{"gene":"BIN3","run_date":"2026-06-09T22:02:44","timeline":{"discoveries":[{"year":2001,"finding":"Human BIN3 is a BAR adaptor protein homologous to yeast RVS161/Hob3p that regulates F-actin localization; expression of BIN3 in S. pombe hob3Δ mutants completely rescued F-actin localization defects (mislocalized patches and absent medial F-actin rings), establishing a conserved role in actin organization.","method":"Genetic complementation of S. pombe hob3Δ mutants with human BIN3; fluorescence microscopy of F-actin localization","journal":"The Journal of biological chemistry","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct complementation rescue with clear phenotypic readout, single lab, two orthogonal methods (genetics + imaging)","pmids":["11274158"],"is_preprint":false},{"year":2007,"finding":"Hob3p (S. pombe ortholog of human BIN3) directly interacts with Cdc42p and forms a complex with the GEF Gef1p; Hob3p facilitates Gef1p-Cdc42p interaction and Cdc42p activation, recruits Cdc42p to the division site, and is required for actomyosin ring contraction and cytokinesis. Human Bin3 partially rescued GTP-Cdc42p levels and Cdc42p localization in hob3Δ cells, indicating functional conservation.","method":"Two-hybrid screening, co-immunoprecipitation, fluorescence localization, FRAP/live imaging of actomyosin ring contraction, genetic complementation with human BIN3, GTP-Cdc42p pull-down assay","journal":"The EMBO journal","confidence":"High","confidence_rationale":"Tier 2 / Strong — multiple orthogonal methods (Y2H, Co-IP, live imaging, biochemical GTPase assay, complementation), independently consistent results in single rigorous study","pmids":["17363901"],"is_preprint":false},{"year":2008,"finding":"Homozygous deletion of Bin3 in mice causes loss of F-actin in lens fiber cells (but not epithelial cells), leading to cataract formation with vacuoles in cortical fibers; Bin3 loss also increases proliferation and invasive motility of SV40-large-T/Ras-transformed cells, while not affecting normal proliferation or F-actin organization, establishing Bin3 as a regulator of F-actin in lens and a suppressor of transformed-cell invasiveness.","method":"Bin3 knockout mouse; histology and fluorescence microscopy of lens F-actin; invasion and proliferation assays in transformed cells","journal":"Cancer research","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — clean genetic knockout with defined phenotypic readout, single lab, multiple cellular assays","pmids":["18339847"],"is_preprint":false},{"year":2011,"finding":"Drosophila Bin3 is required for repression of caudal mRNA translation; bin3 mutant embryos show elevated Caudal protein levels and head involution defects. Mechanistically, Bin3 co-immunoprecipitates with 7SK RNA; 7SK RNA is present in Bicoid complexes; Bin3 loss causes severe reduction of 7SK RNA levels and reduced Bicoid binding to the caudal 3' UTR. Genetic interactions with bicoid, eIF4E, Larp1, PABP, and Ago2 support a model where Bin3 stabilizes 7SK RNA to promote assembly of a repressive RNP on the caudal 3' UTR blocking translation initiation.","method":"Drosophila genetics (bin3 loss-of-function mutants), immunostaining for Caudal protein, RNA immunoprecipitation (co-IP of 7SK with Bin3), Northern blot for 7SK RNA levels, genetic epistasis with eIF4E/Larp1/PABP/Ago2","journal":"Developmental biology","confidence":"High","confidence_rationale":"Tier 2 / Strong — in vivo genetic loss-of-function combined with RNA co-IP, RNA quantification, and genetic epistasis across multiple partner genes in a single rigorous study","pmids":["21262214"],"is_preprint":false},{"year":2012,"finding":"The mammalian Bin3 ortholog MePCE (BCDIN3) methylates the γ-phosphate of the 5' guanosine of 7SK RNA using S-adenosyl methionine, generating an unusual methyl-phosphate cap that protects 7SK RNA from degradation; 7SK RNA then scaffolds an RNP complex that sequesters P-TEFb (positive transcription elongation factor b) to repress RNA Pol II elongation.","method":"Review synthesizing in vitro methyltransferase assays and biochemical reconstitution data from primary literature; enzymatic activity with SAM substrate","journal":"Wiley interdisciplinary reviews. RNA","confidence":"Medium","confidence_rationale":"Tier 1 / Moderate — review synthesizing in vitro enzymatic reconstitution data; moderate because this paper itself is a review, but the underlying biochemistry is well established","pmids":["22740346"],"is_preprint":false},{"year":2013,"finding":"During myogenesis, mouse Bin3 (N-BAR domain protein) co-localizes with F-actin in lamellipodia of differentiating muscle cells and forms a complex with Rho GTPases Rac1 and Cdc42; Bin3 is a major regulator of Rac1 and Cdc42 activity in differentiated muscle cells, promoting myoblast migration and controlling myofiber size in vitro and in vivo.","method":"Bin3 loss-of-function in mouse myogenesis (siRNA/genetic); co-immunoprecipitation of Bin3 with Rac1 and Cdc42; fluorescence co-localization with F-actin; GTPase activity assays; in vivo myofiber size measurement","journal":"Developmental biology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP, GTPase activity assay, in vivo genetics, and imaging in single lab study","pmids":["23872330"],"is_preprint":false},{"year":2022,"finding":"In EGFR-amplified glioblastoma, ligand-activated EGFR upregulates BIN3, which suppresses tumor invasion by inhibiting a DOCK7-regulated Rho GTPase pathway; this BIN3-dependent suppression of invasion can be activated therapeutically by tofacitinib (which increases EGFR ligand levels and upregulates BIN3).","method":"Orthotopic glioblastoma mouse models; BIN3 overexpression/knockdown; invasion assays; signaling pathway analysis (DOCK7, Rho GTPase activity); tofacitinib pharmacological treatment","journal":"Nature cell biology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — in vivo orthotopic models plus pathway epistasis and pharmacological intervention, single lab","pmids":["35915159"],"is_preprint":false},{"year":2022,"finding":"In S. pombe, the Bin3/MePCE ortholog Bmc1 is a stable component of the telomerase holoenzyme; Bmc1 associates with telomerase and U6 snRNA via an interaction with the LARP7-family protein Pof8, promotes TER1 (telomerase RNA) accumulation and Pof8 recruitment to TER1, and facilitates telomerase holoenzyme assembly. This association is independent of Bmc1's methyltransferase catalytic activity.","method":"Affinity purification of telomerase components; co-immunoprecipitation; genetic analysis of bmc1 mutants (methyltransferase-dead and deletion); telomere length assays; RNA accumulation assays","journal":"Nature communications","confidence":"High","confidence_rationale":"Tier 2 / Strong — two independent labs (PMIDs 35217638 and 35277511) using affinity purification, Co-IP, catalytic mutants, and functional telomere assays independently establish the same conclusion","pmids":["35217638","35277511"],"is_preprint":false},{"year":2023,"finding":"Drosophila Bin3 and mammalian MePCE function as U6 snRNA capping enzymes; a 'Bin3-Box' domain present only in enzymes associated with 7SK regulation (not U6 biology) was identified by sequence analysis, and targeted mutagenesis of this domain confirmed its importance for Bin3 function in 7SK (but not U6) biology, revealing a division of labor between the two capping activities.","method":"Drosophila genetics; hybrid Amus-MePCE protein rescue experiments; targeted mutagenesis of Bin3-Box domain; RNA stability assays for U6 and 7SK snRNAs; human cell MePCE loss-of-function","journal":"Science advances","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct mutagenesis plus genetic rescue in multiple organisms, single study with multiple orthogonal approaches","pmids":["38100593"],"is_preprint":false},{"year":2024,"finding":"The catalytic methyltransferase activity of Drosophila Bin3 is dispensable for 7SK snRNP function in vivo: a catalytic-dead mutant (Bin3Y795A) still binds and stabilizes 7SK RNA and rescues all bin3 mutant phenotypes (reduced egg-laying, neuromuscular defects). Furthermore, Bin3 represses P-TEFb activity in vivo (genetic reduction of P-TEFb rescues bin3 mutant phenotypes). A metazoan-specific motif (MSM) outside the methyltransferase domain is required for a 7SK-independent, tissue-specific function of Bin3.","method":"Drosophila genetics; catalytic-dead point mutant (Bin3Y795A) rescue experiments; P-TEFb genetic epistasis; Bin3ΔMSM deletion mutant analysis; RNA binding/stabilization assays","journal":"Genetics","confidence":"High","confidence_rationale":"Tier 1–2 / Strong — active-site mutagenesis combined with in vivo genetic epistasis and domain-deletion analysis in a single rigorous study, peer-reviewed","pmids":["37982586"],"is_preprint":false}],"current_model":"BIN3/MePCE is a conserved BAR-domain and RNA methyltransferase protein with dual mechanistic roles: (1) as a methyl-phosphate capping enzyme that binds and stabilizes 7SK snRNA (using SAM to cap its 5' γ-phosphate), thereby scaffolding a repressive RNP complex that sequesters P-TEFb and represses RNA Pol II elongation—though catalytic activity is dispensable for 7SK stability in vivo, with a non-catalytic scaffold function and a distinct metazoan-specific motif (MSM) being critical; and (2) as a BAR-domain adaptor that recruits and activates Rho GTPases (Cdc42, Rac1) at sites of cell division and in actin-dependent processes such as cytokinesis, myogenesis, and invasion suppression, acting upstream of DOCK7-Rho GTPase signaling; in fission yeast, the ortholog Bmc1/Bin3 is additionally a stable component of the telomerase holoenzyme, promoting telomerase RNA accumulation and holoenzyme assembly independently of its methyltransferase activity."},"narrative":{"mechanistic_narrative":"BIN3 (MePCE/BCDIN3) is a dual-function protein that combines an RNA 5'-cap methyltransferase activity with a BAR-domain cytoskeletal adaptor role, linking transcriptional control to actin-dependent cell behavior [PMID:17363901, PMID:22740346]. As a methyl-phosphate capping enzyme it methylates the γ-phosphate of the 5' guanosine of 7SK snRNA using S-adenosyl methionine, generating a cap that protects 7SK and scaffolds the repressive RNP that sequesters P-TEFb to restrain RNA Pol II elongation [PMID:22740346], and it likewise caps U6 snRNA, with a dedicated 'Bin3-Box' domain partitioning the 7SK-specific function from U6 biology [PMID:38100593]. The catalytic activity itself is dispensable in vivo for 7SK binding, stabilization, and P-TEFb repression: a catalytic-dead Bin3 still stabilizes 7SK and rescues mutant phenotypes, and a separate metazoan-specific motif drives a 7SK-independent tissue function [PMID:37982586]. In its second role, BIN3 acts as a BAR adaptor that binds and activates the Rho GTPases Cdc42 and Rac1 — facilitating GEF (Gef1p)-Cdc42 interaction and Cdc42 recruitment to the division site for actomyosin ring contraction and cytokinesis [PMID:17363901], regulating F-actin in lens fiber cells and myoblast migration/myofiber size [PMID:18339847, PMID:23872330], and suppressing tumor cell invasion through inhibition of a DOCK7-regulated Rho GTPase pathway downstream of EGFR signaling [PMID:35915159]. The fission yeast ortholog Bmc1/Bin3 additionally serves as a stable, catalysis-independent component of the telomerase holoenzyme, promoting telomerase RNA accumulation via the LARP7-family protein Pof8 [PMID:35217638, PMID:35277511]. A Drosophila role in repressing caudal mRNA translation through 7SK-dependent RNP assembly extends its developmental functions [PMID:21262214].","teleology":[{"year":2001,"claim":"Established that human BIN3 is a functionally conserved BAR adaptor governing F-actin organization, by showing it could substitute for a yeast ortholog.","evidence":"Genetic complementation of S. pombe hob3Δ mutants with human BIN3 plus F-actin imaging","pmids":["11274158"],"confidence":"Medium","gaps":["Did not identify the direct molecular partners through which BIN3 organizes actin","No mammalian-cell mechanism defined"]},{"year":2007,"claim":"Connected BIN3's actin role to a specific molecular mechanism — recruitment and activation of Cdc42 via a GEF — resolving how the BAR adaptor drives cytokinesis.","evidence":"Y2H, Co-IP, live imaging of actomyosin ring, GTP-Cdc42 pull-down, and human BIN3 complementation in S. pombe","pmids":["17363901"],"confidence":"High","gaps":["Direct vs. GEF-bridged nature of the Cdc42 interaction in mammalian cells not resolved","Structural basis of the Hob3p-Gef1p-Cdc42 complex unknown"]},{"year":2008,"claim":"Demonstrated a physiological, tissue-selective requirement for Bin3 in F-actin maintenance and revealed an invasion-suppressor role, distinguishing its functions in normal vs. transformed cells.","evidence":"Bin3 knockout mouse, lens histology/F-actin imaging, invasion and proliferation assays in transformed cells","pmids":["18339847"],"confidence":"Medium","gaps":["Molecular basis for tissue selectivity (lens fiber vs. epithelial) unexplained","Did not link the invasion phenotype to a defined signaling pathway"]},{"year":2011,"claim":"Revealed a wholly separate, RNA-based function: Bin3 stabilizes 7SK RNA to assemble a repressive RNP controlling caudal mRNA translation in development.","evidence":"Drosophila bin3 mutants, RNA co-IP of 7SK, Northern blot quantification, and genetic epistasis with bicoid/eIF4E/Larp1/PABP/Ago2","pmids":["21262214"],"confidence":"High","gaps":["Did not establish whether 7SK stabilization requires catalytic methylation","Direct interaction map within the repressive RNP not resolved"]},{"year":2012,"claim":"Defined the enzymatic basis of 7SK stabilization — γ-phosphate methylation generating a protective methyl-phosphate cap that scaffolds P-TEFb sequestration.","evidence":"Review synthesizing in vitro methyltransferase assays with SAM substrate and biochemical reconstitution","pmids":["22740346"],"confidence":"Medium","gaps":["Synthesizes prior biochemistry rather than presenting new primary data","In vivo requirement of the cap for function not tested here"]},{"year":2013,"claim":"Extended the Rho GTPase adaptor role to mammalian myogenesis, showing Bin3 controls both Rac1 and Cdc42 activity to drive myoblast migration and myofiber size.","evidence":"Bin3 loss-of-function in mouse myogenesis, Co-IP with Rac1/Cdc42, F-actin co-localization, GTPase assays, in vivo myofiber measurement","pmids":["23872330"],"confidence":"Medium","gaps":["Whether Bin3 acts via a GEF in muscle, as in yeast, not established","Direct vs. indirect Rac1/Cdc42 binding not distinguished"]},{"year":2022,"claim":"Placed BIN3's invasion-suppressor activity in a defined signaling axis downstream of EGFR and upstream of DOCK7-Rho GTPase signaling, and showed it is pharmacologically actionable.","evidence":"Orthotopic glioblastoma models, BIN3 gain/loss, invasion and Rho GTPase pathway analysis, tofacitinib treatment","pmids":["35915159"],"confidence":"Medium","gaps":["Direct molecular link between BIN3 and DOCK7 not biochemically defined","Relationship to BIN3's 7SK/RNA function untested"]},{"year":2022,"claim":"Uncovered a catalysis-independent scaffolding function for the ortholog Bmc1 within the telomerase holoenzyme, broadening the protein's RNP-assembly roles beyond 7SK.","evidence":"Affinity purification and Co-IP of telomerase components, methyltransferase-dead and deletion mutants, telomere length and TER1 accumulation assays in S. pombe (two independent labs)","pmids":["35217638","35277511"],"confidence":"High","gaps":["Whether mammalian MePCE has an analogous telomerase role unknown","Structural basis of Bmc1-Pof8-TER1 assembly not resolved"]},{"year":2023,"claim":"Resolved a division of labor between BIN3's two capping activities by identifying a 'Bin3-Box' domain specifically required for 7SK, not U6, biology.","evidence":"Drosophila genetics, hybrid Amus-MePCE rescue, Bin3-Box mutagenesis, U6/7SK stability assays, human-cell MePCE loss-of-function","pmids":["38100593"],"confidence":"Medium","gaps":["Mechanism by which the Bin3-Box confers 7SK specificity unknown","Structural definition of the domain not provided"]},{"year":2024,"claim":"Demonstrated that methyltransferase catalysis is dispensable in vivo — BIN3 stabilizes 7SK and represses P-TEFb as a non-catalytic scaffold — and identified a metazoan-specific motif driving a 7SK-independent function.","evidence":"Drosophila catalytic-dead Bin3Y795A rescue, P-TEFb genetic epistasis, Bin3ΔMSM deletion analysis, RNA binding/stabilization assays","pmids":["37982586"],"confidence":"High","gaps":["Identity of the 7SK-independent MSM-dependent function not defined","How a catalytically dead enzyme retains the protective cap function mechanistically unexplained"]},{"year":null,"claim":"It remains unresolved how BIN3's RNA-capping/RNP-scaffolding functions and its BAR-domain Rho GTPase adaptor functions are integrated within a single protein and coordinated in mammalian cells.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No structural model linking the methyltransferase, Bin3-Box, MSM, and BAR domains","Whether the two activities are spatially or temporally separated within a cell is unknown","Direct mammalian DOCK7 and Rho GTPase binding interfaces undefined"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0140098","term_label":"catalytic activity, acting on RNA","supporting_discovery_ids":[4,8]},{"term_id":"GO:0003723","term_label":"RNA binding","supporting_discovery_ids":[3,9]},{"term_id":"GO:0016740","term_label":"transferase activity","supporting_discovery_ids":[4]},{"term_id":"GO:0008092","term_label":"cytoskeletal protein binding","supporting_discovery_ids":[0,1,5]},{"term_id":"GO:0098772","term_label":"molecular function regulator activity","supporting_discovery_ids":[1,6]},{"term_id":"GO:0060090","term_label":"molecular adaptor activity","supporting_discovery_ids":[1,7]}],"localization":[{"term_id":"GO:0005856","term_label":"cytoskeleton","supporting_discovery_ids":[0,2,5]},{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[4]}],"pathway":[{"term_id":"R-HSA-74160","term_label":"Gene expression (Transcription)","supporting_discovery_ids":[4]},{"term_id":"R-HSA-8953854","term_label":"Metabolism of RNA","supporting_discovery_ids":[4,8]},{"term_id":"R-HSA-162582","term_label":"Signal Transduction","supporting_discovery_ids":[1,5,6]},{"term_id":"R-HSA-1640170","term_label":"Cell Cycle","supporting_discovery_ids":[1]},{"term_id":"R-HSA-1266738","term_label":"Developmental Biology","supporting_discovery_ids":[2,3,5]},{"term_id":"R-HSA-1643685","term_label":"Disease","supporting_discovery_ids":[6]}],"complexes":["7SK snRNP","telomerase holoenzyme"],"partners":["CDC42","RAC1","GEF1P","POF8","DOCK7","7SK RNA"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q9NQY0","full_name":"Bridging integrator 3","aliases":[],"length_aa":253,"mass_kda":29.7,"function":"Involved in cytokinesis and septation where it has a role in the localization of F-actin","subcellular_location":"Cytoplasm, cytoskeleton","url":"https://www.uniprot.org/uniprotkb/Q9NQY0/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/BIN3","classification":"Not Classified","n_dependent_lines":0,"n_total_lines":1208,"dependency_fraction":0.0},"opencell":{"profiled":true,"resolved_as":"","ensg_id":"ENSG00000147439","cell_line_id":"CID000668","localizations":[{"compartment":"cytoplasmic","grade":3}],"interactors":[{"gene":"DNMBP","stoichiometry":10.0},{"gene":"TJP2","stoichiometry":0.2},{"gene":"TOP1","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/target/CID000668","total_profiled":1310},"omim":[{"mim_id":"611478","title":"METHYLPHOSPHATE CAPPING ENZYME; MEPCE","url":"https://www.omim.org/entry/611478"},{"mim_id":"606396","title":"BRIDGING INTEGRATOR 3; BIN3","url":"https://www.omim.org/entry/606396"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"","locations":[],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/BIN3"},"hgnc":{"alias_symbol":[],"prev_symbol":[]},"alphafold":{"accession":"Q9NQY0","domains":[{"cath_id":"1.20.1270.60","chopping":"17-122_179-222","consensus_level":"high","plddt":96.6457,"start":17,"end":222}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9NQY0","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q9NQY0-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q9NQY0-F1-predicted_aligned_error_v6.png","plddt_mean":92.75},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=BIN3","jax_strain_url":"https://www.jax.org/strain/search?query=BIN3"},"sequence":{"accession":"Q9NQY0","fasta_url":"https://rest.uniprot.org/uniprotkb/Q9NQY0.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q9NQY0/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9NQY0"}},"corpus_meta":[{"pmid":"35915159","id":"PMC_35915159","title":"EGFR ligand shifts the role of EGFR from oncogene to tumour suppressor in EGFR-amplified glioblastoma by suppressing invasion through BIN3 upregulation.","date":"2022","source":"Nature cell biology","url":"https://pubmed.ncbi.nlm.nih.gov/35915159","citation_count":33,"is_preprint":false},{"pmid":"17363901","id":"PMC_17363901","title":"Hob3p, the fission yeast ortholog of human BIN3, localizes Cdc42p to the division site and regulates cytokinesis.","date":"2007","source":"The EMBO journal","url":"https://pubmed.ncbi.nlm.nih.gov/17363901","citation_count":32,"is_preprint":false},{"pmid":"22740346","id":"PMC_22740346","title":"The Bin3 RNA methyltransferase targets 7SK RNA to control transcription and translation.","date":"2012","source":"Wiley interdisciplinary reviews. RNA","url":"https://pubmed.ncbi.nlm.nih.gov/22740346","citation_count":27,"is_preprint":false},{"pmid":"23872330","id":"PMC_23872330","title":"The N-BAR domain protein, Bin3, regulates Rac1- and Cdc42-dependent processes in myogenesis.","date":"2013","source":"Developmental biology","url":"https://pubmed.ncbi.nlm.nih.gov/23872330","citation_count":25,"is_preprint":false},{"pmid":"18339847","id":"PMC_18339847","title":"Bin3 deletion causes cataracts and increased susceptibility to lymphoma during aging.","date":"2008","source":"Cancer research","url":"https://pubmed.ncbi.nlm.nih.gov/18339847","citation_count":25,"is_preprint":false},{"pmid":"11274158","id":"PMC_11274158","title":"Human BIN3 complements the F-actin localization defects caused by loss of Hob3p, the fission yeast homolog of Rvs161p.","date":"2001","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/11274158","citation_count":24,"is_preprint":false},{"pmid":"21262214","id":"PMC_21262214","title":"The Bin3 RNA methyltransferase is required for repression of caudal translation in the Drosophila embryo.","date":"2011","source":"Developmental biology","url":"https://pubmed.ncbi.nlm.nih.gov/21262214","citation_count":22,"is_preprint":false},{"pmid":"35217638","id":"PMC_35217638","title":"A putative cap binding protein and the methyl phosphate capping enzyme Bin3/MePCE function in telomerase biogenesis.","date":"2022","source":"Nature communications","url":"https://pubmed.ncbi.nlm.nih.gov/35217638","citation_count":11,"is_preprint":false},{"pmid":"35277511","id":"PMC_35277511","title":"The methyl phosphate capping enzyme Bmc1/Bin3 is a stable component of the fission yeast telomerase holoenzyme.","date":"2022","source":"Nature communications","url":"https://pubmed.ncbi.nlm.nih.gov/35277511","citation_count":11,"is_preprint":false},{"pmid":"38100593","id":"PMC_38100593","title":"Drosophila Amus and Bin3 methylases functionally replace mammalian MePCE for capping and the stabilization of U6 and 7SK snRNAs.","date":"2023","source":"Science advances","url":"https://pubmed.ncbi.nlm.nih.gov/38100593","citation_count":3,"is_preprint":false},{"pmid":"37982586","id":"PMC_37982586","title":"Catalytic activity of the Bin3/MePCE methyltransferase domain is dispensable for 7SK snRNP function in Drosophila melanogaster.","date":"2024","source":"Genetics","url":"https://pubmed.ncbi.nlm.nih.gov/37982586","citation_count":2,"is_preprint":false},{"pmid":"37333392","id":"PMC_37333392","title":"Catalytic activity of the Bin3/MEPCE methyltransferase domain is dispensable for 7SK snRNP function in Drosophila melanogaster.","date":"2023","source":"bioRxiv : the preprint server for biology","url":"https://pubmed.ncbi.nlm.nih.gov/37333392","citation_count":1,"is_preprint":false},{"pmid":null,"id":"bio_10.1101_2025.10.10.25337775","title":"Long-read genome sequencing and multi-omics in aging and neurodegeneration","date":"2025-10-13","source":"bioRxiv","url":"https://doi.org/10.1101/2025.10.10.25337775","citation_count":0,"is_preprint":true}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":8247,"output_tokens":3184,"usd":0.03625,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":10594,"output_tokens":4014,"usd":0.07666,"stage2_stop_reason":"end_turn"},"total_usd":0.11291,"stage1_batch_id":"msgbatch_0179Z2pxRYBsXi2xADneafRw","stage2_batch_id":"msgbatch_01LaY9ZaVdgjWArcZo9eqQE5","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2001,\n      \"finding\": \"Human BIN3 is a BAR adaptor protein homologous to yeast RVS161/Hob3p that regulates F-actin localization; expression of BIN3 in S. pombe hob3Δ mutants completely rescued F-actin localization defects (mislocalized patches and absent medial F-actin rings), establishing a conserved role in actin organization.\",\n      \"method\": \"Genetic complementation of S. pombe hob3Δ mutants with human BIN3; fluorescence microscopy of F-actin localization\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct complementation rescue with clear phenotypic readout, single lab, two orthogonal methods (genetics + imaging)\",\n      \"pmids\": [\"11274158\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2007,\n      \"finding\": \"Hob3p (S. pombe ortholog of human BIN3) directly interacts with Cdc42p and forms a complex with the GEF Gef1p; Hob3p facilitates Gef1p-Cdc42p interaction and Cdc42p activation, recruits Cdc42p to the division site, and is required for actomyosin ring contraction and cytokinesis. Human Bin3 partially rescued GTP-Cdc42p levels and Cdc42p localization in hob3Δ cells, indicating functional conservation.\",\n      \"method\": \"Two-hybrid screening, co-immunoprecipitation, fluorescence localization, FRAP/live imaging of actomyosin ring contraction, genetic complementation with human BIN3, GTP-Cdc42p pull-down assay\",\n      \"journal\": \"The EMBO journal\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — multiple orthogonal methods (Y2H, Co-IP, live imaging, biochemical GTPase assay, complementation), independently consistent results in single rigorous study\",\n      \"pmids\": [\"17363901\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2008,\n      \"finding\": \"Homozygous deletion of Bin3 in mice causes loss of F-actin in lens fiber cells (but not epithelial cells), leading to cataract formation with vacuoles in cortical fibers; Bin3 loss also increases proliferation and invasive motility of SV40-large-T/Ras-transformed cells, while not affecting normal proliferation or F-actin organization, establishing Bin3 as a regulator of F-actin in lens and a suppressor of transformed-cell invasiveness.\",\n      \"method\": \"Bin3 knockout mouse; histology and fluorescence microscopy of lens F-actin; invasion and proliferation assays in transformed cells\",\n      \"journal\": \"Cancer research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — clean genetic knockout with defined phenotypic readout, single lab, multiple cellular assays\",\n      \"pmids\": [\"18339847\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"Drosophila Bin3 is required for repression of caudal mRNA translation; bin3 mutant embryos show elevated Caudal protein levels and head involution defects. Mechanistically, Bin3 co-immunoprecipitates with 7SK RNA; 7SK RNA is present in Bicoid complexes; Bin3 loss causes severe reduction of 7SK RNA levels and reduced Bicoid binding to the caudal 3' UTR. Genetic interactions with bicoid, eIF4E, Larp1, PABP, and Ago2 support a model where Bin3 stabilizes 7SK RNA to promote assembly of a repressive RNP on the caudal 3' UTR blocking translation initiation.\",\n      \"method\": \"Drosophila genetics (bin3 loss-of-function mutants), immunostaining for Caudal protein, RNA immunoprecipitation (co-IP of 7SK with Bin3), Northern blot for 7SK RNA levels, genetic epistasis with eIF4E/Larp1/PABP/Ago2\",\n      \"journal\": \"Developmental biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — in vivo genetic loss-of-function combined with RNA co-IP, RNA quantification, and genetic epistasis across multiple partner genes in a single rigorous study\",\n      \"pmids\": [\"21262214\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"The mammalian Bin3 ortholog MePCE (BCDIN3) methylates the γ-phosphate of the 5' guanosine of 7SK RNA using S-adenosyl methionine, generating an unusual methyl-phosphate cap that protects 7SK RNA from degradation; 7SK RNA then scaffolds an RNP complex that sequesters P-TEFb (positive transcription elongation factor b) to repress RNA Pol II elongation.\",\n      \"method\": \"Review synthesizing in vitro methyltransferase assays and biochemical reconstitution data from primary literature; enzymatic activity with SAM substrate\",\n      \"journal\": \"Wiley interdisciplinary reviews. RNA\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — review synthesizing in vitro enzymatic reconstitution data; moderate because this paper itself is a review, but the underlying biochemistry is well established\",\n      \"pmids\": [\"22740346\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"During myogenesis, mouse Bin3 (N-BAR domain protein) co-localizes with F-actin in lamellipodia of differentiating muscle cells and forms a complex with Rho GTPases Rac1 and Cdc42; Bin3 is a major regulator of Rac1 and Cdc42 activity in differentiated muscle cells, promoting myoblast migration and controlling myofiber size in vitro and in vivo.\",\n      \"method\": \"Bin3 loss-of-function in mouse myogenesis (siRNA/genetic); co-immunoprecipitation of Bin3 with Rac1 and Cdc42; fluorescence co-localization with F-actin; GTPase activity assays; in vivo myofiber size measurement\",\n      \"journal\": \"Developmental biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP, GTPase activity assay, in vivo genetics, and imaging in single lab study\",\n      \"pmids\": [\"23872330\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"In EGFR-amplified glioblastoma, ligand-activated EGFR upregulates BIN3, which suppresses tumor invasion by inhibiting a DOCK7-regulated Rho GTPase pathway; this BIN3-dependent suppression of invasion can be activated therapeutically by tofacitinib (which increases EGFR ligand levels and upregulates BIN3).\",\n      \"method\": \"Orthotopic glioblastoma mouse models; BIN3 overexpression/knockdown; invasion assays; signaling pathway analysis (DOCK7, Rho GTPase activity); tofacitinib pharmacological treatment\",\n      \"journal\": \"Nature cell biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — in vivo orthotopic models plus pathway epistasis and pharmacological intervention, single lab\",\n      \"pmids\": [\"35915159\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"In S. pombe, the Bin3/MePCE ortholog Bmc1 is a stable component of the telomerase holoenzyme; Bmc1 associates with telomerase and U6 snRNA via an interaction with the LARP7-family protein Pof8, promotes TER1 (telomerase RNA) accumulation and Pof8 recruitment to TER1, and facilitates telomerase holoenzyme assembly. This association is independent of Bmc1's methyltransferase catalytic activity.\",\n      \"method\": \"Affinity purification of telomerase components; co-immunoprecipitation; genetic analysis of bmc1 mutants (methyltransferase-dead and deletion); telomere length assays; RNA accumulation assays\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — two independent labs (PMIDs 35217638 and 35277511) using affinity purification, Co-IP, catalytic mutants, and functional telomere assays independently establish the same conclusion\",\n      \"pmids\": [\"35217638\", \"35277511\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"Drosophila Bin3 and mammalian MePCE function as U6 snRNA capping enzymes; a 'Bin3-Box' domain present only in enzymes associated with 7SK regulation (not U6 biology) was identified by sequence analysis, and targeted mutagenesis of this domain confirmed its importance for Bin3 function in 7SK (but not U6) biology, revealing a division of labor between the two capping activities.\",\n      \"method\": \"Drosophila genetics; hybrid Amus-MePCE protein rescue experiments; targeted mutagenesis of Bin3-Box domain; RNA stability assays for U6 and 7SK snRNAs; human cell MePCE loss-of-function\",\n      \"journal\": \"Science advances\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct mutagenesis plus genetic rescue in multiple organisms, single study with multiple orthogonal approaches\",\n      \"pmids\": [\"38100593\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"The catalytic methyltransferase activity of Drosophila Bin3 is dispensable for 7SK snRNP function in vivo: a catalytic-dead mutant (Bin3Y795A) still binds and stabilizes 7SK RNA and rescues all bin3 mutant phenotypes (reduced egg-laying, neuromuscular defects). Furthermore, Bin3 represses P-TEFb activity in vivo (genetic reduction of P-TEFb rescues bin3 mutant phenotypes). A metazoan-specific motif (MSM) outside the methyltransferase domain is required for a 7SK-independent, tissue-specific function of Bin3.\",\n      \"method\": \"Drosophila genetics; catalytic-dead point mutant (Bin3Y795A) rescue experiments; P-TEFb genetic epistasis; Bin3ΔMSM deletion mutant analysis; RNA binding/stabilization assays\",\n      \"journal\": \"Genetics\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Strong — active-site mutagenesis combined with in vivo genetic epistasis and domain-deletion analysis in a single rigorous study, peer-reviewed\",\n      \"pmids\": [\"37982586\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"BIN3/MePCE is a conserved BAR-domain and RNA methyltransferase protein with dual mechanistic roles: (1) as a methyl-phosphate capping enzyme that binds and stabilizes 7SK snRNA (using SAM to cap its 5' γ-phosphate), thereby scaffolding a repressive RNP complex that sequesters P-TEFb and represses RNA Pol II elongation—though catalytic activity is dispensable for 7SK stability in vivo, with a non-catalytic scaffold function and a distinct metazoan-specific motif (MSM) being critical; and (2) as a BAR-domain adaptor that recruits and activates Rho GTPases (Cdc42, Rac1) at sites of cell division and in actin-dependent processes such as cytokinesis, myogenesis, and invasion suppression, acting upstream of DOCK7-Rho GTPase signaling; in fission yeast, the ortholog Bmc1/Bin3 is additionally a stable component of the telomerase holoenzyme, promoting telomerase RNA accumulation and holoenzyme assembly independently of its methyltransferase activity.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"BIN3 (MePCE/BCDIN3) is a dual-function protein that combines an RNA 5'-cap methyltransferase activity with a BAR-domain cytoskeletal adaptor role, linking transcriptional control to actin-dependent cell behavior [#1, #4]. As a methyl-phosphate capping enzyme it methylates the γ-phosphate of the 5' guanosine of 7SK snRNA using S-adenosyl methionine, generating a cap that protects 7SK and scaffolds the repressive RNP that sequesters P-TEFb to restrain RNA Pol II elongation [#4], and it likewise caps U6 snRNA, with a dedicated 'Bin3-Box' domain partitioning the 7SK-specific function from U6 biology [#8]. The catalytic activity itself is dispensable in vivo for 7SK binding, stabilization, and P-TEFb repression: a catalytic-dead Bin3 still stabilizes 7SK and rescues mutant phenotypes, and a separate metazoan-specific motif drives a 7SK-independent tissue function [#9]. In its second role, BIN3 acts as a BAR adaptor that binds and activates the Rho GTPases Cdc42 and Rac1 — facilitating GEF (Gef1p)-Cdc42 interaction and Cdc42 recruitment to the division site for actomyosin ring contraction and cytokinesis [#1], regulating F-actin in lens fiber cells and myoblast migration/myofiber size [#2, #5], and suppressing tumor cell invasion through inhibition of a DOCK7-regulated Rho GTPase pathway downstream of EGFR signaling [#6]. The fission yeast ortholog Bmc1/Bin3 additionally serves as a stable, catalysis-independent component of the telomerase holoenzyme, promoting telomerase RNA accumulation via the LARP7-family protein Pof8 [#7]. A Drosophila role in repressing caudal mRNA translation through 7SK-dependent RNP assembly extends its developmental functions [#3].\"\n,\n  \"teleology\": [\n    {\n      \"year\": 2001,\n      \"claim\": \"Established that human BIN3 is a functionally conserved BAR adaptor governing F-actin organization, by showing it could substitute for a yeast ortholog.\",\n      \"evidence\": \"Genetic complementation of S. pombe hob3Δ mutants with human BIN3 plus F-actin imaging\",\n      \"pmids\": [\"11274158\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Did not identify the direct molecular partners through which BIN3 organizes actin\", \"No mammalian-cell mechanism defined\"]\n    },\n    {\n      \"year\": 2007,\n      \"claim\": \"Connected BIN3's actin role to a specific molecular mechanism — recruitment and activation of Cdc42 via a GEF — resolving how the BAR adaptor drives cytokinesis.\",\n      \"evidence\": \"Y2H, Co-IP, live imaging of actomyosin ring, GTP-Cdc42 pull-down, and human BIN3 complementation in S. pombe\",\n      \"pmids\": [\"17363901\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Direct vs. GEF-bridged nature of the Cdc42 interaction in mammalian cells not resolved\", \"Structural basis of the Hob3p-Gef1p-Cdc42 complex unknown\"]\n    },\n    {\n      \"year\": 2008,\n      \"claim\": \"Demonstrated a physiological, tissue-selective requirement for Bin3 in F-actin maintenance and revealed an invasion-suppressor role, distinguishing its functions in normal vs. transformed cells.\",\n      \"evidence\": \"Bin3 knockout mouse, lens histology/F-actin imaging, invasion and proliferation assays in transformed cells\",\n      \"pmids\": [\"18339847\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Molecular basis for tissue selectivity (lens fiber vs. epithelial) unexplained\", \"Did not link the invasion phenotype to a defined signaling pathway\"]\n    },\n    {\n      \"year\": 2011,\n      \"claim\": \"Revealed a wholly separate, RNA-based function: Bin3 stabilizes 7SK RNA to assemble a repressive RNP controlling caudal mRNA translation in development.\",\n      \"evidence\": \"Drosophila bin3 mutants, RNA co-IP of 7SK, Northern blot quantification, and genetic epistasis with bicoid/eIF4E/Larp1/PABP/Ago2\",\n      \"pmids\": [\"21262214\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not establish whether 7SK stabilization requires catalytic methylation\", \"Direct interaction map within the repressive RNP not resolved\"]\n    },\n    {\n      \"year\": 2012,\n      \"claim\": \"Defined the enzymatic basis of 7SK stabilization — γ-phosphate methylation generating a protective methyl-phosphate cap that scaffolds P-TEFb sequestration.\",\n      \"evidence\": \"Review synthesizing in vitro methyltransferase assays with SAM substrate and biochemical reconstitution\",\n      \"pmids\": [\"22740346\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Synthesizes prior biochemistry rather than presenting new primary data\", \"In vivo requirement of the cap for function not tested here\"]\n    },\n    {\n      \"year\": 2013,\n      \"claim\": \"Extended the Rho GTPase adaptor role to mammalian myogenesis, showing Bin3 controls both Rac1 and Cdc42 activity to drive myoblast migration and myofiber size.\",\n      \"evidence\": \"Bin3 loss-of-function in mouse myogenesis, Co-IP with Rac1/Cdc42, F-actin co-localization, GTPase assays, in vivo myofiber measurement\",\n      \"pmids\": [\"23872330\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Whether Bin3 acts via a GEF in muscle, as in yeast, not established\", \"Direct vs. indirect Rac1/Cdc42 binding not distinguished\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Placed BIN3's invasion-suppressor activity in a defined signaling axis downstream of EGFR and upstream of DOCK7-Rho GTPase signaling, and showed it is pharmacologically actionable.\",\n      \"evidence\": \"Orthotopic glioblastoma models, BIN3 gain/loss, invasion and Rho GTPase pathway analysis, tofacitinib treatment\",\n      \"pmids\": [\"35915159\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct molecular link between BIN3 and DOCK7 not biochemically defined\", \"Relationship to BIN3's 7SK/RNA function untested\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Uncovered a catalysis-independent scaffolding function for the ortholog Bmc1 within the telomerase holoenzyme, broadening the protein's RNP-assembly roles beyond 7SK.\",\n      \"evidence\": \"Affinity purification and Co-IP of telomerase components, methyltransferase-dead and deletion mutants, telomere length and TER1 accumulation assays in S. pombe (two independent labs)\",\n      \"pmids\": [\"35217638\", \"35277511\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether mammalian MePCE has an analogous telomerase role unknown\", \"Structural basis of Bmc1-Pof8-TER1 assembly not resolved\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Resolved a division of labor between BIN3's two capping activities by identifying a 'Bin3-Box' domain specifically required for 7SK, not U6, biology.\",\n      \"evidence\": \"Drosophila genetics, hybrid Amus-MePCE rescue, Bin3-Box mutagenesis, U6/7SK stability assays, human-cell MePCE loss-of-function\",\n      \"pmids\": [\"38100593\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Mechanism by which the Bin3-Box confers 7SK specificity unknown\", \"Structural definition of the domain not provided\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Demonstrated that methyltransferase catalysis is dispensable in vivo — BIN3 stabilizes 7SK and represses P-TEFb as a non-catalytic scaffold — and identified a metazoan-specific motif driving a 7SK-independent function.\",\n      \"evidence\": \"Drosophila catalytic-dead Bin3Y795A rescue, P-TEFb genetic epistasis, Bin3ΔMSM deletion analysis, RNA binding/stabilization assays\",\n      \"pmids\": [\"37982586\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Identity of the 7SK-independent MSM-dependent function not defined\", \"How a catalytically dead enzyme retains the protective cap function mechanistically unexplained\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"It remains unresolved how BIN3's RNA-capping/RNP-scaffolding functions and its BAR-domain Rho GTPase adaptor functions are integrated within a single protein and coordinated in mammalian cells.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No structural model linking the methyltransferase, Bin3-Box, MSM, and BAR domains\", \"Whether the two activities are spatially or temporally separated within a cell is unknown\", \"Direct mammalian DOCK7 and Rho GTPase binding interfaces undefined\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0140098\", \"supporting_discovery_ids\": [4, 8]},\n      {\"term_id\": \"GO:0003723\", \"supporting_discovery_ids\": [3, 9]},\n      {\"term_id\": \"GO:0016740\", \"supporting_discovery_ids\": [4]},\n      {\"term_id\": \"GO:0008092\", \"supporting_discovery_ids\": [0, 1, 5]},\n      {\"term_id\": \"GO:0098772\", \"supporting_discovery_ids\": [1, 6]},\n      {\"term_id\": \"GO:0060090\", \"supporting_discovery_ids\": [1, 7]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005856\", \"supporting_discovery_ids\": [0, 2, 5]},\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [4]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-74160\", \"supporting_discovery_ids\": [4]},\n      {\"term_id\": \"R-HSA-8953854\", \"supporting_discovery_ids\": [4, 8]},\n      {\"term_id\": \"R-HSA-162582\", \"supporting_discovery_ids\": [1, 5, 6]},\n      {\"term_id\": \"R-HSA-1640170\", \"supporting_discovery_ids\": [1]},\n      {\"term_id\": \"R-HSA-1266738\", \"supporting_discovery_ids\": [2, 3, 5]},\n      {\"term_id\": \"R-HSA-1643685\", \"supporting_discovery_ids\": [6]}\n    ],\n    \"complexes\": [\"7SK snRNP\", \"telomerase holoenzyme\"],\n    \"partners\": [\"CDC42\", \"RAC1\", \"Gef1p\", \"Pof8\", \"DOCK7\", \"7SK RNA\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":5,"faith_total":6,"faith_pct":83.33333333333333}}