, not directly tested\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Linked RBBP5 to human disease by showing de novo nucleosome-interface variants are partial loss-of-function alleles and that Rbbp5 loss causes microcephaly in vivo.\",\n      \"evidence\": \"Protein structural analysis and transgenic Drosophila rescue/complementation in an Rbbp5 null background for p.T232I and p.E296D\",\n      \"pmids\": [\"39036895\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Molecular consequence of variants on methyltransferase output not quantified\", \"Mammalian neurodevelopmental mechanism not established\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Identified a specific upstream kinase (nuclear HKDC1) and phosphosite (Ser497) controlling MLL1 complex assembly, providing a defined signaling input to RBBP5 function.\",\n      \"evidence\": \"Co-IP, in vitro kinase assay, Ser497 mutagenesis, and ChIP for H3K4me3 with HKDC1 inhibition/knockout in hepatocellular carcinoma cells\",\n      \"pmids\": [\"39891906\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether Ser497 phosphorylation is the same phospho-switch seen structurally not resolved\", \"Generality across non-HCC contexts unknown\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Extended RBBP5 to stress-responsive gene programs, showing it co-activates XBP1s to mark proteostasis genes and that its loss sensitizes mice to proteotoxic stress.\",\n      \"evidence\": \"RBBP5 knockout mice, H3K4me3 ChIP-seq, co-activator interaction assays, and in vitro stress assays (preprint)\",\n      \"pmids\": [\"39314427\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Preprint, not peer-reviewed\", \"Direct RBBP5\\u2013XBP1s contact and recruitment order not biochemically defined\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Showed lncRNA-directed recruitment of RBBP5 to a specific oncogenic promoter, illustrating RNA-guided targeting of RBBP5-containing complexes.\",\n      \"evidence\": \"RNA pulldown, mass spectrometry, ChIP, RNAi knockdown, and dual luciferase reporter at the ODC1 promoter in liver cancer cells\",\n      \"pmids\": [\"41022601\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Whether RBBP5 binds the lncRNA directly or via partners unclear\", \"KAT2B/RBBP5 functional cooperation not dissected\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How RBBP5's methylation-independent functions (replication licensing, pre-mRNA processing, XBP1s co-activation) are mechanistically separated from its WRAD scaffolding role remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No structural model distinguishing methylation-dependent from methylation-independent complexes\", \"Phosphorylation- and RNA-guided targeting mechanisms not integrated into a unified regulatory model\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0140096\", \"supporting_discovery_ids\": [0, 2, 4]},\n      {\"term_id\": \"GO:0060090\", \"supporting_discovery_ids\": [0, 2, 4]},\n      {\"term_id\": \"GO:0003677\", \"supporting_discovery_ids\": [3, 13]},\n      {\"term_id\": \"GO:0042393\", \"supporting_discovery_ids\": [4]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [6, 11]},\n      {\"term_id\": \"GO:0000228\", \"supporting_discovery_ids\": [4, 5]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-4839726\", \"supporting_discovery_ids\": [0, 2, 4]},\n      {\"term_id\": \"R-HSA-74160\", \"supporting_discovery_ids\": [6, 11, 12]},\n      {\"term_id\": \"R-HSA-69306\", \"supporting_discovery_ids\": [5]}\n    ],\n    \"complexes\": [\"WRAD (WDR5\\u2013RBBP5\\u2013ASH2L\\u2013DPY30)\", \"MLL1/SET1 (COMPASS) H3K4 methyltransferase complex\"],\n    \"partners\": [\"WDR5\", \"ASH2L\", \"DPY30\", \"KMT2A\", \"HKDC1\", \"KAT2B\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":7,"faith_total":7,"faith_pct":100.0}}