{"gene":"RBM6","run_date":"2026-06-10T06:43:36","timeline":{"discoveries":[{"year":1999,"finding":"RBM6 (DEF-3/NY-LU-12) encodes an RNA-binding protein containing two RNA recognition motifs (RRMs); recombinant proteins containing the RRMs of RBM6 specifically bound poly(G) RNA homopolymers in vitro, demonstrating direct RNA-binding activity.","method":"In vitro RNA binding assay with recombinant protein containing RRM domains","journal":"Oncogene","confidence":"Medium","confidence_rationale":"Tier 1 / Weak — direct in vitro biochemical assay with recombinant protein, single lab, single method","pmids":["10353602"],"is_preprint":false},{"year":2007,"finding":"RBM6 forms a fusion protein with CSF1R (via t(3;5)(p21;q33) translocation) in acute megakaryoblastic leukemia; the RBM6-CSF1R fusion protein confers IL-3-independent growth in BaF3 cells and induces myeloproliferative disease in a murine transplant model, demonstrating constitutive kinase activation driven by the fusion.","method":"5'RACE cDNA sequencing to identify fusion; BaF3 functional growth assay; murine transplant model","journal":"Blood","confidence":"High","confidence_rationale":"Tier 2 / Moderate — functional validation in two orthogonal systems (cell line growth assay and in vivo murine model), single lab","pmids":["17360941"],"is_preprint":false},{"year":2010,"finding":"RBM6 localizes to splicing speckles/interchromatin granule clusters (IGCs) and to nascent transcripts on lampbrush chromosomes. The repetitive N-terminal region of RBM6 acts as a multimerization/oligomerization domain required for assembly of novel bead-like structures on the IGC surface; without this domain, RBM6 accumulates homogeneously within IGCs rather than at their periphery. Oligomerized RBM6 on lampbrush loops causes them to appear as dense spiral structures distinct from normal extended loops.","method":"Immunostaining of endogenous RBM6 in mammalian cell lines; tagged RBM6 expression; Xenopus oocyte germinal vesicle spread preparations; deletion mapping of oligomerization domain","journal":"Chromosome Research","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct localization with functional domain dissection via deletion mutants in two experimental systems (mammalian cells and Xenopus oocytes), single lab","pmids":["21086038"],"is_preprint":false},{"year":2021,"finding":"RBM6 promotes homologous recombination (HR) repair of DNA double-strand breaks (DSBs) by regulating alternative splicing-coupled nonstop-decay of the HR regulator Fe65/APBB1; RBM6 knockdown severely reduces Fe65 protein levels and impairs HR. RBM6-deficient cancer cells show increased sensitivity to ATM inhibition, PARP inhibition, and cisplatin.","method":"RBM6 knockdown; alternative splicing analysis; HR reporter assays; drug sensitivity assays; mouse xenograft model","journal":"Nucleic Acids Research","confidence":"High","confidence_rationale":"Tier 2 / Moderate — mechanistic pathway defined by knockdown + splicing analysis + functional HR assays + in vivo xenograft, single lab with multiple orthogonal methods","pmids":["34718714"],"is_preprint":false},{"year":2021,"finding":"RBM6 forms a protein complex with the histone deacetylase SIRT7; this complex downregulates H3K18 acetylation at the OSX promoter by recruiting SIRT7 to it, thereby inhibiting expression of OSX isoforms 1 and 2 and suppressing osteogenic differentiation of mesenchymal stem cells.","method":"Co-immunoprecipitation (complex formation); ChIP (H3K18Ac at OSX promoter); RBM6 knockdown; in vivo osteogenesis assay","journal":"Stem Cells","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP for complex, ChIP for histone modification, functional knockdown; single lab with multiple methods","pmids":["33684230"],"is_preprint":false},{"year":2023,"finding":"RBM6 is recruited to DSB sites in a manner indirectly regulated by PARP1 activity. Five glycine residues within the G-patch domain are required for RBM6 accumulation at DNA damage sites but are dispensable for its splicing activity (no effect on Fe65 or Eya2 splicing targets). RBM6 interacts with Rad51 via its G-patch domain; deletion of this domain attenuates Rad51 interaction and reduces Rad51 foci formation after ionizing radiation, impairing HR repair independently of splicing.","method":"Deletion mapping with domain mutants; live-cell imaging of DSB recruitment; Co-IP of RBM6 with Rad51; Rad51 foci quantification after IR; HR reporter assay","journal":"Molecular and Cellular Biology","confidence":"High","confidence_rationale":"Tier 2 / Moderate — domain mutagenesis, Co-IP, functional HR assay, and foci analysis; multiple orthogonal methods, single lab; mechanistically separates splicing-dependent and splicing-independent HR functions","pmids":["36941773"],"is_preprint":false},{"year":2024,"finding":"iRIP-seq analysis in HeLa cells revealed that RBM6 directly interacts with a large number of mRNAs, with preferential binding motifs GGCGAUG and CUCU, enriched for mRNAs of cell proliferation- and apoptosis-associated genes that undergo altered alternative splicing upon RBM6 knockdown.","method":"Improved RNA immunoprecipitation coupled with sequencing (iRIP-seq); whole transcriptome sequencing after shRBM6 knockdown","journal":"Frontiers in Bioscience","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — genome-wide RIP-seq identifies binding targets and motifs with transcriptome validation, single lab, single study","pmids":["39344314"],"is_preprint":false},{"year":2025,"finding":"In prostate cancer cells, RBM6 suppresses CDH1 expression to promote cell migration, but when ZEB1 is overexpressed, RBM6 instead inhibits MMP16, shifting its net effect to reduced migration. RNA pulldown and RNA immunoprecipitation confirmed RBM6 binding to target mRNAs. Thus RBM6's regulatory output on migration-related genes is context-dependent on ZEB1 levels.","method":"Scratch/transwell migration assays; PCR and western blot; RNA pulldown; RNA immunoprecipitation","journal":"Journal of Cellular and Molecular Medicine","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single lab, single paper; RNA pulldown and RIP confirm binding but mechanistic pathway placement is limited and context-specific","pmids":["39900560"],"is_preprint":false}],"current_model":"RBM6 is a nuclear RNA-binding protein that localizes to splicing speckles/IGCs via an N-terminal oligomerization domain and directly binds mRNA targets (preferring GGCGAUG/CUCU motifs); it promotes homologous recombination repair of DNA double-strand breaks through two separable mechanisms — alternative splicing-coupled nonstop-decay of the HR factor Fe65/APBB1, and a splicing-independent function requiring its G-patch domain to recruit Rad51 to break sites — while also forming a complex with SIRT7 to repress H3K18 acetylation at osteogenic gene promoters."},"narrative":{"mechanistic_narrative":"RBM6 is a nuclear RNA-binding protein that couples mRNA recognition to control of DNA double-strand break repair and chromatin-based transcriptional regulation [PMID:34718714, PMID:39344314]. It contains two RNA recognition motifs that confer direct RNA-binding activity, originally shown by specific binding to poly(G) homopolymers [PMID:10353602], and genome-wide it engages a large set of mRNAs through preferential GGCGAUG and CUCU motifs, with targets enriched for proliferation- and apoptosis-associated genes whose alternative splicing depends on RBM6 [PMID:39344314]. Within the nucleus RBM6 localizes to splicing speckles/interchromatin granule clusters and to nascent transcripts, with a repetitive N-terminal region that drives oligomerization and assembly of bead-like structures at the IGC periphery [PMID:21086038]. RBM6 promotes homologous recombination repair through two separable activities: an alternative splicing-coupled nonstop-decay mechanism that maintains levels of the HR regulator Fe65/APBB1 [PMID:34718714], and a splicing-independent function in which its G-patch domain mediates recruitment to break sites and interaction with Rad51 to support Rad51 foci formation, with five G-patch glycine residues required for damage-site accumulation but dispensable for splicing [PMID:36941773]. Consistent with this repair role, RBM6-deficient cancer cells are sensitized to ATM inhibition, PARP inhibition, and cisplatin [PMID:34718714]. RBM6 additionally forms a complex with the deacetylase SIRT7 that lowers H3K18 acetylation at the OSX promoter to suppress osteogenic differentiation [PMID:33684230]. A recurrent t(3;5) translocation fuses RBM6 to CSF1R, generating a constitutively active kinase fusion that drives myeloproliferative disease [PMID:17360941].","teleology":[{"year":1999,"claim":"Establishing that RBM6 is a bona fide RNA-binding protein answered whether its RRM domains were functional, anchoring all later RNA-dependent models.","evidence":"In vitro RNA binding assay with recombinant protein containing the RRM domains","pmids":["10353602"],"confidence":"Medium","gaps":["Binding to poly(G) homopolymers in vitro does not define physiological mRNA targets","No cellular function assigned at this stage","Single method, single lab"]},{"year":2007,"claim":"Identifying the RBM6-CSF1R fusion answered how a chromosomal translocation involving RBM6 contributes to leukemia, showing the fusion drives constitutive kinase signaling.","evidence":"5'RACE fusion identification, IL-3-independent BaF3 growth assay, and murine transplant model","pmids":["17360941"],"confidence":"High","gaps":["The oncogenic driver is CSF1R kinase activity, not native RBM6 function","Contribution of the RBM6 portion to fusion behavior not dissected"]},{"year":2010,"claim":"Mapping RBM6 to splicing speckles/IGCs and defining an N-terminal oligomerization domain answered where RBM6 acts in the nucleus and how it self-assembles on RNP structures.","evidence":"Immunostaining, tagged-protein expression, Xenopus lampbrush spreads, and deletion mapping","pmids":["21086038"],"confidence":"Medium","gaps":["Functional consequence of oligomerization for splicing or repair not established","Molecular partners at IGCs not identified"]},{"year":2021,"claim":"Linking RBM6 to HR repair via splicing-coupled nonstop-decay of Fe65/APBB1 answered how an RNA-binding protein influences DNA repair and revealed a synthetic-lethal therapeutic vulnerability.","evidence":"Knockdown with splicing analysis, HR reporter assays, drug sensitivity tests, and mouse xenografts","pmids":["34718714"],"confidence":"High","gaps":["Whether splicing regulation fully accounts for the HR phenotype was not resolved","Direct binding of RBM6 to the APBB1 transcript not shown in this study"]},{"year":2021,"claim":"Defining the RBM6-SIRT7 complex answered how RBM6 contributes to chromatin regulation, showing it directs histone deacetylation to a developmental gene promoter.","evidence":"Co-immunoprecipitation, ChIP for H3K18Ac at the OSX promoter, knockdown, and in vivo osteogenesis assay","pmids":["33684230"],"confidence":"Medium","gaps":["Whether RBM6 recruitment to OSX depends on its RNA-binding activity is unknown","Co-IP without reciprocal/structural validation of the complex interface"]},{"year":2023,"claim":"Dissecting the G-patch domain answered whether RBM6 has a repair role beyond splicing, separating a splicing-independent Rad51-recruitment function from its splicing activity.","evidence":"Domain mutagenesis, live-cell DSB recruitment imaging, Rad51 Co-IP and foci quantification, and HR reporter assays","pmids":["36941773"],"confidence":"High","gaps":["How PARP1 indirectly governs RBM6 recruitment is unresolved","Structural basis of the G-patch-Rad51 interaction not determined"]},{"year":2024,"claim":"Genome-wide iRIP-seq answered which transcripts RBM6 binds directly and defined its sequence preferences, connecting binding to splicing of proliferation/apoptosis genes.","evidence":"iRIP-seq in HeLa cells with transcriptome sequencing after knockdown","pmids":["39344314"],"confidence":"Medium","gaps":["Which bound transcripts are functionally regulated versus passively bound not resolved","Motif preference not validated by mutagenesis"]},{"year":2025,"claim":"Examining migration genes in prostate cancer addressed whether RBM6's regulatory output is fixed, showing it is context-dependent on ZEB1 levels.","evidence":"Migration assays, RNA pulldown, and RNA immunoprecipitation in prostate cancer cells","pmids":["39900560"],"confidence":"Low","gaps":["Single lab, single paper, context-specific with limited mechanistic pathway placement","How ZEB1 switches RBM6 target preference is unexplained","Direct splicing versus expression mechanism on CDH1/MMP16 not distinguished"]},{"year":null,"claim":"How RBM6's RNA-binding, oligomerization, splicing, and direct Rad51-recruitment activities are coordinated into a single regulatory program remains unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No structural model integrating RRM, N-terminal oligomerization, and G-patch domains","Mechanism linking PARP1 activity to RBM6 recruitment unknown","Whether IGC localization is required for repair or splicing functions untested"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0003723","term_label":"RNA binding","supporting_discovery_ids":[0,6]}],"localization":[{"term_id":"GO:0005654","term_label":"nucleoplasm","supporting_discovery_ids":[2]},{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[2]}],"pathway":[{"term_id":"R-HSA-73894","term_label":"DNA Repair","supporting_discovery_ids":[3,5]},{"term_id":"R-HSA-8953854","term_label":"Metabolism of RNA","supporting_discovery_ids":[3,6]}],"complexes":[],"partners":["SIRT7","RAD51","APBB1","CSF1R"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"P78332","full_name":"RNA-binding protein 6","aliases":["Lung cancer antigen NY-LU-12","Protein G16","RNA-binding motif protein 6","RNA-binding protein DEF-3"],"length_aa":1123,"mass_kda":128.6,"function":"Specifically binds poly(G) RNA homopolymers in vitro","subcellular_location":"Nucleus","url":"https://www.uniprot.org/uniprotkb/P78332/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/RBM6","classification":"Not Classified","n_dependent_lines":13,"n_total_lines":1208,"dependency_fraction":0.01076158940397351},"opencell":{"profiled":true,"resolved_as":"","ensg_id":"ENSG00000004534","cell_line_id":"CID001490","localizations":[{"compartment":"nucleolus_fc_dfc","grade":3},{"compartment":"nucleoplasm","grade":3},{"compartment":"nuclear_punctae","grade":2}],"interactors":[{"gene":"FUS","stoichiometry":0.2},{"gene":"RBM14","stoichiometry":0.2},{"gene":"PRPF8","stoichiometry":0.2},{"gene":"DDX42","stoichiometry":0.2},{"gene":"ERH","stoichiometry":0.2},{"gene":"MFAP1","stoichiometry":0.2},{"gene":"EFTUD2","stoichiometry":0.2},{"gene":"NCBP1","stoichiometry":0.2},{"gene":"LSM2","stoichiometry":0.2},{"gene":"PRPF19","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/target/CID001490","total_profiled":1310},"omim":[{"mim_id":"606886","title":"RNA-BINDING MOTIF PROTEIN 6; RBM6","url":"https://www.omim.org/entry/606886"},{"mim_id":"606884","title":"RNA-BINDING MOTIF PROTEIN 5; RBM5","url":"https://www.omim.org/entry/606884"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Approved","locations":[{"location":"Nuclear speckles","reliability":"Approved"},{"location":"Cytoplasmic bodies","reliability":"Additional"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/RBM6"},"hgnc":{"alias_symbol":["DEF-3","3G2","NY-LU-12","g16","DEF3"],"prev_symbol":[]},"alphafold":{"accession":"P78332","domains":[{"cath_id":"3.30.70.330","chopping":"458-535","consensus_level":"high","plddt":76.2749,"start":458,"end":535},{"cath_id":"3.30.70.330","chopping":"662-738","consensus_level":"high","plddt":84.8539,"start":662,"end":738},{"cath_id":"-","chopping":"950-1006","consensus_level":"high","plddt":86.4347,"start":950,"end":1006}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/P78332","model_url":"https://alphafold.ebi.ac.uk/files/AF-P78332-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-P78332-F1-predicted_aligned_error_v6.png","plddt_mean":49.19},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=RBM6","jax_strain_url":"https://www.jax.org/strain/search?query=RBM6"},"sequence":{"accession":"P78332","fasta_url":"https://rest.uniprot.org/uniprotkb/P78332.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/P78332/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/P78332"}},"corpus_meta":[{"pmid":"10353602","id":"PMC_10353602","title":"DEF-3(g16/NY-LU-12), an RNA binding protein from the 3p21.3 homozygous deletion region in SCLC.","date":"1999","source":"Oncogene","url":"https://pubmed.ncbi.nlm.nih.gov/10353602","citation_count":41,"is_preprint":false},{"pmid":"17360941","id":"PMC_17360941","title":"A novel fusion of RBM6 to CSF1R in acute megakaryoblastic leukemia.","date":"2007","source":"Blood","url":"https://pubmed.ncbi.nlm.nih.gov/17360941","citation_count":38,"is_preprint":false},{"pmid":"17908320","id":"PMC_17908320","title":"RBM6-RBM5 transcription-induced chimeras are differentially expressed in tumours.","date":"2007","source":"BMC genomics","url":"https://pubmed.ncbi.nlm.nih.gov/17908320","citation_count":32,"is_preprint":false},{"pmid":"34718714","id":"PMC_34718714","title":"RBM6 splicing factor promotes homologous recombination repair of double-strand breaks and modulates sensitivity to chemotherapeutic drugs.","date":"2021","source":"Nucleic acids research","url":"https://pubmed.ncbi.nlm.nih.gov/34718714","citation_count":31,"is_preprint":false},{"pmid":"30772516","id":"PMC_30772516","title":"RNA-binding protein RBM6 as a tumor suppressor gene represses the growth and progression in laryngocarcinoma.","date":"2019","source":"Gene","url":"https://pubmed.ncbi.nlm.nih.gov/30772516","citation_count":25,"is_preprint":false},{"pmid":"10825432","id":"PMC_10825432","title":"Targeting of endothelial KDR receptors with 3G2 immunoliposomes in vitro.","date":"2000","source":"Biochimica et biophysica acta","url":"https://pubmed.ncbi.nlm.nih.gov/10825432","citation_count":21,"is_preprint":false},{"pmid":"33684230","id":"PMC_33684230","title":"LncRNA, PLXDC2-OT promoted the osteogenesis potentials of MSCs by inhibiting the deacetylation function of RBM6/SIRT7 complex and OSX specific isoform.","date":"2021","source":"Stem cells (Dayton, Ohio)","url":"https://pubmed.ncbi.nlm.nih.gov/33684230","citation_count":21,"is_preprint":false},{"pmid":"38114270","id":"PMC_38114270","title":"Spindle cell rhabdomyosarcomas: With TFCP2 rearrangements, and novel EWSR1::ZBTB41 and PLOD2::RBM6 gene fusions. A study of five cases and review of the literature.","date":"2023","source":"Histopathology","url":"https://pubmed.ncbi.nlm.nih.gov/38114270","citation_count":14,"is_preprint":false},{"pmid":"21086038","id":"PMC_21086038","title":"Subnuclear targeting of the RNA-binding motif protein RBM6 to splicing speckles and nascent transcripts.","date":"2010","source":"Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology","url":"https://pubmed.ncbi.nlm.nih.gov/21086038","citation_count":10,"is_preprint":false},{"pmid":"36941773","id":"PMC_36941773","title":"Recruitment of RBM6 to DNA Double-Strand Breaks Fosters Homologous Recombination Repair.","date":"2023","source":"Molecular and cellular biology","url":"https://pubmed.ncbi.nlm.nih.gov/36941773","citation_count":6,"is_preprint":false},{"pmid":"34076986","id":"PMC_34076986","title":"RNA-binding protein RBM6 acts as a tumor suppressor gene to inhibit the progression of hepatocellular carcinoma.","date":"2021","source":"Journal of B.U.ON. : official journal of the Balkan Union of Oncology","url":"https://pubmed.ncbi.nlm.nih.gov/34076986","citation_count":3,"is_preprint":false},{"pmid":"39900560","id":"PMC_39900560","title":"The Oncopromoting Gene RBM6 Inhibits Prostate Tumour Cell Migration During Epithelial-to-Mesenchymal Transition.","date":"2025","source":"Journal of cellular and molecular medicine","url":"https://pubmed.ncbi.nlm.nih.gov/39900560","citation_count":1,"is_preprint":false},{"pmid":"39344314","id":"PMC_39344314","title":"Global RNA Interaction and Transcriptome Profiles Demonstrate the Potential Anti-Oncogenic Targets and Pathways of RBM6 in HeLa Cells.","date":"2024","source":"Frontiers in bioscience (Landmark edition)","url":"https://pubmed.ncbi.nlm.nih.gov/39344314","citation_count":1,"is_preprint":false},{"pmid":null,"id":"bio_10.1101_2024.09.01.24310190","title":"Genetic analyses identify shared genetic components related to autoimmune and cardiovascular diseases","date":"2024-09-01","source":"bioRxiv","url":"https://doi.org/10.1101/2024.09.01.24310190","citation_count":0,"is_preprint":true}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":9691,"output_tokens":2181,"usd":0.030894,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":9230,"output_tokens":3034,"usd":0.061,"stage2_stop_reason":"end_turn"},"total_usd":0.091894,"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\": 1999,\n      \"finding\": \"RBM6 (DEF-3/NY-LU-12) encodes an RNA-binding protein containing two RNA recognition motifs (RRMs); recombinant proteins containing the RRMs of RBM6 specifically bound poly(G) RNA homopolymers in vitro, demonstrating direct RNA-binding activity.\",\n      \"method\": \"In vitro RNA binding assay with recombinant protein containing RRM domains\",\n      \"journal\": \"Oncogene\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1 / Weak — direct in vitro biochemical assay with recombinant protein, single lab, single method\",\n      \"pmids\": [\"10353602\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2007,\n      \"finding\": \"RBM6 forms a fusion protein with CSF1R (via t(3;5)(p21;q33) translocation) in acute megakaryoblastic leukemia; the RBM6-CSF1R fusion protein confers IL-3-independent growth in BaF3 cells and induces myeloproliferative disease in a murine transplant model, demonstrating constitutive kinase activation driven by the fusion.\",\n      \"method\": \"5'RACE cDNA sequencing to identify fusion; BaF3 functional growth assay; murine transplant model\",\n      \"journal\": \"Blood\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — functional validation in two orthogonal systems (cell line growth assay and in vivo murine model), single lab\",\n      \"pmids\": [\"17360941\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2010,\n      \"finding\": \"RBM6 localizes to splicing speckles/interchromatin granule clusters (IGCs) and to nascent transcripts on lampbrush chromosomes. The repetitive N-terminal region of RBM6 acts as a multimerization/oligomerization domain required for assembly of novel bead-like structures on the IGC surface; without this domain, RBM6 accumulates homogeneously within IGCs rather than at their periphery. Oligomerized RBM6 on lampbrush loops causes them to appear as dense spiral structures distinct from normal extended loops.\",\n      \"method\": \"Immunostaining of endogenous RBM6 in mammalian cell lines; tagged RBM6 expression; Xenopus oocyte germinal vesicle spread preparations; deletion mapping of oligomerization domain\",\n      \"journal\": \"Chromosome Research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct localization with functional domain dissection via deletion mutants in two experimental systems (mammalian cells and Xenopus oocytes), single lab\",\n      \"pmids\": [\"21086038\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"RBM6 promotes homologous recombination (HR) repair of DNA double-strand breaks (DSBs) by regulating alternative splicing-coupled nonstop-decay of the HR regulator Fe65/APBB1; RBM6 knockdown severely reduces Fe65 protein levels and impairs HR. RBM6-deficient cancer cells show increased sensitivity to ATM inhibition, PARP inhibition, and cisplatin.\",\n      \"method\": \"RBM6 knockdown; alternative splicing analysis; HR reporter assays; drug sensitivity assays; mouse xenograft model\",\n      \"journal\": \"Nucleic Acids Research\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — mechanistic pathway defined by knockdown + splicing analysis + functional HR assays + in vivo xenograft, single lab with multiple orthogonal methods\",\n      \"pmids\": [\"34718714\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"RBM6 forms a protein complex with the histone deacetylase SIRT7; this complex downregulates H3K18 acetylation at the OSX promoter by recruiting SIRT7 to it, thereby inhibiting expression of OSX isoforms 1 and 2 and suppressing osteogenic differentiation of mesenchymal stem cells.\",\n      \"method\": \"Co-immunoprecipitation (complex formation); ChIP (H3K18Ac at OSX promoter); RBM6 knockdown; in vivo osteogenesis assay\",\n      \"journal\": \"Stem Cells\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP for complex, ChIP for histone modification, functional knockdown; single lab with multiple methods\",\n      \"pmids\": [\"33684230\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"RBM6 is recruited to DSB sites in a manner indirectly regulated by PARP1 activity. Five glycine residues within the G-patch domain are required for RBM6 accumulation at DNA damage sites but are dispensable for its splicing activity (no effect on Fe65 or Eya2 splicing targets). RBM6 interacts with Rad51 via its G-patch domain; deletion of this domain attenuates Rad51 interaction and reduces Rad51 foci formation after ionizing radiation, impairing HR repair independently of splicing.\",\n      \"method\": \"Deletion mapping with domain mutants; live-cell imaging of DSB recruitment; Co-IP of RBM6 with Rad51; Rad51 foci quantification after IR; HR reporter assay\",\n      \"journal\": \"Molecular and Cellular Biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — domain mutagenesis, Co-IP, functional HR assay, and foci analysis; multiple orthogonal methods, single lab; mechanistically separates splicing-dependent and splicing-independent HR functions\",\n      \"pmids\": [\"36941773\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"iRIP-seq analysis in HeLa cells revealed that RBM6 directly interacts with a large number of mRNAs, with preferential binding motifs GGCGAUG and CUCU, enriched for mRNAs of cell proliferation- and apoptosis-associated genes that undergo altered alternative splicing upon RBM6 knockdown.\",\n      \"method\": \"Improved RNA immunoprecipitation coupled with sequencing (iRIP-seq); whole transcriptome sequencing after shRBM6 knockdown\",\n      \"journal\": \"Frontiers in Bioscience\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — genome-wide RIP-seq identifies binding targets and motifs with transcriptome validation, single lab, single study\",\n      \"pmids\": [\"39344314\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"In prostate cancer cells, RBM6 suppresses CDH1 expression to promote cell migration, but when ZEB1 is overexpressed, RBM6 instead inhibits MMP16, shifting its net effect to reduced migration. RNA pulldown and RNA immunoprecipitation confirmed RBM6 binding to target mRNAs. Thus RBM6's regulatory output on migration-related genes is context-dependent on ZEB1 levels.\",\n      \"method\": \"Scratch/transwell migration assays; PCR and western blot; RNA pulldown; RNA immunoprecipitation\",\n      \"journal\": \"Journal of Cellular and Molecular Medicine\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single lab, single paper; RNA pulldown and RIP confirm binding but mechanistic pathway placement is limited and context-specific\",\n      \"pmids\": [\"39900560\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"RBM6 is a nuclear RNA-binding protein that localizes to splicing speckles/IGCs via an N-terminal oligomerization domain and directly binds mRNA targets (preferring GGCGAUG/CUCU motifs); it promotes homologous recombination repair of DNA double-strand breaks through two separable mechanisms — alternative splicing-coupled nonstop-decay of the HR factor Fe65/APBB1, and a splicing-independent function requiring its G-patch domain to recruit Rad51 to break sites — while also forming a complex with SIRT7 to repress H3K18 acetylation at osteogenic gene promoters.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"RBM6 is a nuclear RNA-binding protein that couples mRNA recognition to control of DNA double-strand break repair and chromatin-based transcriptional regulation [#3, #6]. It contains two RNA recognition motifs that confer direct RNA-binding activity, originally shown by specific binding to poly(G) homopolymers [#0], and genome-wide it engages a large set of mRNAs through preferential GGCGAUG and CUCU motifs, with targets enriched for proliferation- and apoptosis-associated genes whose alternative splicing depends on RBM6 [#6]. Within the nucleus RBM6 localizes to splicing speckles/interchromatin granule clusters and to nascent transcripts, with a repetitive N-terminal region that drives oligomerization and assembly of bead-like structures at the IGC periphery [#2]. RBM6 promotes homologous recombination repair through two separable activities: an alternative splicing-coupled nonstop-decay mechanism that maintains levels of the HR regulator Fe65/APBB1 [#3], and a splicing-independent function in which its G-patch domain mediates recruitment to break sites and interaction with Rad51 to support Rad51 foci formation, with five G-patch glycine residues required for damage-site accumulation but dispensable for splicing [#5]. Consistent with this repair role, RBM6-deficient cancer cells are sensitized to ATM inhibition, PARP inhibition, and cisplatin [#3]. RBM6 additionally forms a complex with the deacetylase SIRT7 that lowers H3K18 acetylation at the OSX promoter to suppress osteogenic differentiation [#4]. A recurrent t(3;5) translocation fuses RBM6 to CSF1R, generating a constitutively active kinase fusion that drives myeloproliferative disease [#1].\",\n  \"teleology\": [\n    {\n      \"year\": 1999,\n      \"claim\": \"Establishing that RBM6 is a bona fide RNA-binding protein answered whether its RRM domains were functional, anchoring all later RNA-dependent models.\",\n      \"evidence\": \"In vitro RNA binding assay with recombinant protein containing the RRM domains\",\n      \"pmids\": [\"10353602\"],\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"\",\n      \"gaps\": [\"Binding to poly(G) homopolymers in vitro does not define physiological mRNA targets\", \"No cellular function assigned at this stage\", \"Single method, single lab\"]\n    },\n    {\n      \"year\": 2007,\n      \"claim\": \"Identifying the RBM6-CSF1R fusion answered how a chromosomal translocation involving RBM6 contributes to leukemia, showing the fusion drives constitutive kinase signaling.\",\n      \"evidence\": \"5'RACE fusion identification, IL-3-independent BaF3 growth assay, and murine transplant model\",\n      \"pmids\": [\"17360941\"],\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"\",\n      \"gaps\": [\"The oncogenic driver is CSF1R kinase activity, not native RBM6 function\", \"Contribution of the RBM6 portion to fusion behavior not dissected\"]\n    },\n    {\n      \"year\": 2010,\n      \"claim\": \"Mapping RBM6 to splicing speckles/IGCs and defining an N-terminal oligomerization domain answered where RBM6 acts in the nucleus and how it self-assembles on RNP structures.\",\n      \"evidence\": \"Immunostaining, tagged-protein expression, Xenopus lampbrush spreads, and deletion mapping\",\n      \"pmids\": [\"21086038\"],\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"\",\n      \"gaps\": [\"Functional consequence of oligomerization for splicing or repair not established\", \"Molecular partners at IGCs not identified\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Linking RBM6 to HR repair via splicing-coupled nonstop-decay of Fe65/APBB1 answered how an RNA-binding protein influences DNA repair and revealed a synthetic-lethal therapeutic vulnerability.\",\n      \"evidence\": \"Knockdown with splicing analysis, HR reporter assays, drug sensitivity tests, and mouse xenografts\",\n      \"pmids\": [\"34718714\"],\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"\",\n      \"gaps\": [\"Whether splicing regulation fully accounts for the HR phenotype was not resolved\", \"Direct binding of RBM6 to the APBB1 transcript not shown in this study\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Defining the RBM6-SIRT7 complex answered how RBM6 contributes to chromatin regulation, showing it directs histone deacetylation to a developmental gene promoter.\",\n      \"evidence\": \"Co-immunoprecipitation, ChIP for H3K18Ac at the OSX promoter, knockdown, and in vivo osteogenesis assay\",\n      \"pmids\": [\"33684230\"],\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"\",\n      \"gaps\": [\"Whether RBM6 recruitment to OSX depends on its RNA-binding activity is unknown\", \"Co-IP without reciprocal/structural validation of the complex interface\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Dissecting the G-patch domain answered whether RBM6 has a repair role beyond splicing, separating a splicing-independent Rad51-recruitment function from its splicing activity.\",\n      \"evidence\": \"Domain mutagenesis, live-cell DSB recruitment imaging, Rad51 Co-IP and foci quantification, and HR reporter assays\",\n      \"pmids\": [\"36941773\"],\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"\",\n      \"gaps\": [\"How PARP1 indirectly governs RBM6 recruitment is unresolved\", \"Structural basis of the G-patch-Rad51 interaction not determined\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Genome-wide iRIP-seq answered which transcripts RBM6 binds directly and defined its sequence preferences, connecting binding to splicing of proliferation/apoptosis genes.\",\n      \"evidence\": \"iRIP-seq in HeLa cells with transcriptome sequencing after knockdown\",\n      \"pmids\": [\"39344314\"],\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"\",\n      \"gaps\": [\"Which bound transcripts are functionally regulated versus passively bound not resolved\", \"Motif preference not validated by mutagenesis\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Examining migration genes in prostate cancer addressed whether RBM6's regulatory output is fixed, showing it is context-dependent on ZEB1 levels.\",\n      \"evidence\": \"Migration assays, RNA pulldown, and RNA immunoprecipitation in prostate cancer cells\",\n      \"pmids\": [\"39900560\"],\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"\",\n      \"gaps\": [\"Single lab, single paper, context-specific with limited mechanistic pathway placement\", \"How ZEB1 switches RBM6 target preference is unexplained\", \"Direct splicing versus expression mechanism on CDH1/MMP16 not distinguished\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How RBM6's RNA-binding, oligomerization, splicing, and direct Rad51-recruitment activities are coordinated into a single regulatory program remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"\",\n      \"gaps\": [\"No structural model integrating RRM, N-terminal oligomerization, and G-patch domains\", \"Mechanism linking PARP1 activity to RBM6 recruitment unknown\", \"Whether IGC localization is required for repair or splicing functions untested\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0003723\", \"supporting_discovery_ids\": [0, 6]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005654\", \"supporting_discovery_ids\": [2]},\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [2]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-73894\", \"supporting_discovery_ids\": [3, 5]},\n      {\"term_id\": \"R-HSA-8953854\", \"supporting_discovery_ids\": [3, 6]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\"SIRT7\", \"RAD51\", \"APBB1\", \"CSF1R\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"faith_supported":7,"faith_total":7,"faith_pct":100.0}}