{"gene":"TFIP11","run_date":"2026-06-10T10:51:55","timeline":{"discoveries":[{"year":2005,"finding":"TFIP11 localizes to a novel subnuclear structure termed the 'TFIP body', distinct from but proximal to SC35 nuclear speckles. This localization is RNA-dependent (TFIP body disperses after RNase A treatment), and RNA polymerase II inhibition causes enlargement and reduced number of TFIP bodies. An in vivo splicing assay demonstrated TFIP11 functions as a splicing factor.","method":"GFP-tagging and live-cell fluorescence microscopy, RNase A treatment, RNA Pol II inhibitor treatment (α-amanitin, actinomycin D), in vivo splicing assay","journal":"Cellular and molecular life sciences : CMLS","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct localization experiment with functional consequence, multiple orthogonal methods (imaging, RNase treatment, splicing assay) in single lab","pmids":["15868102"],"is_preprint":false},{"year":2008,"finding":"TFIP11 (human homolog of yeast Ntr1) is present in the post-splicing Intron Large (IL) complex containing U2, U5, and U6 snRNAs. A TFIP11 mutant lacking the interaction domain with hPrp43 caused accumulation of the IL complex and reduction of Intron Small (IS) complex formation in vitro, indicating TFIP11 cooperates with hPrp43 to mediate the IL-to-IS transition, enabling debranching and intron turnover.","method":"Two-tag affinity purification of lariat intron RNA-protein complexes, glycerol gradient sedimentation, in vitro splicing assay with TFIP11 interaction-domain mutant","journal":"Nucleic acids research","confidence":"High","confidence_rationale":"Tier 1-2 / Strong — in vitro reconstitution with domain-deletion mutant, multiple orthogonal methods (purification, sedimentation, functional assay), mechanistically specific","pmids":["19103666"],"is_preprint":false},{"year":2008,"finding":"TFIP11 directly interacts with mDEAH9/DHX15 (the mammalian homolog of yeast Prp43). When co-expressed, TFIP11 recruits mDEAH9 to distinct nuclear speckles, whereas mDEAH9 alone shows diffuse nuclear distribution. The G-patch domain in the N-terminal region of TFIP11 is responsible for this interaction.","method":"Co-transfection of GFP-tagged proteins, confocal microscopy co-localization, sequence homology analysis","journal":"International journal of molecular sciences","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — co-localization and recruitment demonstrated by imaging with two orthogonal lines of evidence, single lab, no direct biochemical pulldown reported in abstract","pmids":["19165350"],"is_preprint":false},{"year":2008,"finding":"TFIP11 interacts with cyclin L1 (CCNL1) and Ewing sarcoma breakpoint region 1 protein (EWSR1), both spliceosome-related proteins, and all three co-localize to speckled nuclear domains, suggesting participation in a common RNA splicing activity.","method":"Yeast two-hybrid assay (initial identification), fluorescently-tagged protein co-expression and confocal microscopy co-localization","journal":"International journal of molecular sciences","confidence":"Low","confidence_rationale":"Tier 3 / Weak — co-localization only, no biochemical interaction confirmed, single lab, single method for functional inference","pmids":["19122807"],"is_preprint":false},{"year":2009,"finding":"TFIP11 contains a novel atypical nuclear localization signal (NLS) at amino acids 701-706 (VKDKFN) and a distinct speckle-targeting sequence (STS) within amino acids 711-735, identified by sequential C-terminal deletions and mutational analyses of mouse TFIP11.","method":"Sequential C-terminal deletions and site-directed mutagenesis of GFP-tagged TFIP11, fluorescence microscopy","journal":"Biochemical and biophysical research communications","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct mutagenesis with functional localization readout, multiple deletion constructs tested, single lab","pmids":["19857462"],"is_preprint":false},{"year":2007,"finding":"Yeast Ntr1/Spp382 (ortholog of human TFIP11) and Ntr2 form a stable complex that recruits the DExD/H-box helicase Prp43 dynamically to the spliceosome to catalyze disassembly. Ntr1-Ntr2 can bind the spliceosome prior to Prp43 recruitment; spliceosome binding does not require ATP but disassembly requires ATP hydrolysis. Ntr2 interacts with U5 component Brr2 and is essential for NTR-U5 and NTR-spliceosome interactions.","method":"Co-immunoprecipitation, in vitro binding assays, ATP hydrolysis-deficient mutants, genetic interaction analysis, metabolic depletion","journal":"Molecular and cellular biology","confidence":"High","confidence_rationale":"Tier 1-2 / Strong — multiple orthogonal biochemical methods, ATP dependence established with mutants, reproduced across multiple assays in single study, consistent with independent yeast studies","pmids":["17893323"],"is_preprint":false},{"year":2006,"finding":"Yeast Ntr1/Spp382 (ortholog of TFIP11) associates with a post-splicing complex containing the excised intron and U2, U5, U6 snRNAs. Depletion of Ntr1 reduces splicing activity, causes intron accumulation, decreases free U5 and U6 snRNPs, and disrupts Prp43 association with the excised intron. Ntr1 acts as a spliceosome receptor/RNA-targeting factor for Prp43 to promote intron release and snRNP recycling.","method":"Metabolic depletion of Ntr1, in vitro splicing assays, snRNA/snRNP analysis, co-immunoprecipitation","journal":"Molecular and cellular biology","confidence":"High","confidence_rationale":"Tier 2 / Strong — multiple orthogonal methods (depletion, splicing assay, snRNP analysis, co-IP), consistent with independent reports from other labs","pmids":["16880513"],"is_preprint":false},{"year":2006,"finding":"Yeast Spp382/Ntr1 (ortholog of TFIP11) is required for cellular splicing and intron turnover. Weak spp382 alleles suppress splicing defects caused by mutations in Prp38 and Prp8, defining a Spp382-dependent turnover/discard pathway for defective spliceosomes. Spp382 binds Prp43, and Prp43 requires Spp382 for intron release. Spp382 also interacts with the DnaJ-like protein Cwc23. Defective splicing complexes lacking the 5' exon cleavage intermediate are recovered with tagged Spp382.","method":"Genetic suppressor screen, tandem affinity purification, two-hybrid assay, proteomic analysis, in vivo splicing assays","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"High","confidence_rationale":"Tier 2 / Strong — genetic epistasis plus biochemical pulldown plus proteomic analysis, multiple orthogonal methods, consistent with other yeast studies","pmids":["16945917"],"is_preprint":false},{"year":2007,"finding":"Human TFIP11 (NTR1) and its yeast ortholog Ntr1/Spp382 interact with the DNA ligase IV-associated proteins XRCC4 (human) and Lif1p (yeast), occupying the DNA ligase IV-binding sites and thereby preventing formation of an active NHEJ ligation complex. Excess Ntr1p in yeast reduces NHEJ efficiency in plasmid ligation and chromosomal DSB repair assays. Both yeast and human NTR1 also interact with the G-patch protein PinX1. TFIP11/Ntr1 localizes to telomeres and nucleoli.","method":"Yeast two-hybrid assay, plasmid ligation assay, chromosomal DSB repair assay, subcellular localization (yeast and human cells)","journal":"Nucleic acids research","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — two-hybrid plus functional NHEJ assays, conserved in yeast and human, single lab","pmids":["17389648"],"is_preprint":false},{"year":2009,"finding":"Yeast Spp382/Ntr1 interacts with multiple splicing factors (Prp8, Prp9, Prp11, Prp39, Yhc1) and with Sqs1 and Cwc23. Sqs1 copurifies with Prp43, binds both Prp43 and Spp382, and overexpression of Sqs1 blocks pre-mRNA splicing; increased Prp43 levels buffer Sqs1 cytotoxicity, identifying Prp43 as a target of Sqs1. CWC23 activity is critical for splicing and intron metabolism but the DnaJ motif is dispensable, though genetic interactions between the CWC23 J domain and Ntr1/Prp43 suggest an auxiliary Hsp70 chaperone role in disassembly.","method":"Dosage interference assay, copurification, yeast two-hybrid, overexpression epistasis, in vivo splicing assays","journal":"Genetics","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — multiple methods (copurification, two-hybrid, genetic epistasis, splicing assays), single lab","pmids":["19581443"],"is_preprint":false},{"year":2013,"finding":"C2ORF3 was identified as a novel component of the post-splicing IL (Intron Large) complex via immunoprecipitation with hPrp43 and TFIP11 followed by mass spectrometry. Depletion of C2ORF3 from nuclear extracts significantly represses pre-mRNA splicing in vitro, suggesting its role in intron turnover.","method":"Immunoprecipitation with TFIP11 and hPrp43, mass spectrometry, in vitro splicing with C2ORF3-depleted nuclear extract","journal":"Genes to cells : devoted to molecular & cellular mechanisms","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — reciprocal IP plus MS identification plus functional depletion assay, single lab","pmids":["24304693"],"is_preprint":false},{"year":2017,"finding":"Cryo-EM structure of the yeast intron lariat spliceosome (ILS) at 3.5 Å resolution shows the C-terminal domain of Ntr1/Spp382 (yeast ortholog of TFIP11) associates with the GTPase Snu114, while Ntr2 is anchored to Prp8 and interacts with the superhelical domain of Ntr1. The DEAH helicase Prp43 binds Syf1 at the spliceosome periphery with its RNA-binding site close to the 3' end of U6 snRNA, providing structural basis for ILS disassembly.","method":"Cryo-electron microscopy structure determination at 3.5 Å resolution","journal":"Cell","confidence":"High","confidence_rationale":"Tier 1 / Strong — high-resolution cryo-EM structure with domain-level resolution of interaction interfaces","pmids":["28919079"],"is_preprint":false},{"year":2021,"finding":"TFIP11 localizes to nucleoli and Cajal Bodies and is essential for 2'-O-methylation of U6 snRNA. TFIP11 knockdown reduces association of U6 snRNA with fibrillarin and associated snoRNAs, thereby impairing U6 2'-O-methylation. U6 hypomethylation impairs U4/U6.U5 tri-snRNP assembly, leading to spliceosome assembly defects and altered splicing fidelity. This function of TFIP11 is independent of DHX15.","method":"siRNA knockdown, snRNA methylation analysis, co-immunoprecipitation (U6 with fibrillarin/snoRNAs), tri-snRNP assembly assay, RNA-seq splicing analysis, fluorescence microscopy","journal":"Nature communications","confidence":"High","confidence_rationale":"Tier 2 / Strong — multiple orthogonal methods (knockdown, RNA modification assay, co-IP, assembly assay, transcriptomics), novel mechanistic finding independently validated within study","pmids":["34789764"],"is_preprint":false},{"year":2024,"finding":"Cryo-EM structures of nematode and human terminal intron lariat spliceosomes reveal that TFIP11 and C19L1, together with SYF1, SYF2, and SDE2, dock onto and activate DHX15 on the catalytic U6 snRNA to initiate spliceosome disassembly. TFIP11 and C19L1 probe inner and outer spliceosome surfaces to detect the release of ligated mRNA. U6 snRNA thus controls both the start and end of pre-mRNA splicing.","method":"Cryo-electron microscopy structure determination of nematode and human terminal ILS complexes, biochemical and genetic validation","journal":"Nature","confidence":"High","confidence_rationale":"Tier 1 / Strong — high-resolution cryo-EM of human and nematode complexes plus biochemical and genetic validation, multiple organisms, direct mechanistic visualization","pmids":["38925148"],"is_preprint":false},{"year":2024,"finding":"TFIP11 forms a complex with the BLM helicase and preferentially binds DNA substrates mimicking stalled replication fork structures. Loss of TFIP11 causes abnormal accumulation of BLM at stalled forks, impairs RAD51-mediated fork reversal and fork slowing, sensitizes cells to replication stress-inducing agents, and enhances chromosomal instability.","method":"Co-immunoprecipitation, DNA substrate binding assays, replication fork assays, RAD51 foci analysis, cell survival assays, chromosomal instability analysis, siRNA/genetic knockout","journal":"Nature communications","confidence":"High","confidence_rationale":"Tier 2 / Strong — multiple orthogonal methods (co-IP, DNA binding, fork reversal assays, chromosomal instability), functionally defined phenotype with mechanistic pathway placement","pmids":["38341452"],"is_preprint":false},{"year":2024,"finding":"The N-terminal region of TFIP11 is an intrinsically disordered polyampholytic protein that exhibits structural duality with coexisting ordered and disordered assemblies in a salt-dependent manner. Increasing ionic strength enhances conformational flexibility, promoting a more globule-like shape that may favor liquid-liquid phase separation and protein-RNA interaction. The G-patch domain, essential for TFIP11 function, is among the most conformationally impacted regions.","method":"Disorder prediction, molecular dynamics simulation, spectroscopy (CD, NMR-type methods implied), recombinant protein characterization","journal":"International journal of biological macromolecules","confidence":"Medium","confidence_rationale":"Tier 1-2 / Moderate — computational plus experimental spectroscopy on recombinant domain, single lab, no functional mutagenesis validation","pmids":["39089542"],"is_preprint":false},{"year":2010,"finding":"A partial loss-of-function CWC23 mutant shows reduced interaction with Ntr1/Spp382 (yeast ortholog of TFIP11) and causes accumulation of excised lariat intron and unspliced pre-mRNA, implicating Cwc23 in the spliceosome disassembly pathway coordinated by Ntr1. Genetic interactions between the CWC23 J domain and Ntr1 or Prp43 suggest an auxiliary Hsp70-based chaperone role.","method":"Genetic interaction analysis, co-immunoprecipitation (Cwc23-Ntr1), in vivo splicing assays, site-directed mutagenesis of J domain","journal":"Molecular and cellular biology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — co-IP plus genetic epistasis plus splicing assay, single lab, yeast ortholog data","pmids":["19822657"],"is_preprint":false},{"year":2015,"finding":"The G-patch domain of Spp382/Ntr1 (yeast ortholog of TFIP11) is required for Spp382 function and differs from the G-patches of Sqs1 and Pxr1 in Prp43 two-hybrid response and ability to reconstitute RNA processing factors. G-patch domains are not freely interchangeable between Prp43 cofactors, suggesting G-patch identity specifies pathway-selective DExD/H-box helicase activity beyond simply tethering Prp43.","method":"Yeast two-hybrid, domain-swap experiments, site-directed mutagenesis, in vivo splicing/rRNA processing assays","journal":"Genetics","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — multiple complementary genetic and biochemical approaches, domain-level mechanistic resolution, single lab","pmids":["25808954"],"is_preprint":false}],"current_model":"TFIP11 (human ortholog of yeast Ntr1/Spp382) is a G-patch-containing splicing factor that localizes to nuclear speckles, Cajal Bodies, and nucleoli, where it functions at multiple stages of the spliceosome cycle: it recruits the RNA helicase DHX15/hPrp43 to the post-catalytic intron lariat spliceosome to initiate disassembly (alongside C19L1, SYF1, SYF2, and SDE2 as visualized by cryo-EM), independently promotes 2'-O-methylation of U6 snRNA via fibrillarin/snoRNA association to ensure proper U4/U6.U5 tri-snRNP assembly and splicing fidelity, and additionally participates in genome stability by forming a complex with BLM helicase at stalled replication forks to facilitate RAD51-mediated fork reversal."},"narrative":{"mechanistic_narrative":"TFIP11 (human ortholog of yeast Ntr1/Spp382) is a G-patch splicing factor that governs the final, disassembly stage of the spliceosome cycle and additionally supports replication-fork stability [PMID:19103666, PMID:38925148]. Through its N-terminal G-patch domain, TFIP11 directly engages and activates the DEAH-box RNA helicase DHX15/hPrp43, recruiting the otherwise diffusely distributed helicase to nuclear speckles and to the post-catalytic intron-lariat spliceosome [PMID:19165350, PMID:19103666]. In the human and nematode terminal intron-lariat spliceosome, TFIP11 together with C19L1, SYF1, SYF2 and SDE2 docks onto and activates DHX15 on the catalytic U6 snRNA to detect release of ligated mRNA and trigger disassembly, debranching of the excised intron, and recycling of snRNPs [PMID:38925148, PMID:19103666]. A separate, DHX15-independent function localizes TFIP11 to nucleoli and Cajal bodies, where it promotes fibrillarin/snoRNA-dependent 2'-O-methylation of U6 snRNA required for proper U4/U6.U5 tri-snRNP assembly and splicing fidelity [PMID:34789764]. Beyond RNA metabolism, TFIP11 forms a complex with the BLM helicase, binds stalled-replication-fork-mimicking DNA, and is required for RAD51-mediated fork reversal and genome stability [PMID:38341452]. The conserved yeast ortholog establishes the underlying disassembly machinery: Ntr1/Spp382 binds Prp43 and acts as its spliceosome-targeting factor for intron release and snRNP recycling, defining a turnover/discard pathway for defective spliceosomes [PMID:16880513, PMID:16945917, PMID:17893323].","teleology":[{"year":2005,"claim":"Established that human TFIP11 is a bona fide splicing factor with dynamic, RNA-dependent subnuclear organization, rather than its originally inferred transcription-factor role.","evidence":"GFP live-cell imaging with RNase A and Pol II inhibitor treatment plus an in vivo splicing assay in human cells","pmids":["15868102"],"confidence":"Medium","gaps":["Does not define the molecular step of splicing TFIP11 acts at","No interacting partners identified"]},{"year":2006,"claim":"Defined the core disassembly function in yeast: the ortholog Ntr1/Spp382 targets Prp43 to the post-splicing intron complex to drive intron release and snRNP recycling, and a discard pathway for defective spliceosomes.","evidence":"Metabolic depletion, in vitro splicing/snRNP analysis, co-IP, genetic suppressor screen and TAP in budding yeast","pmids":["16880513","16945917"],"confidence":"High","gaps":["Whether human TFIP11 performs the identical step was not yet shown","Role of the G-patch domain not resolved"]},{"year":2007,"claim":"Resolved how the disassembly factor is delivered to the spliceosome: Ntr1 partners with Ntr2 (which contacts U5/Brr2) to recruit Prp43 dynamically, with spliceosome binding ATP-independent but disassembly requiring ATP hydrolysis.","evidence":"Co-IP, in vitro binding, ATP-hydrolysis-deficient mutants and genetic interaction analysis in yeast","pmids":["17893323"],"confidence":"High","gaps":["Human counterpart of the Ntr1-Ntr2 module not established","Mechanism of helicase activation not defined"]},{"year":2007,"claim":"Uncovered a non-splicing role: NTR1/Ntr1 binds XRCC4/Lif1 and PinX1, occupying DNA ligase IV sites to restrain NHEJ and localizing to telomeres and nucleoli.","evidence":"Yeast two-hybrid, plasmid ligation and chromosomal DSB repair assays, subcellular localization in yeast and human cells","pmids":["17389648"],"confidence":"Medium","gaps":["Physiological significance of NHEJ inhibition in human cells unclear","Relationship between RNA and DNA-repair functions undefined"]},{"year":2008,"claim":"Connected human TFIP11 directly to the disassembly machinery, showing it occupies the post-splicing IL complex and cooperates with hPrp43 to drive the IL-to-IS transition enabling debranching.","evidence":"Two-tag affinity purification of lariat-intron complexes, glycerol gradient sedimentation, and in vitro splicing with an interaction-domain deletion mutant","pmids":["19103666"],"confidence":"High","gaps":["Structural basis of the TFIP11-hPrp43 interaction not resolved","Full IL complex composition incomplete"]},{"year":2008,"claim":"Localized the helicase-recruiting activity to a defined domain and identified additional speckle partners, showing the G-patch mediates DHX15 recruitment and that TFIP11 co-localizes with CCNL1 and EWSR1.","evidence":"GFP co-transfection and confocal co-localization, yeast two-hybrid, sequence homology analysis in mammalian cells","pmids":["19165350","19122807"],"confidence":"Medium","gaps":["CCNL1/EWSR1 interactions shown only by co-localization, no biochemical confirmation","Functional consequence of these partnerships untested"]},{"year":2009,"claim":"Mapped the targeting determinants of TFIP11 and expanded the yeast cofactor network, defining a novel NLS and speckle-targeting sequence and implicating Cwc23/Sqs1 chaperone-helicase coordination.","evidence":"C-terminal deletion/mutagenesis with fluorescence imaging in mouse TFIP11; dosage interference, copurification and two-hybrid in yeast","pmids":["19857462","19581443"],"confidence":"Medium","gaps":["Human counterparts of Sqs1/Cwc23 modulation not addressed","Hsp70 chaperone role inferred only genetically"]},{"year":2010,"claim":"Implicated an Hsp70-coupled chaperone in TFIP11-orchestrated disassembly by showing a Cwc23 mutant with reduced Ntr1 binding accumulates lariat intron and unspliced pre-mRNA.","evidence":"Genetic interaction analysis, co-IP and J-domain mutagenesis with in vivo splicing assays in yeast","pmids":["19822657"],"confidence":"Medium","gaps":["J-domain mechanistic contribution remains genetic, not biochemical","Conservation in human disassembly untested"]},{"year":2013,"claim":"Extended the human post-splicing IL complex composition by identifying C2ORF3 as a functional component required for in vitro splicing.","evidence":"Reciprocal IP with TFIP11 and hPrp43, mass spectrometry, and depletion-rescue in vitro splicing in human extracts","pmids":["24304693"],"confidence":"Medium","gaps":["Direct binding partner of C2ORF3 within the complex undefined","Structural placement not resolved"]},{"year":2015,"claim":"Demonstrated that the G-patch is not merely a Prp43 tether but specifies pathway-selective helicase activity, since G-patches of different cofactors are not interchangeable.","evidence":"Yeast two-hybrid, domain-swap and mutagenesis with in vivo splicing/rRNA processing assays","pmids":["25808954"],"confidence":"Medium","gaps":["Molecular basis of G-patch specificity unresolved","Human G-patch specificity not directly tested"]},{"year":2017,"claim":"Provided structural context for disassembly by visualizing the Ntr1 C-terminal domain on Snu114 and Prp43 bound to Syf1 near the U6 3' end in the intron-lariat spliceosome.","evidence":"3.5 Å cryo-EM of the yeast intron-lariat spliceosome","pmids":["28919079"],"confidence":"High","gaps":["Human ILS architecture not resolved in this study","Dynamics of helicase activation not captured"]},{"year":2021,"claim":"Revealed a second, helicase-independent TFIP11 function in U6 snRNA modification, showing it is required for fibrillarin/snoRNA-dependent 2'-O-methylation that ensures tri-snRNP assembly and splicing fidelity.","evidence":"siRNA knockdown, snRNA methylation analysis, co-IP, tri-snRNP assembly assays and RNA-seq in human cells","pmids":["34789764"],"confidence":"High","gaps":["Direct snoRNA/fibrillarin binding interface on TFIP11 undefined","How nucleolar/Cajal-body and speckle functions are partitioned unclear"]},{"year":2024,"claim":"Established the activated human disassembly machine, showing TFIP11 with C19L1, SYF1, SYF2 and SDE2 docks onto and activates DHX15 on catalytic U6 snRNA to sense ligated-mRNA release.","evidence":"Cryo-EM of human and nematode terminal ILS complexes with biochemical and genetic validation","pmids":["38925148"],"confidence":"High","gaps":["Sequence of conformational events during activation not fully resolved","Regulation of disassembly timing unaddressed"]},{"year":2024,"claim":"Defined a direct genome-stability role, showing TFIP11 complexes with BLM, binds stalled-fork DNA, and is required for RAD51-mediated fork reversal and chromosomal stability.","evidence":"Co-IP, DNA-substrate binding, replication-fork and RAD51 foci assays, survival and chromosomal instability analysis with siRNA/knockout in human cells","pmids":["38341452"],"confidence":"High","gaps":["Whether the G-patch/RNA functions are required for fork protection unknown","Mechanistic link to BLM regulation at the fork incomplete"]},{"year":2024,"claim":"Characterized the biophysical nature of the functional N-terminal region as an intrinsically disordered polyampholyte with salt-dependent structural duality affecting the G-patch.","evidence":"Disorder prediction, molecular dynamics and spectroscopy on recombinant TFIP11 N-terminal domain","pmids":["39089542"],"confidence":"Medium","gaps":["Phase-separation behavior inferred, not demonstrated in cells","No functional mutagenesis linking disorder to activity"]},{"year":null,"claim":"How TFIP11's distinct activities — spliceosome disassembly, U6 methylation, and replication-fork protection — are coordinated, partitioned among subnuclear compartments, and regulated remains unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No unified model linking RNA and DNA functions","Regulation/post-translational control of compartment switching unknown","No disease association established in the corpus"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0003723","term_label":"RNA binding","supporting_discovery_ids":[1,12,13]},{"term_id":"GO:0003677","term_label":"DNA binding","supporting_discovery_ids":[14]},{"term_id":"GO:0098772","term_label":"molecular function regulator activity","supporting_discovery_ids":[2,13,1]},{"term_id":"GO:0060090","term_label":"molecular adaptor activity","supporting_discovery_ids":[2,13]}],"localization":[{"term_id":"GO:0005654","term_label":"nucleoplasm","supporting_discovery_ids":[0,2]},{"term_id":"GO:0005730","term_label":"nucleolus","supporting_discovery_ids":[8,12]},{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[0,4]}],"pathway":[{"term_id":"R-HSA-8953854","term_label":"Metabolism of RNA","supporting_discovery_ids":[1,12,13]},{"term_id":"R-HSA-73894","term_label":"DNA Repair","supporting_discovery_ids":[14,8]}],"complexes":["intron lariat spliceosome (ILS)","post-splicing Intron Large (IL) complex","Ntr1-Ntr2 (NTR) complex","TFIP11-BLM complex"],"partners":["DHX15","C19L1","SYF1","SYF2","SDE2","BLM","CCNL1","EWSR1"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q9UBB9","full_name":"Tuftelin-interacting protein 11","aliases":["Septin and tuftelin-interacting protein 1","STIP-1"],"length_aa":837,"mass_kda":96.8,"function":"Involved in pre-mRNA splicing, specifically in spliceosome disassembly during late-stage splicing events. Intron turnover seems to proceed through reactions in two lariat-intron associated complexes termed Intron Large (IL) and Intron Small (IS). In cooperation with DHX15 seems to mediate the transition of the U2, U5 and U6 snRNP-containing IL complex to the snRNP-free IS complex leading to efficient debranching and turnover of excised introns. May play a role in the differentiation of ameloblasts and odontoblasts or in the forming of the enamel extracellular matrix","subcellular_location":"Cytoplasm; Nucleus","url":"https://www.uniprot.org/uniprotkb/Q9UBB9/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":true,"resolved_as":"","url":"https://depmap.org/portal/gene/TFIP11","classification":"Common Essential","n_dependent_lines":1174,"n_total_lines":1208,"dependency_fraction":0.9718543046357616},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[{"gene":"PRPF4B","stoichiometry":4.0},{"gene":"CD2BP2","stoichiometry":0.2},{"gene":"CSNK2B","stoichiometry":0.2},{"gene":"DDB1","stoichiometry":0.2},{"gene":"RBM39","stoichiometry":0.2},{"gene":"SF3B1","stoichiometry":0.2},{"gene":"SNRPA","stoichiometry":0.2},{"gene":"SNRPB","stoichiometry":0.2},{"gene":"SNRPD2","stoichiometry":0.2},{"gene":"SNRPF","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/search/TFIP11","total_profiled":1310},"omim":[{"mim_id":"612747","title":"TUFTELIN-INTERACTING PROTEIN 11; TFIP11","url":"https://www.omim.org/entry/612747"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Approved","locations":[{"location":"Nucleoplasm","reliability":"Approved"},{"location":"Cytosol","reliability":"Additional"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/TFIP11"},"hgnc":{"alias_symbol":["TIP39","DKFZP434B194","Spp382"],"prev_symbol":[]},"alphafold":{"accession":"Q9UBB9","domains":[{"cath_id":"1.25.40","chopping":"581-732","consensus_level":"medium","plddt":87.5165,"start":581,"end":732},{"cath_id":"3.40.30","chopping":"772-835","consensus_level":"high","plddt":87.5723,"start":772,"end":835}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9UBB9","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q9UBB9-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q9UBB9-F1-predicted_aligned_error_v6.png","plddt_mean":73.88},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=TFIP11","jax_strain_url":"https://www.jax.org/strain/search?query=TFIP11"},"sequence":{"accession":"Q9UBB9","fasta_url":"https://rest.uniprot.org/uniprotkb/Q9UBB9.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q9UBB9/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9UBB9"}},"corpus_meta":[{"pmid":"23790503","id":"PMC_23790503","title":"Genes expressed in dental enamel development are associated with molar-incisor hypomineralization.","date":"2013","source":"Archives of oral biology","url":"https://pubmed.ncbi.nlm.nih.gov/23790503","citation_count":121,"is_preprint":false},{"pmid":"28919079","id":"PMC_28919079","title":"Structure of an Intron Lariat Spliceosome from Saccharomyces cerevisiae.","date":"2017","source":"Cell","url":"https://pubmed.ncbi.nlm.nih.gov/28919079","citation_count":82,"is_preprint":false},{"pmid":"19103666","id":"PMC_19103666","title":"Isolation and characterization of post-splicing lariat-intron complexes.","date":"2008","source":"Nucleic acids research","url":"https://pubmed.ncbi.nlm.nih.gov/19103666","citation_count":81,"is_preprint":false},{"pmid":"29988728","id":"PMC_29988728","title":"A novel role in skeletal segment regeneration of extracellular vesicles released from periodontal-ligament stem cells.","date":"2018","source":"International journal of nanomedicine","url":"https://pubmed.ncbi.nlm.nih.gov/29988728","citation_count":78,"is_preprint":false},{"pmid":"17893323","id":"PMC_17893323","title":"Dynamic interactions of Ntr1-Ntr2 with Prp43 and with U5 govern the recruitment of Prp43 to mediate spliceosome disassembly.","date":"2007","source":"Molecular and cellular biology","url":"https://pubmed.ncbi.nlm.nih.gov/17893323","citation_count":69,"is_preprint":false},{"pmid":"16880513","id":"PMC_16880513","title":"Yeast ntr1/spp382 mediates prp43 function in postspliceosomes.","date":"2006","source":"Molecular and cellular biology","url":"https://pubmed.ncbi.nlm.nih.gov/16880513","citation_count":58,"is_preprint":false},{"pmid":"16945917","id":"PMC_16945917","title":"Inhibition of a spliceosome turnover pathway suppresses splicing defects.","date":"2006","source":"Proceedings of the National Academy of Sciences of the United States of 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\"TFIP11 localizes to a novel subnuclear structure termed the 'TFIP body', distinct from but proximal to SC35 nuclear speckles. This localization is RNA-dependent (TFIP body disperses after RNase A treatment), and RNA polymerase II inhibition causes enlargement and reduced number of TFIP bodies. An in vivo splicing assay demonstrated TFIP11 functions as a splicing factor.\",\n      \"method\": \"GFP-tagging and live-cell fluorescence microscopy, RNase A treatment, RNA Pol II inhibitor treatment (α-amanitin, actinomycin D), in vivo splicing assay\",\n      \"journal\": \"Cellular and molecular life sciences : CMLS\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct localization experiment with functional consequence, multiple orthogonal methods (imaging, RNase treatment, splicing assay) in single lab\",\n      \"pmids\": [\"15868102\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2008,\n      \"finding\": \"TFIP11 (human homolog of yeast Ntr1) is present in the post-splicing Intron Large (IL) complex containing U2, U5, and U6 snRNAs. A TFIP11 mutant lacking the interaction domain with hPrp43 caused accumulation of the IL complex and reduction of Intron Small (IS) complex formation in vitro, indicating TFIP11 cooperates with hPrp43 to mediate the IL-to-IS transition, enabling debranching and intron turnover.\",\n      \"method\": \"Two-tag affinity purification of lariat intron RNA-protein complexes, glycerol gradient sedimentation, in vitro splicing assay with TFIP11 interaction-domain mutant\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 / Strong — in vitro reconstitution with domain-deletion mutant, multiple orthogonal methods (purification, sedimentation, functional assay), mechanistically specific\",\n      \"pmids\": [\"19103666\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2008,\n      \"finding\": \"TFIP11 directly interacts with mDEAH9/DHX15 (the mammalian homolog of yeast Prp43). When co-expressed, TFIP11 recruits mDEAH9 to distinct nuclear speckles, whereas mDEAH9 alone shows diffuse nuclear distribution. The G-patch domain in the N-terminal region of TFIP11 is responsible for this interaction.\",\n      \"method\": \"Co-transfection of GFP-tagged proteins, confocal microscopy co-localization, sequence homology analysis\",\n      \"journal\": \"International journal of molecular sciences\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — co-localization and recruitment demonstrated by imaging with two orthogonal lines of evidence, single lab, no direct biochemical pulldown reported in abstract\",\n      \"pmids\": [\"19165350\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2008,\n      \"finding\": \"TFIP11 interacts with cyclin L1 (CCNL1) and Ewing sarcoma breakpoint region 1 protein (EWSR1), both spliceosome-related proteins, and all three co-localize to speckled nuclear domains, suggesting participation in a common RNA splicing activity.\",\n      \"method\": \"Yeast two-hybrid assay (initial identification), fluorescently-tagged protein co-expression and confocal microscopy co-localization\",\n      \"journal\": \"International journal of molecular sciences\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — co-localization only, no biochemical interaction confirmed, single lab, single method for functional inference\",\n      \"pmids\": [\"19122807\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2009,\n      \"finding\": \"TFIP11 contains a novel atypical nuclear localization signal (NLS) at amino acids 701-706 (VKDKFN) and a distinct speckle-targeting sequence (STS) within amino acids 711-735, identified by sequential C-terminal deletions and mutational analyses of mouse TFIP11.\",\n      \"method\": \"Sequential C-terminal deletions and site-directed mutagenesis of GFP-tagged TFIP11, fluorescence microscopy\",\n      \"journal\": \"Biochemical and biophysical research communications\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct mutagenesis with functional localization readout, multiple deletion constructs tested, single lab\",\n      \"pmids\": [\"19857462\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2007,\n      \"finding\": \"Yeast Ntr1/Spp382 (ortholog of human TFIP11) and Ntr2 form a stable complex that recruits the DExD/H-box helicase Prp43 dynamically to the spliceosome to catalyze disassembly. Ntr1-Ntr2 can bind the spliceosome prior to Prp43 recruitment; spliceosome binding does not require ATP but disassembly requires ATP hydrolysis. Ntr2 interacts with U5 component Brr2 and is essential for NTR-U5 and NTR-spliceosome interactions.\",\n      \"method\": \"Co-immunoprecipitation, in vitro binding assays, ATP hydrolysis-deficient mutants, genetic interaction analysis, metabolic depletion\",\n      \"journal\": \"Molecular and cellular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 / Strong — multiple orthogonal biochemical methods, ATP dependence established with mutants, reproduced across multiple assays in single study, consistent with independent yeast studies\",\n      \"pmids\": [\"17893323\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2006,\n      \"finding\": \"Yeast Ntr1/Spp382 (ortholog of TFIP11) associates with a post-splicing complex containing the excised intron and U2, U5, U6 snRNAs. Depletion of Ntr1 reduces splicing activity, causes intron accumulation, decreases free U5 and U6 snRNPs, and disrupts Prp43 association with the excised intron. Ntr1 acts as a spliceosome receptor/RNA-targeting factor for Prp43 to promote intron release and snRNP recycling.\",\n      \"method\": \"Metabolic depletion of Ntr1, in vitro splicing assays, snRNA/snRNP analysis, co-immunoprecipitation\",\n      \"journal\": \"Molecular and cellular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — multiple orthogonal methods (depletion, splicing assay, snRNP analysis, co-IP), consistent with independent reports from other labs\",\n      \"pmids\": [\"16880513\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2006,\n      \"finding\": \"Yeast Spp382/Ntr1 (ortholog of TFIP11) is required for cellular splicing and intron turnover. Weak spp382 alleles suppress splicing defects caused by mutations in Prp38 and Prp8, defining a Spp382-dependent turnover/discard pathway for defective spliceosomes. Spp382 binds Prp43, and Prp43 requires Spp382 for intron release. Spp382 also interacts with the DnaJ-like protein Cwc23. Defective splicing complexes lacking the 5' exon cleavage intermediate are recovered with tagged Spp382.\",\n      \"method\": \"Genetic suppressor screen, tandem affinity purification, two-hybrid assay, proteomic analysis, in vivo splicing assays\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — genetic epistasis plus biochemical pulldown plus proteomic analysis, multiple orthogonal methods, consistent with other yeast studies\",\n      \"pmids\": [\"16945917\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2007,\n      \"finding\": \"Human TFIP11 (NTR1) and its yeast ortholog Ntr1/Spp382 interact with the DNA ligase IV-associated proteins XRCC4 (human) and Lif1p (yeast), occupying the DNA ligase IV-binding sites and thereby preventing formation of an active NHEJ ligation complex. Excess Ntr1p in yeast reduces NHEJ efficiency in plasmid ligation and chromosomal DSB repair assays. Both yeast and human NTR1 also interact with the G-patch protein PinX1. TFIP11/Ntr1 localizes to telomeres and nucleoli.\",\n      \"method\": \"Yeast two-hybrid assay, plasmid ligation assay, chromosomal DSB repair assay, subcellular localization (yeast and human cells)\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — two-hybrid plus functional NHEJ assays, conserved in yeast and human, single lab\",\n      \"pmids\": [\"17389648\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2009,\n      \"finding\": \"Yeast Spp382/Ntr1 interacts with multiple splicing factors (Prp8, Prp9, Prp11, Prp39, Yhc1) and with Sqs1 and Cwc23. Sqs1 copurifies with Prp43, binds both Prp43 and Spp382, and overexpression of Sqs1 blocks pre-mRNA splicing; increased Prp43 levels buffer Sqs1 cytotoxicity, identifying Prp43 as a target of Sqs1. CWC23 activity is critical for splicing and intron metabolism but the DnaJ motif is dispensable, though genetic interactions between the CWC23 J domain and Ntr1/Prp43 suggest an auxiliary Hsp70 chaperone role in disassembly.\",\n      \"method\": \"Dosage interference assay, copurification, yeast two-hybrid, overexpression epistasis, in vivo splicing assays\",\n      \"journal\": \"Genetics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple methods (copurification, two-hybrid, genetic epistasis, splicing assays), single lab\",\n      \"pmids\": [\"19581443\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"C2ORF3 was identified as a novel component of the post-splicing IL (Intron Large) complex via immunoprecipitation with hPrp43 and TFIP11 followed by mass spectrometry. Depletion of C2ORF3 from nuclear extracts significantly represses pre-mRNA splicing in vitro, suggesting its role in intron turnover.\",\n      \"method\": \"Immunoprecipitation with TFIP11 and hPrp43, mass spectrometry, in vitro splicing with C2ORF3-depleted nuclear extract\",\n      \"journal\": \"Genes to cells : devoted to molecular & cellular mechanisms\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal IP plus MS identification plus functional depletion assay, single lab\",\n      \"pmids\": [\"24304693\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"Cryo-EM structure of the yeast intron lariat spliceosome (ILS) at 3.5 Å resolution shows the C-terminal domain of Ntr1/Spp382 (yeast ortholog of TFIP11) associates with the GTPase Snu114, while Ntr2 is anchored to Prp8 and interacts with the superhelical domain of Ntr1. The DEAH helicase Prp43 binds Syf1 at the spliceosome periphery with its RNA-binding site close to the 3' end of U6 snRNA, providing structural basis for ILS disassembly.\",\n      \"method\": \"Cryo-electron microscopy structure determination at 3.5 Å resolution\",\n      \"journal\": \"Cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — high-resolution cryo-EM structure with domain-level resolution of interaction interfaces\",\n      \"pmids\": [\"28919079\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"TFIP11 localizes to nucleoli and Cajal Bodies and is essential for 2'-O-methylation of U6 snRNA. TFIP11 knockdown reduces association of U6 snRNA with fibrillarin and associated snoRNAs, thereby impairing U6 2'-O-methylation. U6 hypomethylation impairs U4/U6.U5 tri-snRNP assembly, leading to spliceosome assembly defects and altered splicing fidelity. This function of TFIP11 is independent of DHX15.\",\n      \"method\": \"siRNA knockdown, snRNA methylation analysis, co-immunoprecipitation (U6 with fibrillarin/snoRNAs), tri-snRNP assembly assay, RNA-seq splicing analysis, fluorescence microscopy\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — multiple orthogonal methods (knockdown, RNA modification assay, co-IP, assembly assay, transcriptomics), novel mechanistic finding independently validated within study\",\n      \"pmids\": [\"34789764\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"Cryo-EM structures of nematode and human terminal intron lariat spliceosomes reveal that TFIP11 and C19L1, together with SYF1, SYF2, and SDE2, dock onto and activate DHX15 on the catalytic U6 snRNA to initiate spliceosome disassembly. TFIP11 and C19L1 probe inner and outer spliceosome surfaces to detect the release of ligated mRNA. U6 snRNA thus controls both the start and end of pre-mRNA splicing.\",\n      \"method\": \"Cryo-electron microscopy structure determination of nematode and human terminal ILS complexes, biochemical and genetic validation\",\n      \"journal\": \"Nature\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — high-resolution cryo-EM of human and nematode complexes plus biochemical and genetic validation, multiple organisms, direct mechanistic visualization\",\n      \"pmids\": [\"38925148\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"TFIP11 forms a complex with the BLM helicase and preferentially binds DNA substrates mimicking stalled replication fork structures. Loss of TFIP11 causes abnormal accumulation of BLM at stalled forks, impairs RAD51-mediated fork reversal and fork slowing, sensitizes cells to replication stress-inducing agents, and enhances chromosomal instability.\",\n      \"method\": \"Co-immunoprecipitation, DNA substrate binding assays, replication fork assays, RAD51 foci analysis, cell survival assays, chromosomal instability analysis, siRNA/genetic knockout\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — multiple orthogonal methods (co-IP, DNA binding, fork reversal assays, chromosomal instability), functionally defined phenotype with mechanistic pathway placement\",\n      \"pmids\": [\"38341452\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"The N-terminal region of TFIP11 is an intrinsically disordered polyampholytic protein that exhibits structural duality with coexisting ordered and disordered assemblies in a salt-dependent manner. Increasing ionic strength enhances conformational flexibility, promoting a more globule-like shape that may favor liquid-liquid phase separation and protein-RNA interaction. The G-patch domain, essential for TFIP11 function, is among the most conformationally impacted regions.\",\n      \"method\": \"Disorder prediction, molecular dynamics simulation, spectroscopy (CD, NMR-type methods implied), recombinant protein characterization\",\n      \"journal\": \"International journal of biological macromolecules\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1-2 / Moderate — computational plus experimental spectroscopy on recombinant domain, single lab, no functional mutagenesis validation\",\n      \"pmids\": [\"39089542\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2010,\n      \"finding\": \"A partial loss-of-function CWC23 mutant shows reduced interaction with Ntr1/Spp382 (yeast ortholog of TFIP11) and causes accumulation of excised lariat intron and unspliced pre-mRNA, implicating Cwc23 in the spliceosome disassembly pathway coordinated by Ntr1. Genetic interactions between the CWC23 J domain and Ntr1 or Prp43 suggest an auxiliary Hsp70-based chaperone role.\",\n      \"method\": \"Genetic interaction analysis, co-immunoprecipitation (Cwc23-Ntr1), in vivo splicing assays, site-directed mutagenesis of J domain\",\n      \"journal\": \"Molecular and cellular biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — co-IP plus genetic epistasis plus splicing assay, single lab, yeast ortholog data\",\n      \"pmids\": [\"19822657\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"The G-patch domain of Spp382/Ntr1 (yeast ortholog of TFIP11) is required for Spp382 function and differs from the G-patches of Sqs1 and Pxr1 in Prp43 two-hybrid response and ability to reconstitute RNA processing factors. G-patch domains are not freely interchangeable between Prp43 cofactors, suggesting G-patch identity specifies pathway-selective DExD/H-box helicase activity beyond simply tethering Prp43.\",\n      \"method\": \"Yeast two-hybrid, domain-swap experiments, site-directed mutagenesis, in vivo splicing/rRNA processing assays\",\n      \"journal\": \"Genetics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple complementary genetic and biochemical approaches, domain-level mechanistic resolution, single lab\",\n      \"pmids\": [\"25808954\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"TFIP11 (human ortholog of yeast Ntr1/Spp382) is a G-patch-containing splicing factor that localizes to nuclear speckles, Cajal Bodies, and nucleoli, where it functions at multiple stages of the spliceosome cycle: it recruits the RNA helicase DHX15/hPrp43 to the post-catalytic intron lariat spliceosome to initiate disassembly (alongside C19L1, SYF1, SYF2, and SDE2 as visualized by cryo-EM), independently promotes 2'-O-methylation of U6 snRNA via fibrillarin/snoRNA association to ensure proper U4/U6.U5 tri-snRNP assembly and splicing fidelity, and additionally participates in genome stability by forming a complex with BLM helicase at stalled replication forks to facilitate RAD51-mediated fork reversal.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"TFIP11 (human ortholog of yeast Ntr1/Spp382) is a G-patch splicing factor that governs the final, disassembly stage of the spliceosome cycle and additionally supports replication-fork stability [#1, #13]. Through its N-terminal G-patch domain, TFIP11 directly engages and activates the DEAH-box RNA helicase DHX15/hPrp43, recruiting the otherwise diffusely distributed helicase to nuclear speckles and to the post-catalytic intron-lariat spliceosome [#2, #1]. In the human and nematode terminal intron-lariat spliceosome, TFIP11 together with C19L1, SYF1, SYF2 and SDE2 docks onto and activates DHX15 on the catalytic U6 snRNA to detect release of ligated mRNA and trigger disassembly, debranching of the excised intron, and recycling of snRNPs [#13, #1]. A separate, DHX15-independent function localizes TFIP11 to nucleoli and Cajal bodies, where it promotes fibrillarin/snoRNA-dependent 2'-O-methylation of U6 snRNA required for proper U4/U6.U5 tri-snRNP assembly and splicing fidelity [#12]. Beyond RNA metabolism, TFIP11 forms a complex with the BLM helicase, binds stalled-replication-fork-mimicking DNA, and is required for RAD51-mediated fork reversal and genome stability [#14]. The conserved yeast ortholog establishes the underlying disassembly machinery: Ntr1/Spp382 binds Prp43 and acts as its spliceosome-targeting factor for intron release and snRNP recycling, defining a turnover/discard pathway for defective spliceosomes [#6, #7, #5].\",\n  \"teleology\": [\n    {\n      \"year\": 2005,\n      \"claim\": \"Established that human TFIP11 is a bona fide splicing factor with dynamic, RNA-dependent subnuclear organization, rather than its originally inferred transcription-factor role.\",\n      \"evidence\": \"GFP live-cell imaging with RNase A and Pol II inhibitor treatment plus an in vivo splicing assay in human cells\",\n      \"pmids\": [\"15868102\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Does not define the molecular step of splicing TFIP11 acts at\", \"No interacting partners identified\"]\n    },\n    {\n      \"year\": 2006,\n      \"claim\": \"Defined the core disassembly function in yeast: the ortholog Ntr1/Spp382 targets Prp43 to the post-splicing intron complex to drive intron release and snRNP recycling, and a discard pathway for defective spliceosomes.\",\n      \"evidence\": \"Metabolic depletion, in vitro splicing/snRNP analysis, co-IP, genetic suppressor screen and TAP in budding yeast\",\n      \"pmids\": [\"16880513\", \"16945917\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether human TFIP11 performs the identical step was not yet shown\", \"Role of the G-patch domain not resolved\"]\n    },\n    {\n      \"year\": 2007,\n      \"claim\": \"Resolved how the disassembly factor is delivered to the spliceosome: Ntr1 partners with Ntr2 (which contacts U5/Brr2) to recruit Prp43 dynamically, with spliceosome binding ATP-independent but disassembly requiring ATP hydrolysis.\",\n      \"evidence\": \"Co-IP, in vitro binding, ATP-hydrolysis-deficient mutants and genetic interaction analysis in yeast\",\n      \"pmids\": [\"17893323\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Human counterpart of the Ntr1-Ntr2 module not established\", \"Mechanism of helicase activation not defined\"]\n    },\n    {\n      \"year\": 2007,\n      \"claim\": \"Uncovered a non-splicing role: NTR1/Ntr1 binds XRCC4/Lif1 and PinX1, occupying DNA ligase IV sites to restrain NHEJ and localizing to telomeres and nucleoli.\",\n      \"evidence\": \"Yeast two-hybrid, plasmid ligation and chromosomal DSB repair assays, subcellular localization in yeast and human cells\",\n      \"pmids\": [\"17389648\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Physiological significance of NHEJ inhibition in human cells unclear\", \"Relationship between RNA and DNA-repair functions undefined\"]\n    },\n    {\n      \"year\": 2008,\n      \"claim\": \"Connected human TFIP11 directly to the disassembly machinery, showing it occupies the post-splicing IL complex and cooperates with hPrp43 to drive the IL-to-IS transition enabling debranching.\",\n      \"evidence\": \"Two-tag affinity purification of lariat-intron complexes, glycerol gradient sedimentation, and in vitro splicing with an interaction-domain deletion mutant\",\n      \"pmids\": [\"19103666\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Structural basis of the TFIP11-hPrp43 interaction not resolved\", \"Full IL complex composition incomplete\"]\n    },\n    {\n      \"year\": 2008,\n      \"claim\": \"Localized the helicase-recruiting activity to a defined domain and identified additional speckle partners, showing the G-patch mediates DHX15 recruitment and that TFIP11 co-localizes with CCNL1 and EWSR1.\",\n      \"evidence\": \"GFP co-transfection and confocal co-localization, yeast two-hybrid, sequence homology analysis in mammalian cells\",\n      \"pmids\": [\"19165350\", \"19122807\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"CCNL1/EWSR1 interactions shown only by co-localization, no biochemical confirmation\", \"Functional consequence of these partnerships untested\"]\n    },\n    {\n      \"year\": 2009,\n      \"claim\": \"Mapped the targeting determinants of TFIP11 and expanded the yeast cofactor network, defining a novel NLS and speckle-targeting sequence and implicating Cwc23/Sqs1 chaperone-helicase coordination.\",\n      \"evidence\": \"C-terminal deletion/mutagenesis with fluorescence imaging in mouse TFIP11; dosage interference, copurification and two-hybrid in yeast\",\n      \"pmids\": [\"19857462\", \"19581443\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Human counterparts of Sqs1/Cwc23 modulation not addressed\", \"Hsp70 chaperone role inferred only genetically\"]\n    },\n    {\n      \"year\": 2010,\n      \"claim\": \"Implicated an Hsp70-coupled chaperone in TFIP11-orchestrated disassembly by showing a Cwc23 mutant with reduced Ntr1 binding accumulates lariat intron and unspliced pre-mRNA.\",\n      \"evidence\": \"Genetic interaction analysis, co-IP and J-domain mutagenesis with in vivo splicing assays in yeast\",\n      \"pmids\": [\"19822657\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"J-domain mechanistic contribution remains genetic, not biochemical\", \"Conservation in human disassembly untested\"]\n    },\n    {\n      \"year\": 2013,\n      \"claim\": \"Extended the human post-splicing IL complex composition by identifying C2ORF3 as a functional component required for in vitro splicing.\",\n      \"evidence\": \"Reciprocal IP with TFIP11 and hPrp43, mass spectrometry, and depletion-rescue in vitro splicing in human extracts\",\n      \"pmids\": [\"24304693\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct binding partner of C2ORF3 within the complex undefined\", \"Structural placement not resolved\"]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"Demonstrated that the G-patch is not merely a Prp43 tether but specifies pathway-selective helicase activity, since G-patches of different cofactors are not interchangeable.\",\n      \"evidence\": \"Yeast two-hybrid, domain-swap and mutagenesis with in vivo splicing/rRNA processing assays\",\n      \"pmids\": [\"25808954\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Molecular basis of G-patch specificity unresolved\", \"Human G-patch specificity not directly tested\"]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"Provided structural context for disassembly by visualizing the Ntr1 C-terminal domain on Snu114 and Prp43 bound to Syf1 near the U6 3' end in the intron-lariat spliceosome.\",\n      \"evidence\": \"3.5 Å cryo-EM of the yeast intron-lariat spliceosome\",\n      \"pmids\": [\"28919079\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Human ILS architecture not resolved in this study\", \"Dynamics of helicase activation not captured\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Revealed a second, helicase-independent TFIP11 function in U6 snRNA modification, showing it is required for fibrillarin/snoRNA-dependent 2'-O-methylation that ensures tri-snRNP assembly and splicing fidelity.\",\n      \"evidence\": \"siRNA knockdown, snRNA methylation analysis, co-IP, tri-snRNP assembly assays and RNA-seq in human cells\",\n      \"pmids\": [\"34789764\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Direct snoRNA/fibrillarin binding interface on TFIP11 undefined\", \"How nucleolar/Cajal-body and speckle functions are partitioned unclear\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Established the activated human disassembly machine, showing TFIP11 with C19L1, SYF1, SYF2 and SDE2 docks onto and activates DHX15 on catalytic U6 snRNA to sense ligated-mRNA release.\",\n      \"evidence\": \"Cryo-EM of human and nematode terminal ILS complexes with biochemical and genetic validation\",\n      \"pmids\": [\"38925148\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Sequence of conformational events during activation not fully resolved\", \"Regulation of disassembly timing unaddressed\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Defined a direct genome-stability role, showing TFIP11 complexes with BLM, binds stalled-fork DNA, and is required for RAD51-mediated fork reversal and chromosomal stability.\",\n      \"evidence\": \"Co-IP, DNA-substrate binding, replication-fork and RAD51 foci assays, survival and chromosomal instability analysis with siRNA/knockout in human cells\",\n      \"pmids\": [\"38341452\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether the G-patch/RNA functions are required for fork protection unknown\", \"Mechanistic link to BLM regulation at the fork incomplete\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Characterized the biophysical nature of the functional N-terminal region as an intrinsically disordered polyampholyte with salt-dependent structural duality affecting the G-patch.\",\n      \"evidence\": \"Disorder prediction, molecular dynamics and spectroscopy on recombinant TFIP11 N-terminal domain\",\n      \"pmids\": [\"39089542\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Phase-separation behavior inferred, not demonstrated in cells\", \"No functional mutagenesis linking disorder to activity\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How TFIP11's distinct activities — spliceosome disassembly, U6 methylation, and replication-fork protection — are coordinated, partitioned among subnuclear compartments, and regulated remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No unified model linking RNA and DNA functions\", \"Regulation/post-translational control of compartment switching unknown\", \"No disease association established in the corpus\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0003723\", \"supporting_discovery_ids\": [1, 12, 13]},\n      {\"term_id\": \"GO:0003677\", \"supporting_discovery_ids\": [14]},\n      {\"term_id\": \"GO:0098772\", \"supporting_discovery_ids\": [2, 13, 1]},\n      {\"term_id\": \"GO:0060090\", \"supporting_discovery_ids\": [2, 13]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005654\", \"supporting_discovery_ids\": [0, 2]},\n      {\"term_id\": \"GO:0005730\", \"supporting_discovery_ids\": [8, 12]},\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [0, 4]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-8953854\", \"supporting_discovery_ids\": [1, 12, 13]},\n      {\"term_id\": \"R-HSA-73894\", \"supporting_discovery_ids\": [14, 8]}\n    ],\n    \"complexes\": [\n      \"intron lariat spliceosome (ILS)\",\n      \"post-splicing Intron Large (IL) complex\",\n      \"Ntr1-Ntr2 (NTR) complex\",\n      \"TFIP11-BLM complex\"\n    ],\n    \"partners\": [\n      \"DHX15\",\n      \"C19L1\",\n      \"SYF1\",\n      \"SYF2\",\n      \"SDE2\",\n      \"BLM\",\n      \"CCNL1\",\n      \"EWSR1\"\n    ],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":6,"faith_total":6,"faith_pct":100.0}}