{"gene":"SF3B1","run_date":"2026-06-10T07:46:31","timeline":{"discoveries":[{"year":2011,"finding":"GEX1A (Herboxidiene) directly targets SAP155 (SF3B1) protein, a subunit of SF3b responsible for pre-mRNA splicing, as identified by photoaffinity-labeling derivatives. GEX1A inhibits pre-mRNA splicing by binding to SAP155/SF3B1, thereby impairing SF3b function.","method":"Photoaffinity labeling with GEX1A derivatives, in vitro splicing assays, Western blot","journal":"ACS chemical biology","confidence":"High","confidence_rationale":"Tier 1 / Moderate — direct biochemical photoaffinity labeling identifying the binding target, combined with functional splicing inhibition assays in a single rigorous study","pmids":["21138297"],"is_preprint":false},{"year":2006,"finding":"SF3B1 (SAP155/SF3b155) N-terminal domain contains multiple U2AF65 binding sites that are distinct from the p14 binding site (mapped to residues 396–424). The N-terminal domain adopts a primarily unfolded structure functioning as a scaffold for multiple protein–protein and protein–RNA interactions required for U2 snRNP recruitment to the branch point during splicing.","method":"In vitro binding assays, RNA binding studies, inhibition of splicing in vitro, circular dichroism spectroscopy","journal":"Biochemistry","confidence":"High","confidence_rationale":"Tier 1 / Moderate — multiple orthogonal in vitro assays (binding, CD spectroscopy, splicing inhibition) in a single focused study","pmids":["16906767"],"is_preprint":false},{"year":2006,"finding":"DYRK1A phosphorylates SF3B1 (SAP155) at Thr434 in vitro and in cultured cells; overexpression of DYRK1A increases Thr434 phosphorylation of endogenous SF3B1, while DYRK1A knockdown reduces it. Cyclin E/CDK2 phosphorylates SF3B1 at different sites, producing a completely different phosphopeptide pattern.","method":"In vitro kinase assay, phosphopeptide mapping, mass spectrometry, mutational analysis, co-expression/knockdown in COS-7 and HEK293 cells, Western blot with phospho-specific antibody","journal":"BMC biochemistry","confidence":"High","confidence_rationale":"Tier 1 / Strong — in vitro kinase assay plus mutagenesis plus metabolic labeling phosphopeptide mapping, with RNAi validation; replicated across multiple cell lines","pmids":["16512921"],"is_preprint":false},{"year":2006,"finding":"SF3B1 (SAP155) binds via its RRM-like domain to the ceramide-responsive RNA cis-element 1 (CRCE1) of Bcl-x pre-mRNA. SAP155 knockdown shifts splicing toward the pro-apoptotic Bcl-x(s) isoform and is required for ceramide-induced activation of the Bcl-x(s) 5' splice site, sensitizing cells to chemotherapeutic agents.","method":"Mass spectrometry identification, EMSA supershift with anti-SAP155 antibody, RNA interference (RNAi) knockdown, RT-PCR for splice variant quantification, apoptosis assays","journal":"FASEB journal","confidence":"High","confidence_rationale":"Tier 2 / Moderate — reciprocal binding confirmed by EMSA supershift, MS identification, and RNAi functional readout with multiple orthogonal methods in one study","pmids":["16790528"],"is_preprint":false},{"year":2006,"finding":"SF3B155 binds to the β-sheet surface of p14 (SF3b14) through a helical peptide (residues 401–415 form the core epitope), occupying the canonical RNA-binding surface of the p14 RRM. SF3B155 simultaneously binds p14 and U2AF65 through non-overlapping regions, potentially stabilizing U2 snRNP association with pre-mRNA. The p14–SF3B155 complex modulates RNA-binding specificity for the branch point.","method":"NMR spectroscopy, biochemical binding assays, mutagenesis","journal":"RNA","confidence":"High","confidence_rationale":"Tier 1 / Strong — NMR structure determination combined with biochemical and mutagenesis validation, replicated across multiple constructs","pmids":["16495236"],"is_preprint":false},{"year":2005,"finding":"SF3b155 contains five functional tryptophan-containing U2AF65-binding sites in its N-terminal domain, each recognized by the U2AF65 UHM domain via a mechanism similar to SF1 but with lower affinity (3.3 kcal/mol less stable than the SF1/U2AF65 complex), consistent with ATP-dependent exchange of these partners during pre-mRNA splicing.","method":"Intrinsic tryptophan fluorescence spectroscopy, isothermal titration calorimetry, circular dichroism, mutagenesis of SF3b155 variants","journal":"Journal of molecular biology","confidence":"High","confidence_rationale":"Tier 1 / Moderate — thermodynamic and spectroscopic characterization with multiple orthogonal methods and systematic mutagenesis in one study","pmids":["16376933"],"is_preprint":false},{"year":2002,"finding":"The FHA domain of NIPP1 interacts in vitro and in vivo with the TP dipeptide-rich region of SF3B1 (SAP155) in a phosphorylation-dependent manner; phosphorylated TP motifs in SAP155 compete for binding to the same NIPP1 FHA site. SAP155 kinases in cell lysates are blocked by EGTA and roscovitine (CDK inhibitor). SAP155 phosphorylation is dramatically increased during mitosis.","method":"GST pulldown, co-immunoprecipitation, phosphopeptide competition, kinase inhibition in cell lysates, mutagenesis","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 2 / Moderate — reciprocal Co-IP and in vitro pulldown combined with mutagenesis and competition studies; phosphorylation-dependent interaction rigorously established","pmids":["12105215"],"is_preprint":false},{"year":2008,"finding":"NIPP1 recruits PP1 to Sap155 (SF3B1) and promotes Sap155 dephosphorylation; NIPP1 stimulates Sap155 dephosphorylation by PP1 in vitro by facilitating their interaction. NIPP1 acts as a molecular sensor that recognizes hyperphosphorylated Sap155 through its FHA domain and dissociates after dephosphorylation, linking phosphorylation cycling of Sap155 to splicing regulation.","method":"Co-immunoprecipitation, in vitro phosphatase assays, siRNA knockdown of NIPP1, overexpression of truncated NIPP1 mutants, splicing assays","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1 / Moderate — in vitro reconstitution of PP1/NIPP1/SAP155 complex with phosphatase activity assay, complemented by RNAi and overexpression studies with splicing readout","pmids":["18842582"],"is_preprint":false},{"year":2008,"finding":"The p14–SF3b155 complex has two independent RNA-binding sites: a positively charged groove (requiring Tyr28 and Arg85 of p14) and the C-terminal extension of p14. SF3b155 residues Phe408, Tyr412, Val414, and Leu415 are critical contact points for complex formation with p14.","method":"NMR chemical shift perturbation, mutagenesis, in vitro binding assays","journal":"Proteins","confidence":"High","confidence_rationale":"Tier 1 / Moderate — NMR solution structure combined with extensive mutagenesis and functional binding validation in one study","pmids":["18076038"],"is_preprint":false},{"year":2010,"finding":"p14 (SF3b14) specifically recognizes the branch adenosine within the bulged U2/branch-point duplex, with the branch nucleotide buried at the p14/SF3b155-peptide interface; this interaction must be disrupted before the first catalytic step of splicing.","method":"X-ray crystallography (adenine-p14/SF3b155 peptide complex), disulfide cross-linking of protein-RNA complexes, small-angle X-ray scattering (SAXS)","journal":"RNA","confidence":"High","confidence_rationale":"Tier 1 / Strong — crystal structure combined with SAXS and biochemical cross-linking providing orthogonal structural validation","pmids":["21062891"],"is_preprint":false},{"year":2015,"finding":"SF3B1 is strongly associated with nucleosomes at exonic positions in chromatin; disruption of this SF3B1–nucleosome association impairs splicing of short exons flanked by long introns. Co-IP and sedimentation analyses demonstrate SF3B1 physically associates with nucleosomal components, and ChIP-seq shows preferential binding at exonic nucleosomes with differential GC content.","method":"Co-immunoprecipitation, proteomic analysis, sedimentation analysis, ChIP-seq, RNA-seq, SF3B1–nucleosome binding disruption experiments","journal":"Cell reports","confidence":"High","confidence_rationale":"Tier 2 / Moderate — reciprocal Co-IP, ChIP-seq, and functional disruption experiments provide multiple orthogonal lines of evidence in one study","pmids":["25892229"],"is_preprint":false},{"year":2015,"finding":"Cancer-associated SF3B1 hotspot mutations induce aberrant 3' splice site selection by utilizing a different (upstream) branch point sequence (BPS) compared to wild-type SF3B1. The mutant BPS requires the canonical 3' splice site to enable aberrant splicing during the second step. Approximately 50% of aberrantly spliced mRNAs are degraded by nonsense-mediated decay.","method":"RNA-seq analysis of cancer cell lines and patient samples, mutagenesis of predicted branchpoints, NMD inhibition experiments, isogenic cell line comparisons","journal":"Cell reports","confidence":"High","confidence_rationale":"Tier 2 / Strong — branchpoint mutagenesis combined with RNA-seq across multiple cancer types and isogenic cell lines; independently replicated across labs","pmids":["26565915"],"is_preprint":false},{"year":2016,"finding":"SF3B1 R625/K666 cancer mutations act as change-of-function (not loss-of-function) mutants that promote alternative branchpoint usage, leading to aberrant 3' splice site selection; wild-type SF3B1 knockdown or overexpression does not reproduce the mutant splicing pattern. Mutagenesis of predicted branchpoints confirms that the mutant-specific splicing depends directly on alternative branchpoint utilization.","method":"RNA-seq of uveal melanoma, isogenic SF3B1-WT and mutant cell lines, SF3B1 knockdown/overexpression, branchpoint mutagenesis","journal":"Nature communications","confidence":"High","confidence_rationale":"Tier 1 / Strong — branchpoint mutagenesis combined with isogenic cell lines and knockdown/overexpression controls; change-of-function mechanism firmly established","pmids":["26842708"],"is_preprint":false},{"year":2016,"finding":"SF3B1 inhibitors (three structurally distinct compounds) all interact with the same site on SF3B1 and interfere with splicing at multiple stages including both early spliceosome assembly and late exon ligation. Inactive analogs of each compound interchangeably compete with active inhibitors to restore splicing, supporting a shared pharmacophore model in which inhibition results not from binding alone but from inducing a conformational change in SF3B1.","method":"In vitro splicing assays, competition experiments with active and inactive inhibitor analogs, analysis at defined spliceosome assembly stages","journal":"RNA","confidence":"High","confidence_rationale":"Tier 1 / Moderate — in vitro splicing reconstitution with pharmacological competition experiments; multiple inhibitor compounds tested with rigorous controls","pmids":["26742993"],"is_preprint":false},{"year":2016,"finding":"SF3B1 HEAT-repeat mutations (yeast Hsh155 counterparts of human cancer mutations) directly alter the physical interaction between Hsh155 and the spliceosomal ATPase Prp5; this altered interaction changes the fidelity of branch-site (BS)–U2 duplex loading into the SF3B complex during prespliceosome formation, resulting in altered BS selectivity and splicing of suboptimal BS substrates.","method":"Yeast genetic analysis, in vitro direct binding assays (Hsh155–Prp5 interaction), splicing assays with nonconsensus BS pre-mRNAs, epistasis analysis of Hsh155 and Prp5 mutations","journal":"Genes & development","confidence":"High","confidence_rationale":"Tier 1 / Strong — direct protein-protein interaction assays combined with genetic epistasis and in vitro splicing assays; mechanism rigorously established in yeast ortholog with disease-relevant mutations","pmids":["28087715"],"is_preprint":false},{"year":2016,"finding":"Sf3b1(K700E) knock-in mice develop macrocytic anemia due to terminal erythroid maturation defect and erythroid dysplasia; Sf3b1(K700E) myeloid progenitors show aberrant 3' splice-site selection associated with increased nonsense-mediated decay. Tet2 loss cooperates with Sf3b1(K700E) to worsen erythroid and LT-HSC phenotypes.","method":"Conditional knock-in mouse model, RNA-seq (aberrant splice site analysis), NMD pathway analysis, genetic epistasis (Sf3b1(K700E) × Tet2 loss), hematopoietic phenotyping","journal":"Cancer cell","confidence":"High","confidence_rationale":"Tier 2 / Strong — physiological knock-in mouse model with RNA-seq, NMD analysis, and genetic epistasis; replicated in patient samples","pmids":["27622333"],"is_preprint":false},{"year":2017,"finding":"SF3b1/Hsh155 mutations alter branchsite selection fidelity in yeast, changing how the spliceosome recognizes nonconsensus nucleotides at positions -2, -1, and +1 relative to the branchpoint adenosine. Different HSH155 alleles have disparate effects: some increase and others decrease fidelity of BS selection. The data support a model in which SF3B1 conformational changes promote U2 snRNA association with the BS to drive spliceosome assembly, acting independently of Prp5 ATPase in some contexts.","method":"Yeast genetic analysis, in vitro splicing assays with nonconsensus BS substrates, single-molecule fluorescence microscopy of spliceosome assembly","journal":"Nucleic acids research","confidence":"High","confidence_rationale":"Tier 1 / Moderate — in vitro splicing assays combined with genetic analysis and single-molecule microscopy; detailed mechanistic investigation of BS recognition","pmids":["28062854"],"is_preprint":false},{"year":2019,"finding":"Disease-causing SF3B1 hotspot mutations (K700E and others) reduce the level of SUGP1 in mutant spliceosomes. SUGP1 knockdown completely recapitulates SF3B1-mutant splicing errors. SUGP1 overexpression partially rescues aberrant splicing by driving SUGP1 back into mutant spliceosomes. SUGP1 plays an important role in branchsite recognition; loss of SF3B1–SUGP1 interaction is the common molecular defect of disease-causing SF3B1 mutations.","method":"Purification of wild-type and K700E mutant SF3B1 complexes followed by proteomics, SUGP1 knockdown and overexpression with RNA-seq, analysis across multiple SF3B1 hotspot mutants","journal":"Molecular cell","confidence":"High","confidence_rationale":"Tier 2 / Strong — complex purification with proteomics, combined with knockdown/overexpression rescue experiments and RNA-seq; finding validated across multiple SF3B1 hotspot mutants","pmids":["31474574"],"is_preprint":false},{"year":2019,"finding":"Cus2 (yeast) contains a UHM that binds Hsh155 (yeast SF3b1) through a conserved ULM, enforcing the first ATP-dependent step of pre-spliceosome formation. Disruption of this UHM–ULM interaction allows pre-spliceosome formation without ATP. Crystal structure of the human Tat-SF1 (Cus2 homolog) UHM bound to an Hsh155 ULM at 2.0 Å confirms the interaction is conserved between yeast and humans.","method":"Crystal structure determination (2.0 Å), mutagenesis of UHM/ULM motifs, yeast splicing extract complementation assays, in vitro binding assays","journal":"RNA","confidence":"High","confidence_rationale":"Tier 1 / Strong — crystal structure combined with mutagenesis, in vitro binding, and functional splicing assays; yeast-human conservation established","pmids":["31110137"],"is_preprint":false},{"year":2018,"finding":"Conserved amino acids in SF3B1 (Hsh155) that contact the U2 snRNA backbone in the U2/branch-site duplex are nonessential; however, mutations in the branch-point adenosine-housing pocket, while viable, cause defects in splicing pre-mRNAs with nonconsensus BS sequences. Human SF3B1 HEAT repeats substituted into yeast Hsh155 chimeras confer pladienolide B sensitivity to yeast splicing and alter BS usage.","method":"Mutational analysis of yeast Hsh155 guided by spliceosome cryo-EM structures, in vitro splicing assays, yeast-human chimeric protein analysis, pladienolide B inhibition assays","journal":"RNA","confidence":"High","confidence_rationale":"Tier 1 / Moderate — structure-guided mutagenesis with in vitro splicing assays and chimeric protein validation in one rigorous study","pmids":["29752352"],"is_preprint":false},{"year":2019,"finding":"In SF3B1-mutated MDS, mutant SF3B1 generates an alternative ERFE (erythroferrone) transcript in erythroblasts encoding a variant protein that retains capacity to suppress hepcidin transcription, leading to elevated plasma ERFE and iron overload in SF3B1-mutant MDS patients.","method":"RNA-seq identification of alternative ERFE transcript, induction in primary SF3B1-mutated erythroblasts, hepcidin suppression assays, plasma ERFE measurement","journal":"Science translational medicine","confidence":"High","confidence_rationale":"Tier 2 / Moderate — functional validation in primary patient erythroblasts combined with hepcidin suppression assays and patient plasma measurements","pmids":["31292266"],"is_preprint":false},{"year":2020,"finding":"SF3B1 hotspot mutations promote decay of PPP2R5A (PP2A subunit) transcripts via aberrant splicing, increasing MYC S62 and BCL2 S70 phosphorylation, which stabilizes MYC protein and impairs apoptosis. Genetic PPP2R5A restoration or pharmacological PP2A activation impaired SF3B1-mutant tumorigenesis.","method":"RNA-seq across 98 tumors and 12 isogenic cell lines, regulatory network analysis, phosphoprotein analysis, genetic rescue (PPP2R5A restoration), pharmacological PP2A activation in mouse xenograft models","journal":"Cancer discovery","confidence":"High","confidence_rationale":"Tier 2 / Strong — mechanistic link established across human and mouse cells with genetic and pharmacological rescue experiments; multiple orthogonal methods","pmids":["32188705"],"is_preprint":false},{"year":2014,"finding":"CAPERα (a UHM-containing alternative splicing factor) interacts with SF3b155 through a UHM/ULM interaction; crystal structure of the CAPERα UHM bound to a representative SF3b155 ULM at 1.7 Å resolution establishes SF3b155 as the relevant ULM-containing partner of CAPERα in human cell extracts. SF3b155 serves as a platform for coordinated recruitment of multiple UHM-containing splicing factors.","method":"X-ray crystallography (1.7 Å), isothermal titration calorimetry, pulldown from human cell extracts","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1 / Moderate — crystal structure with ITC thermodynamic characterization and cell extract pulldown validation","pmids":["24795046"],"is_preprint":false},{"year":2022,"finding":"CDK11 associates with SF3B1 and phosphorylates threonine residues at its N-terminus during spliceosome activation. This phosphorylation is important for SF3B1 association with U5 and U6 snRNAs in the activated (Bact) spliceosome. Inhibition of CDK11 with OTS964 prevents spliceosomal transition from precatalytic complex B to activated complex Bact, causing widespread intron retention.","method":"Co-immunoprecipitation (CDK11–SF3B1 association), in vitro kinase assays, OTS964 CDK11 inhibitor treatment, spliceosome complex analysis (B vs Bact), RNA-seq for intron retention, CLIP-seq for snRNA association","journal":"Nature","confidence":"High","confidence_rationale":"Tier 1 / Strong — in vitro kinase assay combined with pharmacological inhibition, spliceosome complex analysis, and genome-wide RNA-seq; multiple orthogonal methods in one rigorous study","pmids":["36104565"],"is_preprint":false},{"year":2022,"finding":"Coordinated missplicing of TMEM14C and ABCB7 by mutant SF3B1 (K700E) sequesters iron in mitochondria causing ring sideroblast (RS) formation in MDS. Functional rescue of both TMEM14C and ABCB7 expression nearly abolished RS formation in iPSC-derived erythroid cells, while rescue of PPOX alone had no effect.","method":"iPSC model of SF3B1-mutant MDS with in vitro erythroid differentiation, RNA-seq, functional rescue of TMEM14C and ABCB7, ring sideroblast quantification","journal":"Blood","confidence":"High","confidence_rationale":"Tier 2 / Strong — physiological iPSC model with genetic rescue experiments establishing causal necessity of specific mis-spliced genes for RS formation","pmids":["34861039"],"is_preprint":false},{"year":2022,"finding":"SF3B1 K700E mutation induces mis-splicing of MAP3K7, leading to inactivation of the MAP3K7–p38 MAPK pathway, premature downregulation of GATA1, and accelerated erythroid differentiation followed by apoptosis, causing the anemia characteristic of SF3B1-mutant MDS.","method":"Isogenic SF3B1-WT and mutant cell lines, normal human CD34+ cells, MDS patient cells; p38 MAPK activity assays, GATA1 expression analysis, erythroid differentiation assays","journal":"PNAS","confidence":"High","confidence_rationale":"Tier 2 / Strong — causal pathway established using isogenic cell lines, primary human CD34+ cells, and patient samples with multiple orthogonal functional readouts","pmids":["34930825"],"is_preprint":false},{"year":2022,"finding":"CDK12/13 promote the interaction of SF3B1 with Ser2-phosphorylated RNA polymerase II (RNAPII), facilitating SF3B1 association with chromatin and recruitment to 3' splice sites of promoter-proximal introns. CDK12/13 inhibition disrupts the SF3B1–RNAPII interaction and causes selective retention of promoter-proximal introns with weak 3' splice sites.","method":"Co-IP of SF3B1 with Ser2-phospho-RNAPII, CDK12/13 inhibitor (THZ531) treatment, ChIP-seq for SF3B1 chromatin association, nascent transcript analysis, RNA-seq for intron retention","journal":"Nucleic acids research","confidence":"High","confidence_rationale":"Tier 2 / Moderate — Co-IP combined with ChIP-seq, nascent transcript analysis, and RNA-seq in one study; mechanism linking transcription to SF3B1 recruitment established","pmids":["37026485"],"is_preprint":false},{"year":2022,"finding":"DHX15 is the RNA helicase required for SUGP1 function in branchpoint recognition. Cancer-causing SF3B1 mutations disrupt the SF3B1–SUGP1 interaction, indirectly depriving SUGP1 of its helicase partner DHX15. Crystal structure of DHX15–SUGP1 G-patch complex reveals the molecular basis of their direct interaction. A DHX15–SUGP1 G-patch fusion protein rescues splicing defects of mutant SF3B1.","method":"Protein-protein interaction assays (Co-IP, pulldown), crystal structure of DHX15–SUGP1 G-patch complex, RNA-seq, knockdown/overexpression of DHX15, DHX15–SUGP1 fusion rescue experiments","journal":"PNAS","confidence":"High","confidence_rationale":"Tier 1 / Strong — crystal structure combined with multiple interaction assays, knockdown experiments, and functional rescue; mechanism rigorously established","pmids":["36459648"],"is_preprint":false},{"year":2023,"finding":"Structural modeling and experimental validation show that two regions flanking the SUGP1 G-patch make numerous contacts with the SF3B1 region harboring cancer hotspot mutations. All cancer-associated mutations in these interface regions weaken or disrupt SF3B1–SUGP1 interaction and alter splicing. Structural modeling reveals that the SF3B1–SUGP1 interaction 'loops out' the G-patch for interaction with DHX15.","method":"Structural modeling (AlphaFold-based), mutagenesis of SF3B1–SUGP1 interface residues, Co-IP, RNA-seq for splicing analysis","journal":"Genes & development","confidence":"High","confidence_rationale":"Tier 2 / Moderate — structural modeling validated by systematic mutagenesis and Co-IP with functional RNA-seq readout; comprehensive interface characterization","pmids":["37977822"],"is_preprint":false},{"year":2022,"finding":"SF3B1 K700E mutation promotes centromeric R-loop (cen-R-loop) accumulation, leading to increased chromosome oscillation, impaired chromosome segregation, altered spindle architecture, and aneuploidy. Aberrant splicing of genes involved in R-loop processing underlies cen-R-loop augmentation; overexpression of the normal (not mis-spliced) isoform mitigated mitotic stress. ATM deletion exaggerates these phenotypes.","method":"R-loop detection (DRIP), chromosome segregation analysis, spindle architecture imaging, isogenic cell lines with SF3B1 mutation, genetic epistasis with ATM deletion, isoform rescue experiments","journal":"The Journal of clinical investigation","confidence":"High","confidence_rationale":"Tier 2 / Moderate — multiple orthogonal assays (DRIP, chromosome imaging, isoform rescue) establishing causal link between aberrant splicing and chromosomal instability","pmids":["37463047"],"is_preprint":false},{"year":2023,"finding":"Mis-splicing of COASY (coenzyme A synthase) by mutant SF3B1 depletes both CoA and succinyl-CoA in erythroblasts, impairing heme biosynthesis and erythropoiesis. Supplementation with vitamin B5 (COASY substrate) rescued CoA/succinyl-CoA concentrations in SF3B1-mutant cells and rescued erythropoiesis differentiation in primary MDS-RS patient cells.","method":"Splice variant analysis of COASY in patient samples, COASY silencing in erythroid cultures, CoA/succinyl-CoA metabolite measurement, vitamin B5 supplementation in isogenic cells and primary patient cells","journal":"Science translational medicine","confidence":"High","confidence_rationale":"Tier 2 / Strong — causal metabolic pathway established through COASY knockdown, metabolite measurement, and rescue in patient primary cells using multiple orthogonal approaches","pmids":["36857430"],"is_preprint":false},{"year":2024,"finding":"Cancer-associated SF3B1 mutations reduce RNA polymerase II (RNAPII) elongation rate along gene bodies and decrease RNAPII density at promoters. The elongation defect results from disrupted pre-spliceosome assembly due to impaired protein–protein interactions of mutant SF3B1. Decreased promoter-proximal RNAPII density reduces chromatin accessibility and H3K4me3 at promoters. Sin3/HDAC/H3K4me pathway modulation reverses both transcription and chromatin changes.","method":"RNAPII ChIP-seq, chromatin accessibility (ATAC-seq), H3K4me3 ChIP-seq, isogenic cell lines, patient samples, mutant mouse model, unbiased epigenetic inhibitor screen","journal":"Molecular cell","confidence":"High","confidence_rationale":"Tier 2 / Strong — multiple orthogonal genomic assays (ChIP-seq, ATAC-seq) across isogenic cell lines, patient samples, and mouse model with functional rescue screen","pmids":["38521065"],"is_preprint":false},{"year":2024,"finding":"GPATCH8 is required for mutant SF3B1-induced aberrant splicing activity. GPATCH8 interacts with the RNA helicase DHX15 and functionally opposes SUGP1 in branchpoint quality control. GPATCH8 silencing corrected approximately one-third of mutant SF3B1-dependent splicing defects and improved dysfunctional hematopoiesis in SF3B1-mutant mice and primary human progenitors.","method":"Synthetic intron screen to identify trans factors, Co-IP (GPATCH8–DHX15 interaction), GPATCH8 knockdown in isogenic cell lines and SF3B1-mutant mice, RNA-seq for splicing correction, hematopoiesis assays","journal":"Molecular cell","confidence":"High","confidence_rationale":"Tier 2 / Strong — interaction assay combined with functional genetic rescue in multiple model systems (cell lines, mouse, primary human progenitors) with RNA-seq splicing readout","pmids":["38688280"],"is_preprint":false},{"year":2017,"finding":"Upon genotoxic (alkylation) stress, Hsh155 (yeast SF3B1) disassembles from its spliceosomal partners and localizes to intranuclear and cytoplasmic protein quality control aggregates. This sequestration is regulated by molecular chaperones and requires TORC1 signaling through Sfp1 transcription factor, and is associated with intron retention in ribosomal protein gene transcripts and decreased splicing efficiency during stress recovery.","method":"Cytological screen, live cell imaging, genetic analysis (chaperone mutants, TORC1/Sfp1 pathway), RNA-seq for intron retention, stress recovery assays","journal":"The Journal of cell biology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct localization by imaging with functional pathway analysis; single study but multiple methods","pmids":["28978642"],"is_preprint":false},{"year":2022,"finding":"Cancer-associated SF3B1 mutations disrupt the interaction between SF3B1 and DDX42 (and DDX46). Overexpression of DDX42 suppresses some SF3B1-mutation-associated aberrant splicing, and this suppression requires DDX42 ATP hydrolysis activity.","method":"Co-immunoprecipitation of WT and K700E SF3B1 complexes, DDX42 overexpression with RNA-seq for splicing correction, ATPase-dead DDX42 mutant analysis","journal":"Journal of biochemistry","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — Co-IP interaction assay with functional overexpression rescue; single lab, limited orthogonal validation","pmids":["35652295"],"is_preprint":false},{"year":2013,"finding":"SAP155 (SF3B1) physically interacts with FIR/FIRΔexon2 (a PUF60 splicing variant), forming a complex that bridges c-Myc transcription and P27 (CDKN1B) expression. SAP155/FIR/FIRΔexon2 knockdown reduces p27 expression and inhibits P27 pre-mRNA splicing, reducing CDK2/Cyclin E expression.","method":"Co-immunoprecipitation (SAP155–FIR/FIRΔexon2 complex), siRNA knockdown of SAP155/FIR, RT-PCR for P27 splicing, Western blot for CDK2/Cyclin E","journal":"Molecular cancer research","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — Co-IP and RNAi with functional splicing readout; single lab, limited mechanistic detail in abstract","pmids":["23594796"],"is_preprint":false},{"year":2022,"finding":"SF3B1 mutations lead to aberrant retention of full-length exon 6 of IRAK4, producing a longer IRAK4 isoform (IRAK4-long) containing the full death and kinase domains that maximally activates NF-κB. IRAK4-long expression in SF3B1-mutant cells induces TRAF6 activation and K63-linked ubiquitination of CDK2, causing a block in hematopoietic differentiation. IRAK4 inhibition with CA-4948 reduces NF-κB activation and improves myeloid differentiation.","method":"RNA-seq splicing analysis of SF3B1-mutant MDS samples, IRAK4 isoform functional assays, TRAF6/CDK2 ubiquitination assays, IRAK4 inhibitor in vitro differentiation and xenograft models","journal":"eLife","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — functional isoform analysis combined with downstream signaling assays and in vivo xenograft; multiple methods but primarily in cancer models","pmids":["36040792"],"is_preprint":false},{"year":2021,"finding":"SF3B1 protein is stabilized via deubiquitination (post-translational stabilization of the U2 complex component SF3B1). SF3B1 inhibition blocks T-ALL growth in vivo, perturbs exon skipping leading to NMD-mediated reduction of CHEK2 transcripts, and impairs DNA damage response. SF3B1 inhibition also leads to a general decrease in R-loop formation.","method":"In vivo T-ALL mouse model with SF3B1 inhibitor treatment, deubiquitination assays for SF3B1 stability, RNA-seq for exon skipping/NMD analysis, CHEK2 protein/transcript analysis, R-loop detection","journal":"Science advances","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — multiple assays (deubiquitination, RNA-seq, R-loop detection, in vivo) but abstract is compressed; single lab study","pmids":["35061527"],"is_preprint":false},{"year":2023,"finding":"ALKBH5-driven 5' UTR m6A demethylation fine-tunes SF3B1 translation, and SF3B1 protein abundance levels dynamically regulate MDS-to-leukemia progression in vivo. Changes in SF3B1 levels affect splicing of central DNA repair and epigenetic regulators.","method":"m6A sequencing, ALKBH5 manipulation in human and murine pre-leukemic MDS cells, SF3B1 translation reporter assays, in vivo MDS-to-leukemia progression monitoring","journal":"Molecular cell","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — epitranscriptomic modification identified with functional in vivo validation; abstract compressed, mechanism partially inferred","pmids":["36944332"],"is_preprint":false},{"year":2021,"finding":"SF3B1 physically interacts with HIF1α, facilitating binding of the HIF1 complex to hypoxia response elements (HREs) to activate target gene expression. SF3B1 is a HIF-1 target gene, forming a positive feedback loop. Monoallelic Sf3b1 deletion impedes tumor formation and progression via impaired HIF signaling in a mouse pancreatic cancer model.","method":"Co-IP of SF3B1 with HIF1α, chromatin immunoprecipitation (HIF1 complex binding to HREs), Sf3b1 monoallelic deletion in mouse pancreatic cancer model, tumor formation assays","journal":"Cell reports","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP and ChIP combined with in vivo mouse model; interaction and functional consequence established but in compressed abstract","pmids":["36001976"],"is_preprint":false},{"year":1998,"finding":"Fission yeast prp10+ (SF3B1 ortholog) is essential for viability and encodes a protein homologous to human SAP155. Prp10p-GFP localizes predominantly to the nuclear DNA region. The N-terminal ~300 amino acids are dispensable for viability, unlike the conserved C-terminal region containing HEAT repeats.","method":"Complementation cloning, gene disruption, GFP fusion localization, deletion analysis","journal":"Nucleic acids research","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct localization by GFP imaging and genetic essentiality established by gene disruption; foundational characterization in ortholog","pmids":["9837997"],"is_preprint":false},{"year":2012,"finding":"SAP155 (SF3B1) knockdown generates FIRΔexon2 and novel FIR splicing variants (Δ3, Δ4) that lack c-Myc transcriptional repression activity; these variants are found in human colorectal cancer tissues, establishing a role for SAP155 in regulation of FIR pre-mRNA splicing and c-Myc transcriptional control.","method":"siRNA knockdown of SAP155 in cell lines, RT-PCR identification of FIR splice variants, colorectal cancer tissue analysis","journal":"Cancer science","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single knockdown experiment with splice variant identification; no direct mechanistic assay of SF3B1 binding to FIR pre-mRNA","pmids":["23113893"],"is_preprint":false},{"year":2011,"finding":"SF3B1 inhibitor treatment in HNSCC cells promotes generation of pro-apoptotic MCL1-S splice variant while diminishing anti-apoptotic MCL1-L variant, via SF3B1-dependent splicing regulation of MCL1 pre-mRNA. SF3B1 is also involved in the splicing of HPV16 E6 to produce the non-oncogenic E6* isoform.","method":"RT-PCR and Western blot for MCL1 splice variants upon meayamycin B (SF3B1 inhibitor) treatment, apoptosis assays, pharmacological SF3B1 inhibition","journal":"Scientific reports","confidence":"Low","confidence_rationale":"Tier 3 / Weak — pharmacological inhibition only (no direct SF3B1 binding assay); functional splicing outcome established but mechanism inferred from inhibitor effects","pmids":["25139387"],"is_preprint":false}],"current_model":"SF3B1 is the largest subunit of the SF3b complex within the U2 snRNP of the spliceosome, functioning as a scaffold that recruits U2 snRNP to pre-mRNA branch points through simultaneous interactions with p14, U2AF65 (via multiple ULM sites in its N-terminal domain), and SUGP1 (whose G-patch activates the DHX15 helicase for branchpoint recognition); SF3B1 undergoes CDK11-mediated phosphorylation of N-terminal threonine residues during spliceosomal activation (B-to-Bact transition), is phosphorylated at Thr434 by DYRK1A and dephosphorylated by the NIPP1–PP1 complex, and physically associates with chromatin/nucleosomes at exonic positions to couple transcription elongation (via CDK12/13-mediated interaction with Ser2-phosphorylated RNAPII) to splice-site recognition; recurrent cancer hotspot mutations (K700E, R625H, etc.) act as change-of-function alleles that disrupt the SF3B1–SUGP1 interaction, impair RNAPII elongation and chromatin accessibility, and redirect branchpoint usage to generate hundreds of cryptic 3' splice sites, with downstream consequences including PPP2R5A mis-splicing activating MYC and BCL2, ABCB7/TMEM14C mis-splicing causing ring sideroblast formation, MAP3K7 mis-splicing impairing erythropoiesis, COASY mis-splicing depleting CoA/succinyl-CoA, and IRAK4 exon retention activating NF-κB."},"narrative":{"mechanistic_narrative":"SF3B1 is the largest subunit of the SF3b complex within the U2 snRNP and functions as a scaffold that recruits U2 snRNP to pre-mRNA branch points during spliceosome assembly [PMID:16906767, PMID:21138297]. Its intrinsically disordered N-terminal domain presents multiple tryptophan-containing ULM sites that engage the UHM domain of U2AF65 with tunable, lower-than-SF1 affinity consistent with ATP-dependent partner exchange, and this same platform recruits additional UHM-containing splicing factors such as CAPERα [PMID:16376933, PMID:24795046]. Through a helical epitope (residues ~401–415) SF3B1 binds the p14/SF3b14 RRM surface, and the p14–SF3B1 module directly recognizes and buries the branch-point adenosine within the U2/branch-site duplex before the first catalytic step [PMID:16495236, PMID:18076038, PMID:21062891]. SF3B1 is built around HEAT repeats whose conformation governs branch-site selection fidelity: structure-guided yeast work shows that the branch-point adenosine pocket and the interaction with the ATPase Prp5 set how the U2/branch-site duplex is loaded, and HEAT-repeat substitutions confer pladienolide sensitivity [PMID:28087715, PMID:29752352, PMID:28062854]. SF3B1 activity is regulated by phosphorylation cycling—DYRK1A phosphorylates Thr434, CDK11 phosphorylates N-terminal threonines to drive the B-to-Bact spliceosomal transition, and the NIPP1–PP1 complex senses hyperphosphorylated SF3B1 and reverses these marks [PMID:16512921, PMID:36104565, PMID:12105215, PMID:18842582]. Beyond core splicing, SF3B1 associates with exonic nucleosomes and couples transcription to splice-site recognition by binding Ser2-phosphorylated RNAPII via CDK12/13 [PMID:25892229, PMID:37026485]. SUGP1 binds SF3B1 and supplies the G-patch that activates the DHX15 helicase for branch-point fidelity [PMID:36459648, PMID:37977822]. Recurrent cancer hotspot mutations (e.g., K700E, R625H) are change-of-function alleles that weaken the SF3B1–SUGP1 interaction, redirect branch-point usage to generate cryptic 3' splice sites, and impair RNAPII elongation and chromatin accessibility [PMID:26842708, PMID:31474574, PMID:38521065]. The resulting mis-splicing drives disease-specific phenotypes: PPP2R5A decay stabilizing MYC and BCL2 [PMID:32188705], coordinated TMEM14C/ABCB7 mis-splicing causing ring sideroblasts [PMID:34861039], MAP3K7 mis-splicing impairing erythropoiesis [PMID:34930825], COASY mis-splicing depleting CoA/succinyl-CoA [PMID:36857430], and IRAK4 exon retention activating NF-κB [PMID:36040792], with mutant SF3B1 also promoting centromeric R-loop accumulation and chromosomal instability [PMID:37463047]. A heterozygous K700E knock-in mouse develops macrocytic anemia and erythroid dysplasia modeling SF3B1-mutant myelodysplastic syndrome [PMID:27622333].","teleology":[{"year":1998,"claim":"Established that the SF3B1 ortholog is an essential, conserved nuclear protein, defining the gene as core machinery rather than an accessory factor.","evidence":"Complementation cloning, gene disruption, and GFP localization of fission yeast prp10+","pmids":["9837997"],"confidence":"Medium","gaps":["Molecular function not assigned beyond essentiality","N-terminal dispensability in yeast not connected to human regulatory roles"]},{"year":2006,"claim":"Defined how SF3B1 acts as a scaffold by mapping distinct, non-overlapping binding sites for U2AF65 and p14 within its unfolded N-terminal domain, explaining how it nucleates U2 snRNP at the branch point.","evidence":"In vitro binding, CD spectroscopy, NMR, ITC, and mutagenesis of SF3b155 N-terminal ULM and p14-binding regions","pmids":["16906767","16495236","16376933"],"confidence":"High","gaps":["Affinity hierarchy among the multiple ULM sites in vivo not resolved","How partner exchange is timed during assembly not directly shown"]},{"year":2010,"claim":"Resolved the structural basis of branch-point recognition, showing the branch adenosine is buried at the p14/SF3B1-peptide interface and must be released before catalysis.","evidence":"X-ray crystallography of adenine-p14/SF3b155 peptide, disulfide cross-linking, and SAXS","pmids":["21062891","18076038"],"confidence":"High","gaps":["Trigger for adenosine release before first catalytic step not defined","Structure captures peptide, not full-length SF3B1 in spliceosome"]},{"year":2008,"claim":"Established SF3B1 as a regulated phosphoprotein by identifying DYRK1A as a Thr434 kinase and the NIPP1–PP1 complex as the sensor/phosphatase that reverses hyperphosphorylation, linking phospho-cycling to splicing.","evidence":"In vitro kinase and phosphatase assays, phosphopeptide mapping, FHA-domain pulldowns, and RNAi across cell lines","pmids":["16512921","12105215","18842582"],"confidence":"High","gaps":["Functional consequence of Thr434 phosphorylation on splicing not fully defined","Which spliceosomal stage each phospho-mark governs not resolved here"]},{"year":2011,"claim":"Identified SF3B1 as the direct molecular target of splicing-inhibitor natural products, validating it as a druggable node and providing tools to probe its function.","evidence":"Photoaffinity labeling with GEX1A derivatives and in vitro splicing assays","pmids":["21138297"],"confidence":"High","gaps":["Binding site on SF3B1 not localized at this stage","Mechanism of inhibition beyond SF3b impairment unresolved"]},{"year":2014,"claim":"Generalized the scaffold model by showing SF3B1 ULMs recruit additional UHM splicing factors, establishing it as a coordinating platform for multiple regulators.","evidence":"Crystal structure of CAPERα UHM bound to an SF3b155 ULM, ITC, and cell-extract pulldowns","pmids":["24795046"],"confidence":"High","gaps":["In vivo competition among UHM partners not quantified","Functional output of CAPERα recruitment not defined"]},{"year":2016,"claim":"Determined that cancer hotspot mutations are change-of-function alleles that redirect branch-point usage to create cryptic 3' splice sites, distinguishing the mechanism from simple loss of function.","evidence":"RNA-seq of cancer cell lines and tumors, isogenic comparisons, branchpoint mutagenesis, and knockdown/overexpression controls","pmids":["26565915","26842708"],"confidence":"High","gaps":["Why specific branch points are selected not explained at this stage","Molecular partner whose loss causes the shift unidentified"]},{"year":2017,"claim":"Used yeast genetics to mechanistically connect SF3B1 HEAT-repeat conformation to branch-site selection fidelity through its interaction with the ATPase Prp5.","evidence":"Yeast Hsh155 epistasis, in vitro Hsh155–Prp5 binding, single-molecule assembly imaging, and splicing of nonconsensus branch-site substrates","pmids":["28087715","28062854","29752352"],"confidence":"High","gaps":["Direct extrapolation of allele-specific fidelity effects to human disease mutants incomplete","Conformational states not visualized structurally"]},{"year":2019,"claim":"Identified loss of the SF3B1–SUGP1 interaction as the common molecular defect of disease-causing SF3B1 mutations, since SUGP1 knockdown recapitulates and overexpression rescues mutant splicing errors.","evidence":"Proteomics of WT vs K700E complexes, SUGP1 knockdown/overexpression with RNA-seq across multiple hotspot mutants, plus conserved UHM–ULM structural work","pmids":["31474574","31110137"],"confidence":"High","gaps":["How SUGP1 mechanistically enforces branch-site choice not yet defined","Helicase partner of SUGP1 not identified at this point"]},{"year":2022,"claim":"Completed the SUGP1 module by showing it presents a G-patch that activates the DHX15 helicase, and that hotspot mutations indirectly deprive SUGP1 of DHX15.","evidence":"Co-IP, crystal structure of DHX15–SUGP1 G-patch, knockdown, and a DHX15–SUGP1 fusion that rescues mutant splicing; structural modeling of the SF3B1–SUGP1 interface","pmids":["36459648","37977822"],"confidence":"High","gaps":["In vivo kinetics of helicase activation during assembly not measured","GPATCH8 as an opposing G-patch factor only later defined"]},{"year":2022,"claim":"Connected SF3B1 to transcription and chromatin, showing CDK11 drives the activating B-to-Bact phosphorylation while CDK12/13 couple SF3B1 to elongating RNAPII at exonic nucleosomes.","evidence":"Co-IP, in vitro kinase assays, CDK11 (OTS964) and CDK12/13 (THZ531) inhibition, ChIP-seq, CLIP-seq, and intron-retention RNA-seq","pmids":["36104565","37026485","25892229"],"confidence":"High","gaps":["Hierarchy between transcriptional coupling and core spliceosome recruitment not fully ordered","Direct chromatin-binding determinants of SF3B1 not mapped"]},{"year":2022,"claim":"Established the disease-relevant downstream targets of mutant SF3B1 mis-splicing, defining the molecular causes of ring sideroblasts, anemia, and oncogenic signaling.","evidence":"iPSC and isogenic models with genetic rescue of TMEM14C/ABCB7, MAP3K7/p38 pathway analysis, PPP2R5A/MYC/BCL2 phosphoprotein and rescue studies, IRAK4 isoform and NF-κB assays, and a K700E knock-in mouse","pmids":["34861039","34930825","32188705","36040792","27622333"],"confidence":"High","gaps":["Relative contribution of each mis-splicing event to combined phenotype not quantified","Why erythroid lineage is selectively vulnerable not fully explained"]},{"year":2023,"claim":"Extended the consequences of mutant SF3B1 to metabolism and genome stability, linking COASY mis-splicing to CoA depletion and the K700E allele to centromeric R-loops and aneuploidy.","evidence":"COASY splice-variant and metabolite analysis with vitamin B5 rescue in patient cells; DRIP, chromosome segregation imaging, and isoform rescue in isogenic lines","pmids":["36857430","37463047"],"confidence":"High","gaps":["Whether metabolic and genomic phenotypes are independent or sequential not resolved","Identity of all R-loop-processing transcripts mis-spliced not complete"]},{"year":2024,"claim":"Showed that mutant SF3B1 impairs RNAPII elongation and reduces promoter chromatin accessibility, and identified GPATCH8 as a DHX15-binding factor required for mutant mis-splicing, nominating reversible nodes for intervention.","evidence":"RNAPII/H3K4me3 ChIP-seq, ATAC-seq, epigenetic inhibitor screen across isogenic cells, patients and mouse; synthetic intron screen, Co-IP, and GPATCH8 knockdown rescue across model systems","pmids":["38521065","38688280"],"confidence":"High","gaps":["How GPATCH8 and SUGP1 are balanced at branch points mechanistically unresolved","Causal order between elongation defect and chromatin changes not fully established"]},{"year":null,"claim":"How SF3B1 protein abundance, post-translational modification, and additional helicase partners (e.g., DDX42/DDX46) are integrated to determine branch-point fidelity and disease progression remains incompletely defined.","evidence":"","pmids":[],"confidence":"Medium","gaps":["DDX42/DDX46 interactions characterized only by Co-IP and overexpression rescue without structural detail","Stress-induced SF3B1 sequestration and m6A/ALKBH5 translational control not mechanistically linked to splice-site fidelity in humans","Quantitative rules predicting which introns are mis-spliced by a given mutant remain unknown"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0003723","term_label":"RNA binding","supporting_discovery_ids":[3,9,1]},{"term_id":"GO:0060090","term_label":"molecular adaptor activity","supporting_discovery_ids":[1,5,4,22]},{"term_id":"GO:0140098","term_label":"catalytic activity, acting on RNA","supporting_discovery_ids":[11,12,14]}],"localization":[{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[40]},{"term_id":"GO:0000228","term_label":"nuclear chromosome","supporting_discovery_ids":[10]},{"term_id":"GO:0005654","term_label":"nucleoplasm","supporting_discovery_ids":[1,4]}],"pathway":[{"term_id":"R-HSA-8953854","term_label":"Metabolism of RNA","supporting_discovery_ids":[0,1,9,23]},{"term_id":"R-HSA-74160","term_label":"Gene expression (Transcription)","supporting_discovery_ids":[26,31,10]},{"term_id":"R-HSA-1643685","term_label":"Disease","supporting_discovery_ids":[12,17,15,24]}],"complexes":["SF3b complex","U2 snRNP","spliceosome"],"partners":["U2AF65","SF3B14 (P14)","SUGP1","DHX15","NIPP1","CDK11","RNAPII","GPATCH8"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"O75533","full_name":"Splicing factor 3B subunit 1","aliases":["Pre-mRNA-splicing factor SF3b 155 kDa subunit","SF3b155","Spliceosome-associated protein 155","SAP 155"],"length_aa":1304,"mass_kda":145.8,"function":"Component of the 17S U2 SnRNP complex of the spliceosome, a large ribonucleoprotein complex that removes introns from transcribed pre-mRNAs (PubMed:12234937, PubMed:27720643, PubMed:32494006, PubMed:34822310, PubMed:36104565). The 17S U2 SnRNP complex (1) directly participates in early spliceosome assembly and (2) mediates recognition of the intron branch site during pre-mRNA splicing by promoting the selection of the pre-mRNA branch-site adenosine, the nucleophile for the first step of splicing (PubMed:32494006, PubMed:34822310, PubMed:36104565). Within the 17S U2 SnRNP complex, SF3B1 is part of the SF3B subcomplex, which is required for 'A' complex assembly formed by the stable binding of U2 snRNP to the branchpoint sequence in pre-mRNA (PubMed:12234937, PubMed:36104565). Sequence independent binding of SF3A and SF3B subcomplexes upstream of the branch site is essential, it may anchor U2 snRNP to the pre-mRNA (PubMed:12234937). May also be involved in the assembly of the 'E' complex (PubMed:10882114). Also acts as a component of the minor spliceosome, which is involved in the splicing of U12-type introns in pre-mRNAs (PubMed:15146077, PubMed:33509932). Together with other U2 snRNP complex components may also play a role in the selective processing of microRNAs (miRNAs) from the long primary miRNA transcript, pri-miR-17-92 (By similarity)","subcellular_location":"Nucleus; Nucleus speckle","url":"https://www.uniprot.org/uniprotkb/O75533/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":true,"resolved_as":"","url":"https://depmap.org/portal/gene/SF3B1","classification":"Common Essential","n_dependent_lines":1204,"n_total_lines":1208,"dependency_fraction":0.9966887417218543},"opencell":{"profiled":true,"resolved_as":"","ensg_id":"ENSG00000115524","cell_line_id":"CID001447","localizations":[{"compartment":"chromatin","grade":3}],"interactors":[{"gene":"COMMD6","stoichiometry":10.0},{"gene":"PRPF4B","stoichiometry":10.0},{"gene":"RANBP2","stoichiometry":10.0},{"gene":"RBM17","stoichiometry":10.0},{"gene":"SF3A1","stoichiometry":10.0},{"gene":"SF3A2","stoichiometry":10.0},{"gene":"SF3A3","stoichiometry":10.0},{"gene":"TTC33","stoichiometry":10.0},{"gene":"ERH","stoichiometry":10.0},{"gene":"SNRPD1","stoichiometry":10.0}],"url":"https://opencell.sf.czbiohub.org/target/CID001447","total_profiled":1310},"omim":[{"mim_id":"618465","title":"BROMODOMAIN-CONTAINING PROTEIN 9; BRD9","url":"https://www.omim.org/entry/618465"},{"mim_id":"617848","title":"DEAD-BOX HELICASE 46; DDX46","url":"https://www.omim.org/entry/617848"},{"mim_id":"614286","title":"MYELODYSPLASTIC SYNDROME; MDS","url":"https://www.omim.org/entry/614286"},{"mim_id":"614058","title":"KETOHEXOKINASE; KHK","url":"https://www.omim.org/entry/614058"},{"mim_id":"607835","title":"SPLICING FACTOR 3B, SUBUNIT 6; SF3B6","url":"https://www.omim.org/entry/607835"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Enhanced","locations":[{"location":"Nuclear speckles","reliability":"Enhanced"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/SF3B1"},"hgnc":{"alias_symbol":["SAP155","SF3b155","PRPF10","Prp10","Hsh155"],"prev_symbol":[]},"alphafold":{"accession":"O75533","domains":[{"cath_id":"1.25.40","chopping":"893-1009","consensus_level":"medium","plddt":91.3596,"start":893,"end":1009}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/O75533","model_url":"https://alphafold.ebi.ac.uk/files/AF-O75533-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-O75533-F1-predicted_aligned_error_v6.png","plddt_mean":74.81},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=SF3B1","jax_strain_url":"https://www.jax.org/strain/search?query=SF3B1"},"sequence":{"accession":"O75533","fasta_url":"https://rest.uniprot.org/uniprotkb/O75533.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/O75533/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/O75533"}},"corpus_meta":[{"pmid":"22150006","id":"PMC_22150006","title":"SF3B1 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GEX1A inhibits pre-mRNA splicing by binding to SAP155/SF3B1, thereby impairing SF3b function.\",\n      \"method\": \"Photoaffinity labeling with GEX1A derivatives, in vitro splicing assays, Western blot\",\n      \"journal\": \"ACS chemical biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — direct biochemical photoaffinity labeling identifying the binding target, combined with functional splicing inhibition assays in a single rigorous study\",\n      \"pmids\": [\"21138297\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2006,\n      \"finding\": \"SF3B1 (SAP155/SF3b155) N-terminal domain contains multiple U2AF65 binding sites that are distinct from the p14 binding site (mapped to residues 396–424). The N-terminal domain adopts a primarily unfolded structure functioning as a scaffold for multiple protein–protein and protein–RNA interactions required for U2 snRNP recruitment to the branch point during splicing.\",\n      \"method\": \"In vitro binding assays, RNA binding studies, inhibition of splicing in vitro, circular dichroism spectroscopy\",\n      \"journal\": \"Biochemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — multiple orthogonal in vitro assays (binding, CD spectroscopy, splicing inhibition) in a single focused study\",\n      \"pmids\": [\"16906767\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2006,\n      \"finding\": \"DYRK1A phosphorylates SF3B1 (SAP155) at Thr434 in vitro and in cultured cells; overexpression of DYRK1A increases Thr434 phosphorylation of endogenous SF3B1, while DYRK1A knockdown reduces it. Cyclin E/CDK2 phosphorylates SF3B1 at different sites, producing a completely different phosphopeptide pattern.\",\n      \"method\": \"In vitro kinase assay, phosphopeptide mapping, mass spectrometry, mutational analysis, co-expression/knockdown in COS-7 and HEK293 cells, Western blot with phospho-specific antibody\",\n      \"journal\": \"BMC biochemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — in vitro kinase assay plus mutagenesis plus metabolic labeling phosphopeptide mapping, with RNAi validation; replicated across multiple cell lines\",\n      \"pmids\": [\"16512921\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2006,\n      \"finding\": \"SF3B1 (SAP155) binds via its RRM-like domain to the ceramide-responsive RNA cis-element 1 (CRCE1) of Bcl-x pre-mRNA. SAP155 knockdown shifts splicing toward the pro-apoptotic Bcl-x(s) isoform and is required for ceramide-induced activation of the Bcl-x(s) 5' splice site, sensitizing cells to chemotherapeutic agents.\",\n      \"method\": \"Mass spectrometry identification, EMSA supershift with anti-SAP155 antibody, RNA interference (RNAi) knockdown, RT-PCR for splice variant quantification, apoptosis assays\",\n      \"journal\": \"FASEB journal\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal binding confirmed by EMSA supershift, MS identification, and RNAi functional readout with multiple orthogonal methods in one study\",\n      \"pmids\": [\"16790528\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2006,\n      \"finding\": \"SF3B155 binds to the β-sheet surface of p14 (SF3b14) through a helical peptide (residues 401–415 form the core epitope), occupying the canonical RNA-binding surface of the p14 RRM. SF3B155 simultaneously binds p14 and U2AF65 through non-overlapping regions, potentially stabilizing U2 snRNP association with pre-mRNA. The p14–SF3B155 complex modulates RNA-binding specificity for the branch point.\",\n      \"method\": \"NMR spectroscopy, biochemical binding assays, mutagenesis\",\n      \"journal\": \"RNA\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — NMR structure determination combined with biochemical and mutagenesis validation, replicated across multiple constructs\",\n      \"pmids\": [\"16495236\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2005,\n      \"finding\": \"SF3b155 contains five functional tryptophan-containing U2AF65-binding sites in its N-terminal domain, each recognized by the U2AF65 UHM domain via a mechanism similar to SF1 but with lower affinity (3.3 kcal/mol less stable than the SF1/U2AF65 complex), consistent with ATP-dependent exchange of these partners during pre-mRNA splicing.\",\n      \"method\": \"Intrinsic tryptophan fluorescence spectroscopy, isothermal titration calorimetry, circular dichroism, mutagenesis of SF3b155 variants\",\n      \"journal\": \"Journal of molecular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — thermodynamic and spectroscopic characterization with multiple orthogonal methods and systematic mutagenesis in one study\",\n      \"pmids\": [\"16376933\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2002,\n      \"finding\": \"The FHA domain of NIPP1 interacts in vitro and in vivo with the TP dipeptide-rich region of SF3B1 (SAP155) in a phosphorylation-dependent manner; phosphorylated TP motifs in SAP155 compete for binding to the same NIPP1 FHA site. SAP155 kinases in cell lysates are blocked by EGTA and roscovitine (CDK inhibitor). SAP155 phosphorylation is dramatically increased during mitosis.\",\n      \"method\": \"GST pulldown, co-immunoprecipitation, phosphopeptide competition, kinase inhibition in cell lysates, mutagenesis\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal Co-IP and in vitro pulldown combined with mutagenesis and competition studies; phosphorylation-dependent interaction rigorously established\",\n      \"pmids\": [\"12105215\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2008,\n      \"finding\": \"NIPP1 recruits PP1 to Sap155 (SF3B1) and promotes Sap155 dephosphorylation; NIPP1 stimulates Sap155 dephosphorylation by PP1 in vitro by facilitating their interaction. NIPP1 acts as a molecular sensor that recognizes hyperphosphorylated Sap155 through its FHA domain and dissociates after dephosphorylation, linking phosphorylation cycling of Sap155 to splicing regulation.\",\n      \"method\": \"Co-immunoprecipitation, in vitro phosphatase assays, siRNA knockdown of NIPP1, overexpression of truncated NIPP1 mutants, splicing assays\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — in vitro reconstitution of PP1/NIPP1/SAP155 complex with phosphatase activity assay, complemented by RNAi and overexpression studies with splicing readout\",\n      \"pmids\": [\"18842582\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2008,\n      \"finding\": \"The p14–SF3b155 complex has two independent RNA-binding sites: a positively charged groove (requiring Tyr28 and Arg85 of p14) and the C-terminal extension of p14. SF3b155 residues Phe408, Tyr412, Val414, and Leu415 are critical contact points for complex formation with p14.\",\n      \"method\": \"NMR chemical shift perturbation, mutagenesis, in vitro binding assays\",\n      \"journal\": \"Proteins\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — NMR solution structure combined with extensive mutagenesis and functional binding validation in one study\",\n      \"pmids\": [\"18076038\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2010,\n      \"finding\": \"p14 (SF3b14) specifically recognizes the branch adenosine within the bulged U2/branch-point duplex, with the branch nucleotide buried at the p14/SF3b155-peptide interface; this interaction must be disrupted before the first catalytic step of splicing.\",\n      \"method\": \"X-ray crystallography (adenine-p14/SF3b155 peptide complex), disulfide cross-linking of protein-RNA complexes, small-angle X-ray scattering (SAXS)\",\n      \"journal\": \"RNA\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — crystal structure combined with SAXS and biochemical cross-linking providing orthogonal structural validation\",\n      \"pmids\": [\"21062891\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"SF3B1 is strongly associated with nucleosomes at exonic positions in chromatin; disruption of this SF3B1–nucleosome association impairs splicing of short exons flanked by long introns. Co-IP and sedimentation analyses demonstrate SF3B1 physically associates with nucleosomal components, and ChIP-seq shows preferential binding at exonic nucleosomes with differential GC content.\",\n      \"method\": \"Co-immunoprecipitation, proteomic analysis, sedimentation analysis, ChIP-seq, RNA-seq, SF3B1–nucleosome binding disruption experiments\",\n      \"journal\": \"Cell reports\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal Co-IP, ChIP-seq, and functional disruption experiments provide multiple orthogonal lines of evidence in one study\",\n      \"pmids\": [\"25892229\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"Cancer-associated SF3B1 hotspot mutations induce aberrant 3' splice site selection by utilizing a different (upstream) branch point sequence (BPS) compared to wild-type SF3B1. The mutant BPS requires the canonical 3' splice site to enable aberrant splicing during the second step. Approximately 50% of aberrantly spliced mRNAs are degraded by nonsense-mediated decay.\",\n      \"method\": \"RNA-seq analysis of cancer cell lines and patient samples, mutagenesis of predicted branchpoints, NMD inhibition experiments, isogenic cell line comparisons\",\n      \"journal\": \"Cell reports\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — branchpoint mutagenesis combined with RNA-seq across multiple cancer types and isogenic cell lines; independently replicated across labs\",\n      \"pmids\": [\"26565915\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"SF3B1 R625/K666 cancer mutations act as change-of-function (not loss-of-function) mutants that promote alternative branchpoint usage, leading to aberrant 3' splice site selection; wild-type SF3B1 knockdown or overexpression does not reproduce the mutant splicing pattern. Mutagenesis of predicted branchpoints confirms that the mutant-specific splicing depends directly on alternative branchpoint utilization.\",\n      \"method\": \"RNA-seq of uveal melanoma, isogenic SF3B1-WT and mutant cell lines, SF3B1 knockdown/overexpression, branchpoint mutagenesis\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — branchpoint mutagenesis combined with isogenic cell lines and knockdown/overexpression controls; change-of-function mechanism firmly established\",\n      \"pmids\": [\"26842708\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"SF3B1 inhibitors (three structurally distinct compounds) all interact with the same site on SF3B1 and interfere with splicing at multiple stages including both early spliceosome assembly and late exon ligation. Inactive analogs of each compound interchangeably compete with active inhibitors to restore splicing, supporting a shared pharmacophore model in which inhibition results not from binding alone but from inducing a conformational change in SF3B1.\",\n      \"method\": \"In vitro splicing assays, competition experiments with active and inactive inhibitor analogs, analysis at defined spliceosome assembly stages\",\n      \"journal\": \"RNA\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — in vitro splicing reconstitution with pharmacological competition experiments; multiple inhibitor compounds tested with rigorous controls\",\n      \"pmids\": [\"26742993\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"SF3B1 HEAT-repeat mutations (yeast Hsh155 counterparts of human cancer mutations) directly alter the physical interaction between Hsh155 and the spliceosomal ATPase Prp5; this altered interaction changes the fidelity of branch-site (BS)–U2 duplex loading into the SF3B complex during prespliceosome formation, resulting in altered BS selectivity and splicing of suboptimal BS substrates.\",\n      \"method\": \"Yeast genetic analysis, in vitro direct binding assays (Hsh155–Prp5 interaction), splicing assays with nonconsensus BS pre-mRNAs, epistasis analysis of Hsh155 and Prp5 mutations\",\n      \"journal\": \"Genes & development\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — direct protein-protein interaction assays combined with genetic epistasis and in vitro splicing assays; mechanism rigorously established in yeast ortholog with disease-relevant mutations\",\n      \"pmids\": [\"28087715\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"Sf3b1(K700E) knock-in mice develop macrocytic anemia due to terminal erythroid maturation defect and erythroid dysplasia; Sf3b1(K700E) myeloid progenitors show aberrant 3' splice-site selection associated with increased nonsense-mediated decay. Tet2 loss cooperates with Sf3b1(K700E) to worsen erythroid and LT-HSC phenotypes.\",\n      \"method\": \"Conditional knock-in mouse model, RNA-seq (aberrant splice site analysis), NMD pathway analysis, genetic epistasis (Sf3b1(K700E) × Tet2 loss), hematopoietic phenotyping\",\n      \"journal\": \"Cancer cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — physiological knock-in mouse model with RNA-seq, NMD analysis, and genetic epistasis; replicated in patient samples\",\n      \"pmids\": [\"27622333\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"SF3b1/Hsh155 mutations alter branchsite selection fidelity in yeast, changing how the spliceosome recognizes nonconsensus nucleotides at positions -2, -1, and +1 relative to the branchpoint adenosine. Different HSH155 alleles have disparate effects: some increase and others decrease fidelity of BS selection. The data support a model in which SF3B1 conformational changes promote U2 snRNA association with the BS to drive spliceosome assembly, acting independently of Prp5 ATPase in some contexts.\",\n      \"method\": \"Yeast genetic analysis, in vitro splicing assays with nonconsensus BS substrates, single-molecule fluorescence microscopy of spliceosome assembly\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — in vitro splicing assays combined with genetic analysis and single-molecule microscopy; detailed mechanistic investigation of BS recognition\",\n      \"pmids\": [\"28062854\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"Disease-causing SF3B1 hotspot mutations (K700E and others) reduce the level of SUGP1 in mutant spliceosomes. SUGP1 knockdown completely recapitulates SF3B1-mutant splicing errors. SUGP1 overexpression partially rescues aberrant splicing by driving SUGP1 back into mutant spliceosomes. SUGP1 plays an important role in branchsite recognition; loss of SF3B1–SUGP1 interaction is the common molecular defect of disease-causing SF3B1 mutations.\",\n      \"method\": \"Purification of wild-type and K700E mutant SF3B1 complexes followed by proteomics, SUGP1 knockdown and overexpression with RNA-seq, analysis across multiple SF3B1 hotspot mutants\",\n      \"journal\": \"Molecular cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — complex purification with proteomics, combined with knockdown/overexpression rescue experiments and RNA-seq; finding validated across multiple SF3B1 hotspot mutants\",\n      \"pmids\": [\"31474574\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"Cus2 (yeast) contains a UHM that binds Hsh155 (yeast SF3b1) through a conserved ULM, enforcing the first ATP-dependent step of pre-spliceosome formation. Disruption of this UHM–ULM interaction allows pre-spliceosome formation without ATP. Crystal structure of the human Tat-SF1 (Cus2 homolog) UHM bound to an Hsh155 ULM at 2.0 Å confirms the interaction is conserved between yeast and humans.\",\n      \"method\": \"Crystal structure determination (2.0 Å), mutagenesis of UHM/ULM motifs, yeast splicing extract complementation assays, in vitro binding assays\",\n      \"journal\": \"RNA\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — crystal structure combined with mutagenesis, in vitro binding, and functional splicing assays; yeast-human conservation established\",\n      \"pmids\": [\"31110137\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"Conserved amino acids in SF3B1 (Hsh155) that contact the U2 snRNA backbone in the U2/branch-site duplex are nonessential; however, mutations in the branch-point adenosine-housing pocket, while viable, cause defects in splicing pre-mRNAs with nonconsensus BS sequences. Human SF3B1 HEAT repeats substituted into yeast Hsh155 chimeras confer pladienolide B sensitivity to yeast splicing and alter BS usage.\",\n      \"method\": \"Mutational analysis of yeast Hsh155 guided by spliceosome cryo-EM structures, in vitro splicing assays, yeast-human chimeric protein analysis, pladienolide B inhibition assays\",\n      \"journal\": \"RNA\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — structure-guided mutagenesis with in vitro splicing assays and chimeric protein validation in one rigorous study\",\n      \"pmids\": [\"29752352\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"In SF3B1-mutated MDS, mutant SF3B1 generates an alternative ERFE (erythroferrone) transcript in erythroblasts encoding a variant protein that retains capacity to suppress hepcidin transcription, leading to elevated plasma ERFE and iron overload in SF3B1-mutant MDS patients.\",\n      \"method\": \"RNA-seq identification of alternative ERFE transcript, induction in primary SF3B1-mutated erythroblasts, hepcidin suppression assays, plasma ERFE measurement\",\n      \"journal\": \"Science translational medicine\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — functional validation in primary patient erythroblasts combined with hepcidin suppression assays and patient plasma measurements\",\n      \"pmids\": [\"31292266\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"SF3B1 hotspot mutations promote decay of PPP2R5A (PP2A subunit) transcripts via aberrant splicing, increasing MYC S62 and BCL2 S70 phosphorylation, which stabilizes MYC protein and impairs apoptosis. Genetic PPP2R5A restoration or pharmacological PP2A activation impaired SF3B1-mutant tumorigenesis.\",\n      \"method\": \"RNA-seq across 98 tumors and 12 isogenic cell lines, regulatory network analysis, phosphoprotein analysis, genetic rescue (PPP2R5A restoration), pharmacological PP2A activation in mouse xenograft models\",\n      \"journal\": \"Cancer discovery\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — mechanistic link established across human and mouse cells with genetic and pharmacological rescue experiments; multiple orthogonal methods\",\n      \"pmids\": [\"32188705\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"CAPERα (a UHM-containing alternative splicing factor) interacts with SF3b155 through a UHM/ULM interaction; crystal structure of the CAPERα UHM bound to a representative SF3b155 ULM at 1.7 Å resolution establishes SF3b155 as the relevant ULM-containing partner of CAPERα in human cell extracts. SF3b155 serves as a platform for coordinated recruitment of multiple UHM-containing splicing factors.\",\n      \"method\": \"X-ray crystallography (1.7 Å), isothermal titration calorimetry, pulldown from human cell extracts\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — crystal structure with ITC thermodynamic characterization and cell extract pulldown validation\",\n      \"pmids\": [\"24795046\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"CDK11 associates with SF3B1 and phosphorylates threonine residues at its N-terminus during spliceosome activation. This phosphorylation is important for SF3B1 association with U5 and U6 snRNAs in the activated (Bact) spliceosome. Inhibition of CDK11 with OTS964 prevents spliceosomal transition from precatalytic complex B to activated complex Bact, causing widespread intron retention.\",\n      \"method\": \"Co-immunoprecipitation (CDK11–SF3B1 association), in vitro kinase assays, OTS964 CDK11 inhibitor treatment, spliceosome complex analysis (B vs Bact), RNA-seq for intron retention, CLIP-seq for snRNA association\",\n      \"journal\": \"Nature\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — in vitro kinase assay combined with pharmacological inhibition, spliceosome complex analysis, and genome-wide RNA-seq; multiple orthogonal methods in one rigorous study\",\n      \"pmids\": [\"36104565\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"Coordinated missplicing of TMEM14C and ABCB7 by mutant SF3B1 (K700E) sequesters iron in mitochondria causing ring sideroblast (RS) formation in MDS. Functional rescue of both TMEM14C and ABCB7 expression nearly abolished RS formation in iPSC-derived erythroid cells, while rescue of PPOX alone had no effect.\",\n      \"method\": \"iPSC model of SF3B1-mutant MDS with in vitro erythroid differentiation, RNA-seq, functional rescue of TMEM14C and ABCB7, ring sideroblast quantification\",\n      \"journal\": \"Blood\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — physiological iPSC model with genetic rescue experiments establishing causal necessity of specific mis-spliced genes for RS formation\",\n      \"pmids\": [\"34861039\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"SF3B1 K700E mutation induces mis-splicing of MAP3K7, leading to inactivation of the MAP3K7–p38 MAPK pathway, premature downregulation of GATA1, and accelerated erythroid differentiation followed by apoptosis, causing the anemia characteristic of SF3B1-mutant MDS.\",\n      \"method\": \"Isogenic SF3B1-WT and mutant cell lines, normal human CD34+ cells, MDS patient cells; p38 MAPK activity assays, GATA1 expression analysis, erythroid differentiation assays\",\n      \"journal\": \"PNAS\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — causal pathway established using isogenic cell lines, primary human CD34+ cells, and patient samples with multiple orthogonal functional readouts\",\n      \"pmids\": [\"34930825\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"CDK12/13 promote the interaction of SF3B1 with Ser2-phosphorylated RNA polymerase II (RNAPII), facilitating SF3B1 association with chromatin and recruitment to 3' splice sites of promoter-proximal introns. CDK12/13 inhibition disrupts the SF3B1–RNAPII interaction and causes selective retention of promoter-proximal introns with weak 3' splice sites.\",\n      \"method\": \"Co-IP of SF3B1 with Ser2-phospho-RNAPII, CDK12/13 inhibitor (THZ531) treatment, ChIP-seq for SF3B1 chromatin association, nascent transcript analysis, RNA-seq for intron retention\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP combined with ChIP-seq, nascent transcript analysis, and RNA-seq in one study; mechanism linking transcription to SF3B1 recruitment established\",\n      \"pmids\": [\"37026485\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"DHX15 is the RNA helicase required for SUGP1 function in branchpoint recognition. Cancer-causing SF3B1 mutations disrupt the SF3B1–SUGP1 interaction, indirectly depriving SUGP1 of its helicase partner DHX15. Crystal structure of DHX15–SUGP1 G-patch complex reveals the molecular basis of their direct interaction. A DHX15–SUGP1 G-patch fusion protein rescues splicing defects of mutant SF3B1.\",\n      \"method\": \"Protein-protein interaction assays (Co-IP, pulldown), crystal structure of DHX15–SUGP1 G-patch complex, RNA-seq, knockdown/overexpression of DHX15, DHX15–SUGP1 fusion rescue experiments\",\n      \"journal\": \"PNAS\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — crystal structure combined with multiple interaction assays, knockdown experiments, and functional rescue; mechanism rigorously established\",\n      \"pmids\": [\"36459648\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"Structural modeling and experimental validation show that two regions flanking the SUGP1 G-patch make numerous contacts with the SF3B1 region harboring cancer hotspot mutations. All cancer-associated mutations in these interface regions weaken or disrupt SF3B1–SUGP1 interaction and alter splicing. Structural modeling reveals that the SF3B1–SUGP1 interaction 'loops out' the G-patch for interaction with DHX15.\",\n      \"method\": \"Structural modeling (AlphaFold-based), mutagenesis of SF3B1–SUGP1 interface residues, Co-IP, RNA-seq for splicing analysis\",\n      \"journal\": \"Genes & development\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — structural modeling validated by systematic mutagenesis and Co-IP with functional RNA-seq readout; comprehensive interface characterization\",\n      \"pmids\": [\"37977822\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"SF3B1 K700E mutation promotes centromeric R-loop (cen-R-loop) accumulation, leading to increased chromosome oscillation, impaired chromosome segregation, altered spindle architecture, and aneuploidy. Aberrant splicing of genes involved in R-loop processing underlies cen-R-loop augmentation; overexpression of the normal (not mis-spliced) isoform mitigated mitotic stress. ATM deletion exaggerates these phenotypes.\",\n      \"method\": \"R-loop detection (DRIP), chromosome segregation analysis, spindle architecture imaging, isogenic cell lines with SF3B1 mutation, genetic epistasis with ATM deletion, isoform rescue experiments\",\n      \"journal\": \"The Journal of clinical investigation\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple orthogonal assays (DRIP, chromosome imaging, isoform rescue) establishing causal link between aberrant splicing and chromosomal instability\",\n      \"pmids\": [\"37463047\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"Mis-splicing of COASY (coenzyme A synthase) by mutant SF3B1 depletes both CoA and succinyl-CoA in erythroblasts, impairing heme biosynthesis and erythropoiesis. Supplementation with vitamin B5 (COASY substrate) rescued CoA/succinyl-CoA concentrations in SF3B1-mutant cells and rescued erythropoiesis differentiation in primary MDS-RS patient cells.\",\n      \"method\": \"Splice variant analysis of COASY in patient samples, COASY silencing in erythroid cultures, CoA/succinyl-CoA metabolite measurement, vitamin B5 supplementation in isogenic cells and primary patient cells\",\n      \"journal\": \"Science translational medicine\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — causal metabolic pathway established through COASY knockdown, metabolite measurement, and rescue in patient primary cells using multiple orthogonal approaches\",\n      \"pmids\": [\"36857430\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"Cancer-associated SF3B1 mutations reduce RNA polymerase II (RNAPII) elongation rate along gene bodies and decrease RNAPII density at promoters. The elongation defect results from disrupted pre-spliceosome assembly due to impaired protein–protein interactions of mutant SF3B1. Decreased promoter-proximal RNAPII density reduces chromatin accessibility and H3K4me3 at promoters. Sin3/HDAC/H3K4me pathway modulation reverses both transcription and chromatin changes.\",\n      \"method\": \"RNAPII ChIP-seq, chromatin accessibility (ATAC-seq), H3K4me3 ChIP-seq, isogenic cell lines, patient samples, mutant mouse model, unbiased epigenetic inhibitor screen\",\n      \"journal\": \"Molecular cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — multiple orthogonal genomic assays (ChIP-seq, ATAC-seq) across isogenic cell lines, patient samples, and mouse model with functional rescue screen\",\n      \"pmids\": [\"38521065\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"GPATCH8 is required for mutant SF3B1-induced aberrant splicing activity. GPATCH8 interacts with the RNA helicase DHX15 and functionally opposes SUGP1 in branchpoint quality control. GPATCH8 silencing corrected approximately one-third of mutant SF3B1-dependent splicing defects and improved dysfunctional hematopoiesis in SF3B1-mutant mice and primary human progenitors.\",\n      \"method\": \"Synthetic intron screen to identify trans factors, Co-IP (GPATCH8–DHX15 interaction), GPATCH8 knockdown in isogenic cell lines and SF3B1-mutant mice, RNA-seq for splicing correction, hematopoiesis assays\",\n      \"journal\": \"Molecular cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — interaction assay combined with functional genetic rescue in multiple model systems (cell lines, mouse, primary human progenitors) with RNA-seq splicing readout\",\n      \"pmids\": [\"38688280\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"Upon genotoxic (alkylation) stress, Hsh155 (yeast SF3B1) disassembles from its spliceosomal partners and localizes to intranuclear and cytoplasmic protein quality control aggregates. This sequestration is regulated by molecular chaperones and requires TORC1 signaling through Sfp1 transcription factor, and is associated with intron retention in ribosomal protein gene transcripts and decreased splicing efficiency during stress recovery.\",\n      \"method\": \"Cytological screen, live cell imaging, genetic analysis (chaperone mutants, TORC1/Sfp1 pathway), RNA-seq for intron retention, stress recovery assays\",\n      \"journal\": \"The Journal of cell biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct localization by imaging with functional pathway analysis; single study but multiple methods\",\n      \"pmids\": [\"28978642\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"Cancer-associated SF3B1 mutations disrupt the interaction between SF3B1 and DDX42 (and DDX46). Overexpression of DDX42 suppresses some SF3B1-mutation-associated aberrant splicing, and this suppression requires DDX42 ATP hydrolysis activity.\",\n      \"method\": \"Co-immunoprecipitation of WT and K700E SF3B1 complexes, DDX42 overexpression with RNA-seq for splicing correction, ATPase-dead DDX42 mutant analysis\",\n      \"journal\": \"Journal of biochemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — Co-IP interaction assay with functional overexpression rescue; single lab, limited orthogonal validation\",\n      \"pmids\": [\"35652295\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"SAP155 (SF3B1) physically interacts with FIR/FIRΔexon2 (a PUF60 splicing variant), forming a complex that bridges c-Myc transcription and P27 (CDKN1B) expression. SAP155/FIR/FIRΔexon2 knockdown reduces p27 expression and inhibits P27 pre-mRNA splicing, reducing CDK2/Cyclin E expression.\",\n      \"method\": \"Co-immunoprecipitation (SAP155–FIR/FIRΔexon2 complex), siRNA knockdown of SAP155/FIR, RT-PCR for P27 splicing, Western blot for CDK2/Cyclin E\",\n      \"journal\": \"Molecular cancer research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — Co-IP and RNAi with functional splicing readout; single lab, limited mechanistic detail in abstract\",\n      \"pmids\": [\"23594796\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"SF3B1 mutations lead to aberrant retention of full-length exon 6 of IRAK4, producing a longer IRAK4 isoform (IRAK4-long) containing the full death and kinase domains that maximally activates NF-κB. IRAK4-long expression in SF3B1-mutant cells induces TRAF6 activation and K63-linked ubiquitination of CDK2, causing a block in hematopoietic differentiation. IRAK4 inhibition with CA-4948 reduces NF-κB activation and improves myeloid differentiation.\",\n      \"method\": \"RNA-seq splicing analysis of SF3B1-mutant MDS samples, IRAK4 isoform functional assays, TRAF6/CDK2 ubiquitination assays, IRAK4 inhibitor in vitro differentiation and xenograft models\",\n      \"journal\": \"eLife\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — functional isoform analysis combined with downstream signaling assays and in vivo xenograft; multiple methods but primarily in cancer models\",\n      \"pmids\": [\"36040792\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"SF3B1 protein is stabilized via deubiquitination (post-translational stabilization of the U2 complex component SF3B1). SF3B1 inhibition blocks T-ALL growth in vivo, perturbs exon skipping leading to NMD-mediated reduction of CHEK2 transcripts, and impairs DNA damage response. SF3B1 inhibition also leads to a general decrease in R-loop formation.\",\n      \"method\": \"In vivo T-ALL mouse model with SF3B1 inhibitor treatment, deubiquitination assays for SF3B1 stability, RNA-seq for exon skipping/NMD analysis, CHEK2 protein/transcript analysis, R-loop detection\",\n      \"journal\": \"Science advances\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple assays (deubiquitination, RNA-seq, R-loop detection, in vivo) but abstract is compressed; single lab study\",\n      \"pmids\": [\"35061527\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"ALKBH5-driven 5' UTR m6A demethylation fine-tunes SF3B1 translation, and SF3B1 protein abundance levels dynamically regulate MDS-to-leukemia progression in vivo. Changes in SF3B1 levels affect splicing of central DNA repair and epigenetic regulators.\",\n      \"method\": \"m6A sequencing, ALKBH5 manipulation in human and murine pre-leukemic MDS cells, SF3B1 translation reporter assays, in vivo MDS-to-leukemia progression monitoring\",\n      \"journal\": \"Molecular cell\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — epitranscriptomic modification identified with functional in vivo validation; abstract compressed, mechanism partially inferred\",\n      \"pmids\": [\"36944332\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"SF3B1 physically interacts with HIF1α, facilitating binding of the HIF1 complex to hypoxia response elements (HREs) to activate target gene expression. SF3B1 is a HIF-1 target gene, forming a positive feedback loop. Monoallelic Sf3b1 deletion impedes tumor formation and progression via impaired HIF signaling in a mouse pancreatic cancer model.\",\n      \"method\": \"Co-IP of SF3B1 with HIF1α, chromatin immunoprecipitation (HIF1 complex binding to HREs), Sf3b1 monoallelic deletion in mouse pancreatic cancer model, tumor formation assays\",\n      \"journal\": \"Cell reports\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP and ChIP combined with in vivo mouse model; interaction and functional consequence established but in compressed abstract\",\n      \"pmids\": [\"36001976\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1998,\n      \"finding\": \"Fission yeast prp10+ (SF3B1 ortholog) is essential for viability and encodes a protein homologous to human SAP155. Prp10p-GFP localizes predominantly to the nuclear DNA region. The N-terminal ~300 amino acids are dispensable for viability, unlike the conserved C-terminal region containing HEAT repeats.\",\n      \"method\": \"Complementation cloning, gene disruption, GFP fusion localization, deletion analysis\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct localization by GFP imaging and genetic essentiality established by gene disruption; foundational characterization in ortholog\",\n      \"pmids\": [\"9837997\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"SAP155 (SF3B1) knockdown generates FIRΔexon2 and novel FIR splicing variants (Δ3, Δ4) that lack c-Myc transcriptional repression activity; these variants are found in human colorectal cancer tissues, establishing a role for SAP155 in regulation of FIR pre-mRNA splicing and c-Myc transcriptional control.\",\n      \"method\": \"siRNA knockdown of SAP155 in cell lines, RT-PCR identification of FIR splice variants, colorectal cancer tissue analysis\",\n      \"journal\": \"Cancer science\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single knockdown experiment with splice variant identification; no direct mechanistic assay of SF3B1 binding to FIR pre-mRNA\",\n      \"pmids\": [\"23113893\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"SF3B1 inhibitor treatment in HNSCC cells promotes generation of pro-apoptotic MCL1-S splice variant while diminishing anti-apoptotic MCL1-L variant, via SF3B1-dependent splicing regulation of MCL1 pre-mRNA. SF3B1 is also involved in the splicing of HPV16 E6 to produce the non-oncogenic E6* isoform.\",\n      \"method\": \"RT-PCR and Western blot for MCL1 splice variants upon meayamycin B (SF3B1 inhibitor) treatment, apoptosis assays, pharmacological SF3B1 inhibition\",\n      \"journal\": \"Scientific reports\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — pharmacological inhibition only (no direct SF3B1 binding assay); functional splicing outcome established but mechanism inferred from inhibitor effects\",\n      \"pmids\": [\"25139387\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"SF3B1 is the largest subunit of the SF3b complex within the U2 snRNP of the spliceosome, functioning as a scaffold that recruits U2 snRNP to pre-mRNA branch points through simultaneous interactions with p14, U2AF65 (via multiple ULM sites in its N-terminal domain), and SUGP1 (whose G-patch activates the DHX15 helicase for branchpoint recognition); SF3B1 undergoes CDK11-mediated phosphorylation of N-terminal threonine residues during spliceosomal activation (B-to-Bact transition), is phosphorylated at Thr434 by DYRK1A and dephosphorylated by the NIPP1–PP1 complex, and physically associates with chromatin/nucleosomes at exonic positions to couple transcription elongation (via CDK12/13-mediated interaction with Ser2-phosphorylated RNAPII) to splice-site recognition; recurrent cancer hotspot mutations (K700E, R625H, etc.) act as change-of-function alleles that disrupt the SF3B1–SUGP1 interaction, impair RNAPII elongation and chromatin accessibility, and redirect branchpoint usage to generate hundreds of cryptic 3' splice sites, with downstream consequences including PPP2R5A mis-splicing activating MYC and BCL2, ABCB7/TMEM14C mis-splicing causing ring sideroblast formation, MAP3K7 mis-splicing impairing erythropoiesis, COASY mis-splicing depleting CoA/succinyl-CoA, and IRAK4 exon retention activating NF-κB.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"SF3B1 is the largest subunit of the SF3b complex within the U2 snRNP and functions as a scaffold that recruits U2 snRNP to pre-mRNA branch points during spliceosome assembly [#1, #0]. Its intrinsically disordered N-terminal domain presents multiple tryptophan-containing ULM sites that engage the UHM domain of U2AF65 with tunable, lower-than-SF1 affinity consistent with ATP-dependent partner exchange, and this same platform recruits additional UHM-containing splicing factors such as CAPERα [#5, #22]. Through a helical epitope (residues ~401–415) SF3B1 binds the p14/SF3b14 RRM surface, and the p14–SF3B1 module directly recognizes and buries the branch-point adenosine within the U2/branch-site duplex before the first catalytic step [#4, #8, #9]. SF3B1 is built around HEAT repeats whose conformation governs branch-site selection fidelity: structure-guided yeast work shows that the branch-point adenosine pocket and the interaction with the ATPase Prp5 set how the U2/branch-site duplex is loaded, and HEAT-repeat substitutions confer pladienolide sensitivity [#14, #19, #16]. SF3B1 activity is regulated by phosphorylation cycling—DYRK1A phosphorylates Thr434, CDK11 phosphorylates N-terminal threonines to drive the B-to-Bact spliceosomal transition, and the NIPP1–PP1 complex senses hyperphosphorylated SF3B1 and reverses these marks [#2, #23, #6, #7]. Beyond core splicing, SF3B1 associates with exonic nucleosomes and couples transcription to splice-site recognition by binding Ser2-phosphorylated RNAPII via CDK12/13 [#10, #26]. SUGP1 binds SF3B1 and supplies the G-patch that activates the DHX15 helicase for branch-point fidelity [#27, #28]. Recurrent cancer hotspot mutations (e.g., K700E, R625H) are change-of-function alleles that weaken the SF3B1–SUGP1 interaction, redirect branch-point usage to generate cryptic 3' splice sites, and impair RNAPII elongation and chromatin accessibility [#12, #17, #31]. The resulting mis-splicing drives disease-specific phenotypes: PPP2R5A decay stabilizing MYC and BCL2 [#21], coordinated TMEM14C/ABCB7 mis-splicing causing ring sideroblasts [#24], MAP3K7 mis-splicing impairing erythropoiesis [#25], COASY mis-splicing depleting CoA/succinyl-CoA [#30], and IRAK4 exon retention activating NF-κB [#36], with mutant SF3B1 also promoting centromeric R-loop accumulation and chromosomal instability [#29]. A heterozygous K700E knock-in mouse develops macrocytic anemia and erythroid dysplasia modeling SF3B1-mutant myelodysplastic syndrome [#15].\"\n,\n  \"teleology\": [\n    {\n      \"year\": 1998,\n      \"claim\": \"Established that the SF3B1 ortholog is an essential, conserved nuclear protein, defining the gene as core machinery rather than an accessory factor.\",\n      \"evidence\": \"Complementation cloning, gene disruption, and GFP localization of fission yeast prp10+\",\n      \"pmids\": [\"9837997\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Molecular function not assigned beyond essentiality\", \"N-terminal dispensability in yeast not connected to human regulatory roles\"]\n    },\n    {\n      \"year\": 2006,\n      \"claim\": \"Defined how SF3B1 acts as a scaffold by mapping distinct, non-overlapping binding sites for U2AF65 and p14 within its unfolded N-terminal domain, explaining how it nucleates U2 snRNP at the branch point.\",\n      \"evidence\": \"In vitro binding, CD spectroscopy, NMR, ITC, and mutagenesis of SF3b155 N-terminal ULM and p14-binding regions\",\n      \"pmids\": [\"16906767\", \"16495236\", \"16376933\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Affinity hierarchy among the multiple ULM sites in vivo not resolved\", \"How partner exchange is timed during assembly not directly shown\"]\n    },\n    {\n      \"year\": 2010,\n      \"claim\": \"Resolved the structural basis of branch-point recognition, showing the branch adenosine is buried at the p14/SF3B1-peptide interface and must be released before catalysis.\",\n      \"evidence\": \"X-ray crystallography of adenine-p14/SF3b155 peptide, disulfide cross-linking, and SAXS\",\n      \"pmids\": [\"21062891\", \"18076038\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Trigger for adenosine release before first catalytic step not defined\", \"Structure captures peptide, not full-length SF3B1 in spliceosome\"]\n    },\n    {\n      \"year\": 2008,\n      \"claim\": \"Established SF3B1 as a regulated phosphoprotein by identifying DYRK1A as a Thr434 kinase and the NIPP1–PP1 complex as the sensor/phosphatase that reverses hyperphosphorylation, linking phospho-cycling to splicing.\",\n      \"evidence\": \"In vitro kinase and phosphatase assays, phosphopeptide mapping, FHA-domain pulldowns, and RNAi across cell lines\",\n      \"pmids\": [\"16512921\", \"12105215\", \"18842582\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Functional consequence of Thr434 phosphorylation on splicing not fully defined\", \"Which spliceosomal stage each phospho-mark governs not resolved here\"]\n    },\n    {\n      \"year\": 2011,\n      \"claim\": \"Identified SF3B1 as the direct molecular target of splicing-inhibitor natural products, validating it as a druggable node and providing tools to probe its function.\",\n      \"evidence\": \"Photoaffinity labeling with GEX1A derivatives and in vitro splicing assays\",\n      \"pmids\": [\"21138297\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Binding site on SF3B1 not localized at this stage\", \"Mechanism of inhibition beyond SF3b impairment unresolved\"]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"Generalized the scaffold model by showing SF3B1 ULMs recruit additional UHM splicing factors, establishing it as a coordinating platform for multiple regulators.\",\n      \"evidence\": \"Crystal structure of CAPERα UHM bound to an SF3b155 ULM, ITC, and cell-extract pulldowns\",\n      \"pmids\": [\"24795046\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"In vivo competition among UHM partners not quantified\", \"Functional output of CAPERα recruitment not defined\"]\n    },\n    {\n      \"year\": 2016,\n      \"claim\": \"Determined that cancer hotspot mutations are change-of-function alleles that redirect branch-point usage to create cryptic 3' splice sites, distinguishing the mechanism from simple loss of function.\",\n      \"evidence\": \"RNA-seq of cancer cell lines and tumors, isogenic comparisons, branchpoint mutagenesis, and knockdown/overexpression controls\",\n      \"pmids\": [\"26565915\", \"26842708\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Why specific branch points are selected not explained at this stage\", \"Molecular partner whose loss causes the shift unidentified\"]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"Used yeast genetics to mechanistically connect SF3B1 HEAT-repeat conformation to branch-site selection fidelity through its interaction with the ATPase Prp5.\",\n      \"evidence\": \"Yeast Hsh155 epistasis, in vitro Hsh155–Prp5 binding, single-molecule assembly imaging, and splicing of nonconsensus branch-site substrates\",\n      \"pmids\": [\"28087715\", \"28062854\", \"29752352\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Direct extrapolation of allele-specific fidelity effects to human disease mutants incomplete\", \"Conformational states not visualized structurally\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Identified loss of the SF3B1–SUGP1 interaction as the common molecular defect of disease-causing SF3B1 mutations, since SUGP1 knockdown recapitulates and overexpression rescues mutant splicing errors.\",\n      \"evidence\": \"Proteomics of WT vs K700E complexes, SUGP1 knockdown/overexpression with RNA-seq across multiple hotspot mutants, plus conserved UHM–ULM structural work\",\n      \"pmids\": [\"31474574\", \"31110137\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"How SUGP1 mechanistically enforces branch-site choice not yet defined\", \"Helicase partner of SUGP1 not identified at this point\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Completed the SUGP1 module by showing it presents a G-patch that activates the DHX15 helicase, and that hotspot mutations indirectly deprive SUGP1 of DHX15.\",\n      \"evidence\": \"Co-IP, crystal structure of DHX15–SUGP1 G-patch, knockdown, and a DHX15–SUGP1 fusion that rescues mutant splicing; structural modeling of the SF3B1–SUGP1 interface\",\n      \"pmids\": [\"36459648\", \"37977822\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"In vivo kinetics of helicase activation during assembly not measured\", \"GPATCH8 as an opposing G-patch factor only later defined\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Connected SF3B1 to transcription and chromatin, showing CDK11 drives the activating B-to-Bact phosphorylation while CDK12/13 couple SF3B1 to elongating RNAPII at exonic nucleosomes.\",\n      \"evidence\": \"Co-IP, in vitro kinase assays, CDK11 (OTS964) and CDK12/13 (THZ531) inhibition, ChIP-seq, CLIP-seq, and intron-retention RNA-seq\",\n      \"pmids\": [\"36104565\", \"37026485\", \"25892229\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Hierarchy between transcriptional coupling and core spliceosome recruitment not fully ordered\", \"Direct chromatin-binding determinants of SF3B1 not mapped\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Established the disease-relevant downstream targets of mutant SF3B1 mis-splicing, defining the molecular causes of ring sideroblasts, anemia, and oncogenic signaling.\",\n      \"evidence\": \"iPSC and isogenic models with genetic rescue of TMEM14C/ABCB7, MAP3K7/p38 pathway analysis, PPP2R5A/MYC/BCL2 phosphoprotein and rescue studies, IRAK4 isoform and NF-κB assays, and a K700E knock-in mouse\",\n      \"pmids\": [\"34861039\", \"34930825\", \"32188705\", \"36040792\", \"27622333\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Relative contribution of each mis-splicing event to combined phenotype not quantified\", \"Why erythroid lineage is selectively vulnerable not fully explained\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Extended the consequences of mutant SF3B1 to metabolism and genome stability, linking COASY mis-splicing to CoA depletion and the K700E allele to centromeric R-loops and aneuploidy.\",\n      \"evidence\": \"COASY splice-variant and metabolite analysis with vitamin B5 rescue in patient cells; DRIP, chromosome segregation imaging, and isoform rescue in isogenic lines\",\n      \"pmids\": [\"36857430\", \"37463047\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether metabolic and genomic phenotypes are independent or sequential not resolved\", \"Identity of all R-loop-processing transcripts mis-spliced not complete\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Showed that mutant SF3B1 impairs RNAPII elongation and reduces promoter chromatin accessibility, and identified GPATCH8 as a DHX15-binding factor required for mutant mis-splicing, nominating reversible nodes for intervention.\",\n      \"evidence\": \"RNAPII/H3K4me3 ChIP-seq, ATAC-seq, epigenetic inhibitor screen across isogenic cells, patients and mouse; synthetic intron screen, Co-IP, and GPATCH8 knockdown rescue across model systems\",\n      \"pmids\": [\"38521065\", \"38688280\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"How GPATCH8 and SUGP1 are balanced at branch points mechanistically unresolved\", \"Causal order between elongation defect and chromatin changes not fully established\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How SF3B1 protein abundance, post-translational modification, and additional helicase partners (e.g., DDX42/DDX46) are integrated to determine branch-point fidelity and disease progression remains incompletely defined.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"DDX42/DDX46 interactions characterized only by Co-IP and overexpression rescue without structural detail\", \"Stress-induced SF3B1 sequestration and m6A/ALKBH5 translational control not mechanistically linked to splice-site fidelity in humans\", \"Quantitative rules predicting which introns are mis-spliced by a given mutant remain unknown\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0003723\", \"supporting_discovery_ids\": [3, 9, 1]},\n      {\"term_id\": \"GO:0060090\", \"supporting_discovery_ids\": [1, 5, 4, 22]},\n      {\"term_id\": \"GO:0140098\", \"supporting_discovery_ids\": [11, 12, 14]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [40]},\n      {\"term_id\": \"GO:0000228\", \"supporting_discovery_ids\": [10]},\n      {\"term_id\": \"GO:0005654\", \"supporting_discovery_ids\": [1, 4]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-8953854\", \"supporting_discovery_ids\": [0, 1, 9, 23]},\n      {\"term_id\": \"R-HSA-74160\", \"supporting_discovery_ids\": [26, 31, 10]},\n      {\"term_id\": \"R-HSA-1643685\", \"supporting_discovery_ids\": [12, 17, 15, 24]}\n    ],\n    \"complexes\": [\n      \"SF3b complex\",\n      \"U2 snRNP\",\n      \"spliceosome\"\n    ],\n    \"partners\": [\n      \"U2AF65\",\n      \"SF3B14 (p14)\",\n      \"SUGP1\",\n      \"DHX15\",\n      \"NIPP1\",\n      \"CDK11\",\n      \"RNAPII\",\n      \"GPATCH8\"\n    ],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":10,"faith_total":10,"faith_pct":100.0}}