{"gene":"RBBP6","run_date":"2026-06-10T06:43:36","timeline":{"discoveries":[{"year":1995,"finding":"RBBP6 (RBQ-1) binds to the retinoblastoma gene product (pRB) through a small region near its C-terminus, as demonstrated by GST pull-down of pRB from cellular extracts, with binding competed by adenovirus E1a protein indicating the interaction occurs through the pocket domain of Rb1.","method":"GST fusion protein pull-down, competition with E1a protein","journal":"Genomics","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — GST pull-down with competitive inhibition control, single lab, two orthogonal lines of evidence","pmids":["8595913"],"is_preprint":false},{"year":1997,"finding":"P2P-R (RBBP6) encodes protein domains that bind single-stranded nucleic acids and associate with hnRNP proteins, as demonstrated by binding of cDNA-derived fusion proteins to ssDNA and recognition by anti-hnRNP monoclonal antibodies.","method":"GST fusion protein binding assay, monoclonal antibody recognition, antisense oligonucleotide experiments","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — multiple biochemical methods in single lab, direct binding demonstrated","pmids":["9037032"],"is_preprint":false},{"year":2002,"finding":"P2P-R (RBBP6) localizes to nucleoli in interphase cells and to the periphery of chromosomes in mitotic cells, with protein levels increasing >10-fold during mitosis without a concomitant change in mRNA, suggesting post-transcriptional regulation.","method":"Confocal microscopy, Western blot, mitotic cell synchronization (nocodazole, vinblastine, shake-select)","journal":"Journal of cellular physiology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct localization by confocal microscopy with functional context, multiple synchronization methods, single lab","pmids":["12064457"],"is_preprint":false},{"year":2002,"finding":"Overexpression of near full-length P2P-R (RBBP6) in Saos2 cells restricts mitotic progression at prometaphase and promotes mitotic apoptosis, with P2P-R protein dissociating from chromosomes and appearing in cytoplasm and apoptotic cell surface blebs during mitotic apoptosis.","method":"Stable transfection, flow cytometry, confocal microscopy, Western blot of enriched apoptotic blebs","journal":"Journal of cellular physiology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — gain-of-function with multiple readouts, single lab, direct localization during apoptosis confirmed biochemically","pmids":["12384997"],"is_preprint":false},{"year":2002,"finding":"P2P-R (RBBP6) deficiency restricts cell cycle progression from G1 through S to mitosis in a microtubule-dependent manner and represses UV irradiation-induced apoptosis.","method":"Antisense oligonucleotide knockdown, flow cytometry, nocodazole treatment","journal":"Anticancer research","confidence":"Low","confidence_rationale":"Tier 3 / Weak — antisense knockdown with phenotypic readout, no direct molecular mechanism identified, single lab single method","pmids":["12553003"],"is_preprint":false},{"year":2003,"finding":"P2P-R (RBBP6) is phosphorylated by cdc2 and SRPK1a kinases, interacts with scaffold attachment factor-B (SAF-B), and co-immunoprecipitates with nucleolin.","method":"Co-immunoprecipitation, in vitro kinase assay (inferred from review-style paper)","journal":"Journal of cellular biochemistry","confidence":"Low","confidence_rationale":"Tier 3 / Weak — summary/review paper citing prior data, single lab, methods not fully described in this abstract","pmids":["12938151"],"is_preprint":false},{"year":2003,"finding":"Overexpression of P2P-R (RBBP6) segments spanning residues 1156-1314 promotes camptothecin-induced apoptosis 3-5 fold in MCF-7 cells; the p53-binding domain overlaps with this apoptosis-associated region.","method":"Stable transfection, flow cytometry, TUNEL assay","journal":"Journal of cellular physiology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — domain mapping with two orthogonal apoptosis assays, functional region identified, single lab","pmids":["14566974"],"is_preprint":false},{"year":2005,"finding":"PUM2 binds P2P-R (RBBP6) mRNA through consensus sequences in its 3' UTR, as confirmed by PUM2 pull-down followed by RT-PCR, suggesting translational regulation of RBBP6 by PUM2.","method":"RNA pull-down (PUM2 immunoprecipitation) followed by RT-PCR","journal":"Journal of cellular physiology","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single RNA pull-down method, single lab, functional consequence not directly tested","pmids":["15617101"],"is_preprint":false},{"year":2005,"finding":"SNAMA, the Drosophila homolog of RBBP6, contains a DWNN domain and a RING finger-like motif; homozygous P-element insertion mutants show embryonic lethality with widespread apoptosis throughout the gastrula, establishing an essential developmental role for this gene family.","method":"P-element insertion genetics, embryo phenotype analysis","journal":"Biochimica et biophysica acta","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — genetic loss-of-function in Drosophila ortholog with clear developmental phenotype, single lab","pmids":["15733535"],"is_preprint":false},{"year":2006,"finding":"The N-terminal 81 amino acids of RBBP6 form a novel ubiquitin-like domain (DWNN) as determined by heteronuclear NMR; the domain lacks conserved K48/K63 equivalents but contains a di-glycine motif in human/mouse, and is independently expressed as a single-domain protein in vertebrates.","method":"Heteronuclear NMR structure determination","journal":"BMC structural biology","confidence":"High","confidence_rationale":"Tier 1 / Strong — NMR structure with detailed sequence and structural analysis, foundational domain characterization","pmids":["16396680"],"is_preprint":false},{"year":2008,"finding":"RBBP6 acts as an E3 ubiquitin ligase for YB-1: the RING finger domain of RBBP6 binds the last 62 residues of YB-1 (identified by yeast two-hybrid), and both full-length RBBP6 and the isolated RING finger domain ubiquitinate YB-1 leading to its proteasomal degradation, suppressing YB-1 transactivational activity in vivo.","method":"Yeast two-hybrid, in vitro ubiquitination assay, proteasome degradation assay, reporter transactivation assay","journal":"Journal of molecular biology","confidence":"High","confidence_rationale":"Tier 1 / Strong — in vitro ubiquitination reconstitution plus yeast two-hybrid plus in vivo degradation, multiple orthogonal methods, single lab","pmids":["18851979"],"is_preprint":false},{"year":2010,"finding":"P2P-R (RBBP6) functions as a transcriptional co-repressor of estrogen-dependent transcription: it represses estrogen-induced transcription by 50-70% when transfected into four cell types, and co-immunoprecipitates with SRC-1 (steroid receptor co-activator 1) and estrogen receptor alpha.","method":"Transient transfection reporter assay, antisense knockdown, co-immunoprecipitation","journal":"BMC systems biology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — co-IP plus functional reporter assay in multiple cell types, single lab","pmids":["20184719"],"is_preprint":false},{"year":2011,"finding":"The RING finger-like domain of RBBP6 adopts a homodimeric structure similar to U-box proteins despite coordinating two zinc ions (replaceable with cadmium); RBBP6 interacts with chaperones Hsp70 and Hsp40 through its N-terminal DWNN ubiquitin-like domain, suggesting a role in chaperone-mediated ubiquitination.","method":"Solution NMR structure, zinc/cadmium substitution assays, thermal stability assays, yeast two-hybrid","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1 / Strong — NMR structure determination with functional domain validation, multiple biophysical methods, single lab","pmids":["22130672"],"is_preprint":false},{"year":2013,"finding":"RBPL-1, the C. elegans homolog of RBBP6, is required for germ cell proliferation, oocyte production, embryonic development, and intestine development; RNAi silencing causes embryonic lethality and defects in mitosis, consistent with a role as an mRNA cleavage/polyadenylation factor.","method":"RNAi knockdown, phenotypic analysis, microarray expression profiling","journal":"PloS one","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — genetic loss-of-function in C. elegans ortholog with defined developmental phenotypes, multiple readouts, single lab","pmids":["23536819"],"is_preprint":false},{"year":2014,"finding":"RBBP6 ubiquitinates and destabilizes the transcriptional repressor ZBTB38; loss of RBBP6 causes ZBTB38 accumulation, leading to MCM10 downregulation on chromatin, reduced replication fork progression, and increased DNA damage at common fragile sites.","method":"shRNA knockdown, ubiquitination assay, chromatin fractionation, DNA fiber assay, FISH for fragile site stability","journal":"Cell reports","confidence":"High","confidence_rationale":"Tier 1-2 / Strong — pathway reconstituted with E3 ligase substrate identification, multiple orthogonal methods including ubiquitination assay and replication fork analysis","pmids":["24726359"],"is_preprint":false},{"year":2014,"finding":"RBBP6 is a component of the mRNA 3' processing complex and functions in 3' processing in vitro and in vivo; its DWNN ubiquitin-like domain mediates interaction with core cleavage/polyadenylation factors and is required for 3' processing activity. RBBP6 isoform 3 (iso3, DWNN-only) competes with full-length RBBP6 for binding to the core machinery, thereby inhibiting 3' processing. RBBP6 knockdown decreases transcript levels of AU-rich 3' UTR mRNAs (e.g., c-Fos, c-Jun) and increases usage of distal poly(A) sites.","method":"In vitro 3' processing assay, co-immunoprecipitation, genome-wide poly(A) site analysis, siRNA knockdown","journal":"Genes & development","confidence":"High","confidence_rationale":"Tier 1 / Strong — in vitro reconstitution assay plus co-IP plus genome-wide analysis, multiple orthogonal methods, mechanistic domain mapping","pmids":["25319826"],"is_preprint":false},{"year":2018,"finding":"RBBP6 interacts with Ebola virus VP30 (transcription regulator) through a 23 amino acid region that mimics the viral nucleoprotein (NP) binding interface on VP30; a crystal structure of the VP30-RBBP6 peptide complex revealed competitive mimicry. RBBP6 knockdown stimulates viral transcription and increases EBOV replication; RBBP6 overexpression inhibits both.","method":"AP-MS, domain mapping, X-ray crystallography, siRNA knockdown, viral replication assays","journal":"Cell","confidence":"High","confidence_rationale":"Tier 1 / Strong — crystal structure plus AP-MS plus functional knockdown/overexpression, multiple orthogonal methods in single study","pmids":["30550789"],"is_preprint":false},{"year":2019,"finding":"RBBP6 ubiquitinates IκBα (inhibitor of NF-κB), leading to its degradation and consequent p65 nuclear translocation, NF-κB pathway activation, EMT induction, and cancer cell metastasis in colorectal cancer.","method":"Co-immunoprecipitation, ubiquitination assay, nuclear fractionation, ChIP analysis, loss-of-function/gain-of-function experiments, mouse metastasis model","journal":"Cell death & disease","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — ubiquitination assay plus co-IP plus nuclear fractionation, single lab with multiple orthogonal methods","pmids":["31685801"],"is_preprint":false},{"year":2021,"finding":"The RING finger domain of RBBP6 binds SNRPG (small nuclear ribonucleoprotein polypeptide G) with a dissociation constant of ~3.16 nM as measured by microscale thermophoresis, confirming a physical interaction between these two splicing-related proteins.","method":"Microscale thermophoresis (MST) binding assay","journal":"American journal of translational research","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single biophysical binding assay, no functional follow-up, single lab","pmids":["34956492"],"is_preprint":false},{"year":2022,"finding":"RBBP6 is required to activate the human CPSF endonuclease for specific and efficient pre-mRNA 3' cleavage; unlike its yeast homolog Mpe1, RBBP6 does not stably copurify with CPSF but is recruited in an RNA-dependent manner. Sequence and mutational analyses indicate RBBP6 interacts with WDR33 and CPSF73 subunits of CPSF.","method":"In vitro reconstitution of 3' endonuclease activity with purified proteins, mutagenesis, co-purification experiments","journal":"Genes & development","confidence":"High","confidence_rationale":"Tier 1 / Strong — in vitro reconstitution with purified proteins plus mutagenesis plus interaction mapping, independent replication by second lab same year","pmids":["35177536"],"is_preprint":false},{"year":2022,"finding":"RBBP6 is required for pre-mRNA 3' end cleavage in a minimal reconstituted mammalian system; structural data show the RBBP6 DWNN domain contacts and presumably activates the endonuclease CPSF73. RBBP6 is among 14 polypeptides essential for RNA processing in vitro, and its role is conserved from yeast (Mpe1) to humans.","method":"In vitro reconstitution with 14 purified polypeptides, structural analysis, RNA cleavage assay at physiological poly(A) site","journal":"Genes & development","confidence":"High","confidence_rationale":"Tier 1 / Strong — in vitro reconstitution from purified components plus structural data, independent replication confirming prior study in same year","pmids":["35177537"],"is_preprint":false},{"year":2024,"finding":"RBBP6 mediates K63-linked ubiquitination of CPSF3 (Cleavage and Polyadenylation Specific Factor 3), which stabilizes CPSF3 and regulates alternative polyadenylation events in glioblastoma stem cells; RBBP6 depletion induces shortening of 3' UTRs of MYC competing-endogenous RNAs, releasing miR-590-3p to decrease MYC expression.","method":"CRISPR/Cas9 knockout screens, ubiquitination assay (K63-linkage specific), alternative polyadenylation profiling, miRNA-mRNA interaction analysis","journal":"Cell discovery","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — CRISPR screens plus ubiquitination assay plus APA profiling, single lab with multiple orthogonal methods","pmids":["38503731"],"is_preprint":false},{"year":2024,"finding":"RBBP6 promotes K48-linked polyubiquitination of ERRα at the K100 residue, leading to its proteasomal degradation; this contributes to mitochondrial injury in proximal renal tubular cells in diabetic kidney disease. RBBP6 inhibition or ERRα overexpression reduces mitochondrial damage in diabetic mice.","method":"Co-immunoprecipitation, ubiquitination assay (K48-linkage and site-specific mutagenesis), conditional knockout/overexpression mouse models, cellular fractionation","journal":"Advanced science (Weinheim, Baden-Wurttemberg, Germany)","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — site-specific ubiquitination with mutagenesis plus in vivo validation, single lab","pmids":["39441040"],"is_preprint":false},{"year":2024,"finding":"Rbbp6 promotes K48-linked ubiquitination and proteasomal degradation of Bmal1, which suppresses the YAP1 signaling pathway and promotes ferroptosis in diabetic testicular damage; co-immunoprecipitation confirmed the Rbbp6-Bmal1 interaction.","method":"Co-immunoprecipitation, ubiquitination assay, Western blot, ferroptosis marker analysis, knockdown/overexpression experiments","journal":"Diabetes & metabolism journal","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — co-IP plus ubiquitination assay plus functional rescue experiments, single lab","pmids":["39501569"],"is_preprint":false},{"year":2024,"finding":"SRSF1-mediated alternative splicing regulates relative levels of RBBP6 isoform 1 vs isoform 3; knockdown of RBBP6 isoform 1 increases p53 protein levels in multiple myeloma cells, consistent with RBBP6 isoform 1 negatively regulating p53 through its ubiquitin ligase activity.","method":"siRNA knockdown, overexpression, Western blot, CCK-8 proliferation assay, RT-PCR","journal":"Zhongguo shi yan xue ye xue za zhi","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single lab, Western blot for p53 levels after knockdown, no direct ubiquitination assay performed","pmids":["39743259"],"is_preprint":false},{"year":2025,"finding":"RBBP6 inhibits Yellow Fever Virus (YFV) genome replication by interacting with the viral polymerase NS5, identifying RBBP6 as a restriction factor for YFV.","method":"AP-MS (affinity purification-mass spectrometry), functional viral replication assays","journal":"bioRxiv","confidence":"Low","confidence_rationale":"Tier 3 / Weak — preprint, single lab, interaction identified by AP-MS with functional assay but limited mechanistic detail in abstract","pmids":[],"is_preprint":true},{"year":2025,"finding":"RBBP6 ubiquitinates and destabilizes FOXP3 via the ubiquitin-proteasome pathway in HBV-related hepatocellular carcinoma; RBBP6 knockdown restores FOXP3 expression and inhibits tumor formation in vivo. RFX5 transcriptionally activates RBBP6 in HBV-positive HCC cells. The interaction between FOXP3 and RBBP6 was confirmed by GST pull-down and co-immunoprecipitation.","method":"GST pull-down, co-immunoprecipitation, ubiquitination assay, ChIP, dual-luciferase reporter assay, xenograft mouse model","journal":"Pathology, research and practice","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — multiple biochemical methods including GST pull-down, co-IP, ubiquitination assay, and in vivo validation, single lab","pmids":["40934694"],"is_preprint":false},{"year":2026,"finding":"RBBP6 ubiquitinates and degrades STAT1, suppressing DPP4 transcription; KMT2B enhances RBBP6 expression through H3K4me3 modification at the RBBP6 promoter. The RBBP6-STAT1 interaction was confirmed by co-immunoprecipitation and GST pull-down.","method":"ChIP-re-ChIP assay, co-immunoprecipitation, GST pull-down, ubiquitination assay","journal":"Epigenomics","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — multiple biochemical methods including ChIP, co-IP, GST pull-down and ubiquitination assay, single lab","pmids":["42011633"],"is_preprint":false}],"current_model":"RBBP6 is a multidomain E3 ubiquitin ligase whose N-terminal DWNN domain adopts a ubiquitin-like fold and directly contacts/activates the CPSF73 endonuclease to enable efficient pre-mRNA 3' cleavage and polyadenylation (recruited to the CPSF complex in an RNA-dependent manner, unlike its constitutive yeast homolog Mpe1); its RING finger/U-box-like domain ubiquitinates multiple substrates including YB-1, ZBTB38 (regulating MCM10 levels and DNA replication fork stability), IκBα (activating NF-κB), ERRα (K48-linked, promoting proteasomal degradation), Bmal1, FOXP3, and STAT1, with K63-linked ubiquitination of CPSF3 stabilizing it for alternative polyadenylation; RBBP6 isoform 3 (DWNN-only) acts as an endogenous competitor that inhibits 3' processing by competing with full-length RBBP6 for the core machinery; RBBP6 also localizes to nucleoli in interphase and to chromosome periphery in mitosis (with >10-fold protein enrichment during mitosis), functions as a co-repressor of estrogen receptor-dependent transcription through interaction with SRC-1/ERα, and restricts viral replication of both Ebola virus (by mimicking NP binding to VP30) and Yellow Fever Virus (by interacting with NS5 polymerase)."},"narrative":{"mechanistic_narrative":"RBBP6 is a multidomain nuclear protein that couples pre-mRNA 3' end processing to ubiquitin-dependent protein turnover [PMID:25319826, PMID:18851979]. Through its N-terminal DWNN domain — a ubiquitin-like fold first defined by NMR [PMID:16396680] — RBBP6 functions as an essential component of the mRNA 3' cleavage and polyadenylation machinery: it contacts core CPSF subunits including WDR33 and the endonuclease CPSF73/CPSF3 and is required to activate specific, efficient pre-mRNA cleavage; unlike its yeast homolog Mpe1 it is recruited to CPSF in an RNA-dependent manner rather than stably copurifying [PMID:35177536, PMID:35177537]. The DWNN-only isoform 3 acts as an endogenous competitor that inhibits 3' processing by competing with full-length RBBP6 for the core machinery, and RBBP6 levels shape poly(A) site choice and the stability of AU-rich transcripts such as c-Fos and c-Jun [PMID:25319826]. In parallel, RBBP6 is an E3 ubiquitin ligase whose RING finger/U-box-like domain adopts a homodimeric, zinc-coordinating fold [PMID:22130672] and directs ubiquitination of numerous substrates: it mediates K48-linked degradation of YB-1 [PMID:18851979], the replication regulator ZBTB38 (controlling MCM10 chromatin loading and replication fork progression) [PMID:24726359], IκBα to activate NF-κB-driven EMT [PMID:31685801], ERRα [PMID:39441040], Bmal1 [PMID:39501569], FOXP3 [PMID:40934694], and STAT1 [PMID:42011633], while K63-linked ubiquitination of CPSF3 stabilizes it to regulate alternative polyadenylation [PMID:38503731]. RBBP6 localizes to nucleoli in interphase and to the chromosome periphery in mitosis, with protein levels rising over 10-fold during mitosis through post-transcriptional control [PMID:12064457], and it acts as a co-repressor of estrogen receptor-dependent transcription via SRC-1/ERα [PMID:20184719]. RBBP6 additionally restricts viral replication, mimicking nucleoprotein binding to Ebola virus VP30 [PMID:30550789]. The gene family is essential for development across metazoans [PMID:15733535, PMID:23536819].","teleology":[{"year":1995,"claim":"Established the founding interaction that named the gene, placing RBBP6 in the orbit of retinoblastoma tumor-suppressor biology.","evidence":"GST pull-down of pRB with E1a competition mapping binding to the Rb pocket domain","pmids":["8595913"],"confidence":"Medium","gaps":["Functional consequence of pRB binding not defined","No cellular pathway linked to the interaction"]},{"year":1997,"claim":"First implicated RBBP6 in nucleic-acid and RNP biology, hinting at an RNA-associated function later resolved as 3' processing.","evidence":"GST fusion binding to ssDNA and recognition by anti-hnRNP antibodies","pmids":["9037032"],"confidence":"Medium","gaps":["No specific RNA target identified","Link to mRNA processing not yet established"]},{"year":2002,"claim":"Defined the cell-cycle-coupled localization and abundance of RBBP6, showing nucleolar-to-chromosome-periphery relocalization and >10-fold mitotic upregulation indicative of post-transcriptional control.","evidence":"Confocal microscopy and Western blot across synchronized mitotic cells; antisense knockdown and overexpression phenotyping","pmids":["12064457","12384997","12553003"],"confidence":"Medium","gaps":["Molecular basis of post-transcriptional regulation unknown","Mechanism connecting localization to mitotic/apoptotic phenotypes unresolved"]},{"year":2005,"claim":"Began assembling the RBBP6 interactome and its post-translational/translational regulation, linking it to splicing scaffolds and PUM2-mediated control.","evidence":"Co-IP with SAF-B and nucleolin, kinase assays, and PUM2 RNA pull-down with RT-PCR","pmids":["12938151","15617101"],"confidence":"Low","gaps":["Review-style/single-method evidence not independently confirmed","Functional impact of PUM2 binding on RBBP6 translation untested"]},{"year":2006,"claim":"Resolved the DWNN domain as a novel ubiquitin-like fold, establishing the structural basis for RBBP6's later-defined roles in ubiquitination and 3' processing.","evidence":"Heteronuclear NMR structure of the N-terminal 81 residues","pmids":["16396680"],"confidence":"High","gaps":["Whether DWNN is conjugated like ubiquitin not determined","Binding partners of DWNN not yet mapped"]},{"year":2008,"claim":"Provided the first direct demonstration that RBBP6 is a functional E3 ligase, identifying YB-1 as a degradation substrate and establishing the RING domain's catalytic role.","evidence":"Yeast two-hybrid, in vitro ubiquitination, proteasomal degradation and reporter transactivation assays","pmids":["18851979"],"confidence":"High","gaps":["Ubiquitin chain linkage type not defined","Physiological contexts of YB-1 regulation not mapped"]},{"year":2011,"claim":"Solved the RING/U-box-like domain structure and linked the DWNN to chaperones, framing RBBP6 as a chaperone-associated ubiquitination platform.","evidence":"Solution NMR structure with zinc/cadmium substitution and yeast two-hybrid with Hsp70/Hsp40","pmids":["22130672"],"confidence":"High","gaps":["Functional role of Hsp70/Hsp40 binding in substrate selection untested","Dimerization requirement for ligase activity not demonstrated"]},{"year":2014,"claim":"Connected RBBP6's ligase activity to genome stability and definitively placed it in the mRNA 3' processing complex, unifying its two principal activities.","evidence":"shRNA/siRNA knockdown, ubiquitination and DNA fiber assays, in vitro 3' processing reconstitution, co-IP, and genome-wide poly(A) site analysis","pmids":["24726359","25319826"],"confidence":"High","gaps":["How ubiquitination and 3' processing activities are coordinated unclear","Regulation of isoform 3 competition in vivo not defined"]},{"year":2018,"claim":"Revealed RBBP6 as a host restriction factor that disrupts Ebola virus transcription by molecular mimicry of viral nucleoprotein.","evidence":"AP-MS, domain mapping, X-ray crystallography of the VP30-RBBP6 peptide complex, and viral replication assays","pmids":["30550789"],"confidence":"High","gaps":["Whether antiviral activity requires ligase function unknown","Endogenous cellular role of the mimicry motif not addressed"]},{"year":2022,"claim":"Established by reconstitution from purified components that RBBP6 is essential to activate the CPSF73 endonuclease, with RNA-dependent recruitment distinguishing it from yeast Mpe1.","evidence":"In vitro reconstitution of 3' cleavage with purified polypeptides, mutagenesis, structural analysis, and co-purification — independently replicated in two studies the same year","pmids":["35177536","35177537"],"confidence":"High","gaps":["Atomic-resolution structure of the activated RBBP6-CPSF73 state not yet defined","Regulation of RNA-dependent recruitment unknown"]},{"year":2024,"claim":"Expanded the substrate repertoire and disease relevance of RBBP6 ubiquitination, including linkage-specific control of CPSF3 stability governing alternative polyadenylation.","evidence":"CRISPR screens, K63- and K48-linkage-specific ubiquitination assays, APA profiling, and conditional mouse models for ERRα and Bmal1","pmids":["38503731","39441040","39501569","39743259"],"confidence":"Medium","gaps":["Determinants of K48 vs K63 linkage choice unresolved","Tissue specificity of substrate selection not mechanistically explained"]},{"year":2027,"claim":"Continued cataloguing RBBP6 degradation substrates in cancer contexts, linking it to FOXP3 and STAT1 turnover under defined transcriptional regulators.","evidence":"GST pull-down, co-IP, ubiquitination assays, ChIP/ChIP-re-ChIP and xenograft models","pmids":["40934694","42011633"],"confidence":"Medium","gaps":["Whether these substrates share a common recognition motif unknown","Reciprocal validation of each interaction limited to single labs"]},{"year":null,"claim":"How RBBP6 partitions its activity between 3' end processing and substrate ubiquitination, and what governs substrate and chain-type selection, remains unresolved.","evidence":"","pmids":[],"confidence":"High","gaps":["No unifying model coordinating the RNA-processing and E3-ligase functions","No defined degron or recognition logic across the diverse substrate set","Structural basis of RNA-dependent CPSF recruitment not solved"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0016874","term_label":"ligase activity","supporting_discovery_ids":[10,14,17,21,22,23,26,27]},{"term_id":"GO:0140096","term_label":"catalytic activity, acting on a protein","supporting_discovery_ids":[10,14,21,22]},{"term_id":"GO:0140098","term_label":"catalytic activity, acting on RNA","supporting_discovery_ids":[15,19,20]},{"term_id":"GO:0003723","term_label":"RNA binding","supporting_discovery_ids":[1,15,19]},{"term_id":"GO:0140110","term_label":"transcription regulator activity","supporting_discovery_ids":[11]},{"term_id":"GO:0031386","term_label":"protein tag activity","supporting_discovery_ids":[9]}],"localization":[{"term_id":"GO:0005730","term_label":"nucleolus","supporting_discovery_ids":[2]},{"term_id":"GO:0005694","term_label":"chromosome","supporting_discovery_ids":[2]},{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[2,14,15]}],"pathway":[{"term_id":"R-HSA-8953854","term_label":"Metabolism of RNA","supporting_discovery_ids":[15,19,20,21]},{"term_id":"R-HSA-392499","term_label":"Metabolism of proteins","supporting_discovery_ids":[10,14,22,26,27]},{"term_id":"R-HSA-74160","term_label":"Gene expression (Transcription)","supporting_discovery_ids":[11,17]},{"term_id":"R-HSA-69306","term_label":"DNA Replication","supporting_discovery_ids":[14]},{"term_id":"R-HSA-1643685","term_label":"Disease","supporting_discovery_ids":[16,17,22,26]}],"complexes":["mRNA 3' cleavage and polyadenylation complex (CPSF)"],"partners":["CPSF3","WDR33","YB-1","ZBTB38","ERRA","FOXP3","STAT1","SRC-1"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q7Z6E9","full_name":"E3 ubiquitin-protein ligase RBBP6","aliases":["Proliferation potential-related protein","Protein P2P-R","RING-type E3 ubiquitin transferase RBBP6","Retinoblastoma-binding Q protein 1","RBQ-1","Retinoblastoma-binding protein 6","p53-associated cellular protein of testis"],"length_aa":1792,"mass_kda":201.6,"function":"E3 ubiquitin-protein ligase which promotes ubiquitination of YBX1, leading to its degradation by the proteasome (PubMed:18851979). May play a role as a scaffold protein to promote the assembly of the p53/TP53-MDM2 complex, resulting in increase of MDM2-mediated ubiquitination and degradation of p53/TP53; may function as negative regulator of p53/TP53, leading to both apoptosis and cell growth (By similarity). Regulates DNA-replication and the stability of chromosomal common fragile sites (CFSs) in a ZBTB38- and MCM10-dependent manner. Controls ZBTB38 protein stability and abundance via ubiquitination and proteasomal degradation, and ZBTB38 in turn negatively regulates the expression of MCM10 which plays an important role in DNA-replication (PubMed:24726359) (Microbial infection) [Isoform 1]: Restricts ebolavirus replication probably by impairing the vp30-NP interaction, and thus viral transcription","subcellular_location":"Nucleus, nucleolus; Chromosome; Cytoplasm, cytoskeleton, microtubule organizing center, centrosome","url":"https://www.uniprot.org/uniprotkb/Q7Z6E9/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":true,"resolved_as":"","url":"https://depmap.org/portal/gene/RBBP6","classification":"Common Essential","n_dependent_lines":1101,"n_total_lines":1208,"dependency_fraction":0.9114238410596026},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[{"gene":"CAPZB","stoichiometry":0.2},{"gene":"CPSF6","stoichiometry":0.2},{"gene":"SF3A1","stoichiometry":0.2},{"gene":"SNRPA","stoichiometry":0.2},{"gene":"SNRPB","stoichiometry":0.2},{"gene":"SNRPC","stoichiometry":0.2},{"gene":"SSRP1","stoichiometry":0.2},{"gene":"TOP1","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/search/RBBP6","total_profiled":1310},"omim":[{"mim_id":"600938","title":"RETINOBLASTOMA-BINDING PROTEIN 6; RBBP6","url":"https://www.omim.org/entry/600938"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Enhanced","locations":[{"location":"Nuclear speckles","reliability":"Enhanced"}],"tissue_specificity":"Tissue enhanced","tissue_distribution":"Detected in all","driving_tissues":[{"tissue":"bone marrow","ntpm":135.4}],"url":"https://www.proteinatlas.org/search/RBBP6"},"hgnc":{"alias_symbol":["P2P-R","PACT","SNAMA"],"prev_symbol":[]},"alphafold":{"accession":"Q7Z6E9","domains":[{"cath_id":"3.10.20.90","chopping":"2-80","consensus_level":"medium","plddt":89.9468,"start":2,"end":80},{"cath_id":"-","chopping":"151-186","consensus_level":"medium","plddt":76.7725,"start":151,"end":186},{"cath_id":"-","chopping":"188-237","consensus_level":"medium","plddt":80.1472,"start":188,"end":237},{"cath_id":"3.30.40.10","chopping":"256-327","consensus_level":"medium","plddt":89.5857,"start":256,"end":327},{"cath_id":"1.10.1200","chopping":"114-147","consensus_level":"medium","plddt":79.8135,"start":114,"end":147}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q7Z6E9","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q7Z6E9-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q7Z6E9-F1-predicted_aligned_error_v6.png","plddt_mean":46.81},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=RBBP6","jax_strain_url":"https://www.jax.org/strain/search?query=RBBP6"},"sequence":{"accession":"Q7Z6E9","fasta_url":"https://rest.uniprot.org/uniprotkb/Q7Z6E9.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q7Z6E9/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q7Z6E9"}},"corpus_meta":[{"pmid":"30550789","id":"PMC_30550789","title":"Protein Interaction Mapping Identifies RBBP6 as a Negative Regulator of Ebola Virus Replication.","date":"2018","source":"Cell","url":"https://pubmed.ncbi.nlm.nih.gov/30550789","citation_count":129,"is_preprint":false},{"pmid":"25319826","id":"PMC_25319826","title":"RBBP6 isoforms regulate the human polyadenylation machinery and modulate expression of mRNAs with AU-rich 3' UTRs.","date":"2014","source":"Genes & development","url":"https://pubmed.ncbi.nlm.nih.gov/25319826","citation_count":76,"is_preprint":false},{"pmid":"18851979","id":"PMC_18851979","title":"RBBP6 interacts with multifunctional protein YB-1 through its RING finger domain, leading to ubiquitination and proteosomal degradation of YB-1.","date":"2008","source":"Journal of molecular biology","url":"https://pubmed.ncbi.nlm.nih.gov/18851979","citation_count":75,"is_preprint":false},{"pmid":"24726359","id":"PMC_24726359","title":"The RBBP6/ZBTB38/MCM10 axis regulates DNA replication and common fragile site stability.","date":"2014","source":"Cell reports","url":"https://pubmed.ncbi.nlm.nih.gov/24726359","citation_count":61,"is_preprint":false},{"pmid":"16396680","id":"PMC_16396680","title":"DWNN, a novel ubiquitin-like domain, implicates RBBP6 in mRNA processing and ubiquitin-like pathways.","date":"2006","source":"BMC structural biology","url":"https://pubmed.ncbi.nlm.nih.gov/16396680","citation_count":59,"is_preprint":false},{"pmid":"35177536","id":"PMC_35177536","title":"RBBP6 activates the pre-mRNA 3' end processing machinery in humans.","date":"2022","source":"Genes & development","url":"https://pubmed.ncbi.nlm.nih.gov/35177536","citation_count":47,"is_preprint":false},{"pmid":"8595913","id":"PMC_8595913","title":"cDNA sequence and chromosomal localization of a novel human protein, RBQ-1 (RBBP6), that binds to the retinoblastoma gene product.","date":"1995","source":"Genomics","url":"https://pubmed.ncbi.nlm.nih.gov/8595913","citation_count":47,"is_preprint":false},{"pmid":"35177537","id":"PMC_35177537","title":"Reconstitution of 3' end processing of mammalian pre-mRNA reveals a central role of RBBP6.","date":"2022","source":"Genes & development","url":"https://pubmed.ncbi.nlm.nih.gov/35177537","citation_count":38,"is_preprint":false},{"pmid":"9037032","id":"PMC_9037032","title":"The proliferation potential protein-related (P2P-R) gene with domains encoding heterogeneous nuclear ribonucleoprotein association and Rb1 binding shows repressed expression during terminal differentiation.","date":"1997","source":"Proceedings of the National Academy of Sciences of the United States of America","url":"https://pubmed.ncbi.nlm.nih.gov/9037032","citation_count":37,"is_preprint":false},{"pmid":"21676486","id":"PMC_21676486","title":"Expression and function of retinoblastoma binding protein 6 (RBBP6) in human lung cancer.","date":"2011","source":"Immunobiology","url":"https://pubmed.ncbi.nlm.nih.gov/21676486","citation_count":34,"is_preprint":false},{"pmid":"31685801","id":"PMC_31685801","title":"RBBP6, a RING finger-domain E3 ubiquitin ligase, induces epithelial-mesenchymal transition and promotes metastasis of colorectal cancer.","date":"2019","source":"Cell death & disease","url":"https://pubmed.ncbi.nlm.nih.gov/31685801","citation_count":34,"is_preprint":false},{"pmid":"24703106","id":"PMC_24703106","title":"Silencing RBBP6 (Retinoblastoma Binding Protein 6) sensitises breast cancer cells MCF7 to staurosporine and camptothecin-induced cell death.","date":"2014","source":"Immunobiology","url":"https://pubmed.ncbi.nlm.nih.gov/24703106","citation_count":32,"is_preprint":false},{"pmid":"22139301","id":"PMC_22139301","title":"De-regulation of the RBBP6 isoform 3/DWNN in human cancers.","date":"2011","source":"Molecular and cellular biochemistry","url":"https://pubmed.ncbi.nlm.nih.gov/22139301","citation_count":30,"is_preprint":false},{"pmid":"12384997","id":"PMC_12384997","title":"P2P-R protein overexpression restricts mitotic progression at prometaphase and promotes mitotic apoptosis.","date":"2002","source":"Journal of cellular physiology","url":"https://pubmed.ncbi.nlm.nih.gov/12384997","citation_count":24,"is_preprint":false},{"pmid":"12064457","id":"PMC_12064457","title":"P2P-R protein localizes to the nucleolus of interphase cells and the periphery of chromosomes in mitotic cells which show maximum P2P-R immunoreactivity.","date":"2002","source":"Journal of cellular physiology","url":"https://pubmed.ncbi.nlm.nih.gov/12064457","citation_count":24,"is_preprint":false},{"pmid":"29369481","id":"PMC_29369481","title":"RBBP6 increases radioresistance and serves as a therapeutic target for preoperative radiotherapy in colorectal cancer.","date":"2018","source":"Cancer science","url":"https://pubmed.ncbi.nlm.nih.gov/29369481","citation_count":21,"is_preprint":false},{"pmid":"22130672","id":"PMC_22130672","title":"Solution structure of RING finger-like domain of retinoblastoma-binding protein-6 (RBBP6) suggests it functions as a U-box.","date":"2011","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/22130672","citation_count":20,"is_preprint":false},{"pmid":"12938151","id":"PMC_12938151","title":"Functional potential of P2P-R: a role in the cell cycle and cell differentiation related to its interactions with proteins that bind to matrix associated regions of DNA?","date":"2003","source":"Journal of cellular biochemistry","url":"https://pubmed.ncbi.nlm.nih.gov/12938151","citation_count":19,"is_preprint":false},{"pmid":"14566974","id":"PMC_14566974","title":"Stable overexpression of specific segments of the P2P-R protein in human MCF-7 cells promotes camptothecin-induced apoptosis.","date":"2003","source":"Journal of cellular physiology","url":"https://pubmed.ncbi.nlm.nih.gov/14566974","citation_count":19,"is_preprint":false},{"pmid":"39441040","id":"PMC_39441040","title":"RBBP6-Mediated ERRα Degradation Contributes to Mitochondrial Injury in Renal Tubular Cells in Diabetic Kidney Disease.","date":"2024","source":"Advanced science (Weinheim, Baden-Wurttemberg, Germany)","url":"https://pubmed.ncbi.nlm.nih.gov/39441040","citation_count":16,"is_preprint":false},{"pmid":"31274515","id":"PMC_31274515","title":"Expression Analysis of RbBP6 in human cancers: a Prospective biomarker.","date":"2019","source":"Anti-cancer drugs","url":"https://pubmed.ncbi.nlm.nih.gov/31274515","citation_count":15,"is_preprint":false},{"pmid":"27536134","id":"PMC_27536134","title":"RBBP6: a potential biomarker of apoptosis induction in human cervical cancer cell lines.","date":"2016","source":"OncoTargets and therapy","url":"https://pubmed.ncbi.nlm.nih.gov/27536134","citation_count":15,"is_preprint":false},{"pmid":"38503731","id":"PMC_38503731","title":"RBBP6 maintains glioblastoma stem cells through CPSF3-dependent alternative polyadenylation.","date":"2024","source":"Cell discovery","url":"https://pubmed.ncbi.nlm.nih.gov/38503731","citation_count":14,"is_preprint":false},{"pmid":"29501043","id":"PMC_29501043","title":"RBBP6 promotes human cervical carcinoma malignancy via JNK signaling pathway.","date":"2018","source":"Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie","url":"https://pubmed.ncbi.nlm.nih.gov/29501043","citation_count":14,"is_preprint":false},{"pmid":"15617101","id":"PMC_15617101","title":"P2P-R expression is genetically coregulated with components of the translation machinery and with PUM2, a translational repressor that associates with the P2P-R mRNA.","date":"2005","source":"Journal of cellular physiology","url":"https://pubmed.ncbi.nlm.nih.gov/15617101","citation_count":12,"is_preprint":false},{"pmid":"15733535","id":"PMC_15733535","title":"SNAMA, a novel protein with a DWNN domain and a RING finger-like motif: a possible role in apoptosis.","date":"2005","source":"Biochimica et biophysica acta","url":"https://pubmed.ncbi.nlm.nih.gov/15733535","citation_count":11,"is_preprint":false},{"pmid":"34132380","id":"PMC_34132380","title":"MicroRNA‑193a‑5p exerts a tumor suppressive role in epithelial ovarian cancer by modulating RBBP6.","date":"2021","source":"Molecular medicine reports","url":"https://pubmed.ncbi.nlm.nih.gov/34132380","citation_count":10,"is_preprint":false},{"pmid":"26905308","id":"PMC_26905308","title":"Expression analysis and association of RBBP6 with apoptosis in colon cancers.","date":"2016","source":"Journal of molecular histology","url":"https://pubmed.ncbi.nlm.nih.gov/26905308","citation_count":9,"is_preprint":false},{"pmid":"36853473","id":"PMC_36853473","title":"Cannabidiol and Cannabis Sativa as a potential treatment in vitro prostate cancer cells silenced with RBBp6 and PC3 xenograft.","date":"2023","source":"Molecular biology reports","url":"https://pubmed.ncbi.nlm.nih.gov/36853473","citation_count":9,"is_preprint":false},{"pmid":"23536819","id":"PMC_23536819","title":"The C. elegans Homolog of RBBP6 (RBPL-1) regulates fertility through controlling cell proliferation in the germline and nutrient synthesis in the intestine.","date":"2013","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/23536819","citation_count":9,"is_preprint":false},{"pmid":"12553003","id":"PMC_12553003","title":"P2P-R deficiency modifies nocodazole-induced mitotic arrest and UV-induced apoptosis.","date":"2002","source":"Anticancer research","url":"https://pubmed.ncbi.nlm.nih.gov/12553003","citation_count":9,"is_preprint":false},{"pmid":"33683013","id":"PMC_33683013","title":"The lncRNA SLCO4A1-AS1/miR-876-3p/RBBP6 axis regulates cell proliferation and apoptosis in acute lymphocytic leukemia via the JNK signaling pathway.","date":"2021","source":"International journal of laboratory hematology","url":"https://pubmed.ncbi.nlm.nih.gov/33683013","citation_count":8,"is_preprint":false},{"pmid":"30237738","id":"PMC_30237738","title":"RBBP6 expressional effects on cell proliferation and apoptosis in breast cancer cell lines with distinct p53 statuses.","date":"2018","source":"Cancer management and research","url":"https://pubmed.ncbi.nlm.nih.gov/30237738","citation_count":7,"is_preprint":false},{"pmid":"20184719","id":"PMC_20184719","title":"Systems genetics analyses predict a transcription role for P2P-R: molecular confirmation that P2P-R is a transcriptional co-repressor.","date":"2010","source":"BMC systems biology","url":"https://pubmed.ncbi.nlm.nih.gov/20184719","citation_count":7,"is_preprint":false},{"pmid":"33155192","id":"PMC_33155192","title":"RBBP6 aggravates the progression of ovarian cancer by targeting PIK3R6.","date":"2020","source":"European review for medical and pharmacological sciences","url":"https://pubmed.ncbi.nlm.nih.gov/33155192","citation_count":6,"is_preprint":false},{"pmid":"39501569","id":"PMC_39501569","title":"Rbbp6-Mediated Bmal1 Ubiquitination Inhibits YAP1 Signaling Pathway to Promote Ferroptosis in Diabetes-Induced Testicular Damage.","date":"2024","source":"Diabetes & metabolism journal","url":"https://pubmed.ncbi.nlm.nih.gov/39501569","citation_count":6,"is_preprint":false},{"pmid":"31534777","id":"PMC_31534777","title":"Downregulation of RBBP6 variant 1 during arsenic trioxide-mediated cell cycle arrest and curcumin-induced apoptosis in MCF-7 breast cancer cells.","date":"2019","source":"Future science OA","url":"https://pubmed.ncbi.nlm.nih.gov/31534777","citation_count":5,"is_preprint":false},{"pmid":"30886526","id":"PMC_30886526","title":"RBBP6 Is Abundantly Expressed in Human Cervical Carcinoma and May Be Implicated in Its Malignant Progression.","date":"2019","source":"Biomarkers in cancer","url":"https://pubmed.ncbi.nlm.nih.gov/30886526","citation_count":4,"is_preprint":false},{"pmid":"38667315","id":"PMC_38667315","title":"Probing the Effects of Retinoblastoma Binding Protein 6 (RBBP6) Knockdown on the Sensitivity of Cisplatin in Cervical Cancer Cells.","date":"2024","source":"Cells","url":"https://pubmed.ncbi.nlm.nih.gov/38667315","citation_count":4,"is_preprint":false},{"pmid":"36763571","id":"PMC_36763571","title":"Expression, purification, and characterisation of the p53 binding domain of Retinoblastoma binding protein 6 (RBBP6).","date":"2023","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/36763571","citation_count":3,"is_preprint":false},{"pmid":"37322627","id":"PMC_37322627","title":"Abnormal expression of long non-coding RNA FGD5-AS1 affects the development of ovarian cancer through regulating miR-107/RBBP6 axis.","date":"2023","source":"The Chinese journal of physiology","url":"https://pubmed.ncbi.nlm.nih.gov/37322627","citation_count":2,"is_preprint":false},{"pmid":"34956492","id":"PMC_34956492","title":"Microscale thermophoresis analysis of the molecular interaction between small nuclear ribonucleoprotein polypeptide G and the RING finger domain of RBBP6 towards anti-cancer drug discovery.","date":"2021","source":"American journal of translational research","url":"https://pubmed.ncbi.nlm.nih.gov/34956492","citation_count":2,"is_preprint":false},{"pmid":"39580381","id":"PMC_39580381","title":"Mbnl1-mediated alternative splicing of circMlxipl regulates Rbbp6-involved ChREBP turnover to inhibit lipotoxicity-induced β-cell damage.","date":"2024","source":"Molecular medicine (Cambridge, Mass.)","url":"https://pubmed.ncbi.nlm.nih.gov/39580381","citation_count":1,"is_preprint":false},{"pmid":"25910411","id":"PMC_25910411","title":"The association of RBBP6 variant 3 expressions with apoptosis in human immunodeficiency virus-associated nephropathy (HIVAN).","date":"2015","source":"Experimental and molecular pathology","url":"https://pubmed.ncbi.nlm.nih.gov/25910411","citation_count":1,"is_preprint":false},{"pmid":"39743259","id":"PMC_39743259","title":"[The Impact of SRSF1 -Mediated Alternative Splicing of RBBP6 on the Proliferation of Multiple Myeloma Cells].","date":"2024","source":"Zhongguo shi yan xue ye xue za zhi","url":"https://pubmed.ncbi.nlm.nih.gov/39743259","citation_count":1,"is_preprint":false},{"pmid":"40934694","id":"PMC_40934694","title":"RBBP6-induced destabilization of FOXP3 promotes glucose metabolism and malignant progression of HBV-related hepatocellular carcinoma.","date":"2025","source":"Pathology, research and practice","url":"https://pubmed.ncbi.nlm.nih.gov/40934694","citation_count":0,"is_preprint":false},{"pmid":"42239902","id":"PMC_42239902","title":"RBBP6 and cancer: from molecular mechanisms to clinical implications.","date":"2026","source":"Frontiers in oncology","url":"https://pubmed.ncbi.nlm.nih.gov/42239902","citation_count":0,"is_preprint":false},{"pmid":"42011633","id":"PMC_42011633","title":"KMT2B induces the H3K4 trimethylation of RBBP6 promoter to enhance the 131I sensitivity in thyroid carcinoma by restraining STAT1/DPP4 axis.","date":"2026","source":"Epigenomics","url":"https://pubmed.ncbi.nlm.nih.gov/42011633","citation_count":0,"is_preprint":false},{"pmid":null,"id":"bio_10.1101_2025.06.14.659623","title":"Yellow Fever Virus Interactomes Reveal Common and Divergent Strategies of Replication and Evolution for Mosquito-borne Flaviviruses","date":"2025-06-18","source":"bioRxiv","url":"https://doi.org/10.1101/2025.06.14.659623","citation_count":0,"is_preprint":true}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":27022,"output_tokens":6595,"usd":0.089996,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":15346,"output_tokens":4281,"usd":0.091878,"stage2_stop_reason":"end_turn"},"total_usd":0.181874,"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\": 1995,\n      \"finding\": \"RBBP6 (RBQ-1) binds to the retinoblastoma gene product (pRB) through a small region near its C-terminus, as demonstrated by GST pull-down of pRB from cellular extracts, with binding competed by adenovirus E1a protein indicating the interaction occurs through the pocket domain of Rb1.\",\n      \"method\": \"GST fusion protein pull-down, competition with E1a protein\",\n      \"journal\": \"Genomics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — GST pull-down with competitive inhibition control, single lab, two orthogonal lines of evidence\",\n      \"pmids\": [\"8595913\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1997,\n      \"finding\": \"P2P-R (RBBP6) encodes protein domains that bind single-stranded nucleic acids and associate with hnRNP proteins, as demonstrated by binding of cDNA-derived fusion proteins to ssDNA and recognition by anti-hnRNP monoclonal antibodies.\",\n      \"method\": \"GST fusion protein binding assay, monoclonal antibody recognition, antisense oligonucleotide experiments\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple biochemical methods in single lab, direct binding demonstrated\",\n      \"pmids\": [\"9037032\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2002,\n      \"finding\": \"P2P-R (RBBP6) localizes to nucleoli in interphase cells and to the periphery of chromosomes in mitotic cells, with protein levels increasing >10-fold during mitosis without a concomitant change in mRNA, suggesting post-transcriptional regulation.\",\n      \"method\": \"Confocal microscopy, Western blot, mitotic cell synchronization (nocodazole, vinblastine, shake-select)\",\n      \"journal\": \"Journal of cellular physiology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct localization by confocal microscopy with functional context, multiple synchronization methods, single lab\",\n      \"pmids\": [\"12064457\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2002,\n      \"finding\": \"Overexpression of near full-length P2P-R (RBBP6) in Saos2 cells restricts mitotic progression at prometaphase and promotes mitotic apoptosis, with P2P-R protein dissociating from chromosomes and appearing in cytoplasm and apoptotic cell surface blebs during mitotic apoptosis.\",\n      \"method\": \"Stable transfection, flow cytometry, confocal microscopy, Western blot of enriched apoptotic blebs\",\n      \"journal\": \"Journal of cellular physiology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — gain-of-function with multiple readouts, single lab, direct localization during apoptosis confirmed biochemically\",\n      \"pmids\": [\"12384997\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2002,\n      \"finding\": \"P2P-R (RBBP6) deficiency restricts cell cycle progression from G1 through S to mitosis in a microtubule-dependent manner and represses UV irradiation-induced apoptosis.\",\n      \"method\": \"Antisense oligonucleotide knockdown, flow cytometry, nocodazole treatment\",\n      \"journal\": \"Anticancer research\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — antisense knockdown with phenotypic readout, no direct molecular mechanism identified, single lab single method\",\n      \"pmids\": [\"12553003\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2003,\n      \"finding\": \"P2P-R (RBBP6) is phosphorylated by cdc2 and SRPK1a kinases, interacts with scaffold attachment factor-B (SAF-B), and co-immunoprecipitates with nucleolin.\",\n      \"method\": \"Co-immunoprecipitation, in vitro kinase assay (inferred from review-style paper)\",\n      \"journal\": \"Journal of cellular biochemistry\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — summary/review paper citing prior data, single lab, methods not fully described in this abstract\",\n      \"pmids\": [\"12938151\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2003,\n      \"finding\": \"Overexpression of P2P-R (RBBP6) segments spanning residues 1156-1314 promotes camptothecin-induced apoptosis 3-5 fold in MCF-7 cells; the p53-binding domain overlaps with this apoptosis-associated region.\",\n      \"method\": \"Stable transfection, flow cytometry, TUNEL assay\",\n      \"journal\": \"Journal of cellular physiology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — domain mapping with two orthogonal apoptosis assays, functional region identified, single lab\",\n      \"pmids\": [\"14566974\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2005,\n      \"finding\": \"PUM2 binds P2P-R (RBBP6) mRNA through consensus sequences in its 3' UTR, as confirmed by PUM2 pull-down followed by RT-PCR, suggesting translational regulation of RBBP6 by PUM2.\",\n      \"method\": \"RNA pull-down (PUM2 immunoprecipitation) followed by RT-PCR\",\n      \"journal\": \"Journal of cellular physiology\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single RNA pull-down method, single lab, functional consequence not directly tested\",\n      \"pmids\": [\"15617101\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2005,\n      \"finding\": \"SNAMA, the Drosophila homolog of RBBP6, contains a DWNN domain and a RING finger-like motif; homozygous P-element insertion mutants show embryonic lethality with widespread apoptosis throughout the gastrula, establishing an essential developmental role for this gene family.\",\n      \"method\": \"P-element insertion genetics, embryo phenotype analysis\",\n      \"journal\": \"Biochimica et biophysica acta\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — genetic loss-of-function in Drosophila ortholog with clear developmental phenotype, single lab\",\n      \"pmids\": [\"15733535\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2006,\n      \"finding\": \"The N-terminal 81 amino acids of RBBP6 form a novel ubiquitin-like domain (DWNN) as determined by heteronuclear NMR; the domain lacks conserved K48/K63 equivalents but contains a di-glycine motif in human/mouse, and is independently expressed as a single-domain protein in vertebrates.\",\n      \"method\": \"Heteronuclear NMR structure determination\",\n      \"journal\": \"BMC structural biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — NMR structure with detailed sequence and structural analysis, foundational domain characterization\",\n      \"pmids\": [\"16396680\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2008,\n      \"finding\": \"RBBP6 acts as an E3 ubiquitin ligase for YB-1: the RING finger domain of RBBP6 binds the last 62 residues of YB-1 (identified by yeast two-hybrid), and both full-length RBBP6 and the isolated RING finger domain ubiquitinate YB-1 leading to its proteasomal degradation, suppressing YB-1 transactivational activity in vivo.\",\n      \"method\": \"Yeast two-hybrid, in vitro ubiquitination assay, proteasome degradation assay, reporter transactivation assay\",\n      \"journal\": \"Journal of molecular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — in vitro ubiquitination reconstitution plus yeast two-hybrid plus in vivo degradation, multiple orthogonal methods, single lab\",\n      \"pmids\": [\"18851979\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2010,\n      \"finding\": \"P2P-R (RBBP6) functions as a transcriptional co-repressor of estrogen-dependent transcription: it represses estrogen-induced transcription by 50-70% when transfected into four cell types, and co-immunoprecipitates with SRC-1 (steroid receptor co-activator 1) and estrogen receptor alpha.\",\n      \"method\": \"Transient transfection reporter assay, antisense knockdown, co-immunoprecipitation\",\n      \"journal\": \"BMC systems biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — co-IP plus functional reporter assay in multiple cell types, single lab\",\n      \"pmids\": [\"20184719\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"The RING finger-like domain of RBBP6 adopts a homodimeric structure similar to U-box proteins despite coordinating two zinc ions (replaceable with cadmium); RBBP6 interacts with chaperones Hsp70 and Hsp40 through its N-terminal DWNN ubiquitin-like domain, suggesting a role in chaperone-mediated ubiquitination.\",\n      \"method\": \"Solution NMR structure, zinc/cadmium substitution assays, thermal stability assays, yeast two-hybrid\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — NMR structure determination with functional domain validation, multiple biophysical methods, single lab\",\n      \"pmids\": [\"22130672\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"RBPL-1, the C. elegans homolog of RBBP6, is required for germ cell proliferation, oocyte production, embryonic development, and intestine development; RNAi silencing causes embryonic lethality and defects in mitosis, consistent with a role as an mRNA cleavage/polyadenylation factor.\",\n      \"method\": \"RNAi knockdown, phenotypic analysis, microarray expression profiling\",\n      \"journal\": \"PloS one\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — genetic loss-of-function in C. elegans ortholog with defined developmental phenotypes, multiple readouts, single lab\",\n      \"pmids\": [\"23536819\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"RBBP6 ubiquitinates and destabilizes the transcriptional repressor ZBTB38; loss of RBBP6 causes ZBTB38 accumulation, leading to MCM10 downregulation on chromatin, reduced replication fork progression, and increased DNA damage at common fragile sites.\",\n      \"method\": \"shRNA knockdown, ubiquitination assay, chromatin fractionation, DNA fiber assay, FISH for fragile site stability\",\n      \"journal\": \"Cell reports\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 / Strong — pathway reconstituted with E3 ligase substrate identification, multiple orthogonal methods including ubiquitination assay and replication fork analysis\",\n      \"pmids\": [\"24726359\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"RBBP6 is a component of the mRNA 3' processing complex and functions in 3' processing in vitro and in vivo; its DWNN ubiquitin-like domain mediates interaction with core cleavage/polyadenylation factors and is required for 3' processing activity. RBBP6 isoform 3 (iso3, DWNN-only) competes with full-length RBBP6 for binding to the core machinery, thereby inhibiting 3' processing. RBBP6 knockdown decreases transcript levels of AU-rich 3' UTR mRNAs (e.g., c-Fos, c-Jun) and increases usage of distal poly(A) sites.\",\n      \"method\": \"In vitro 3' processing assay, co-immunoprecipitation, genome-wide poly(A) site analysis, siRNA knockdown\",\n      \"journal\": \"Genes & development\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — in vitro reconstitution assay plus co-IP plus genome-wide analysis, multiple orthogonal methods, mechanistic domain mapping\",\n      \"pmids\": [\"25319826\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"RBBP6 interacts with Ebola virus VP30 (transcription regulator) through a 23 amino acid region that mimics the viral nucleoprotein (NP) binding interface on VP30; a crystal structure of the VP30-RBBP6 peptide complex revealed competitive mimicry. RBBP6 knockdown stimulates viral transcription and increases EBOV replication; RBBP6 overexpression inhibits both.\",\n      \"method\": \"AP-MS, domain mapping, X-ray crystallography, siRNA knockdown, viral replication assays\",\n      \"journal\": \"Cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — crystal structure plus AP-MS plus functional knockdown/overexpression, multiple orthogonal methods in single study\",\n      \"pmids\": [\"30550789\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"RBBP6 ubiquitinates IκBα (inhibitor of NF-κB), leading to its degradation and consequent p65 nuclear translocation, NF-κB pathway activation, EMT induction, and cancer cell metastasis in colorectal cancer.\",\n      \"method\": \"Co-immunoprecipitation, ubiquitination assay, nuclear fractionation, ChIP analysis, loss-of-function/gain-of-function experiments, mouse metastasis model\",\n      \"journal\": \"Cell death & disease\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — ubiquitination assay plus co-IP plus nuclear fractionation, single lab with multiple orthogonal methods\",\n      \"pmids\": [\"31685801\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"The RING finger domain of RBBP6 binds SNRPG (small nuclear ribonucleoprotein polypeptide G) with a dissociation constant of ~3.16 nM as measured by microscale thermophoresis, confirming a physical interaction between these two splicing-related proteins.\",\n      \"method\": \"Microscale thermophoresis (MST) binding assay\",\n      \"journal\": \"American journal of translational research\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single biophysical binding assay, no functional follow-up, single lab\",\n      \"pmids\": [\"34956492\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"RBBP6 is required to activate the human CPSF endonuclease for specific and efficient pre-mRNA 3' cleavage; unlike its yeast homolog Mpe1, RBBP6 does not stably copurify with CPSF but is recruited in an RNA-dependent manner. Sequence and mutational analyses indicate RBBP6 interacts with WDR33 and CPSF73 subunits of CPSF.\",\n      \"method\": \"In vitro reconstitution of 3' endonuclease activity with purified proteins, mutagenesis, co-purification experiments\",\n      \"journal\": \"Genes & development\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — in vitro reconstitution with purified proteins plus mutagenesis plus interaction mapping, independent replication by second lab same year\",\n      \"pmids\": [\"35177536\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"RBBP6 is required for pre-mRNA 3' end cleavage in a minimal reconstituted mammalian system; structural data show the RBBP6 DWNN domain contacts and presumably activates the endonuclease CPSF73. RBBP6 is among 14 polypeptides essential for RNA processing in vitro, and its role is conserved from yeast (Mpe1) to humans.\",\n      \"method\": \"In vitro reconstitution with 14 purified polypeptides, structural analysis, RNA cleavage assay at physiological poly(A) site\",\n      \"journal\": \"Genes & development\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — in vitro reconstitution from purified components plus structural data, independent replication confirming prior study in same year\",\n      \"pmids\": [\"35177537\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"RBBP6 mediates K63-linked ubiquitination of CPSF3 (Cleavage and Polyadenylation Specific Factor 3), which stabilizes CPSF3 and regulates alternative polyadenylation events in glioblastoma stem cells; RBBP6 depletion induces shortening of 3' UTRs of MYC competing-endogenous RNAs, releasing miR-590-3p to decrease MYC expression.\",\n      \"method\": \"CRISPR/Cas9 knockout screens, ubiquitination assay (K63-linkage specific), alternative polyadenylation profiling, miRNA-mRNA interaction analysis\",\n      \"journal\": \"Cell discovery\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — CRISPR screens plus ubiquitination assay plus APA profiling, single lab with multiple orthogonal methods\",\n      \"pmids\": [\"38503731\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"RBBP6 promotes K48-linked polyubiquitination of ERRα at the K100 residue, leading to its proteasomal degradation; this contributes to mitochondrial injury in proximal renal tubular cells in diabetic kidney disease. RBBP6 inhibition or ERRα overexpression reduces mitochondrial damage in diabetic mice.\",\n      \"method\": \"Co-immunoprecipitation, ubiquitination assay (K48-linkage and site-specific mutagenesis), conditional knockout/overexpression mouse models, cellular fractionation\",\n      \"journal\": \"Advanced science (Weinheim, Baden-Wurttemberg, Germany)\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — site-specific ubiquitination with mutagenesis plus in vivo validation, single lab\",\n      \"pmids\": [\"39441040\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"Rbbp6 promotes K48-linked ubiquitination and proteasomal degradation of Bmal1, which suppresses the YAP1 signaling pathway and promotes ferroptosis in diabetic testicular damage; co-immunoprecipitation confirmed the Rbbp6-Bmal1 interaction.\",\n      \"method\": \"Co-immunoprecipitation, ubiquitination assay, Western blot, ferroptosis marker analysis, knockdown/overexpression experiments\",\n      \"journal\": \"Diabetes & metabolism journal\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — co-IP plus ubiquitination assay plus functional rescue experiments, single lab\",\n      \"pmids\": [\"39501569\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"SRSF1-mediated alternative splicing regulates relative levels of RBBP6 isoform 1 vs isoform 3; knockdown of RBBP6 isoform 1 increases p53 protein levels in multiple myeloma cells, consistent with RBBP6 isoform 1 negatively regulating p53 through its ubiquitin ligase activity.\",\n      \"method\": \"siRNA knockdown, overexpression, Western blot, CCK-8 proliferation assay, RT-PCR\",\n      \"journal\": \"Zhongguo shi yan xue ye xue za zhi\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single lab, Western blot for p53 levels after knockdown, no direct ubiquitination assay performed\",\n      \"pmids\": [\"39743259\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"RBBP6 inhibits Yellow Fever Virus (YFV) genome replication by interacting with the viral polymerase NS5, identifying RBBP6 as a restriction factor for YFV.\",\n      \"method\": \"AP-MS (affinity purification-mass spectrometry), functional viral replication assays\",\n      \"journal\": \"bioRxiv\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — preprint, single lab, interaction identified by AP-MS with functional assay but limited mechanistic detail in abstract\",\n      \"pmids\": [],\n      \"is_preprint\": true\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"RBBP6 ubiquitinates and destabilizes FOXP3 via the ubiquitin-proteasome pathway in HBV-related hepatocellular carcinoma; RBBP6 knockdown restores FOXP3 expression and inhibits tumor formation in vivo. RFX5 transcriptionally activates RBBP6 in HBV-positive HCC cells. The interaction between FOXP3 and RBBP6 was confirmed by GST pull-down and co-immunoprecipitation.\",\n      \"method\": \"GST pull-down, co-immunoprecipitation, ubiquitination assay, ChIP, dual-luciferase reporter assay, xenograft mouse model\",\n      \"journal\": \"Pathology, research and practice\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple biochemical methods including GST pull-down, co-IP, ubiquitination assay, and in vivo validation, single lab\",\n      \"pmids\": [\"40934694\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"RBBP6 ubiquitinates and degrades STAT1, suppressing DPP4 transcription; KMT2B enhances RBBP6 expression through H3K4me3 modification at the RBBP6 promoter. The RBBP6-STAT1 interaction was confirmed by co-immunoprecipitation and GST pull-down.\",\n      \"method\": \"ChIP-re-ChIP assay, co-immunoprecipitation, GST pull-down, ubiquitination assay\",\n      \"journal\": \"Epigenomics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple biochemical methods including ChIP, co-IP, GST pull-down and ubiquitination assay, single lab\",\n      \"pmids\": [\"42011633\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"RBBP6 is a multidomain E3 ubiquitin ligase whose N-terminal DWNN domain adopts a ubiquitin-like fold and directly contacts/activates the CPSF73 endonuclease to enable efficient pre-mRNA 3' cleavage and polyadenylation (recruited to the CPSF complex in an RNA-dependent manner, unlike its constitutive yeast homolog Mpe1); its RING finger/U-box-like domain ubiquitinates multiple substrates including YB-1, ZBTB38 (regulating MCM10 levels and DNA replication fork stability), IκBα (activating NF-κB), ERRα (K48-linked, promoting proteasomal degradation), Bmal1, FOXP3, and STAT1, with K63-linked ubiquitination of CPSF3 stabilizing it for alternative polyadenylation; RBBP6 isoform 3 (DWNN-only) acts as an endogenous competitor that inhibits 3' processing by competing with full-length RBBP6 for the core machinery; RBBP6 also localizes to nucleoli in interphase and to chromosome periphery in mitosis (with >10-fold protein enrichment during mitosis), functions as a co-repressor of estrogen receptor-dependent transcription through interaction with SRC-1/ERα, and restricts viral replication of both Ebola virus (by mimicking NP binding to VP30) and Yellow Fever Virus (by interacting with NS5 polymerase).\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"RBBP6 is a multidomain nuclear protein that couples pre-mRNA 3' end processing to ubiquitin-dependent protein turnover [#15, #10]. Through its N-terminal DWNN domain — a ubiquitin-like fold first defined by NMR [#9] — RBBP6 functions as an essential component of the mRNA 3' cleavage and polyadenylation machinery: it contacts core CPSF subunits including WDR33 and the endonuclease CPSF73/CPSF3 and is required to activate specific, efficient pre-mRNA cleavage; unlike its yeast homolog Mpe1 it is recruited to CPSF in an RNA-dependent manner rather than stably copurifying [#19, #20]. The DWNN-only isoform 3 acts as an endogenous competitor that inhibits 3' processing by competing with full-length RBBP6 for the core machinery, and RBBP6 levels shape poly(A) site choice and the stability of AU-rich transcripts such as c-Fos and c-Jun [#15]. In parallel, RBBP6 is an E3 ubiquitin ligase whose RING finger/U-box-like domain adopts a homodimeric, zinc-coordinating fold [#12] and directs ubiquitination of numerous substrates: it mediates K48-linked degradation of YB-1 [#10], the replication regulator ZBTB38 (controlling MCM10 chromatin loading and replication fork progression) [#14], IκBα to activate NF-κB-driven EMT [#17], ERRα [#22], Bmal1 [#23], FOXP3 [#26], and STAT1 [#27], while K63-linked ubiquitination of CPSF3 stabilizes it to regulate alternative polyadenylation [#21]. RBBP6 localizes to nucleoli in interphase and to the chromosome periphery in mitosis, with protein levels rising over 10-fold during mitosis through post-transcriptional control [#2], and it acts as a co-repressor of estrogen receptor-dependent transcription via SRC-1/ERα [#11]. RBBP6 additionally restricts viral replication, mimicking nucleoprotein binding to Ebola virus VP30 [#16]. The gene family is essential for development across metazoans [#8, #13].\",\n  \"teleology\": [\n    {\n      \"year\": 1995,\n      \"claim\": \"Established the founding interaction that named the gene, placing RBBP6 in the orbit of retinoblastoma tumor-suppressor biology.\",\n      \"evidence\": \"GST pull-down of pRB with E1a competition mapping binding to the Rb pocket domain\",\n      \"pmids\": [\"8595913\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Functional consequence of pRB binding not defined\", \"No cellular pathway linked to the interaction\"]\n    },\n    {\n      \"year\": 1997,\n      \"claim\": \"First implicated RBBP6 in nucleic-acid and RNP biology, hinting at an RNA-associated function later resolved as 3' processing.\",\n      \"evidence\": \"GST fusion binding to ssDNA and recognition by anti-hnRNP antibodies\",\n      \"pmids\": [\"9037032\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No specific RNA target identified\", \"Link to mRNA processing not yet established\"]\n    },\n    {\n      \"year\": 2002,\n      \"claim\": \"Defined the cell-cycle-coupled localization and abundance of RBBP6, showing nucleolar-to-chromosome-periphery relocalization and >10-fold mitotic upregulation indicative of post-transcriptional control.\",\n      \"evidence\": \"Confocal microscopy and Western blot across synchronized mitotic cells; antisense knockdown and overexpression phenotyping\",\n      \"pmids\": [\"12064457\", \"12384997\", \"12553003\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Molecular basis of post-transcriptional regulation unknown\", \"Mechanism connecting localization to mitotic/apoptotic phenotypes unresolved\"]\n    },\n    {\n      \"year\": 2005,\n      \"claim\": \"Began assembling the RBBP6 interactome and its post-translational/translational regulation, linking it to splicing scaffolds and PUM2-mediated control.\",\n      \"evidence\": \"Co-IP with SAF-B and nucleolin, kinase assays, and PUM2 RNA pull-down with RT-PCR\",\n      \"pmids\": [\"12938151\", \"15617101\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"Review-style/single-method evidence not independently confirmed\", \"Functional impact of PUM2 binding on RBBP6 translation untested\"]\n    },\n    {\n      \"year\": 2006,\n      \"claim\": \"Resolved the DWNN domain as a novel ubiquitin-like fold, establishing the structural basis for RBBP6's later-defined roles in ubiquitination and 3' processing.\",\n      \"evidence\": \"Heteronuclear NMR structure of the N-terminal 81 residues\",\n      \"pmids\": [\"16396680\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether DWNN is conjugated like ubiquitin not determined\", \"Binding partners of DWNN not yet mapped\"]\n    },\n    {\n      \"year\": 2008,\n      \"claim\": \"Provided the first direct demonstration that RBBP6 is a functional E3 ligase, identifying YB-1 as a degradation substrate and establishing the RING domain's catalytic role.\",\n      \"evidence\": \"Yeast two-hybrid, in vitro ubiquitination, proteasomal degradation and reporter transactivation assays\",\n      \"pmids\": [\"18851979\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Ubiquitin chain linkage type not defined\", \"Physiological contexts of YB-1 regulation not mapped\"]\n    },\n    {\n      \"year\": 2011,\n      \"claim\": \"Solved the RING/U-box-like domain structure and linked the DWNN to chaperones, framing RBBP6 as a chaperone-associated ubiquitination platform.\",\n      \"evidence\": \"Solution NMR structure with zinc/cadmium substitution and yeast two-hybrid with Hsp70/Hsp40\",\n      \"pmids\": [\"22130672\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Functional role of Hsp70/Hsp40 binding in substrate selection untested\", \"Dimerization requirement for ligase activity not demonstrated\"]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"Connected RBBP6's ligase activity to genome stability and definitively placed it in the mRNA 3' processing complex, unifying its two principal activities.\",\n      \"evidence\": \"shRNA/siRNA knockdown, ubiquitination and DNA fiber assays, in vitro 3' processing reconstitution, co-IP, and genome-wide poly(A) site analysis\",\n      \"pmids\": [\"24726359\", \"25319826\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"How ubiquitination and 3' processing activities are coordinated unclear\", \"Regulation of isoform 3 competition in vivo not defined\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Revealed RBBP6 as a host restriction factor that disrupts Ebola virus transcription by molecular mimicry of viral nucleoprotein.\",\n      \"evidence\": \"AP-MS, domain mapping, X-ray crystallography of the VP30-RBBP6 peptide complex, and viral replication assays\",\n      \"pmids\": [\"30550789\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether antiviral activity requires ligase function unknown\", \"Endogenous cellular role of the mimicry motif not addressed\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Established by reconstitution from purified components that RBBP6 is essential to activate the CPSF73 endonuclease, with RNA-dependent recruitment distinguishing it from yeast Mpe1.\",\n      \"evidence\": \"In vitro reconstitution of 3' cleavage with purified polypeptides, mutagenesis, structural analysis, and co-purification — independently replicated in two studies the same year\",\n      \"pmids\": [\"35177536\", \"35177537\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Atomic-resolution structure of the activated RBBP6-CPSF73 state not yet defined\", \"Regulation of RNA-dependent recruitment unknown\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Expanded the substrate repertoire and disease relevance of RBBP6 ubiquitination, including linkage-specific control of CPSF3 stability governing alternative polyadenylation.\",\n      \"evidence\": \"CRISPR screens, K63- and K48-linkage-specific ubiquitination assays, APA profiling, and conditional mouse models for ERRα and Bmal1\",\n      \"pmids\": [\"38503731\", \"39441040\", \"39501569\", \"39743259\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Determinants of K48 vs K63 linkage choice unresolved\", \"Tissue specificity of substrate selection not mechanistically explained\"]\n    },\n    {\n      \"year\": 2027,\n      \"claim\": \"Continued cataloguing RBBP6 degradation substrates in cancer contexts, linking it to FOXP3 and STAT1 turnover under defined transcriptional regulators.\",\n      \"evidence\": \"GST pull-down, co-IP, ubiquitination assays, ChIP/ChIP-re-ChIP and xenograft models\",\n      \"pmids\": [\"40934694\", \"42011633\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Whether these substrates share a common recognition motif unknown\", \"Reciprocal validation of each interaction limited to single labs\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How RBBP6 partitions its activity between 3' end processing and substrate ubiquitination, and what governs substrate and chain-type selection, remains unresolved.\",\n      \"evidence\": null,\n      \"pmids\": [],\n      \"confidence\": \"High\",\n      \"gaps\": [\"No unifying model coordinating the RNA-processing and E3-ligase functions\", \"No defined degron or recognition logic across the diverse substrate set\", \"Structural basis of RNA-dependent CPSF recruitment not solved\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0016874\", \"supporting_discovery_ids\": [10, 14, 17, 21, 22, 23, 26, 27]},\n      {\"term_id\": \"GO:0140096\", \"supporting_discovery_ids\": [10, 14, 21, 22]},\n      {\"term_id\": \"GO:0140098\", \"supporting_discovery_ids\": [15, 19, 20]},\n      {\"term_id\": \"GO:0003723\", \"supporting_discovery_ids\": [1, 15, 19]},\n      {\"term_id\": \"GO:0140110\", \"supporting_discovery_ids\": [11]},\n      {\"term_id\": \"GO:0031386\", \"supporting_discovery_ids\": [9]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005730\", \"supporting_discovery_ids\": [2]},\n      {\"term_id\": \"GO:0005694\", \"supporting_discovery_ids\": [2]},\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [2, 14, 15]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-8953854\", \"supporting_discovery_ids\": [15, 19, 20, 21]},\n      {\"term_id\": \"R-HSA-392499\", \"supporting_discovery_ids\": [10, 14, 22, 26, 27]},\n      {\"term_id\": \"R-HSA-74160\", \"supporting_discovery_ids\": [11, 17]},\n      {\"term_id\": \"R-HSA-69306\", \"supporting_discovery_ids\": [14]},\n      {\"term_id\": \"R-HSA-1643685\", \"supporting_discovery_ids\": [16, 17, 22, 26]}\n    ],\n    \"complexes\": [\n      \"mRNA 3' cleavage and polyadenylation complex (CPSF)\"\n    ],\n    \"partners\": [\n      \"CPSF3\",\n      \"WDR33\",\n      \"YB-1\",\n      \"ZBTB38\",\n      \"ERRA\",\n      \"FOXP3\",\n      \"STAT1\",\n      \"SRC-1\"\n    ],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":7,"faith_total":7,"faith_pct":100.0}}