{"gene":"BUD13","run_date":"2026-04-28T17:12:38","timeline":{"discoveries":[{"year":2019,"finding":"BUD13 functions as an RNA-binding protein that acts at a specific intron of Irf7 to promote splicing and counteract intron retention (IR). Deficiency of BUD13 leads to increased IR, decreased mature Irf7 transcript and protein levels, and a dampened type I interferon response, impairing macrophage resistance to VSV infection. Global CLIP analysis revealed a subset of introns with shared characteristics that are spliced in a BUD13-dependent manner.","method":"RNA-binding protein identification, BUD13 knockdown, cross-linking immunoprecipitation (CLIP), global IR analysis, VSV infection assay","journal":"Molecular Cell","confidence":"High","confidence_rationale":"Tier 2 — multiple orthogonal methods (CLIP, KD with defined phenotype, global transcriptomics) in a single rigorous study","pmids":["30639243"],"is_preprint":false},{"year":2022,"finding":"BUD13 is a component of the retention and splicing (RES) complex. A homozygous nonsense variant in BUD13 causing alternative splicing leads to a stable truncated protein. Loss of full-length BUD13 results in elevated intron retention genome-wide, global reduction of spliceosomal proteins, and nuclear morphology defects (multiple invaginations) in patient dermal fibroblasts. Overexpression of either BUD13 isoform normalized nuclear morphology.","method":"Exome sequencing, RNA sequencing, proteomics, immunoblotting, immunostaining, electron microscopy, overexpression rescue studies","journal":"Genetics in Medicine","confidence":"High","confidence_rationale":"Tier 1-2 — multiple orthogonal methods (RNA-seq, proteomics, rescue) with patient-derived fibroblasts","pmids":["35670808"],"is_preprint":false},{"year":2023,"finding":"BUD13 functions as an endogenous inhibitor of the E3 ubiquitin ligase Fbw7, stabilizing Fbw7 oncogenic substrates. Cancer-associated BUD13 mutations R156C and R230Q evade RSK3-mediated phosphorylation and interfere with Fbw7-Cul1 complex formation, thereby enhancing oncogenicity and promoting colon cancer growth.","method":"Algorithm-based somatic mutation analysis, in vitro phosphorylation assays, Co-IP (Fbw7-Cul1 complex), cancer cell growth assays, mechanistic mutagenesis","journal":"Journal of Experimental Medicine","confidence":"Medium","confidence_rationale":"Tier 2 — multiple methods (Co-IP, mutagenesis, functional assays) but single study","pmids":["37382881"],"is_preprint":false},{"year":2022,"finding":"METTL3-mediated m6A methylation enhances BUD13 mRNA stability and upregulates BUD13 expression. BUD13 in turn enhances CDK12 mRNA stability, and CDK12 phosphorylates MBNL1 to regulate vasculogenic mimicry formation in glioblastoma cells. Knockdown of BUD13 inhibited VM formation and reduced tumor volume in vivo.","method":"m6A methylation assay, mRNA stability assay, knockdown (siRNA/shRNA), in vivo xenograft, immunoblotting","journal":"Cell Death & Disease","confidence":"Medium","confidence_rationale":"Tier 2-3 — multiple functional assays but mechanistic links between BUD13 and CDK12 mRNA stability rely primarily on KD experiments without direct binding reconstitution","pmids":["36463205"],"is_preprint":false},{"year":2020,"finding":"BUD13 binds to the long non-coding RNA DBH-AS1 and stabilizes FN1 mRNA, promoting FN1 expression. The DBH-AS1/BUD13/FN1 axis regulates proliferation, migration, and invasion of diffuse large B-cell lymphoma cells.","method":"RNA immunoprecipitation (RIP), knockdown/overexpression rescue assays, mRNA stability assay","journal":"Cell Biology International","confidence":"Low","confidence_rationale":"Tier 3 — single lab, limited mechanistic detail on BUD13-RNA binding","pmids":["32091157"],"is_preprint":false},{"year":2021,"finding":"CircSERPINA3 recruits BUD13 to stabilize SERPINA3 mRNA, thereby promoting SERPINA3 expression and inhibiting apoptosis while promoting aerobic glycolysis and autophagy in prostate cancer cells.","method":"RIP, RNA pull-down, mRNA stability assay, gain/loss-of-function assays","journal":"Journal of Translational Medicine","confidence":"Low","confidence_rationale":"Tier 3 — single lab, single method for BUD13-RNA interaction","pmids":["34861864"],"is_preprint":false},{"year":2024,"finding":"Circ_001653 recruits BUD13 to activate the KEAP1/Nrf2/HO-1 signaling pathway, attenuating apoptosis, oxidative stress, and inflammation in sepsis-associated acute kidney injury models.","method":"RIP, gain/loss-of-function assays, LPS-stimulated cell model, CLP rat model, western blot","journal":"Journal of Inflammation","confidence":"Low","confidence_rationale":"Tier 3 — single lab, mechanistic link between BUD13 and KEAP1/Nrf2/HO-1 not directly demonstrated","pmids":["39289683"],"is_preprint":false},{"year":2023,"finding":"RNASEH1-AS1 lncRNA recruits BUD13 to stabilize ANXA2 mRNA, thereby activating the Wnt/β-catenin pathway and promoting colorectal cancer progression.","method":"RIP, RNA pull-down, ChIP, nucleoplasmic separation, FISH, in vivo tumor model","journal":"Neoplasma","confidence":"Low","confidence_rationale":"Tier 3 — single lab, BUD13 role inferred from recruitment assays without direct mechanistic dissection","pmids":["38053379"],"is_preprint":false},{"year":2021,"finding":"Rare variants in BUD13, a component of the retention and splicing (RES) complex, co-segregate with specific language impairment (SLI) in a family study, and loss-of-function mutations in BUD13 cause profound neural phenotypes in animal models, implicating BUD13's splicing function in neural/language development.","method":"Whole-exome sequencing, Sanger sequencing, co-segregation analysis, animal model loss-of-function","journal":"Brain Sciences","confidence":"Medium","confidence_rationale":"Tier 2 — genetic evidence with animal model support, though mechanistic detail on BUD13's neural role is limited","pmids":["35053791"],"is_preprint":false}],"current_model":"BUD13 is a component of the retention and splicing (RES) complex that functions as an RNA-binding protein to promote splicing and counteract intron retention at specific introns (most clearly demonstrated for Irf7), thereby regulating mature transcript levels and downstream signaling (e.g., type I interferon response); it also acts as an endogenous inhibitor of the Fbw7 ubiquitin ligase complex, stabilizing Fbw7 substrates, and is subject to RSK3-mediated phosphorylation and METTL3-mediated m6A regulation of its own mRNA stability."},"narrative":{"teleology":[{"year":2019,"claim":"The mechanistic question of how specific introns are protected from retention was answered by showing BUD13 directly binds a defined intron subset (via CLIP) and that its loss at the Irf7 locus impairs mature mRNA production and type I interferon signaling, establishing BUD13 as a selective splicing-promoting RNA-binding protein.","evidence":"CLIP, BUD13 knockdown with global IR analysis, and VSV infection assay in macrophages","pmids":["30639243"],"confidence":"High","gaps":["Structural basis for BUD13 recognition of its target intron features not determined","Whether BUD13 splicing targets beyond Irf7 have comparable functional consequences remains unexplored","Relationship between BUD13 and other RES complex subunits in target selection not dissected"]},{"year":2020,"claim":"BUD13 was shown to stabilize specific mRNAs when recruited by non-coding RNAs (lncRNA DBH-AS1 stabilizing FN1 mRNA), extending its function beyond splicing to post-transcriptional mRNA stabilization in cancer contexts.","evidence":"RIP, knockdown/overexpression rescue, and mRNA stability assays in diffuse large B-cell lymphoma cells","pmids":["32091157"],"confidence":"Low","gaps":["Direct binding between BUD13 and FN1 mRNA not demonstrated with purified components","Whether mRNA stabilization is independent of BUD13's splicing function not addressed","Single-laboratory finding without independent replication"]},{"year":2021,"claim":"Genetic evidence linked BUD13 to neural development and language function, answering whether its splicing role has neurodevelopmental consequences: rare BUD13 variants co-segregated with specific language impairment in a family, and animal models confirmed neural phenotypes upon loss of function.","evidence":"Whole-exome sequencing with co-segregation analysis in an SLI family, plus animal model loss-of-function studies","pmids":["35053791"],"confidence":"Medium","gaps":["Specific splicing targets disrupted in neural tissue not identified","Mechanistic pathway from BUD13 loss to language impairment not delineated","Small family study; broader cohort replication needed"]},{"year":2022,"claim":"Human genetic evidence established that BUD13 is essential for genome-wide splicing fidelity and nuclear architecture: a homozygous nonsense variant caused global intron retention, reduced spliceosomal protein levels, and nuclear envelope invaginations — all rescued by BUD13 re-expression — confirming its non-redundant role in the RES complex.","evidence":"Patient exome sequencing, RNA-seq, proteomics, electron microscopy, and overexpression rescue in patient-derived dermal fibroblasts","pmids":["35670808"],"confidence":"High","gaps":["Whether nuclear morphology defects are a direct consequence of splicing failure or reflect an independent BUD13 function is unresolved","Which spliceosomal proteins are downregulated due to intron retention versus other mechanisms not distinguished","Genotype-phenotype correlation across additional patients not available"]},{"year":2022,"claim":"METTL3-mediated m6A modification was shown to regulate BUD13 expression itself by stabilizing BUD13 mRNA, and BUD13 in turn stabilized CDK12 mRNA to drive vasculogenic mimicry in glioblastoma, placing BUD13 within an epitranscriptomic regulatory circuit.","evidence":"m6A methylation and mRNA stability assays, knockdown, and in vivo xenograft in glioblastoma models","pmids":["36463205"],"confidence":"Medium","gaps":["Direct binding of BUD13 to CDK12 mRNA not reconstituted in vitro","Whether m6A regulation of BUD13 occurs in non-cancer contexts is unknown","Contribution of BUD13's splicing versus mRNA stabilization function not separated"]},{"year":2023,"claim":"BUD13 was found to have a splicing-independent oncogenic function as an endogenous Fbw7 inhibitor: it disrupts Fbw7–Cul1 complex formation, and cancer-associated mutations (R156C, R230Q) that evade RSK3 phosphorylation amplify this inhibitory activity, stabilizing Fbw7 substrates and promoting colon cancer.","evidence":"Co-immunoprecipitation of Fbw7–Cul1 complex, in vitro phosphorylation assays, cancer-associated mutagenesis, and tumor growth assays","pmids":["37382881"],"confidence":"Medium","gaps":["Structural basis for BUD13–Fbw7 interaction not resolved","Whether wild-type BUD13 inhibition of Fbw7 is physiologically relevant in non-cancer settings remains unclear","Independent validation of BUD13 as an Fbw7 inhibitor by another group not yet available"]},{"year":null,"claim":"It remains unknown how BUD13's dual roles — as a splicing factor within the RES complex and as an Fbw7 inhibitor — are coordinated, what determines its allocation between these functions, and which BUD13 domains mediate each activity independently.","evidence":"","pmids":[],"confidence":"High","gaps":["No structural model of BUD13 in complex with RES subunits or Fbw7","Domain-specific separation of splicing versus Fbw7-inhibitory functions not performed","Full spectrum of BUD13-dependent splicing targets across tissues not mapped"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0003723","term_label":"RNA binding","supporting_discovery_ids":[0,1,4,5]},{"term_id":"GO:0098772","term_label":"molecular function regulator activity","supporting_discovery_ids":[2]}],"localization":[{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[1]}],"pathway":[{"term_id":"R-HSA-8953854","term_label":"Metabolism of RNA","supporting_discovery_ids":[0,1]},{"term_id":"R-HSA-168256","term_label":"Immune System","supporting_discovery_ids":[0]},{"term_id":"R-HSA-1643685","term_label":"Disease","supporting_discovery_ids":[2]}],"complexes":["RES complex"],"partners":["FBW7","RSK3","CUL1","IRF7"],"other_free_text":[]},"mechanistic_narrative":"BUD13 is a core component of the retention and splicing (RES) complex that functions as an RNA-binding protein to promote efficient pre-mRNA splicing and counteract intron retention genome-wide. CLIP-based studies demonstrate that BUD13 binds directly to a subset of introns with shared sequence characteristics, and its loss leads to elevated intron retention, reduced spliceosomal protein levels, nuclear morphology defects, and impaired production of mature transcripts such as Irf7, thereby dampening the type I interferon response [PMID:30639243, PMID:35670808]. Beyond splicing, BUD13 acts as an endogenous inhibitor of the Fbw7 E3 ubiquitin ligase by interfering with Fbw7–Cul1 complex assembly; cancer-associated BUD13 mutations that evade RSK3-mediated phosphorylation enhance Fbw7 substrate stability and promote colon cancer growth [PMID:37382881]. Homozygous loss-of-function variants in BUD13 cause a Mendelian disorder characterized by global intron retention and nuclear envelope abnormalities, and rare variants co-segregate with specific language impairment in family studies [PMID:35670808, PMID:35053791]."},"prefetch_data":{"uniprot":{"accession":"Q9BRD0","full_name":"BUD13 homolog","aliases":[],"length_aa":619,"mass_kda":70.5,"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","subcellular_location":"Nucleus","url":"https://www.uniprot.org/uniprotkb/Q9BRD0/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":true,"resolved_as":"","url":"https://depmap.org/portal/gene/BUD13","classification":"Common Essential","n_dependent_lines":933,"n_total_lines":1208,"dependency_fraction":0.7723509933774835},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[{"gene":"CPSF6","stoichiometry":0.2},{"gene":"TOP1","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/search/BUD13","total_profiled":1310},"omim":[{"mim_id":"621123","title":"ACHALASIA-PROGEROID SYNDROME; ACHPS","url":"https://www.omim.org/entry/621123"},{"mim_id":"620691","title":"BUD13 HOMOLOG; BUD13","url":"https://www.omim.org/entry/620691"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Enhanced","locations":[{"location":"Nucleoplasm","reliability":"Enhanced"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/BUD13"},"hgnc":{"alias_symbol":["MGC13125","fSAP71","Cwc26"],"prev_symbol":[]},"alphafold":{"accession":"Q9BRD0","domains":[{"cath_id":"-","chopping":"462-521","consensus_level":"medium","plddt":86.7165,"start":462,"end":521}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9BRD0","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q9BRD0-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q9BRD0-F1-predicted_aligned_error_v6.png","plddt_mean":59.94},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=BUD13","jax_strain_url":"https://www.jax.org/strain/search?query=BUD13"},"sequence":{"accession":"Q9BRD0","fasta_url":"https://rest.uniprot.org/uniprotkb/Q9BRD0.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q9BRD0/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9BRD0"}},"corpus_meta":[{"pmid":"27827461","id":"PMC_27827461","title":"Association and interaction of APOA5, BUD13, CETP, LIPA and health-related behavior with metabolic syndrome in a Taiwanese population.","date":"2016","source":"Scientific reports","url":"https://pubmed.ncbi.nlm.nih.gov/27827461","citation_count":49,"is_preprint":false},{"pmid":"30639243","id":"PMC_30639243","title":"BUD13 Promotes a Type I Interferon Response by Countering Intron Retention in Irf7.","date":"2019","source":"Molecular cell","url":"https://pubmed.ncbi.nlm.nih.gov/30639243","citation_count":40,"is_preprint":false},{"pmid":"24780069","id":"PMC_24780069","title":"Association of the variants in the BUD13-ZNF259 genes and the risk of hyperlipidaemia.","date":"2014","source":"Journal of cellular and molecular medicine","url":"https://pubmed.ncbi.nlm.nih.gov/24780069","citation_count":38,"is_preprint":false},{"pmid":"32091157","id":"PMC_32091157","title":"Long non-coding RNA DBH-AS1 promotes cancer progression in diffuse large B-cell lymphoma by targeting FN1 via RNA-binding protein BUD13.","date":"2020","source":"Cell biology international","url":"https://pubmed.ncbi.nlm.nih.gov/32091157","citation_count":25,"is_preprint":false},{"pmid":"24989072","id":"PMC_24989072","title":"Association between the MLX interacting protein-like, BUD13 homolog and zinc finger protein 259 gene polymorphisms and serum lipid levels.","date":"2014","source":"Scientific reports","url":"https://pubmed.ncbi.nlm.nih.gov/24989072","citation_count":25,"is_preprint":false},{"pmid":"34861864","id":"PMC_34861864","title":"CircSERPINA3 regulates SERPINA3-mediated apoptosis, autophagy and aerobic glycolysis of prostate cancer cells by competitively binding to MiR-653-5p and recruiting BUD13.","date":"2021","source":"Journal of translational medicine","url":"https://pubmed.ncbi.nlm.nih.gov/34861864","citation_count":22,"is_preprint":false},{"pmid":"26397108","id":"PMC_26397108","title":"Effects of Polymorphisms in APOA4-APOA5-ZNF259-BUD13 Gene Cluster on Plasma Levels of Triglycerides and Risk of Coronary Heart Disease in a Chinese Han Population.","date":"2015","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/26397108","citation_count":20,"is_preprint":false},{"pmid":"36463205","id":"PMC_36463205","title":"The mechanism of BUD13 m6A methylation mediated MBNL1-phosphorylation by CDK12 regulating the vasculogenic mimicry in glioblastoma cells.","date":"2022","source":"Cell death & disease","url":"https://pubmed.ncbi.nlm.nih.gov/36463205","citation_count":18,"is_preprint":false},{"pmid":"28245265","id":"PMC_28245265","title":"Admixture mapping in two Mexican samples identifies significant associations of locus ancestry with triglyceride levels in the BUD13/ZNF259/APOA5 region and fine mapping points to rs964184 as the main driver of the association signal.","date":"2017","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/28245265","citation_count":17,"is_preprint":false},{"pmid":"35053791","id":"PMC_35053791","title":"Family-Based Whole-Exome Analysis of Specific Language Impairment (SLI) Identifies Rare Variants in BUD13, a Component of the Retention and Splicing (RES) Complex.","date":"2021","source":"Brain sciences","url":"https://pubmed.ncbi.nlm.nih.gov/35053791","citation_count":16,"is_preprint":false},{"pmid":"31165758","id":"PMC_31165758","title":"Association of BUD13-ZNF259-APOA5-APOA1-SIK3 cluster polymorphism in 11q23.3 and structure of APOA5 with increased plasma triglyceride levels in a Korean population.","date":"2019","source":"Scientific reports","url":"https://pubmed.ncbi.nlm.nih.gov/31165758","citation_count":14,"is_preprint":false},{"pmid":"33986338","id":"PMC_33986338","title":"Kernel machine SNP set analysis finds the association of BUD13, ZPR1, and APOA5 variants with metabolic syndrome in Tehran Cardio-metabolic Genetics Study.","date":"2021","source":"Scientific reports","url":"https://pubmed.ncbi.nlm.nih.gov/33986338","citation_count":13,"is_preprint":false},{"pmid":"30631647","id":"PMC_30631647","title":"Functional polymorphisms of the APOA1/C3/A4/A5-ZPR1-BUD13 gene cluster are associated with dyslipidemia in a sex-specific pattern.","date":"2019","source":"PeerJ","url":"https://pubmed.ncbi.nlm.nih.gov/30631647","citation_count":12,"is_preprint":false},{"pmid":"26885234","id":"PMC_26885234","title":"Association study of BUD13-ZNF259 gene rs964184 polymorphism and hemorrhagic stroke risk.","date":"2015","source":"International journal of clinical and experimental medicine","url":"https://pubmed.ncbi.nlm.nih.gov/26885234","citation_count":8,"is_preprint":false},{"pmid":"39289683","id":"PMC_39289683","title":"Circ_001653 alleviates sepsis associated-acute kidney injury by recruiting BUD13 to regulate KEAP1/NRF2/HO-1 signaling pathway.","date":"2024","source":"Journal of inflammation (London, England)","url":"https://pubmed.ncbi.nlm.nih.gov/39289683","citation_count":8,"is_preprint":false},{"pmid":"31181149","id":"PMC_31181149","title":"Interaction of polymorphisms in APOA4-APOA5-ZPR1-BUD13 gene cluster and sleep duration on 5-year lipid changes in middle aged and older Chinese.","date":"2019","source":"Sleep","url":"https://pubmed.ncbi.nlm.nih.gov/31181149","citation_count":8,"is_preprint":false},{"pmid":"25900265","id":"PMC_25900265","title":"Differential Lipid Response to Statins Is Associated With Variants in the BUD13-APOA5 Gene Region.","date":"2015","source":"Journal of cardiovascular pharmacology","url":"https://pubmed.ncbi.nlm.nih.gov/25900265","citation_count":5,"is_preprint":false},{"pmid":"35670808","id":"PMC_35670808","title":"Alternative splicing of BUD13 determines the severity of a developmental disorder with lipodystrophy and progeroid features.","date":"2022","source":"Genetics in medicine : official journal of the American College of Medical Genetics","url":"https://pubmed.ncbi.nlm.nih.gov/35670808","citation_count":4,"is_preprint":false},{"pmid":"37641415","id":"PMC_37641415","title":"Regularized Machine Learning Models for Prediction of Metabolic Syndrome Using GCKR, APOA5, and BUD13 Gene Variants: Tehran Cardiometabolic Genetic Study.","date":"2023","source":"Cell journal","url":"https://pubmed.ncbi.nlm.nih.gov/37641415","citation_count":2,"is_preprint":false},{"pmid":"37382881","id":"PMC_37382881","title":"Somatic gain-of-function mutations in BUD13 promote oncogenesis by disrupting Fbw7 function.","date":"2023","source":"The Journal of experimental medicine","url":"https://pubmed.ncbi.nlm.nih.gov/37382881","citation_count":2,"is_preprint":false},{"pmid":"40665476","id":"PMC_40665476","title":"Genome-wide study links cardiometabolic factors to cognition via APOA4-APOA5-ZPR1-BUD13 and other loci in rural Indians.","date":"2025","source":"Alzheimer's & dementia : the journal of the Alzheimer's Association","url":"https://pubmed.ncbi.nlm.nih.gov/40665476","citation_count":1,"is_preprint":false},{"pmid":"38053379","id":"PMC_38053379","title":"RNASEH1-AS1 induced by H3K27ac stabilizes ANXA2 mRNA to promote the progression of colorectal cancer through recruiting BUD13.","date":"2023","source":"Neoplasma","url":"https://pubmed.ncbi.nlm.nih.gov/38053379","citation_count":0,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":13328,"output_tokens":2129,"usd":0.035959},"stage2":{"model":"claude-opus-4-6","input_tokens":5421,"output_tokens":2173,"usd":0.122145},"total_usd":0.158104,"stage1_batch_id":"msgbatch_01TqNM6p6FsoMBT2jzQTwKBr","stage2_batch_id":"msgbatch_01Ya473eco8sTHbvRymQaU8o","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2019,\n      \"finding\": \"BUD13 functions as an RNA-binding protein that acts at a specific intron of Irf7 to promote splicing and counteract intron retention (IR). Deficiency of BUD13 leads to increased IR, decreased mature Irf7 transcript and protein levels, and a dampened type I interferon response, impairing macrophage resistance to VSV infection. Global CLIP analysis revealed a subset of introns with shared characteristics that are spliced in a BUD13-dependent manner.\",\n      \"method\": \"RNA-binding protein identification, BUD13 knockdown, cross-linking immunoprecipitation (CLIP), global IR analysis, VSV infection assay\",\n      \"journal\": \"Molecular Cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — multiple orthogonal methods (CLIP, KD with defined phenotype, global transcriptomics) in a single rigorous study\",\n      \"pmids\": [\"30639243\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"BUD13 is a component of the retention and splicing (RES) complex. A homozygous nonsense variant in BUD13 causing alternative splicing leads to a stable truncated protein. Loss of full-length BUD13 results in elevated intron retention genome-wide, global reduction of spliceosomal proteins, and nuclear morphology defects (multiple invaginations) in patient dermal fibroblasts. Overexpression of either BUD13 isoform normalized nuclear morphology.\",\n      \"method\": \"Exome sequencing, RNA sequencing, proteomics, immunoblotting, immunostaining, electron microscopy, overexpression rescue studies\",\n      \"journal\": \"Genetics in Medicine\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 — multiple orthogonal methods (RNA-seq, proteomics, rescue) with patient-derived fibroblasts\",\n      \"pmids\": [\"35670808\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"BUD13 functions as an endogenous inhibitor of the E3 ubiquitin ligase Fbw7, stabilizing Fbw7 oncogenic substrates. Cancer-associated BUD13 mutations R156C and R230Q evade RSK3-mediated phosphorylation and interfere with Fbw7-Cul1 complex formation, thereby enhancing oncogenicity and promoting colon cancer growth.\",\n      \"method\": \"Algorithm-based somatic mutation analysis, in vitro phosphorylation assays, Co-IP (Fbw7-Cul1 complex), cancer cell growth assays, mechanistic mutagenesis\",\n      \"journal\": \"Journal of Experimental Medicine\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — multiple methods (Co-IP, mutagenesis, functional assays) but single study\",\n      \"pmids\": [\"37382881\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"METTL3-mediated m6A methylation enhances BUD13 mRNA stability and upregulates BUD13 expression. BUD13 in turn enhances CDK12 mRNA stability, and CDK12 phosphorylates MBNL1 to regulate vasculogenic mimicry formation in glioblastoma cells. Knockdown of BUD13 inhibited VM formation and reduced tumor volume in vivo.\",\n      \"method\": \"m6A methylation assay, mRNA stability assay, knockdown (siRNA/shRNA), in vivo xenograft, immunoblotting\",\n      \"journal\": \"Cell Death & Disease\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2-3 — multiple functional assays but mechanistic links between BUD13 and CDK12 mRNA stability rely primarily on KD experiments without direct binding reconstitution\",\n      \"pmids\": [\"36463205\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"BUD13 binds to the long non-coding RNA DBH-AS1 and stabilizes FN1 mRNA, promoting FN1 expression. The DBH-AS1/BUD13/FN1 axis regulates proliferation, migration, and invasion of diffuse large B-cell lymphoma cells.\",\n      \"method\": \"RNA immunoprecipitation (RIP), knockdown/overexpression rescue assays, mRNA stability assay\",\n      \"journal\": \"Cell Biology International\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 — single lab, limited mechanistic detail on BUD13-RNA binding\",\n      \"pmids\": [\"32091157\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"CircSERPINA3 recruits BUD13 to stabilize SERPINA3 mRNA, thereby promoting SERPINA3 expression and inhibiting apoptosis while promoting aerobic glycolysis and autophagy in prostate cancer cells.\",\n      \"method\": \"RIP, RNA pull-down, mRNA stability assay, gain/loss-of-function assays\",\n      \"journal\": \"Journal of Translational Medicine\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 — single lab, single method for BUD13-RNA interaction\",\n      \"pmids\": [\"34861864\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"Circ_001653 recruits BUD13 to activate the KEAP1/Nrf2/HO-1 signaling pathway, attenuating apoptosis, oxidative stress, and inflammation in sepsis-associated acute kidney injury models.\",\n      \"method\": \"RIP, gain/loss-of-function assays, LPS-stimulated cell model, CLP rat model, western blot\",\n      \"journal\": \"Journal of Inflammation\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 — single lab, mechanistic link between BUD13 and KEAP1/Nrf2/HO-1 not directly demonstrated\",\n      \"pmids\": [\"39289683\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"RNASEH1-AS1 lncRNA recruits BUD13 to stabilize ANXA2 mRNA, thereby activating the Wnt/β-catenin pathway and promoting colorectal cancer progression.\",\n      \"method\": \"RIP, RNA pull-down, ChIP, nucleoplasmic separation, FISH, in vivo tumor model\",\n      \"journal\": \"Neoplasma\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 — single lab, BUD13 role inferred from recruitment assays without direct mechanistic dissection\",\n      \"pmids\": [\"38053379\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"Rare variants in BUD13, a component of the retention and splicing (RES) complex, co-segregate with specific language impairment (SLI) in a family study, and loss-of-function mutations in BUD13 cause profound neural phenotypes in animal models, implicating BUD13's splicing function in neural/language development.\",\n      \"method\": \"Whole-exome sequencing, Sanger sequencing, co-segregation analysis, animal model loss-of-function\",\n      \"journal\": \"Brain Sciences\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — genetic evidence with animal model support, though mechanistic detail on BUD13's neural role is limited\",\n      \"pmids\": [\"35053791\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"BUD13 is a component of the retention and splicing (RES) complex that functions as an RNA-binding protein to promote splicing and counteract intron retention at specific introns (most clearly demonstrated for Irf7), thereby regulating mature transcript levels and downstream signaling (e.g., type I interferon response); it also acts as an endogenous inhibitor of the Fbw7 ubiquitin ligase complex, stabilizing Fbw7 substrates, and is subject to RSK3-mediated phosphorylation and METTL3-mediated m6A regulation of its own mRNA stability.\"\n}\n```","stage2_raw":"```json\n{\n  \"mechanistic_narrative\": \"BUD13 is a core component of the retention and splicing (RES) complex that functions as an RNA-binding protein to promote efficient pre-mRNA splicing and counteract intron retention genome-wide. CLIP-based studies demonstrate that BUD13 binds directly to a subset of introns with shared sequence characteristics, and its loss leads to elevated intron retention, reduced spliceosomal protein levels, nuclear morphology defects, and impaired production of mature transcripts such as Irf7, thereby dampening the type I interferon response [PMID:30639243, PMID:35670808]. Beyond splicing, BUD13 acts as an endogenous inhibitor of the Fbw7 E3 ubiquitin ligase by interfering with Fbw7–Cul1 complex assembly; cancer-associated BUD13 mutations that evade RSK3-mediated phosphorylation enhance Fbw7 substrate stability and promote colon cancer growth [PMID:37382881]. Homozygous loss-of-function variants in BUD13 cause a Mendelian disorder characterized by global intron retention and nuclear envelope abnormalities, and rare variants co-segregate with specific language impairment in family studies [PMID:35670808, PMID:35053791].\",\n  \"teleology\": [\n    {\n      \"year\": 2019,\n      \"claim\": \"The mechanistic question of how specific introns are protected from retention was answered by showing BUD13 directly binds a defined intron subset (via CLIP) and that its loss at the Irf7 locus impairs mature mRNA production and type I interferon signaling, establishing BUD13 as a selective splicing-promoting RNA-binding protein.\",\n      \"evidence\": \"CLIP, BUD13 knockdown with global IR analysis, and VSV infection assay in macrophages\",\n      \"pmids\": [\"30639243\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Structural basis for BUD13 recognition of its target intron features not determined\",\n        \"Whether BUD13 splicing targets beyond Irf7 have comparable functional consequences remains unexplored\",\n        \"Relationship between BUD13 and other RES complex subunits in target selection not dissected\"\n      ]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"BUD13 was shown to stabilize specific mRNAs when recruited by non-coding RNAs (lncRNA DBH-AS1 stabilizing FN1 mRNA), extending its function beyond splicing to post-transcriptional mRNA stabilization in cancer contexts.\",\n      \"evidence\": \"RIP, knockdown/overexpression rescue, and mRNA stability assays in diffuse large B-cell lymphoma cells\",\n      \"pmids\": [\"32091157\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"Direct binding between BUD13 and FN1 mRNA not demonstrated with purified components\",\n        \"Whether mRNA stabilization is independent of BUD13's splicing function not addressed\",\n        \"Single-laboratory finding without independent replication\"\n      ]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Genetic evidence linked BUD13 to neural development and language function, answering whether its splicing role has neurodevelopmental consequences: rare BUD13 variants co-segregated with specific language impairment in a family, and animal models confirmed neural phenotypes upon loss of function.\",\n      \"evidence\": \"Whole-exome sequencing with co-segregation analysis in an SLI family, plus animal model loss-of-function studies\",\n      \"pmids\": [\"35053791\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Specific splicing targets disrupted in neural tissue not identified\",\n        \"Mechanistic pathway from BUD13 loss to language impairment not delineated\",\n        \"Small family study; broader cohort replication needed\"\n      ]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Human genetic evidence established that BUD13 is essential for genome-wide splicing fidelity and nuclear architecture: a homozygous nonsense variant caused global intron retention, reduced spliceosomal protein levels, and nuclear envelope invaginations — all rescued by BUD13 re-expression — confirming its non-redundant role in the RES complex.\",\n      \"evidence\": \"Patient exome sequencing, RNA-seq, proteomics, electron microscopy, and overexpression rescue in patient-derived dermal fibroblasts\",\n      \"pmids\": [\"35670808\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Whether nuclear morphology defects are a direct consequence of splicing failure or reflect an independent BUD13 function is unresolved\",\n        \"Which spliceosomal proteins are downregulated due to intron retention versus other mechanisms not distinguished\",\n        \"Genotype-phenotype correlation across additional patients not available\"\n      ]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"METTL3-mediated m6A modification was shown to regulate BUD13 expression itself by stabilizing BUD13 mRNA, and BUD13 in turn stabilized CDK12 mRNA to drive vasculogenic mimicry in glioblastoma, placing BUD13 within an epitranscriptomic regulatory circuit.\",\n      \"evidence\": \"m6A methylation and mRNA stability assays, knockdown, and in vivo xenograft in glioblastoma models\",\n      \"pmids\": [\"36463205\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Direct binding of BUD13 to CDK12 mRNA not reconstituted in vitro\",\n        \"Whether m6A regulation of BUD13 occurs in non-cancer contexts is unknown\",\n        \"Contribution of BUD13's splicing versus mRNA stabilization function not separated\"\n      ]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"BUD13 was found to have a splicing-independent oncogenic function as an endogenous Fbw7 inhibitor: it disrupts Fbw7–Cul1 complex formation, and cancer-associated mutations (R156C, R230Q) that evade RSK3 phosphorylation amplify this inhibitory activity, stabilizing Fbw7 substrates and promoting colon cancer.\",\n      \"evidence\": \"Co-immunoprecipitation of Fbw7–Cul1 complex, in vitro phosphorylation assays, cancer-associated mutagenesis, and tumor growth assays\",\n      \"pmids\": [\"37382881\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Structural basis for BUD13–Fbw7 interaction not resolved\",\n        \"Whether wild-type BUD13 inhibition of Fbw7 is physiologically relevant in non-cancer settings remains unclear\",\n        \"Independent validation of BUD13 as an Fbw7 inhibitor by another group not yet available\"\n      ]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"It remains unknown how BUD13's dual roles — as a splicing factor within the RES complex and as an Fbw7 inhibitor — are coordinated, what determines its allocation between these functions, and which BUD13 domains mediate each activity independently.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"No structural model of BUD13 in complex with RES subunits or Fbw7\",\n        \"Domain-specific separation of splicing versus Fbw7-inhibitory functions not performed\",\n        \"Full spectrum of BUD13-dependent splicing targets across tissues not mapped\"\n      ]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0003723\", \"supporting_discovery_ids\": [0, 1, 4, 5]},\n      {\"term_id\": \"GO:0098772\", \"supporting_discovery_ids\": [2]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [1]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"GO:0008380\", \"supporting_discovery_ids\": [0, 1]},\n      {\"term_id\": \"R-HSA-8953854\", \"supporting_discovery_ids\": [0, 1]},\n      {\"term_id\": \"R-HSA-168256\", \"supporting_discovery_ids\": [0]},\n      {\"term_id\": \"R-HSA-1643685\", \"supporting_discovery_ids\": [2]}\n    ],\n    \"complexes\": [\n      \"RES complex\"\n    ],\n    \"partners\": [\n      \"FBW7\",\n      \"RSK3\",\n      \"CUL1\",\n      \"IRF7\"\n    ],\n    \"other_free_text\": []\n  }\n}\n```"}