Affinage

RBBP5

Retinoblastoma-binding protein 5 · UniProt Q15291

Round 2 corrected
Length
538 aa
Mass
59.2 kDa
Annotated
2026-04-28
51 papers in source corpus 14 papers cited in narrative 15 extracted findings

Mechanistic narrative

Synthesis pass · prose summary of the discoveries below

RBBP5 is a core scaffold subunit of SET1/COMPASS-family histone H3K4 methyltransferase complexes, essential for catalytic activation, nucleosome recognition, and chromatin-templated gene regulation. It forms a heterodimer with Ash2L via a D/E box–SPRY domain interface and binds WDR5 through a distinct surface, together constituting the WRAD subcomplex that allosterically stimulates MLL1 SET domain activity and contributes a second active site required for H3K4 dimethylation (PMID:16878130, PMID:20716525, PMID:25593305, PMID:24680668). Phosphorylation of RBBP5—including at Ser497 by the kinase HKDC1—promotes MLL1 complex assembly and H3K4me3 deposition at cell-cycle gene promoters, while a vertebrate-specific C-terminal motif enables nucleosome recognition and a WD40 β-propeller surface mediates direct nucleic acid binding for chromatin targeting (PMID:39891906, PMID:31544921, PMID:29897600). De novo heterozygous loss-of-function RBBP5 variants cause a syndromic neurodevelopmental disorder with microcephaly, with disease-associated missense mutations mapping to the nucleosome-interaction surface and producing partial loss of function in Drosophila rescue assays (PMID:39036895).

Mechanistic history

Synthesis pass · year-by-year structured walk · 10 steps
  1. 2006 High

    The first reconstitution of the MLL1 core complex established that RBBP5, together with Ash2L and WDR5, forms a structural platform required for full H3K4 methyltransferase activity, answering whether MLL1 catalysis is intrinsic or requires accessory subunits.

    Evidence Biochemical reconstitution of purified MLL1/RBBP5/Ash2L/WDR5, in vitro HMT assays, crystal structure analysis

    PMID:16878130

    Open questions at the time
    • How individual WRAD subunits contact MLL1 and each other was not resolved
    • Whether RBBP5 contributes catalytically versus purely structurally was unknown
  2. 2010 High

    Structural determination of the WDR5–RBBP5 interface revealed that RBBP5 binds a WDR5 surface distinct from the MLL1-binding arginine cavity, resolving how WRAD is assembled without competition between subunits for WDR5 binding.

    Evidence X-ray crystallography of WDR5–RBBP5 complex, mutagenesis, in vitro HMT assays

    PMID:20716525

    Open questions at the time
    • The RBBP5–Ash2L interface remained structurally undefined
    • Whether RBBP5 directly contacts the histone substrate was unknown
  3. 2014 High

    Two advances clarified RBBP5 function beyond scaffolding: identification of the MLL1 SET domain Kabuki interaction surface (KIS) showed that the RBBP5/Ash2L heterodimer contributes a second active site for H3K4 dimethylation, and depletion of WRAD components revealed an unexpected role in co-transcriptional pre-mRNA processing independent of H3K4me3 levels.

    Evidence SET domain mutagenesis with HMT assays (KIS); siRNA knockdown with RT-PCR for spliced/unspliced FOS transcripts and ChIP for H3K4me3

    PMID:24680668 PMID:24715476

    Open questions at the time
    • The structural basis of the second active site was not resolved
    • The mechanism by which WRAD influences splicing independently of methylation was unexplained
    • Whether the pre-mRNA processing role is genome-wide or locus-specific was not determined
  4. 2015 High

    Crystal structures of the Ash2L SPRY domain bound to the RBBP5 D/E box defined the heterodimer interface and revealed a phosphorylation switch on RBBP5 that stimulates WRAD assembly and KMT2 catalytic rates, connecting signaling input to complex activation.

    Evidence X-ray crystallography, mutational analysis, in vitro HMT assays, erythroid differentiation assays

    PMID:25593305

    Open questions at the time
    • The kinase responsible for the phosphoswitch was not identified
    • How phosphorylation modulates WRAD conformation was unclear
  5. 2016 Medium

    RBBP5 was linked to DNA replication origin licensing: it co-localizes with ORC and MCM2-7 at origins, and its depletion reduces H3K4 methylation and MCM loading, connecting the MLL/WRAD complex to genome duplication beyond transcription.

    Evidence siRNA knockdown, ChIP at replication origins, flow cytometry for polyploidy, co-localization with ORC/MCM

    PMID:27744293

    Open questions at the time
    • Whether RBBP5 acts at origins via H3K4me or through a methylation-independent mechanism was not distinguished
    • Direct physical interaction between RBBP5 and origin-licensing factors was not demonstrated
  6. 2018 Medium

    Determination of the RBBP5 WD40 β-propeller crystal structure revealed arginine-rich clusters that directly bind nucleic acids by NMR, suggesting a chromatin-targeting function independent of catalytic activation.

    Evidence X-ray crystallography of WD40 domain, NMR nucleic acid binding assays

    PMID:29897600

    Open questions at the time
    • Functional consequence of nucleic acid binding for MLL complex recruitment in cells was not validated
    • Whether the binding is DNA- or RNA-specific was not resolved
  7. 2019 High

    Full-length RBBP5 structure revealed an intramolecular WD40–C-terminal interaction that maintains compact MLL1 complex architecture, and a vertebrate-specific C-terminal motif was shown to enable nucleosome recognition and methylation, resolving how RBBP5 senses the physiological substrate.

    Evidence X-ray crystallography of full-length RBBP5, biochemical reconstitution, nucleosome methylation assays, mutagenesis

    PMID:31544921

    Open questions at the time
    • Whether the C-terminal nucleosome-recognition motif contacts the histone octamer or nucleosomal DNA was not resolved
    • How this motif cooperates with WDR5 and Ash2L for substrate engagement was unclear
  8. 2021 Medium

    An RNAi screen in C. elegans identified RBBP-5 as a germ cell reprogramming barrier, extending the biological role of RBBP5 from transcriptional regulation to maintenance of cell fate identity.

    Evidence Double RNAi screen (CONJUDOR) in C. elegans, germ cell conversion assay

    PMID:33290523

    Open questions at the time
    • Whether the reprogramming barrier function is conserved in mammals was not tested
    • The specific target genes through which RBBP5 maintains germ cell identity were not identified
  9. 2024 Medium

    Human genetic studies identified de novo heterozygous RBBP5 loss-of-function variants as the cause of a syndromic neurodevelopmental disorder with microcephaly, with disease-associated missense variants mapping to the nucleosome-interaction surface and producing partial loss of function in Drosophila rescue.

    Evidence Patient variant identification, structural mapping, Drosophila transgenic rescue and brain size measurements

    PMID:39036895

    Open questions at the time
    • Only a small patient cohort was reported; broader genotype-phenotype correlations are lacking
    • Whether partial loss of nucleosome recognition specifically or of overall complex activity drives pathogenesis was not distinguished
  10. 2025 High

    Identification of HKDC1 as the kinase phosphorylating RBBP5 at Ser497 closed the gap on which kinase activates MLL1 complex assembly, directly linking this phosphorylation to H3K4me3 deposition at mitotic gene promoters and tumor growth in hepatocellular carcinoma.

    Evidence In vitro kinase assay, mass spectrometry phosphosite mapping, Co-IP, ChIP-seq, siRNA knockdown, xenograft tumor models

    PMID:39891906

    Open questions at the time
    • Whether HKDC1 is the sole kinase for Ser497 or whether the previously described phosphoswitch involves the same residue is unresolved
    • Whether HKDC1-dependent RBBP5 phosphorylation operates in non-cancer cell types was not tested

Open questions

Synthesis pass · forward-looking unresolved questions
  • Key unresolved questions include the structural basis of the RBBP5/Ash2L second active site, the mechanism by which WRAD influences pre-mRNA processing independently of H3K4me, and whether the nucleic acid binding, nucleosome recognition, and replication-origin functions of RBBP5 are coordinated or represent independent modalities.
  • No high-resolution structure of the assembled WRAD second active site exists
  • The splicing/pre-mRNA processing mechanism is documented at a single locus only
  • Functional interplay between nucleic acid binding, nucleosome recognition, and replication licensing has not been dissected

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0042393 histone binding 4 GO:0005198 structural molecule activity 3 GO:0098772 molecular function regulator activity 3 GO:0003677 DNA binding 1
Localization
GO:0005634 nucleus 3 GO:0000228 nuclear chromosome 2
Pathway
R-HSA-4839726 Chromatin organization 6 R-HSA-74160 Gene expression (Transcription) 2 R-HSA-1266738 Developmental Biology 1 R-HSA-1640170 Cell Cycle 1 R-HSA-69306 DNA Replication 1
Partners
ASH2LDPY30HKDC1KAT2BMLL1WDR5
Complex memberships
SET1/COMPASS (MLL/SET1-family H3K4 methyltransferase complex)WRAD subcomplex (WDR5–RBBP5–Ash2L–DPY30)

Evidence

Reading pass · 15 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
2006 RbBP5, together with Ash2L and WDR5, forms a structural platform within the MLL1 core complex. Biochemical reconstitution of the four-component MLL1 core complex (MLL1 + RbBP5 + Ash2L + WDR5) demonstrated that RbBP5 and Ash2L are required for full MLL1 H3K4 methyltransferase activity, and WDR5 mediates interactions of the MLL1 catalytic unit with this structural platform and with the histone substrate. Biochemical reconstitution of purified components, in vitro histone methyltransferase assay, crystal structure analysis Nature structural & molecular biology High 16878130
2010 WDR5 contains a novel interaction site that recruits RbBP5 through a conserved motif (distinct from the WDR5 arginine-binding cavity used for MLL1 interaction). X-ray crystallography defined the WDR5–RbBP5 interface, and biochemical assays showed this interaction is fundamental to assembly of the MLL1 core complex and to stimulation of MLL1 methyltransferase activity. A specific region of RbBP5 was shown to contribute directly to MLL1 activation. X-ray crystallography, in vitro binding assays, histone methyltransferase activity assays The Journal of biological chemistry High 20716525
2014 A non-active-site surface of the MLL1 SET domain (termed the Kabuki interaction surface, KIS) is required for interaction with WRAD and specifically with the RbBP5/Ash2L heterodimer. Mutations at the KIS abolish H3K4 dimethylation by the MLL1 core complex by disrupting RbBP5/Ash2L heterodimer recruitment, establishing that WRAD-dependent dimethylation requires a second active site contributed by the RbBP5/Ash2L heterodimer. In vitro histone methyltransferase assays, co-immunoprecipitation, site-directed mutagenesis of SET domain Journal of molecular biology High 24680668
2015 The Ash2L SPRY domain binds a cluster of acidic residues (D/E box) in RbBP5, forming an Ash2L–RbBP5 heterodimer. Mutations at this interface impair heterodimer formation and stimulation of MLL1 catalytic activity. A phosphorylation switch on RbBP5 stimulates WRAD complex formation and significantly increases KMT2 methylation rates. This phosphorylation was shown to be functionally important for erythroid cell terminal differentiation. X-ray crystallography, mutational analysis, in vitro methyltransferase assays, cell differentiation assays Genes & development High 25593305
2018 The crystal structure of the RbBP5 β-propeller (WD40 repeat) domain reveals a feature-rich surface dominated by clusters of arginine residues. NMR binding data support direct interaction of this β-propeller surface with nucleic acids, suggesting that RbBP5 participates in recruiting MLL complexes to chromatin targets through direct nucleic acid binding, a function independent of its role in catalytic activation. X-ray crystallography, NMR binding assays Nucleic acids research Medium 29897600
2019 The structure of full-length human RBBP5 was determined, revealing an internal interaction between the WD40 propeller and a 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. X-ray crystallography, biochemical reconstitution, nucleosome methylation assays, mutagenesis Nucleic acids research High 31544921
2016 siRNA-mediated knockdown of RBBP5 (or WDR5) suppressed DNA re-replication and chromosomal polyploidy induced by downregulation of Geminin or CRL4CDT2 ligase. RBBP5/WDR5 co-localized with origin recognition complex (ORC) and MCM2-7 helicase at replication origins, and their knockdown reduced H3K4 methylation and impaired MCM2-7 recruitment to replication origins, indicating a role for the MLL–WDR5–RBBP5 complex in licensing DNA replication. siRNA knockdown, ChIP at replication origins, flow cytometry for polyploidy, co-localization with ORC/MCM complexes Biology open Medium 27744293
2016 In TGF-β1-induced epithelial-mesenchymal transition (EMT) in prostate cancer cells, RbBP5 binding and H3K4me3 enrichment increase at the Snail (SNAI1) transcription start site. Knockdown of RbBP5 decreased Snail expression and suppressed EMT. Recruitment of RbBP5 to the Snail TSS was shown to depend on SMAD2/3 and CBP binding at that locus, linking TGF-β/SMAD signaling to H3K4me3 deposition via RbBP5. ChIP assay, RbBP5 knockdown, gene expression analysis Oncotarget Medium 27566588
2014 Depletion of WDR5, ASH2L, or RBBP5 (WAR subcomplex) led to increased levels of unspliced FOS transcripts without necessarily changing mature FOS transcript levels, demonstrating a role for the WRAD subcomplex in coordinating efficient pre-mRNA transcript processing at the FOS immediate-early gene, independent of changes in H3K4me3 levels at the promoter. siRNA knockdown of WAR subcomplex components, RT-PCR for spliced vs. unspliced transcripts, ChIP for H3K4me3 Cellular & molecular biology letters Medium 24715476
2021 In C. elegans, RBBP-5 (the RBBP5 ortholog) was identified as a novel germ cell reprogramming barrier. Double RNAi knockdown of lin-53 and rbbp-5 revealed that RBBP-5 loss facilitates germ cell conversion, establishing RBBP-5 as part of the Set1/MLL methyltransferase complex functioning to maintain germ cell identity. Double RNAi screen (CONJUDOR), C. elegans germ cell reprogramming assay Nucleic acids research Medium 33290523
2025 Nuclear-localized HKDC1 acts as a protein kinase that phosphorylates RBBP5 at Ser497. This phosphorylation is crucial for MLL1 complex assembly and subsequent H3K4me3 modification at promoters of mitosis-related genes, driving cell cycle progression. Blocking HKDC1 kinase activity inhibited RBBP5 phosphorylation and suppressed tumor growth in hepatocellular carcinoma models. In vitro kinase assay, mass spectrometry phosphorylation mapping, Co-IP, ChIP-seq, siRNA knockdown, tumor xenograft models Cell reports High 39891906
2024 De novo heterozygous loss-of-function variants in RBBP5 cause a syndromic neurodevelopmental disorder with microcephaly. Two missense variants (p.T232I and p.E296D) affect evolutionarily conserved residues at the RBBP5–nucleosome interface. In Drosophila, loss of Rbbp5 reduces brain size, and expression of either missense variant in a null background produces less severe microcephaly than the reference transgene, demonstrating partial loss-of-function at the nucleosome interaction surface. Protein structural analysis, transgenic Drosophila overexpression/rescue experiments, brain size measurement Genetics in medicine Medium 39036895
2025 RBBP5, as the core subunit of SET1/COMPASS, co-activates XBP1s to regulate proteostasis gene expression by depositing H3K4me3 at promoter-proximal regions, which further recruits the Integrator Complex and SWI/SNF chromatin remodelers. RBBP5 ablation in mice causes increased susceptibility to proteotoxic stress, chronic inflammation, hepatic steatosis, impaired autophagy, and disrupts both the 12-hour ultradian oscillator of proteostasis genes and acute transcriptional stress responses. Mouse knockout, ChIP-seq for H3K4me3, Co-IP for complex assembly, transcriptomic analysis, in vitro stress assays bioRxivpreprint Medium 39314427
2024 The WRAD core complex (including RBBP5) interacts with the replisome complex in pancreatic ductal adenocarcinoma cells. Disruption of WRAD (via DPY30 loss) caused DNA re-replication, DNA damage, and chromosomal instability without affecting cancer cell proliferation, indicating WRAD/RBBP5 sustains genome stability during DNA replication. Co-immunoprecipitation with replisome components, DNA fiber assays, flow cytometry for DNA content, karyotyping bioRxivpreprint Low
2025 lncRNA HClnc1 simultaneously binds RBBP5 and KAT2B proteins (identified by pull-down and mass spectrometry). The HClnc1/RBBP5/KAT2B complex binds the ODC1 promoter and enhances ODC1 transcription; knockdown of RBBP5 reduces KAT2B binding to the ODC1 promoter and blocks HClnc1-induced ODC1 upregulation, demonstrating RBBP5 participates in an lncRNA-scaffolded epigenetic activation complex at specific gene promoters. RNA pull-down, mass spectrometry, Co-IP, ChIP assay, siRNA knockdown, dual luciferase reporter assay Nan fang yi ke da xue xue bao Low 41022601

Source papers

Stage 0 corpus · 51 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
2006 Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. Cell 2861 17081983
2002 Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Proceedings of the National Academy of Sciences of the United States of America 1479 12477932
2015 The BioPlex Network: A Systematic Exploration of the Human Interactome. Cell 1118 26186194
2017 Architecture of the human interactome defines protein communities and disease networks. Nature 1085 28514442
2015 A human interactome in three quantitative dimensions organized by stoichiometries and abundances. Cell 1015 26496610
2014 A proteome-scale map of the human interactome network. Cell 977 25416956
2020 A reference map of the human binary protein interactome. Nature 849 32296183
2018 VIRMA mediates preferential m6A mRNA methylation in 3'UTR and near stop codon and associates with alternative polyadenylation. Cell discovery 829 29507755
2007 The histone H3 lysine-27 demethylase Jmjd3 links inflammation to inhibition of polycomb-mediated gene silencing. Cell 783 17825402
2021 Dual proteome-scale networks reveal cell-specific remodeling of the human interactome. Cell 705 33961781
2012 A census of human soluble protein complexes. Cell 689 22939629
2005 WDR5 associates with histone H3 methylated at K4 and is essential for H3 K4 methylation and vertebrate development. Cell 668 15960974
2011 Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Briefings in bioinformatics 656 21873635
2006 Regulation of MLL1 H3K4 methyltransferase activity by its core components. Nature structural & molecular biology 623 16878130
2007 Demethylation of H3K27 regulates polycomb recruitment and H2A ubiquitination. Science (New York, N.Y.) 615 17761849
2005 Physical association and coordinate function of the H3 K4 methyltransferase MLL1 and the H4 K16 acetyltransferase MOF. Cell 551 15960975
2004 Leukemia proto-oncoprotein MLL forms a SET1-like histone methyltransferase complex with menin to regulate Hox gene expression. Molecular and cellular biology 551 15199122
2004 Menin associates with a trithorax family histone methyltransferase complex and with the hoxc8 locus. Molecular cell 523 14992727
2007 PTIP associates with MLL3- and MLL4-containing histone H3 lysine 4 methyltransferase complex. The Journal of biological chemistry 442 17500065
2022 OpenCell: Endogenous tagging for the cartography of human cellular organization. Science (New York, N.Y.) 432 35271311
2009 RAD6-Mediated transcription-coupled H2B ubiquitylation directly stimulates H3K4 methylation in human cells. Cell 426 19410543
2013 H3K4 mono- and di-methyltransferase MLL4 is required for enhancer activation during cell differentiation. eLife 425 24368734
2005 Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. Genome research 409 16344560
2015 Panorama of ancient metazoan macromolecular complexes. Nature 407 26344197
2015 Gain-of-function p53 mutants co-opt chromatin pathways to drive cancer growth. Nature 391 26331536
1996 Generation and analysis of 280,000 human expressed sequence tags. Genome research 376 8889549
2006 CUL4-DDB1 ubiquitin ligase interacts with multiple WD40-repeat proteins and regulates histone methylation. Nature cell biology 371 17041588
2013 The MLL3/MLL4 branches of the COMPASS family function as major histone H3K4 monomethylases at enhancers. Molecular and cellular biology 349 24081332
2021 A proximity-dependent biotinylation map of a human cell. Nature 339 34079125
2006 The APC tumor suppressor counteracts beta-catenin activation and H3K4 methylation at Wnt target genes. Genes & development 320 16510874
2010 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. The Journal of biological chemistry 94 20716525
2015 A phosphorylation switch on RbBP5 regulates histone H3 Lys4 methylation. Genes & development 42 25593305
2014 A non-active-site SET domain surface crucial for the interaction of MLL1 and the RbBP5/Ash2L heterodimer within MLL family core complexes. Journal of molecular biology 39 24680668
2017 Diverse roles of WDR5-RbBP5-ASH2L-DPY30 (WRAD) complex in the functions of the SET1 histone methyltransferase family. Journal of biosciences 33 28229975
2019 The internal interaction in RBBP5 regulates assembly and activity of MLL1 methyltransferase complex. Nucleic acids research 19 31544921
2020 Long non‑coding RNA AC245100.4 promotes prostate cancer tumorigenesis via the microRNA‑145‑5p/RBBP5 axis. Oncology reports 16 33416179
2016 Role of RbBP5 and H3K4me3 in the vicinity of Snail transcription start site during epithelial-mesenchymal transition in prostate cancer cell. Oncotarget 16 27566588
2017 Somatic cancer mutations in the MLL1 histone methyltransferase modulate its enzymatic activity and dependence on the WDR5/RBBP5/ASH2L complex. Molecular oncology 14 28182322
2018 The structure of the RbBP5 β-propeller domain reveals a surface with potential nucleic acid binding sites. Nucleic acids research 12 29897600
2016 Regulation of DNA replication and chromosomal polyploidy by the MLL-WDR5-RBBP5 methyltransferases. Biology open 12 27744293
2015 Expression and clinical role of RBQ3 in gliomas. Journal of the neurological sciences 8 26671109
2014 WDR5, ASH2L, and RBBP5 control the efficiency of FOS transcript processing. Cellular & molecular biology letters 8 24715476
2021 Distinct requirements for the COMPASS core subunits Set1, Swd1, and Swd3 during meiosis in the budding yeast Saccharomyces cerevisiae. G3 (Bethesda, Md.) 7 34849786
2016 RBQ3 participates in multiple myeloma cell proliferation, adhesion and chemoresistance. International journal of biological macromolecules 5 27189701
2024 Loss-of-function in RBBP5 results in a syndromic neurodevelopmental disorder associated with microcephaly. Genetics in medicine : official journal of the American College of Medical Genetics 4 39036895
2023 Genome-wide in silico analysis leads to identification of deleterious L290V mutation in RBBP5 gene in Bos indicus. Animal biotechnology 4 37051916
2021 The CONJUDOR pipeline for multiplexed knockdown of gene pairs identifies RBBP-5 as a germ cell reprogramming barrier in C. elegans. Nucleic acids research 4 33290523
2025 Nuclear-localized HKDC1 promotes hepatocellular carcinoma through phosphorylating RBBP5 to upregulate H3K4me3. Cell reports 3 39891906
2025 The SET1/COMPASS subunit RBBP5 orchestrates epigenetic control of global proteostasis and the 12h oscillator to safeguard metabolic and cellular homeostasis. bioRxiv : the preprint server for biology 1 39314427
2023 [Corrigendum] Long non‑coding RNA AC245100.4 promotes prostate cancer tumorigenesis via the microRNA‑145‑5p/RBBP5 axis. Oncology reports 1 36799194
2025 [Long noncoding RNA HClnc1 promotes proliferation and migration of liver cancer cells by targeting RBBP5/KAT2B complex to enhance ODC1 transcription]. Nan fang yi ke da xue xue bao = Journal of Southern Medical University 0 41022601