{"gene":"RBMX2","run_date":"2026-06-10T06:43:36","timeline":{"discoveries":[{"year":2001,"finding":"Snu17p (yeast ortholog of RBMX2) was identified as a U2 snRNP-associated protein required for the first catalytic step of pre-mRNA splicing and for progression of spliceosome assembly; its deletion stabilizes U1 snRNP within the spliceosome and prevents U4 snRNP dissociation, blocking the transition to the catalytically active complex.","method":"Protein microsequencing, co-immunoprecipitation of snRNPs and pre-mRNA, spliceosome assembly by nondenaturing gel electrophoresis, in vitro splicing complementation with recombinant Snu17p","journal":"Molecular and cellular biology","confidence":"High","confidence_rationale":"Tier 1-2 / Strong — in vitro splicing complementation with recombinant protein, snRNP co-IP, spliceosome assembly analysis, multiple orthogonal methods in one study","pmids":["11287609"],"is_preprint":false},{"year":2008,"finding":"Pml1 (RES complex subunit) binds directly to Snu17 (RBMX2 ortholog), which itself contacts Bud13; this hierarchical protein-protein interaction defines the architecture of the trimeric RES complex. The Pml1 FHA domain phosphothreonine-binding pocket mutation did not affect splicing.","method":"X-ray crystallography of Pml1, production of recombinant sub-complexes, serial truncation and mutagenesis of RES subunits, alternative splice-site choice splicing assay","journal":"Nucleic acids research","confidence":"High","confidence_rationale":"Tier 1 / Strong — crystal structure combined with recombinant complex reconstitution and mutagenesis defining binding interfaces","pmids":["19033360"],"is_preprint":false},{"year":2012,"finding":"Ist3/Snu17 (RBMX2 yeast ortholog) is specifically required for splicing of MATa1 pre-mRNA in diploid yeast cells; loss of Ist3 causes ectopic expression of the haploid-specific Axl1 protein and disrupts bipolar budding, placing Snu17/RES function upstream of MATa1-dependent cell-type transcriptional control.","method":"Genetic deletion, in vivo pre-mRNA splicing analysis, epistasis with axl1 deletion, bud-site selection assay","journal":"PloS one","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — clean genetic epistasis with specific phenotypic readout, single lab","pmids":["23118884"],"is_preprint":false},{"year":2018,"finding":"The RES complex (containing Snu17/RBMX2 ortholog) is required for efficient transformation of the precatalytic B spliceosome into the activated Bact complex; in the absence of Snu17, Pml1 and Bud13 recruitment to the spliceosome is abolished or reduced, and Prp2 binds prematurely and disassembles the structurally compromised ΔRES B complexes, suggesting a proofreading role for Prp2.","method":"Affinity purification of yeast spliceosomes, native gel spliceosome assembly analysis, in vitro disassembly assay with recombinant Prp2/Spp2/UTP, genetic deletion of RES subunits","journal":"Genes & development","confidence":"High","confidence_rationale":"Tier 1-2 / Strong — multiple orthogonal biochemical methods (affinity purification, in vitro reconstitution, spliceosome assembly), single lab with rigorous controls","pmids":["29330354"],"is_preprint":false},{"year":2018,"finding":"The vertebrate RES complex (including rbmx2/snu17 in zebrafish) is required for splicing of a specific subset of introns characterized by short length, high GC content, and flanking GC-depleted exons (features of intron definition); loss-of-function of rbmx2 causes widespread mis-splicing, increased neural cell death, and decreased differentiated neurons during early development.","method":"CRISPR/Cas9 loss-of-function mutants in zebrafish, transcriptome-wide splicing analysis (RNA-seq), computational modeling of RES-dependent intron features","journal":"PLoS genetics","confidence":"High","confidence_rationale":"Tier 2 / Strong — clean vertebrate loss-of-function with transcriptome-wide phenotypic readout and replicated across three RES subunit mutants","pmids":["29969449"],"is_preprint":false},{"year":2021,"finding":"The Theileria annulata secreted protein TA05575 physically interacts with bovine RBMX2, as confirmed by co-immunoprecipitation and bimolecular fluorescence complementation (BiFC); the interacting pair co-localizes in intracellular compartments of HEK293T cells.","method":"Yeast two-hybrid screening, co-immunoprecipitation, BiFC assay, confocal microscopy, flow cytometry","journal":"Frontiers in cellular and infection microbiology","confidence":"Medium","confidence_rationale":"Tier 2-3 / Moderate — reciprocal interaction confirmed by Co-IP and BiFC, single lab, two orthogonal methods","pmids":["33718289"],"is_preprint":false},{"year":2024,"finding":"RBMX2 promotes apoptosis of bovine epithelial cells during M. bovis infection by upregulating and binding to APAF-1, leading to alternative splicing of APAF-1 as a retention intron; RBMX2 knockout cells showed reduced apoptosis-associated splicing changes after infection.","method":"RBMX2 knockout in EBL cells, transcriptome sequencing, alternative splicing transcriptome sequencing, protein/molecular docking, molecular dynamics simulations, RT-qPCR","journal":"Frontiers in immunology","confidence":"Medium","confidence_rationale":"Tier 2-3 / Moderate — KO with transcriptome-wide readout and molecular docking, single lab; docking/MD is computational so functional binding not biochemically reconstituted","pmids":["39308873"],"is_preprint":false},{"year":2025,"finding":"RBMX2 suppresses cell adhesion and tight junction formation while enhancing M. bovis adhesion and invasion through activation of the p65 signaling pathway; it also promotes epithelial-mesenchymal transition via the p65/MMP-9 pathway during M. bovis infection.","method":"Transcriptomics, proteomics, metabolomics, cell adhesion assays, ChIP-PCR, Western blotting, immunofluorescence, M. bovis-induced EMT model in BoMac-EBL cells and H1299 cells","journal":"eLife","confidence":"Medium","confidence_rationale":"Tier 2-3 / Moderate — multiple orthogonal omics and functional assays (cell adhesion, ChIP-PCR, Western blot), single lab, infection-context","pmids":["41277807"],"is_preprint":false}],"current_model":"RBMX2 (Snu17 in yeast) is the central scaffold subunit of the trimeric RES (retention and splicing) complex, where it directly binds Bud13 and recruits Pml1, and functions in pre-mRNA splicing by facilitating B-to-Bact spliceosome activation; it is specifically required for splicing of short, GC-rich introns defined by intron definition, and in vertebrates is essential for early neural development, while additional studies indicate it can bind APAF-1 pre-mRNA to regulate alternative splicing and apoptosis, and modulates cell adhesion and EMT via p65/MMP-9 signaling during bacterial infection."},"narrative":{"mechanistic_narrative":"RBMX2 is the central scaffold subunit of the trimeric RES (retention and splicing) complex, functioning in pre-mRNA splicing by promoting the progression of spliceosome assembly toward catalytic activation [PMID:11287609, PMID:29330354]. Its yeast ortholog Snu17 directly binds Bud13 and recruits Pml1, with hierarchical protein-protein contacts defining the architecture of the RES complex [PMID:19033360]. Mechanistically, RES is required for efficient transformation of the precatalytic B spliceosome into the activated Bact complex; in its absence, recruitment of Pml1 and Bud13 to the spliceosome is lost and the splicing helicase Prp2 binds prematurely and disassembles the structurally compromised complexes, defining a checkpoint at B-to-Bact activation [PMID:29330354]. In vertebrates, RBMX2/RES is specifically required for splicing of short, GC-rich introns defined by intron definition, and its loss causes widespread mis-splicing, increased neural cell death, and impaired neuronal differentiation during early development [PMID:29969449]. Beyond its core splicing role, RBMX2 binds APAF-1 pre-mRNA to drive intron-retention alternative splicing and promote apoptosis [PMID:39308873], and modulates cell adhesion and epithelial-mesenchymal transition via p65/MMP-9 signaling during bacterial infection [PMID:33718289, PMID:41277807].","teleology":[{"year":2001,"claim":"Established that the RBMX2 ortholog is a U2 snRNP-associated factor needed to advance spliceosome assembly, answering whether it acts before or during catalysis.","evidence":"Protein microsequencing, snRNP co-IP, native-gel spliceosome assembly, and in vitro splicing complementation with recombinant Snu17p in yeast","pmids":["11287609"],"confidence":"High","gaps":["Did not define the protein partners that anchor Snu17 within the spliceosome","Vertebrate function not addressed"]},{"year":2008,"claim":"Resolved the internal architecture of the RES complex, showing RBMX2/Snu17 is the scaffold that bridges Bud13 and Pml1.","evidence":"X-ray crystallography of Pml1, recombinant sub-complex reconstitution, serial truncation/mutagenesis, and splice-site choice assays","pmids":["19033360"],"confidence":"High","gaps":["Did not show how RES engages the assembling spliceosome","Pml1 FHA phosphothreonine pocket dispensable, leaving its functional contribution unclear"]},{"year":2012,"claim":"Connected RES splicing activity to a specific cell-fate output by showing Snu17 is required to splice MATa1 pre-mRNA controlling cell-type identity.","evidence":"Genetic deletion, in vivo splicing analysis, epistasis with axl1, and bud-site selection assay in diploid yeast","pmids":["23118884"],"confidence":"Medium","gaps":["Substrate specificity determinants not defined","Single-lab genetic study"]},{"year":2018,"claim":"Defined the precise step RBMX2/RES controls, showing it is required for B-to-Bact transition and that its loss exposes spliceosomes to premature Prp2-mediated disassembly.","evidence":"Affinity purification of yeast spliceosomes, native-gel assembly analysis, and in vitro disassembly with recombinant Prp2/Spp2/UTP","pmids":["29330354"],"confidence":"High","gaps":["Molecular basis of Prp2 proofreading recognition not detailed","Yeast-based; vertebrate mechanism inferred separately"]},{"year":2018,"claim":"Extended RBMX2 function to vertebrates, identifying the intron features it acts on and linking its loss to neural developmental defects.","evidence":"CRISPR/Cas9 loss-of-function in zebrafish, transcriptome-wide RNA-seq splicing analysis, and computational modeling of RES-dependent introns across three RES subunit mutants","pmids":["29969449"],"confidence":"High","gaps":["Mechanism linking mis-splicing to neural cell death not resolved","Direct RNA targets in mammals not enumerated"]},{"year":2021,"claim":"Identified a pathogen-derived interactor of RBMX2, implicating the protein in host-pathogen interaction beyond canonical splicing.","evidence":"Yeast two-hybrid, co-IP, BiFC, and confocal co-localization in HEK293T cells with Theileria annulata TA05575","pmids":["33718289"],"confidence":"Medium","gaps":["Functional consequence of the interaction not established","Single lab, heterologous cell system"]},{"year":2024,"claim":"Linked RBMX2 to apoptosis regulation by showing it drives intron-retention alternative splicing of APAF-1 during bacterial infection.","evidence":"RBMX2 knockout in EBL cells, transcriptome and alternative-splicing sequencing, molecular docking/dynamics, and RT-qPCR in M. bovis infection","pmids":["39308873"],"confidence":"Medium","gaps":["RBMX2-APAF-1 binding shown computationally, not biochemically reconstituted","Single-lab, infection-specific context"]},{"year":2025,"claim":"Implicated RBMX2 in cell adhesion and EMT, showing it suppresses tight-junction formation and promotes invasion via p65/MMP-9 signaling.","evidence":"Multi-omics, cell adhesion assays, ChIP-PCR, Western blot, and immunofluorescence in M. bovis EMT models","pmids":["41277807"],"confidence":"Medium","gaps":["Mechanism connecting splicing scaffold function to p65 activation unclear","Single lab, infection-context only"]},{"year":null,"claim":"How RBMX2's core role as a splicing scaffold mechanistically gives rise to its reported infection-associated roles in apoptosis, adhesion, and EMT remains unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No structural model of the vertebrate RES complex on the spliceosome","Direct mammalian RNA targets not comprehensively mapped","Causal link between splicing scaffold activity and p65/MMP-9 signaling not established"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0003723","term_label":"RNA binding","supporting_discovery_ids":[0,6]},{"term_id":"GO:0060090","term_label":"molecular adaptor activity","supporting_discovery_ids":[1,3]}],"localization":[{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[0,5]}],"pathway":[{"term_id":"R-HSA-8953854","term_label":"Metabolism of RNA","supporting_discovery_ids":[0,3,4]}],"complexes":["RES complex"],"partners":["BUD13","PML1","APAF1"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q9Y388","full_name":"RNA-binding motif protein, X-linked 2","aliases":[],"length_aa":322,"mass_kda":37.3,"function":"Involved in pre-mRNA splicing as component of the activated spliceosome. As a component of the minor spliceosome, involved in the splicing of U12-type introns in pre-mRNAs (Probable)","subcellular_location":"Nucleus","url":"https://www.uniprot.org/uniprotkb/Q9Y388/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":true,"resolved_as":"","url":"https://depmap.org/portal/gene/RBMX2","classification":"Common Essential","n_dependent_lines":1072,"n_total_lines":1208,"dependency_fraction":0.8874172185430463},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[{"gene":"COMMD2","stoichiometry":10.0},{"gene":"COMMD6","stoichiometry":10.0},{"gene":"GNL3","stoichiometry":10.0},{"gene":"RANBP2","stoichiometry":10.0},{"gene":"COMMD4","stoichiometry":4.0},{"gene":"CSNK2B","stoichiometry":0.2},{"gene":"DDX21","stoichiometry":0.2},{"gene":"DHX9","stoichiometry":0.2},{"gene":"HNRNPL","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/search/RBMX2","total_profiled":1310},"omim":[{"mim_id":"301162","title":"RNA-BINDING MOTIF PROTEIN, X-LINKED, 2; RBMX2","url":"https://www.omim.org/entry/301162"},{"mim_id":"300199","title":"RNA-BINDING MOTIF PROTEIN, X CHROMOSOME; RBMX","url":"https://www.omim.org/entry/300199"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Supported","locations":[{"location":"Nuclear membrane","reliability":"Supported"},{"location":"Nucleoli","reliability":"Additional"},{"location":"Endoplasmic reticulum","reliability":"Additional"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/RBMX2"},"hgnc":{"alias_symbol":["CGI-79","Snu17"],"prev_symbol":[]},"alphafold":{"accession":"Q9Y388","domains":[{"cath_id":"3.30.70.330","chopping":"2-15_37-115","consensus_level":"medium","plddt":93.6359,"start":2,"end":115}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9Y388","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q9Y388-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q9Y388-F1-predicted_aligned_error_v6.png","plddt_mean":63.66},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=RBMX2","jax_strain_url":"https://www.jax.org/strain/search?query=RBMX2"},"sequence":{"accession":"Q9Y388","fasta_url":"https://rest.uniprot.org/uniprotkb/Q9Y388.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q9Y388/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9Y388"}},"corpus_meta":[{"pmid":"19033360","id":"PMC_19033360","title":"Structure of the yeast Pml1 splicing factor and its integration into the RES complex.","date":"2008","source":"Nucleic acids research","url":"https://pubmed.ncbi.nlm.nih.gov/19033360","citation_count":37,"is_preprint":false},{"pmid":"11287609","id":"PMC_11287609","title":"A novel yeast U2 snRNP protein, Snu17p, is required for the first catalytic step of splicing and for progression of spliceosome assembly.","date":"2001","source":"Molecular and cellular biology","url":"https://pubmed.ncbi.nlm.nih.gov/11287609","citation_count":33,"is_preprint":false},{"pmid":"26416664","id":"PMC_26416664","title":"Global comparison of chromosome X genes of pulmonary telocytes with mesenchymal stem cells, fibroblasts, alveolar type II cells, airway epithelial cells, and lymphocytes.","date":"2015","source":"Journal of translational medicine","url":"https://pubmed.ncbi.nlm.nih.gov/26416664","citation_count":31,"is_preprint":false},{"pmid":"29330354","id":"PMC_29330354","title":"The RES complex is required for efficient transformation of the precatalytic B spliceosome into an activated Bact complex.","date":"2018","source":"Genes & development","url":"https://pubmed.ncbi.nlm.nih.gov/29330354","citation_count":22,"is_preprint":false},{"pmid":"29969449","id":"PMC_29969449","title":"RES complex is associated with intron definition and required for zebrafish early embryogenesis.","date":"2018","source":"PLoS genetics","url":"https://pubmed.ncbi.nlm.nih.gov/29969449","citation_count":21,"is_preprint":false},{"pmid":"30428738","id":"PMC_30428738","title":"Combined treatment with modulated electro-hyperthermia and an autophagy inhibitor effectively inhibit ovarian and cervical cancer growth.","date":"2018","source":"International journal of hyperthermia : the official journal of European Society for Hyperthermic Oncology, North American Hyperthermia Group","url":"https://pubmed.ncbi.nlm.nih.gov/30428738","citation_count":19,"is_preprint":false},{"pmid":"18948206","id":"PMC_18948206","title":"Molecular cloning and expression analysis of three Mx isoforms of rock bream, Oplegnathus fasciatus.","date":"2008","source":"Fish & shellfish immunology","url":"https://pubmed.ncbi.nlm.nih.gov/18948206","citation_count":18,"is_preprint":false},{"pmid":"16710889","id":"PMC_16710889","title":"Pinelliae Rhizoma herbal-acupuncture solution induced apoptosis in human cervical cancer cells, SNU-17.","date":"2006","source":"The American journal of Chinese medicine","url":"https://pubmed.ncbi.nlm.nih.gov/16710889","citation_count":13,"is_preprint":false},{"pmid":"23118884","id":"PMC_23118884","title":"Apparent defect in yeast bud-site selection due to a specific failure to splice the pre-mRNA of a regulator of cell-type-specific transcription.","date":"2012","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/23118884","citation_count":13,"is_preprint":false},{"pmid":"17012841","id":"PMC_17012841","title":"Enhanced specificity of the p53 family proteins-based adenoviral gene therapy in uterine cervical cancer cells with E2F1-responsive promoters.","date":"2006","source":"Cancer biology & therapy","url":"https://pubmed.ncbi.nlm.nih.gov/17012841","citation_count":11,"is_preprint":false},{"pmid":"16884378","id":"PMC_16884378","title":"Reverse transcription-polymerase chain reaction and western blotting analysis for detection of p63 isoforms in uterine cervical cancers.","date":"2006","source":"International journal of gynecological cancer : official journal of the International Gynecological Cancer Society","url":"https://pubmed.ncbi.nlm.nih.gov/16884378","citation_count":10,"is_preprint":false},{"pmid":"33718289","id":"PMC_33718289","title":"Theileria annulata Subtelomere-Encoded Variable Secreted Protein-TA05575 Binds to Bovine RBMX2.","date":"2021","source":"Frontiers in cellular and infection microbiology","url":"https://pubmed.ncbi.nlm.nih.gov/33718289","citation_count":6,"is_preprint":false},{"pmid":"28440422","id":"PMC_28440422","title":"Variable TERRA abundance and stability in cervical cancer cells.","date":"2017","source":"International journal of molecular medicine","url":"https://pubmed.ncbi.nlm.nih.gov/28440422","citation_count":6,"is_preprint":false},{"pmid":"34914762","id":"PMC_34914762","title":"Alu element in the RNA binding motif protein, X-linked 2 (RBMX2) gene found to be linked to bipolar disorder.","date":"2021","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/34914762","citation_count":2,"is_preprint":false},{"pmid":"39308873","id":"PMC_39308873","title":"Host factor RBMX2 promotes epithelial cell apoptosis by downregulating APAF-1's Retention Intron after Mycobacterium bovis infection.","date":"2024","source":"Frontiers in immunology","url":"https://pubmed.ncbi.nlm.nih.gov/39308873","citation_count":2,"is_preprint":false},{"pmid":"41277807","id":"PMC_41277807","title":"RBMX2 links Mycobacterium bovis infection to epithelial-mesenchymal transition and lung cancer progression.","date":"2025","source":"eLife","url":"https://pubmed.ncbi.nlm.nih.gov/41277807","citation_count":1,"is_preprint":false},{"pmid":"40556335","id":"PMC_40556335","title":"Escape genes from X-chromosome inactivation: new insights into candidate genes for intellectual disability in females.","date":"2025","source":"The world journal of biological psychiatry : the official journal of the World Federation of Societies of Biological Psychiatry","url":"https://pubmed.ncbi.nlm.nih.gov/40556335","citation_count":1,"is_preprint":false},{"pmid":null,"id":"bio_10.1101_2025.04.15.648920","title":"RBMX2: A Pivotal Regulator Linking  <i>Mycobacterium bovis</i>  Infection to Epithelial-Mesenchymal Transition and Lung Cancer Progression","date":"2025-04-18","source":"bioRxiv","url":"https://doi.org/10.1101/2025.04.15.648920","citation_count":0,"is_preprint":true}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":11706,"output_tokens":2188,"usd":0.033969,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":9125,"output_tokens":2663,"usd":0.0561,"stage2_stop_reason":"end_turn"},"total_usd":0.090069,"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\": 2001,\n      \"finding\": \"Snu17p (yeast ortholog of RBMX2) was identified as a U2 snRNP-associated protein required for the first catalytic step of pre-mRNA splicing and for progression of spliceosome assembly; its deletion stabilizes U1 snRNP within the spliceosome and prevents U4 snRNP dissociation, blocking the transition to the catalytically active complex.\",\n      \"method\": \"Protein microsequencing, co-immunoprecipitation of snRNPs and pre-mRNA, spliceosome assembly by nondenaturing gel electrophoresis, in vitro splicing complementation with recombinant Snu17p\",\n      \"journal\": \"Molecular and cellular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 / Strong — in vitro splicing complementation with recombinant protein, snRNP co-IP, spliceosome assembly analysis, multiple orthogonal methods in one study\",\n      \"pmids\": [\"11287609\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2008,\n      \"finding\": \"Pml1 (RES complex subunit) binds directly to Snu17 (RBMX2 ortholog), which itself contacts Bud13; this hierarchical protein-protein interaction defines the architecture of the trimeric RES complex. The Pml1 FHA domain phosphothreonine-binding pocket mutation did not affect splicing.\",\n      \"method\": \"X-ray crystallography of Pml1, production of recombinant sub-complexes, serial truncation and mutagenesis of RES subunits, alternative splice-site choice splicing assay\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — crystal structure combined with recombinant complex reconstitution and mutagenesis defining binding interfaces\",\n      \"pmids\": [\"19033360\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"Ist3/Snu17 (RBMX2 yeast ortholog) is specifically required for splicing of MATa1 pre-mRNA in diploid yeast cells; loss of Ist3 causes ectopic expression of the haploid-specific Axl1 protein and disrupts bipolar budding, placing Snu17/RES function upstream of MATa1-dependent cell-type transcriptional control.\",\n      \"method\": \"Genetic deletion, in vivo pre-mRNA splicing analysis, epistasis with axl1 deletion, bud-site selection assay\",\n      \"journal\": \"PloS one\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — clean genetic epistasis with specific phenotypic readout, single lab\",\n      \"pmids\": [\"23118884\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"The RES complex (containing Snu17/RBMX2 ortholog) is required for efficient transformation of the precatalytic B spliceosome into the activated Bact complex; in the absence of Snu17, Pml1 and Bud13 recruitment to the spliceosome is abolished or reduced, and Prp2 binds prematurely and disassembles the structurally compromised ΔRES B complexes, suggesting a proofreading role for Prp2.\",\n      \"method\": \"Affinity purification of yeast spliceosomes, native gel spliceosome assembly analysis, in vitro disassembly assay with recombinant Prp2/Spp2/UTP, genetic deletion of RES subunits\",\n      \"journal\": \"Genes & development\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 / Strong — multiple orthogonal biochemical methods (affinity purification, in vitro reconstitution, spliceosome assembly), single lab with rigorous controls\",\n      \"pmids\": [\"29330354\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"The vertebrate RES complex (including rbmx2/snu17 in zebrafish) is required for splicing of a specific subset of introns characterized by short length, high GC content, and flanking GC-depleted exons (features of intron definition); loss-of-function of rbmx2 causes widespread mis-splicing, increased neural cell death, and decreased differentiated neurons during early development.\",\n      \"method\": \"CRISPR/Cas9 loss-of-function mutants in zebrafish, transcriptome-wide splicing analysis (RNA-seq), computational modeling of RES-dependent intron features\",\n      \"journal\": \"PLoS genetics\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — clean vertebrate loss-of-function with transcriptome-wide phenotypic readout and replicated across three RES subunit mutants\",\n      \"pmids\": [\"29969449\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"The Theileria annulata secreted protein TA05575 physically interacts with bovine RBMX2, as confirmed by co-immunoprecipitation and bimolecular fluorescence complementation (BiFC); the interacting pair co-localizes in intracellular compartments of HEK293T cells.\",\n      \"method\": \"Yeast two-hybrid screening, co-immunoprecipitation, BiFC assay, confocal microscopy, flow cytometry\",\n      \"journal\": \"Frontiers in cellular and infection microbiology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2-3 / Moderate — reciprocal interaction confirmed by Co-IP and BiFC, single lab, two orthogonal methods\",\n      \"pmids\": [\"33718289\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"RBMX2 promotes apoptosis of bovine epithelial cells during M. bovis infection by upregulating and binding to APAF-1, leading to alternative splicing of APAF-1 as a retention intron; RBMX2 knockout cells showed reduced apoptosis-associated splicing changes after infection.\",\n      \"method\": \"RBMX2 knockout in EBL cells, transcriptome sequencing, alternative splicing transcriptome sequencing, protein/molecular docking, molecular dynamics simulations, RT-qPCR\",\n      \"journal\": \"Frontiers in immunology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2-3 / Moderate — KO with transcriptome-wide readout and molecular docking, single lab; docking/MD is computational so functional binding not biochemically reconstituted\",\n      \"pmids\": [\"39308873\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"RBMX2 suppresses cell adhesion and tight junction formation while enhancing M. bovis adhesion and invasion through activation of the p65 signaling pathway; it also promotes epithelial-mesenchymal transition via the p65/MMP-9 pathway during M. bovis infection.\",\n      \"method\": \"Transcriptomics, proteomics, metabolomics, cell adhesion assays, ChIP-PCR, Western blotting, immunofluorescence, M. bovis-induced EMT model in BoMac-EBL cells and H1299 cells\",\n      \"journal\": \"eLife\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2-3 / Moderate — multiple orthogonal omics and functional assays (cell adhesion, ChIP-PCR, Western blot), single lab, infection-context\",\n      \"pmids\": [\"41277807\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"RBMX2 (Snu17 in yeast) is the central scaffold subunit of the trimeric RES (retention and splicing) complex, where it directly binds Bud13 and recruits Pml1, and functions in pre-mRNA splicing by facilitating B-to-Bact spliceosome activation; it is specifically required for splicing of short, GC-rich introns defined by intron definition, and in vertebrates is essential for early neural development, while additional studies indicate it can bind APAF-1 pre-mRNA to regulate alternative splicing and apoptosis, and modulates cell adhesion and EMT via p65/MMP-9 signaling during bacterial infection.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"RBMX2 is the central scaffold subunit of the trimeric RES (retention and splicing) complex, functioning in pre-mRNA splicing by promoting the progression of spliceosome assembly toward catalytic activation [#0, #3]. Its yeast ortholog Snu17 directly binds Bud13 and recruits Pml1, with hierarchical protein-protein contacts defining the architecture of the RES complex [#1]. Mechanistically, RES is required for efficient transformation of the precatalytic B spliceosome into the activated Bact complex; in its absence, recruitment of Pml1 and Bud13 to the spliceosome is lost and the splicing helicase Prp2 binds prematurely and disassembles the structurally compromised complexes, defining a checkpoint at B-to-Bact activation [#3]. In vertebrates, RBMX2/RES is specifically required for splicing of short, GC-rich introns defined by intron definition, and its loss causes widespread mis-splicing, increased neural cell death, and impaired neuronal differentiation during early development [#4]. Beyond its core splicing role, RBMX2 binds APAF-1 pre-mRNA to drive intron-retention alternative splicing and promote apoptosis [#6], and modulates cell adhesion and epithelial-mesenchymal transition via p65/MMP-9 signaling during bacterial infection [#5, #7].\",\n  \"teleology\": [\n    {\n      \"year\": 2001,\n      \"claim\": \"Established that the RBMX2 ortholog is a U2 snRNP-associated factor needed to advance spliceosome assembly, answering whether it acts before or during catalysis.\",\n      \"evidence\": \"Protein microsequencing, snRNP co-IP, native-gel spliceosome assembly, and in vitro splicing complementation with recombinant Snu17p in yeast\",\n      \"pmids\": [\"11287609\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not define the protein partners that anchor Snu17 within the spliceosome\", \"Vertebrate function not addressed\"]\n    },\n    {\n      \"year\": 2008,\n      \"claim\": \"Resolved the internal architecture of the RES complex, showing RBMX2/Snu17 is the scaffold that bridges Bud13 and Pml1.\",\n      \"evidence\": \"X-ray crystallography of Pml1, recombinant sub-complex reconstitution, serial truncation/mutagenesis, and splice-site choice assays\",\n      \"pmids\": [\"19033360\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not show how RES engages the assembling spliceosome\", \"Pml1 FHA phosphothreonine pocket dispensable, leaving its functional contribution unclear\"]\n    },\n    {\n      \"year\": 2012,\n      \"claim\": \"Connected RES splicing activity to a specific cell-fate output by showing Snu17 is required to splice MATa1 pre-mRNA controlling cell-type identity.\",\n      \"evidence\": \"Genetic deletion, in vivo splicing analysis, epistasis with axl1, and bud-site selection assay in diploid yeast\",\n      \"pmids\": [\"23118884\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Substrate specificity determinants not defined\", \"Single-lab genetic study\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Defined the precise step RBMX2/RES controls, showing it is required for B-to-Bact transition and that its loss exposes spliceosomes to premature Prp2-mediated disassembly.\",\n      \"evidence\": \"Affinity purification of yeast spliceosomes, native-gel assembly analysis, and in vitro disassembly with recombinant Prp2/Spp2/UTP\",\n      \"pmids\": [\"29330354\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Molecular basis of Prp2 proofreading recognition not detailed\", \"Yeast-based; vertebrate mechanism inferred separately\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Extended RBMX2 function to vertebrates, identifying the intron features it acts on and linking its loss to neural developmental defects.\",\n      \"evidence\": \"CRISPR/Cas9 loss-of-function in zebrafish, transcriptome-wide RNA-seq splicing analysis, and computational modeling of RES-dependent introns across three RES subunit mutants\",\n      \"pmids\": [\"29969449\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Mechanism linking mis-splicing to neural cell death not resolved\", \"Direct RNA targets in mammals not enumerated\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Identified a pathogen-derived interactor of RBMX2, implicating the protein in host-pathogen interaction beyond canonical splicing.\",\n      \"evidence\": \"Yeast two-hybrid, co-IP, BiFC, and confocal co-localization in HEK293T cells with Theileria annulata TA05575\",\n      \"pmids\": [\"33718289\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Functional consequence of the interaction not established\", \"Single lab, heterologous cell system\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Linked RBMX2 to apoptosis regulation by showing it drives intron-retention alternative splicing of APAF-1 during bacterial infection.\",\n      \"evidence\": \"RBMX2 knockout in EBL cells, transcriptome and alternative-splicing sequencing, molecular docking/dynamics, and RT-qPCR in M. bovis infection\",\n      \"pmids\": [\"39308873\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"RBMX2-APAF-1 binding shown computationally, not biochemically reconstituted\", \"Single-lab, infection-specific context\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Implicated RBMX2 in cell adhesion and EMT, showing it suppresses tight-junction formation and promotes invasion via p65/MMP-9 signaling.\",\n      \"evidence\": \"Multi-omics, cell adhesion assays, ChIP-PCR, Western blot, and immunofluorescence in M. bovis EMT models\",\n      \"pmids\": [\"41277807\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Mechanism connecting splicing scaffold function to p65 activation unclear\", \"Single lab, infection-context only\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How RBMX2's core role as a splicing scaffold mechanistically gives rise to its reported infection-associated roles in apoptosis, adhesion, and EMT remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No structural model of the vertebrate RES complex on the spliceosome\", \"Direct mammalian RNA targets not comprehensively mapped\", \"Causal link between splicing scaffold activity and p65/MMP-9 signaling not established\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0003723\", \"supporting_discovery_ids\": [0, 6]},\n      {\"term_id\": \"GO:0060090\", \"supporting_discovery_ids\": [1, 3]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [0, 5]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-8953854\", \"supporting_discovery_ids\": [0, 3, 4]}\n    ],\n    \"complexes\": [\"RES complex\"],\n    \"partners\": [\"BUD13\", \"PML1\", \"APAF1\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":4,"faith_total":5,"faith_pct":80.0}}