{"gene":"HTATSF1","run_date":"2026-06-10T01:55:22","timeline":{"discoveries":[{"year":1996,"finding":"Tat-SF1 is a cellular cofactor required for HIV-1 Tat-mediated stimulation of transcriptional elongation; it is a substrate of an associated cellular kinase and contains two RNA recognition motifs. Tat may stimulate elongation by recruiting a complex containing Tat-SF1 and this kinase to the HIV-1 promoter through a Tat-TAR interaction.","method":"cDNA isolation, in vitro reconstituted transcription, cotransfection/complementation, kinase assay","journal":"Science","confidence":"High","confidence_rationale":"Tier 2 / Strong — cDNA cloning with in vitro reconstitution, complementation assay, and kinase substrate assay; foundational paper replicated by multiple subsequent studies","pmids":["8849451"],"is_preprint":false},{"year":1998,"finding":"Tat-SF1 is a general transcription elongation factor, not solely a Tat-specific coactivator; a Tat-affinity column bound Tat-SF1 efficiently and selectively, and Tat-SF1 activity requires an ATP-inactivatable general elongation factor (AIEF) for which Tat can substitute functionally.","method":"Protein-affinity chromatography, in vitro transcription elongation assay","journal":"Genes & development","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — affinity chromatography plus functional in vitro transcription assay, single lab, two complementary methods","pmids":["9765201"],"is_preprint":false},{"year":1998,"finding":"The yeast homolog of Tat-SF1, CUS2, associates with U2 snRNA in splicing extracts, interacts with PRP11 (a subunit of SF3a), and is required to refold misfolded U2 RNA into a structure permissive for SF3b/SF3a binding prior to spliceosome assembly; anti-Tat-SF1 antibodies co-immunoprecipitate the human SF3a subunit SF3a66/SAP62, indicating a parallel splicing function in human cells.","method":"Suppressor screen, co-immunoprecipitation, in vitro RNA binding assay, RRM mutagenesis, genetic analysis","journal":"Molecular and cellular biology","confidence":"High","confidence_rationale":"Tier 1–2 / Strong — genetic suppressor screen combined with in vitro binding, mutagenesis, and co-IP; replicated in human cells by antibody co-IP","pmids":["9710584"],"is_preprint":false},{"year":1999,"finding":"Tat-SF1 physically associates with RAP30 (but not RAP74) subunit of TFIIF and with human SPT5 (hSPT5); both hSPT5 and Tat-SF1 are required for Tat transactivation as shown by immunodepletion and complementation with recombinant proteins; overexpression of both factors specifically stimulates Tat-dependent transcription in vivo.","method":"Co-immunoprecipitation, immunodepletion, recombinant protein complementation, overexpression","journal":"Molecular and cellular biology","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal co-IP, immunodepletion/complementation, and in vivo overexpression across two labs","pmids":["10454543"],"is_preprint":false},{"year":2007,"finding":"Tat-SF1 acts as a stimulatory host factor for influenza virus RNA synthesis by interacting with free nucleoprotein (NP) but not RNA-associated NP, thereby facilitating formation of RNA-NP complexes, suggesting a molecular chaperone role for NP.","method":"Yeast replicon system, genome-wide deletion screen, co-immunoprecipitation, RNA-NP complex formation assay","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — genome-wide yeast screen plus biochemical interaction assay; single study, two orthogonal approaches","pmids":["17991777"],"is_preprint":false},{"year":2009,"finding":"Tat-SF1 is not required for Tat-dependent or basal HIV-1 transcription from the LTR in vivo; instead, depletion of Tat-SF1 by shRNA increases the ratio of unspliced to spliced HIV-1 RNAs, revealing a post-transcriptional (splicing) role in regulating viral transcript classes.","method":"shRNA knockdown in HeLa and T-REx-293 cells, HIV-1 infectivity assay, RT-PCR for spliced/unspliced RNA ratios","journal":"PloS one","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — shRNA knockdown with two cell lines and specific molecular readout; contradicts in vitro reconstitution data from earlier studies","pmids":["19479034"],"is_preprint":false},{"year":2009,"finding":"Tat-SF1 collaborates non-redundantly with DSIF (Spt4-Spt5) and the Paf1 complex to facilitate transcription elongation by RNA Pol II; these factors are recruited to the FOS gene in a temporally coordinated manner; elongation activation depends on P-TEFb-mediated phosphorylation of the Spt5 C-terminal region.","method":"Biochemical activity-based fractionation, chromatin immunoprecipitation (ChIP), in vitro transcription elongation assay, P-TEFb inhibition","journal":"Genes & development","confidence":"High","confidence_rationale":"Tier 2 / Strong — biochemical reconstitution plus ChIP in human cells, multiple orthogonal methods, clear functional differentiation of factors","pmids":["19952111"],"is_preprint":false},{"year":2011,"finding":"Genome-wide RNAi and exon-array analysis shows Tat-SF1 generally activates transcript levels (98% of affected genes down-regulated upon depletion) and independently regulates alternative splicing of a distinct gene set; the two functions show minimal overlap, indicating Tat-SF1 does not functionally couple transcription and splicing at the cellular level.","method":"RNAi knockdown, exon-specific microarray, bioinformatics","journal":"RNA","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — genome-wide functional screen with specific cellular readouts; single lab, one primary method (array) plus RNAi","pmids":["21282347"],"is_preprint":false},{"year":2017,"finding":"In Drosophila, Barricade (Barc)/Tat-SF1 associates with components of the U2 snRNP complex and its depletion causes intron retention in a subset of introns characterized as short, GC-rich, with weak 3′ splice sites; loss of Barc impairs neural progenitor proliferation and differentiation during brain development.","method":"Genetic loss-of-function (Drosophila mutants), co-immunoprecipitation, RNA-seq/splicing assay, bioinformatics, cell culture splicing assay","journal":"Development","confidence":"High","confidence_rationale":"Tier 2 / Strong — in vivo genetic KO with defined cellular phenotype, co-IP for complex membership, splicing assay defining substrate class; multiple orthogonal methods","pmids":["28935704"],"is_preprint":false},{"year":2018,"finding":"Tat-SF1 contains a U2AF homology motif (UHM) that directly and preferentially binds the SF3b1 subunit of U2 snRNP via ULM motifs (particularly through SF3b1 Trp338 and electrostatic interactions with a basic ULM tail); crystal structures at 1.1 Å (free UHM), 1.9 Å, and 2.1 Å (UHM-ULM complexes) define the canonical binding interface; SF3b1 regulates Tat-SF1 protein levels and the two factors influence overlapping transcript sets.","method":"X-ray crystallography (1.1 Å, 1.9 Å, 2.1 Å resolution), co-immunoprecipitation, UHM mutagenesis, binding affinity measurements, RNAi/expression analysis","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1 / Strong — high-resolution crystal structures plus mutagenesis, direct binding assays, and functional gene-expression validation; multiple orthogonal methods in one study","pmids":["30567737"],"is_preprint":false},{"year":2024,"finding":"CK2 kinase phosphorylates HTATSF1 at Ser748, which facilitates HTATSF1 interaction with TOPBP1, leading to RAD51 recruitment to DNA damage sites and promotion of homologous recombination (HR) repair; loss-of-function mutations in this axis increase HR deficiency.","method":"Phosphorylation assay, co-immunoprecipitation, HR repair assay, mutant cell lines, tumor data analysis","journal":"The Journal of biological chemistry","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — biochemical phosphorylation/interaction assay plus HR repair functional readout; single lab, two orthogonal methods","pmids":["38762174"],"is_preprint":false},{"year":2025,"finding":"HTATSF1 positively regulates innate antiviral immune signaling: upon viral infection it promotes HECTD3-catalyzed K63-linked polyubiquitination of TRAF3 (enabling TBK1 recruitment and IRF3 activation) and independently promotes TAK1 recruitment to TRAF6 (activating the TAK1-IKK-NF-κB axis); HTATSF1-deficient mice show decreased cytokine production and increased mortality upon viral infection.","method":"Co-immunoprecipitation, ubiquitination assay, gene knockout (mouse and cell), cytokine measurement, viral infection model","journal":"Cell insight","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — co-IP and ubiquitination assays plus in vivo KO mouse phenotype; single lab, multiple orthogonal methods","pmids":["41466838"],"is_preprint":false},{"year":2026,"finding":"Crystal structure of TopBP1 BRCT0-2 in complex with a phospho-HTATSF1 C-terminal peptide (at 1.9 Å resolution) reveals that TopBP1 cooperatively binds phosphorylated HTATSF1 through its BRCT1 and BRCT2 domains; key residue V158 in BRCT1 mediates specific hydrophobic contacts with the HTATSF1 ECT peptide, discriminating HTATSF1 from other phosphorylated ligands.","method":"X-ray crystallography (1.9 Å), mutagenesis, binding assays, AlphaFold3 modeling with biochemical validation","journal":"Biochemical and biophysical research communications","confidence":"High","confidence_rationale":"Tier 1 / Moderate — crystal structure with mutagenesis and binding validation; single lab but multiple orthogonal structural and biochemical methods","pmids":["42251821"],"is_preprint":false},{"year":2024,"finding":"HTATSF1 is found in complex with SF3B1 and P-TEFb on chromatin, along with the splicing factor SNW1; SF3B1 inhibition does not cause nuclear export of HTATSF1 (unlike SNW1), indicating HTATSF1 remains chromatin-associated after SF3B1 perturbation and its role in coupling transcription and splicing is partially separable from SNW1.","method":"Co-immunoprecipitation, nuclear fractionation/localization, SF3B1 inhibitor treatment","journal":"bioRxiv","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single co-IP and fractionation from a preprint; HTATSF1 is not the primary focus of the study","pmids":[],"is_preprint":true},{"year":2025,"finding":"Computational simulations indicate TAT-SF1 acts as a 'molecular latch' maintaining the U2 snRNA branch-stem loop (BSL) in a supercoiled, high-energy 'loaded-spring' conformation; displacement of TAT-SF1 releases stored conformational energy that drives strand invasion for branch-site recognition during spliceosome assembly.","method":"All-atom and coarse-grained molecular dynamics simulations (computational only)","journal":"bioRxiv","confidence":"Low","confidence_rationale":"Tier 4 / Weak — computational prediction only, no experimental validation; preprint","pmids":[],"is_preprint":true}],"current_model":"HTATSF1/Tat-SF1 is a multifunctional RNA-binding and transcription-splicing factor that (1) stimulates RNA Pol II transcription elongation by associating with P-TEFb, DSIF/hSPT5, Paf1C, and TFIIF subunit RAP30; (2) promotes pre-mRNA splicing by binding U2 snRNP through a UHM–SF3b1 ULM interface (crystal-structure defined) and cooperating with the U2 snRNP to facilitate branch-site recognition; (3) regulates viral RNA biology, including modulating HIV-1 spliced/unspliced transcript ratios; (4) undergoes CK2-mediated phosphorylation at Ser748, enabling TOPBP1 recruitment and homologous recombination repair via RAD51 loading (structural basis defined by TopBP1 BRCT1/2 co-crystal); and (5) acts as a positive regulator of innate antiviral immunity by orchestrating HECTD3-dependent K63-ubiquitination of TRAF3 and TRAF6-TAK1 signaling."},"narrative":{"mechanistic_narrative":"HTATSF1 (Tat-SF1) is a multifunctional nuclear RNA-binding protein that links RNA polymerase II transcription elongation to pre-mRNA splicing [PMID:8849451, PMID:19952111]. It was first identified as a cellular cofactor required for HIV-1 Tat-mediated stimulation of transcriptional elongation, containing two RNA recognition motifs and serving as a substrate of an associated cellular kinase [PMID:8849451], and was subsequently shown to act as a general elongation factor rather than a strictly Tat-specific coactivator [PMID:9765201]. Mechanistically, it associates with the RAP30 subunit of TFIIF and with hSPT5 [PMID:10454543] and collaborates non-redundantly with DSIF (Spt4-Spt5) and the Paf1 complex to promote elongation, in a process dependent on P-TEFb-mediated phosphorylation of the Spt5 C-terminal region [PMID:19952111]. In splicing, HTATSF1 functions through U2 snRNP: its yeast homolog CUS2 binds U2 snRNA and refolds it into an assembly-competent structure [PMID:9710584], and the human protein engages the SF3b1 subunit of U2 snRNP through a U2AF homology motif (UHM)–ULM interface defined by high-resolution crystal structures [PMID:30567737]. Depletion causes intron retention in short, GC-rich introns with weak 3' splice sites and impairs neural progenitor proliferation, establishing a developmental requirement for its splicing activity [PMID:28935704]. Genome-wide analyses show it broadly activates transcript levels and independently regulates a distinct alternative-splicing program [PMID:21282347]. Beyond gene expression, CK2 phosphorylates HTATSF1 at Ser748 to recruit TOPBP1 via its BRCT1/2 domains, loading RAD51 to drive homologous recombination repair [PMID:38762174, PMID:42251821], and HTATSF1 positively regulates innate antiviral immunity by promoting HECTD3-dependent K63-ubiquitination of TRAF3 and TAK1 recruitment to TRAF6 [PMID:41466838]. In viral RNA biology it modulates the ratio of unspliced to spliced HIV-1 transcripts [PMID:19479034] and stimulates influenza RNA synthesis by chaperoning nucleoprotein [PMID:17991777].","teleology":[{"year":1996,"claim":"Established HTATSF1 as a discrete cellular factor needed for HIV-1 Tat-stimulated transcription elongation, defining its first molecular role and RNA-binding architecture.","evidence":"cDNA cloning with in vitro reconstituted transcription, complementation, and kinase substrate assay","pmids":["8849451"],"confidence":"High","gaps":["Did not distinguish Tat-specific from general elongation roles","Identity of the associated kinase unresolved","No direct RNA target defined"]},{"year":1998,"claim":"Reframed HTATSF1 as a general elongation factor rather than a Tat-only coactivator, broadening its mechanistic relevance to host transcription.","evidence":"protein-affinity chromatography and in vitro transcription elongation assay","pmids":["9765201"],"confidence":"Medium","gaps":["Identity of the required AIEF factor undefined","No in vivo confirmation"]},{"year":1998,"claim":"Revealed a conserved splicing function through the yeast homolog CUS2, linking HTATSF1 to U2 snRNA folding and SF3a/SF3b association prior to spliceosome assembly.","evidence":"suppressor screen, co-IP, in vitro RNA binding, RRM mutagenesis; human SF3a66 co-IP","pmids":["9710584"],"confidence":"High","gaps":["Human splicing role inferred largely from yeast","Direct human U2 binding interface not yet mapped"]},{"year":1999,"claim":"Identified direct physical partners in the transcription machinery (TFIIF RAP30 and hSPT5), providing a recruitment mechanism for elongation control.","evidence":"co-IP, immunodepletion/recombinant complementation, in vivo overexpression","pmids":["10454543"],"confidence":"High","gaps":["Structural basis of RAP30/hSPT5 contacts undefined","Stoichiometry of the complex unknown"]},{"year":2007,"claim":"Extended HTATSF1 function to influenza RNA synthesis via chaperoning of free nucleoprotein, indicating a role in viral RNP assembly.","evidence":"yeast replicon system, genome-wide deletion screen, co-IP, RNA-NP complex assay","pmids":["17991777"],"confidence":"Medium","gaps":["Mechanism of NP chaperoning not structurally defined","Single study"]},{"year":2009,"claim":"Resolved the HIV-1 role as post-transcriptional, showing depletion shifts the unspliced/spliced transcript ratio rather than blocking LTR transcription.","evidence":"shRNA knockdown in two cell lines, RT-PCR of transcript ratios, infectivity assay","pmids":["19479034"],"confidence":"Medium","gaps":["Contradicts earlier in vitro elongation reconstitution","Direct splicing mechanism on HIV RNA not mapped"]},{"year":2009,"claim":"Defined HTATSF1's non-redundant cooperation with DSIF and Paf1C and dependence on P-TEFb, integrating it into the elongation control circuit at a model gene.","evidence":"activity-based fractionation, ChIP at FOS, in vitro elongation, P-TEFb inhibition","pmids":["19952111"],"confidence":"High","gaps":["Generality beyond FOS not established here","Order of recruitment events partly inferred"]},{"year":2011,"claim":"Genome-wide analysis showed transcription-activating and alternative-splicing functions are largely separable, arguing HTATSF1 does not obligately couple the two processes cellularly.","evidence":"RNAi knockdown, exon-array, bioinformatics","pmids":["21282347"],"confidence":"Medium","gaps":["Mechanistic basis for two separable functions unexplained","Single primary method"]},{"year":2017,"claim":"In vivo Drosophila genetics defined the splicing substrate class (short, GC-rich, weak 3' splice site introns) and a developmental requirement in neural progenitors.","evidence":"Drosophila loss-of-function, co-IP with U2 snRNP, RNA-seq splicing analysis","pmids":["28935704"],"confidence":"High","gaps":["Whether human introns share the same features not directly tested","Direct vs indirect splicing effects not fully separated"]},{"year":2018,"claim":"Provided the structural basis for U2 snRNP engagement, defining the UHM–ULM interface with SF3b1 at atomic resolution and mutual regulation of protein levels.","evidence":"X-ray crystallography (1.1–2.1 Å), UHM mutagenesis, binding affinity, RNAi","pmids":["30567737"],"confidence":"High","gaps":["Functional consequence of disrupting interface in cells not exhaustively tested","Role within the assembling spliceosome not visualized"]},{"year":2024,"claim":"Uncovered a DNA repair function: CK2 phosphorylation at Ser748 recruits TOPBP1 to load RAD51 and promote homologous recombination.","evidence":"phosphorylation assay, co-IP, HR repair assay, mutant cells, tumor data","pmids":["38762174"],"confidence":"Medium","gaps":["How a splicing/transcription factor accesses damage sites unclear","Single lab"]},{"year":2026,"claim":"Defined the structural basis of TOPBP1 recognition, showing cooperative BRCT1/BRCT2 binding of phospho-HTATSF1 with V158 conferring ligand specificity.","evidence":"X-ray crystallography (1.9 Å), mutagenesis, binding assays, AlphaFold3 modeling","pmids":["42251821"],"confidence":"High","gaps":["In-cell validation of V158-dependent specificity limited","Integration with full HR machinery not shown"]},{"year":2025,"claim":"Established HTATSF1 as a positive regulator of innate antiviral immunity via HECTD3-dependent K63-ubiquitination of TRAF3 and TAK1-TRAF6 signaling, with an in vivo survival phenotype.","evidence":"co-IP, ubiquitination assays, mouse and cell knockouts, cytokine and viral infection models","pmids":["41466838"],"confidence":"Medium","gaps":["Relationship between immune role and nuclear RNA functions unclear","Direct vs scaffolding role in ubiquitination not fully separated"]},{"year":null,"claim":"How HTATSF1's distinct activities — elongation, U2-dependent splicing, HR repair, and antiviral signaling — are coordinated or partitioned within a single protein remains unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No unified model linking nuclear RNA roles to repair and immune functions","Domain-level partitioning of the four activities undefined","Regulatory cues switching between functions unknown"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0003723","term_label":"RNA binding","supporting_discovery_ids":[0,2]},{"term_id":"GO:0060090","term_label":"molecular adaptor activity","supporting_discovery_ids":[3,9]},{"term_id":"GO:0140110","term_label":"transcription regulator activity","supporting_discovery_ids":[0,6]}],"localization":[{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[6,8]},{"term_id":"GO:0000228","term_label":"nuclear chromosome","supporting_discovery_ids":[6]}],"pathway":[{"term_id":"R-HSA-74160","term_label":"Gene expression (Transcription)","supporting_discovery_ids":[0,6]},{"term_id":"R-HSA-8953854","term_label":"Metabolism of RNA","supporting_discovery_ids":[2,9]},{"term_id":"R-HSA-73894","term_label":"DNA Repair","supporting_discovery_ids":[10,12]},{"term_id":"R-HSA-168256","term_label":"Immune System","supporting_discovery_ids":[11]}],"complexes":["U2 snRNP","P-TEFb-associated elongation complex"],"partners":["SF3B1","SUPT5H","GTF2F2","TOPBP1","HECTD3","TRAF3","TRAF6","PRPF11"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"O43719","full_name":"17S U2 SnRNP complex component HTATSF1","aliases":["HIV Tat-specific factor 1","Tat-SF1"],"length_aa":755,"mass_kda":85.9,"function":"Component of the 17S U2 SnRNP complex of the spliceosome, a large ribonucleoprotein complex that removes introns from transcribed pre-mRNAs (PubMed:30567737, PubMed:32494006, PubMed:34822310). 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:30567737, PubMed:32494006, PubMed:34822310). Within the 17S U2 SnRNP complex, HTATSF1 is required to stabilize the branchpoint-interacting stem loop (PubMed:34822310). HTATSF1 is displaced from the 17S U2 SnRNP complex before the stable addition of the 17S U2 SnRNP complex to the spliceosome, destabilizing the branchpoint-interacting stem loop and allowing to probe intron branch site sequences (PubMed:32494006, PubMed:34822310). Also acts as a regulator of transcriptional elongation, possibly by mediating the reciprocal stimulatory effect of splicing on transcriptional elongation (PubMed:10454543, PubMed:10913173, PubMed:11780068). Involved in double-strand break (DSB) repair via homologous recombination in S-phase by promoting the recruitment of TOPBP1 to DNA damage sites (PubMed:35597237). Mechanistically, HTATSF1 is (1) recruited to DNA damage sites in S-phase via interaction with poly-ADP-ribosylated RPA1 and (2) phosphorylated by CK2, promoting recruitment of TOPBP1, thereby facilitating RAD51 nucleofilaments formation and RPA displacement, followed by homologous recombination (PubMed:35597237) (Microbial infection) In case of infection by HIV-1, it is up-regulated by the HIV-1 proteins NEF and gp120, acts as a cofactor required for the Tat-enhanced transcription of the virus","subcellular_location":"Nucleus; Chromosome","url":"https://www.uniprot.org/uniprotkb/O43719/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":true,"resolved_as":"","url":"https://depmap.org/portal/gene/HTATSF1","classification":"Common Essential","n_dependent_lines":1112,"n_total_lines":1208,"dependency_fraction":0.9205298013245033},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[{"gene":"SF3A2","stoichiometry":10.0},{"gene":"SF3B1","stoichiometry":10.0},{"gene":"SF3B6","stoichiometry":10.0},{"gene":"SRP9","stoichiometry":10.0},{"gene":"SF3A1","stoichiometry":4.0},{"gene":"SF3B2","stoichiometry":4.0},{"gene":"SNRPB2","stoichiometry":4.0},{"gene":"SEC61B","stoichiometry":0.2},{"gene":"SNRPB","stoichiometry":0.2},{"gene":"SNRPD2","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/search/HTATSF1","total_profiled":1310},"omim":[{"mim_id":"300346","title":"HIV-1 TAT STIMULATORY FACTOR 1; HTATSF1","url":"https://www.omim.org/entry/300346"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Enhanced","locations":[{"location":"Nucleoplasm","reliability":"Enhanced"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/HTATSF1"},"hgnc":{"alias_symbol":["TAT-SF1"],"prev_symbol":[]},"alphafold":{"accession":"O43719","domains":[{"cath_id":"3.30.70.330","chopping":"130-220_236-244","consensus_level":"high","plddt":90.5127,"start":130,"end":244},{"cath_id":"3.30.70.330","chopping":"266-375","consensus_level":"high","plddt":88.8024,"start":266,"end":375}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/O43719","model_url":"https://alphafold.ebi.ac.uk/files/AF-O43719-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-O43719-F1-predicted_aligned_error_v6.png","plddt_mean":59.09},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=HTATSF1","jax_strain_url":"https://www.jax.org/strain/search?query=HTATSF1"},"sequence":{"accession":"O43719","fasta_url":"https://rest.uniprot.org/uniprotkb/O43719.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/O43719/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/O43719"}},"corpus_meta":[{"pmid":"8849451","id":"PMC_8849451","title":"Tat-SF1: cofactor for stimulation of transcriptional elongation by HIV-1 Tat.","date":"1996","source":"Science (New York, N.Y.)","url":"https://pubmed.ncbi.nlm.nih.gov/8849451","citation_count":144,"is_preprint":false},{"pmid":"19952111","id":"PMC_19952111","title":"DSIF, the Paf1 complex, and Tat-SF1 have nonredundant, cooperative roles in RNA polymerase II elongation.","date":"2009","source":"Genes & development","url":"https://pubmed.ncbi.nlm.nih.gov/19952111","citation_count":95,"is_preprint":false},{"pmid":"9710584","id":"PMC_9710584","title":"CUS2, a yeast homolog of human Tat-SF1, rescues function of misfolded U2 through an unusual RNA recognition motif.","date":"1998","source":"Molecular and cellular biology","url":"https://pubmed.ncbi.nlm.nih.gov/9710584","citation_count":74,"is_preprint":false},{"pmid":"17991777","id":"PMC_17991777","title":"An influenza virus replicon system in yeast identified Tat-SF1 as a stimulatory host factor for viral RNA synthesis.","date":"2007","source":"Proceedings of the National Academy of Sciences of the United States of America","url":"https://pubmed.ncbi.nlm.nih.gov/17991777","citation_count":74,"is_preprint":false},{"pmid":"9765201","id":"PMC_9765201","title":"The HIV-1 Tat cellular coactivator Tat-SF1 is a general transcription elongation factor.","date":"1998","source":"Genes & development","url":"https://pubmed.ncbi.nlm.nih.gov/9765201","citation_count":61,"is_preprint":false},{"pmid":"10454543","id":"PMC_10454543","title":"Tat-SF1 protein associates with RAP30 and human SPT5 proteins.","date":"1999","source":"Molecular and cellular biology","url":"https://pubmed.ncbi.nlm.nih.gov/10454543","citation_count":49,"is_preprint":false},{"pmid":"30567737","id":"PMC_30567737","title":"The pre-mRNA splicing and transcription factor Tat-SF1 is a functional partner of the spliceosome SF3b1 subunit via a U2AF homology motif interface.","date":"2018","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/30567737","citation_count":35,"is_preprint":false},{"pmid":"19479034","id":"PMC_19479034","title":"Tat-SF1 is not required for Tat transactivation but does regulate the relative levels of unspliced and spliced HIV-1 RNAs.","date":"2009","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/19479034","citation_count":17,"is_preprint":false},{"pmid":"21282347","id":"PMC_21282347","title":"Identification of Tat-SF1 cellular targets by exon array analysis reveals dual roles in transcription and splicing.","date":"2011","source":"RNA (New York, N.Y.)","url":"https://pubmed.ncbi.nlm.nih.gov/21282347","citation_count":16,"is_preprint":false},{"pmid":"28935704","id":"PMC_28935704","title":"The splicing co-factor Barricade/Tat-SF1 is required for cell cycle and lineage progression in Drosophila neural stem cells.","date":"2017","source":"Development (Cambridge, England)","url":"https://pubmed.ncbi.nlm.nih.gov/28935704","citation_count":12,"is_preprint":false},{"pmid":"23153325","id":"PMC_23153325","title":"Impact of sustained RNAi-mediated suppression of cellular cofactor Tat-SF1 on HIV-1 replication in CD4+ T cells.","date":"2012","source":"Virology journal","url":"https://pubmed.ncbi.nlm.nih.gov/23153325","citation_count":7,"is_preprint":false},{"pmid":"41466838","id":"PMC_41466838","title":"HTATSF1 regulates innate antiviral immune response by orchestrating TRAF3-IRF3 and TRAF6-NF-κB pathways.","date":"2025","source":"Cell insight","url":"https://pubmed.ncbi.nlm.nih.gov/41466838","citation_count":2,"is_preprint":false},{"pmid":"38762174","id":"PMC_38762174","title":"CK2-HTATSF1-TOPBP1 signaling axis modulates tumor chemotherapy response.","date":"2024","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/38762174","citation_count":0,"is_preprint":false},{"pmid":"42251821","id":"PMC_42251821","title":"Structural mechanism of TopBP1 recognizing phosphorylated HTATSF1 in homologous recombination repair.","date":"2026","source":"Biochemical and biophysical research communications","url":"https://pubmed.ncbi.nlm.nih.gov/42251821","citation_count":0,"is_preprint":false},{"pmid":null,"id":"bio_10.1101_2025.10.31.685824","title":"U2 snRNP recognizes the branch site through a loaded-spring strand-invasion mechanism","date":"2025-10-31","source":"bioRxiv","url":"https://doi.org/10.1101/2025.10.31.685824","citation_count":0,"is_preprint":true},{"pmid":null,"id":"bio_10.1101_2024.06.26.600844","title":"Inhibition of SF3B1 affects recruitment of P-TEFb to chromatin through multiple mechanisms","date":"2024-06-27","source":"bioRxiv","url":"https://doi.org/10.1101/2024.06.26.600844","citation_count":0,"is_preprint":true}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":9217,"output_tokens":3920,"usd":0.043226,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":11618,"output_tokens":4019,"usd":0.079283,"stage2_stop_reason":"end_turn"},"total_usd":0.122509,"stage1_batch_id":"msgbatch_01DUPACZi7AAWwuZiUjseQF4","stage2_batch_id":"msgbatch_018yt7chE3f48PEFtDwtj6AE","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 1996,\n      \"finding\": \"Tat-SF1 is a cellular cofactor required for HIV-1 Tat-mediated stimulation of transcriptional elongation; it is a substrate of an associated cellular kinase and contains two RNA recognition motifs. Tat may stimulate elongation by recruiting a complex containing Tat-SF1 and this kinase to the HIV-1 promoter through a Tat-TAR interaction.\",\n      \"method\": \"cDNA isolation, in vitro reconstituted transcription, cotransfection/complementation, kinase assay\",\n      \"journal\": \"Science\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — cDNA cloning with in vitro reconstitution, complementation assay, and kinase substrate assay; foundational paper replicated by multiple subsequent studies\",\n      \"pmids\": [\"8849451\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1998,\n      \"finding\": \"Tat-SF1 is a general transcription elongation factor, not solely a Tat-specific coactivator; a Tat-affinity column bound Tat-SF1 efficiently and selectively, and Tat-SF1 activity requires an ATP-inactivatable general elongation factor (AIEF) for which Tat can substitute functionally.\",\n      \"method\": \"Protein-affinity chromatography, in vitro transcription elongation assay\",\n      \"journal\": \"Genes & development\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — affinity chromatography plus functional in vitro transcription assay, single lab, two complementary methods\",\n      \"pmids\": [\"9765201\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1998,\n      \"finding\": \"The yeast homolog of Tat-SF1, CUS2, associates with U2 snRNA in splicing extracts, interacts with PRP11 (a subunit of SF3a), and is required to refold misfolded U2 RNA into a structure permissive for SF3b/SF3a binding prior to spliceosome assembly; anti-Tat-SF1 antibodies co-immunoprecipitate the human SF3a subunit SF3a66/SAP62, indicating a parallel splicing function in human cells.\",\n      \"method\": \"Suppressor screen, co-immunoprecipitation, in vitro RNA binding assay, RRM mutagenesis, genetic analysis\",\n      \"journal\": \"Molecular and cellular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Strong — genetic suppressor screen combined with in vitro binding, mutagenesis, and co-IP; replicated in human cells by antibody co-IP\",\n      \"pmids\": [\"9710584\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1999,\n      \"finding\": \"Tat-SF1 physically associates with RAP30 (but not RAP74) subunit of TFIIF and with human SPT5 (hSPT5); both hSPT5 and Tat-SF1 are required for Tat transactivation as shown by immunodepletion and complementation with recombinant proteins; overexpression of both factors specifically stimulates Tat-dependent transcription in vivo.\",\n      \"method\": \"Co-immunoprecipitation, immunodepletion, recombinant protein complementation, overexpression\",\n      \"journal\": \"Molecular and cellular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal co-IP, immunodepletion/complementation, and in vivo overexpression across two labs\",\n      \"pmids\": [\"10454543\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2007,\n      \"finding\": \"Tat-SF1 acts as a stimulatory host factor for influenza virus RNA synthesis by interacting with free nucleoprotein (NP) but not RNA-associated NP, thereby facilitating formation of RNA-NP complexes, suggesting a molecular chaperone role for NP.\",\n      \"method\": \"Yeast replicon system, genome-wide deletion screen, co-immunoprecipitation, RNA-NP complex formation assay\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — genome-wide yeast screen plus biochemical interaction assay; single study, two orthogonal approaches\",\n      \"pmids\": [\"17991777\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2009,\n      \"finding\": \"Tat-SF1 is not required for Tat-dependent or basal HIV-1 transcription from the LTR in vivo; instead, depletion of Tat-SF1 by shRNA increases the ratio of unspliced to spliced HIV-1 RNAs, revealing a post-transcriptional (splicing) role in regulating viral transcript classes.\",\n      \"method\": \"shRNA knockdown in HeLa and T-REx-293 cells, HIV-1 infectivity assay, RT-PCR for spliced/unspliced RNA ratios\",\n      \"journal\": \"PloS one\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — shRNA knockdown with two cell lines and specific molecular readout; contradicts in vitro reconstitution data from earlier studies\",\n      \"pmids\": [\"19479034\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2009,\n      \"finding\": \"Tat-SF1 collaborates non-redundantly with DSIF (Spt4-Spt5) and the Paf1 complex to facilitate transcription elongation by RNA Pol II; these factors are recruited to the FOS gene in a temporally coordinated manner; elongation activation depends on P-TEFb-mediated phosphorylation of the Spt5 C-terminal region.\",\n      \"method\": \"Biochemical activity-based fractionation, chromatin immunoprecipitation (ChIP), in vitro transcription elongation assay, P-TEFb inhibition\",\n      \"journal\": \"Genes & development\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — biochemical reconstitution plus ChIP in human cells, multiple orthogonal methods, clear functional differentiation of factors\",\n      \"pmids\": [\"19952111\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"Genome-wide RNAi and exon-array analysis shows Tat-SF1 generally activates transcript levels (98% of affected genes down-regulated upon depletion) and independently regulates alternative splicing of a distinct gene set; the two functions show minimal overlap, indicating Tat-SF1 does not functionally couple transcription and splicing at the cellular level.\",\n      \"method\": \"RNAi knockdown, exon-specific microarray, bioinformatics\",\n      \"journal\": \"RNA\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — genome-wide functional screen with specific cellular readouts; single lab, one primary method (array) plus RNAi\",\n      \"pmids\": [\"21282347\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"In Drosophila, Barricade (Barc)/Tat-SF1 associates with components of the U2 snRNP complex and its depletion causes intron retention in a subset of introns characterized as short, GC-rich, with weak 3′ splice sites; loss of Barc impairs neural progenitor proliferation and differentiation during brain development.\",\n      \"method\": \"Genetic loss-of-function (Drosophila mutants), co-immunoprecipitation, RNA-seq/splicing assay, bioinformatics, cell culture splicing assay\",\n      \"journal\": \"Development\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — in vivo genetic KO with defined cellular phenotype, co-IP for complex membership, splicing assay defining substrate class; multiple orthogonal methods\",\n      \"pmids\": [\"28935704\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"Tat-SF1 contains a U2AF homology motif (UHM) that directly and preferentially binds the SF3b1 subunit of U2 snRNP via ULM motifs (particularly through SF3b1 Trp338 and electrostatic interactions with a basic ULM tail); crystal structures at 1.1 Å (free UHM), 1.9 Å, and 2.1 Å (UHM-ULM complexes) define the canonical binding interface; SF3b1 regulates Tat-SF1 protein levels and the two factors influence overlapping transcript sets.\",\n      \"method\": \"X-ray crystallography (1.1 Å, 1.9 Å, 2.1 Å resolution), co-immunoprecipitation, UHM mutagenesis, binding affinity measurements, RNAi/expression analysis\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — high-resolution crystal structures plus mutagenesis, direct binding assays, and functional gene-expression validation; multiple orthogonal methods in one study\",\n      \"pmids\": [\"30567737\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"CK2 kinase phosphorylates HTATSF1 at Ser748, which facilitates HTATSF1 interaction with TOPBP1, leading to RAD51 recruitment to DNA damage sites and promotion of homologous recombination (HR) repair; loss-of-function mutations in this axis increase HR deficiency.\",\n      \"method\": \"Phosphorylation assay, co-immunoprecipitation, HR repair assay, mutant cell lines, tumor data analysis\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — biochemical phosphorylation/interaction assay plus HR repair functional readout; single lab, two orthogonal methods\",\n      \"pmids\": [\"38762174\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"HTATSF1 positively regulates innate antiviral immune signaling: upon viral infection it promotes HECTD3-catalyzed K63-linked polyubiquitination of TRAF3 (enabling TBK1 recruitment and IRF3 activation) and independently promotes TAK1 recruitment to TRAF6 (activating the TAK1-IKK-NF-κB axis); HTATSF1-deficient mice show decreased cytokine production and increased mortality upon viral infection.\",\n      \"method\": \"Co-immunoprecipitation, ubiquitination assay, gene knockout (mouse and cell), cytokine measurement, viral infection model\",\n      \"journal\": \"Cell insight\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — co-IP and ubiquitination assays plus in vivo KO mouse phenotype; single lab, multiple orthogonal methods\",\n      \"pmids\": [\"41466838\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"Crystal structure of TopBP1 BRCT0-2 in complex with a phospho-HTATSF1 C-terminal peptide (at 1.9 Å resolution) reveals that TopBP1 cooperatively binds phosphorylated HTATSF1 through its BRCT1 and BRCT2 domains; key residue V158 in BRCT1 mediates specific hydrophobic contacts with the HTATSF1 ECT peptide, discriminating HTATSF1 from other phosphorylated ligands.\",\n      \"method\": \"X-ray crystallography (1.9 Å), mutagenesis, binding assays, AlphaFold3 modeling with biochemical validation\",\n      \"journal\": \"Biochemical and biophysical research communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — crystal structure with mutagenesis and binding validation; single lab but multiple orthogonal structural and biochemical methods\",\n      \"pmids\": [\"42251821\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"HTATSF1 is found in complex with SF3B1 and P-TEFb on chromatin, along with the splicing factor SNW1; SF3B1 inhibition does not cause nuclear export of HTATSF1 (unlike SNW1), indicating HTATSF1 remains chromatin-associated after SF3B1 perturbation and its role in coupling transcription and splicing is partially separable from SNW1.\",\n      \"method\": \"Co-immunoprecipitation, nuclear fractionation/localization, SF3B1 inhibitor treatment\",\n      \"journal\": \"bioRxiv\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single co-IP and fractionation from a preprint; HTATSF1 is not the primary focus of the study\",\n      \"pmids\": [],\n      \"is_preprint\": true\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"Computational simulations indicate TAT-SF1 acts as a 'molecular latch' maintaining the U2 snRNA branch-stem loop (BSL) in a supercoiled, high-energy 'loaded-spring' conformation; displacement of TAT-SF1 releases stored conformational energy that drives strand invasion for branch-site recognition during spliceosome assembly.\",\n      \"method\": \"All-atom and coarse-grained molecular dynamics simulations (computational only)\",\n      \"journal\": \"bioRxiv\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 4 / Weak — computational prediction only, no experimental validation; preprint\",\n      \"pmids\": [],\n      \"is_preprint\": true\n    }\n  ],\n  \"current_model\": \"HTATSF1/Tat-SF1 is a multifunctional RNA-binding and transcription-splicing factor that (1) stimulates RNA Pol II transcription elongation by associating with P-TEFb, DSIF/hSPT5, Paf1C, and TFIIF subunit RAP30; (2) promotes pre-mRNA splicing by binding U2 snRNP through a UHM–SF3b1 ULM interface (crystal-structure defined) and cooperating with the U2 snRNP to facilitate branch-site recognition; (3) regulates viral RNA biology, including modulating HIV-1 spliced/unspliced transcript ratios; (4) undergoes CK2-mediated phosphorylation at Ser748, enabling TOPBP1 recruitment and homologous recombination repair via RAD51 loading (structural basis defined by TopBP1 BRCT1/2 co-crystal); and (5) acts as a positive regulator of innate antiviral immunity by orchestrating HECTD3-dependent K63-ubiquitination of TRAF3 and TRAF6-TAK1 signaling.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"HTATSF1 (Tat-SF1) is a multifunctional nuclear RNA-binding protein that links RNA polymerase II transcription elongation to pre-mRNA splicing [#0, #6]. It was first identified as a cellular cofactor required for HIV-1 Tat-mediated stimulation of transcriptional elongation, containing two RNA recognition motifs and serving as a substrate of an associated cellular kinase [#0], and was subsequently shown to act as a general elongation factor rather than a strictly Tat-specific coactivator [#1]. Mechanistically, it associates with the RAP30 subunit of TFIIF and with hSPT5 [#3] and collaborates non-redundantly with DSIF (Spt4-Spt5) and the Paf1 complex to promote elongation, in a process dependent on P-TEFb-mediated phosphorylation of the Spt5 C-terminal region [#6]. In splicing, HTATSF1 functions through U2 snRNP: its yeast homolog CUS2 binds U2 snRNA and refolds it into an assembly-competent structure [#2], and the human protein engages the SF3b1 subunit of U2 snRNP through a U2AF homology motif (UHM)–ULM interface defined by high-resolution crystal structures [#9]. Depletion causes intron retention in short, GC-rich introns with weak 3' splice sites and impairs neural progenitor proliferation, establishing a developmental requirement for its splicing activity [#8]. Genome-wide analyses show it broadly activates transcript levels and independently regulates a distinct alternative-splicing program [#7]. Beyond gene expression, CK2 phosphorylates HTATSF1 at Ser748 to recruit TOPBP1 via its BRCT1/2 domains, loading RAD51 to drive homologous recombination repair [#10, #12], and HTATSF1 positively regulates innate antiviral immunity by promoting HECTD3-dependent K63-ubiquitination of TRAF3 and TAK1 recruitment to TRAF6 [#11]. In viral RNA biology it modulates the ratio of unspliced to spliced HIV-1 transcripts [#5] and stimulates influenza RNA synthesis by chaperoning nucleoprotein [#4].\",\n  \"teleology\": [\n    {\n      \"year\": 1996,\n      \"claim\": \"Established HTATSF1 as a discrete cellular factor needed for HIV-1 Tat-stimulated transcription elongation, defining its first molecular role and RNA-binding architecture.\",\n      \"evidence\": \"cDNA cloning with in vitro reconstituted transcription, complementation, and kinase substrate assay\",\n      \"pmids\": [\"8849451\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not distinguish Tat-specific from general elongation roles\", \"Identity of the associated kinase unresolved\", \"No direct RNA target defined\"]\n    },\n    {\n      \"year\": 1998,\n      \"claim\": \"Reframed HTATSF1 as a general elongation factor rather than a Tat-only coactivator, broadening its mechanistic relevance to host transcription.\",\n      \"evidence\": \"protein-affinity chromatography and in vitro transcription elongation assay\",\n      \"pmids\": [\"9765201\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Identity of the required AIEF factor undefined\", \"No in vivo confirmation\"]\n    },\n    {\n      \"year\": 1998,\n      \"claim\": \"Revealed a conserved splicing function through the yeast homolog CUS2, linking HTATSF1 to U2 snRNA folding and SF3a/SF3b association prior to spliceosome assembly.\",\n      \"evidence\": \"suppressor screen, co-IP, in vitro RNA binding, RRM mutagenesis; human SF3a66 co-IP\",\n      \"pmids\": [\"9710584\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Human splicing role inferred largely from yeast\", \"Direct human U2 binding interface not yet mapped\"]\n    },\n    {\n      \"year\": 1999,\n      \"claim\": \"Identified direct physical partners in the transcription machinery (TFIIF RAP30 and hSPT5), providing a recruitment mechanism for elongation control.\",\n      \"evidence\": \"co-IP, immunodepletion/recombinant complementation, in vivo overexpression\",\n      \"pmids\": [\"10454543\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Structural basis of RAP30/hSPT5 contacts undefined\", \"Stoichiometry of the complex unknown\"]\n    },\n    {\n      \"year\": 2007,\n      \"claim\": \"Extended HTATSF1 function to influenza RNA synthesis via chaperoning of free nucleoprotein, indicating a role in viral RNP assembly.\",\n      \"evidence\": \"yeast replicon system, genome-wide deletion screen, co-IP, RNA-NP complex assay\",\n      \"pmids\": [\"17991777\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Mechanism of NP chaperoning not structurally defined\", \"Single study\"]\n    },\n    {\n      \"year\": 2009,\n      \"claim\": \"Resolved the HIV-1 role as post-transcriptional, showing depletion shifts the unspliced/spliced transcript ratio rather than blocking LTR transcription.\",\n      \"evidence\": \"shRNA knockdown in two cell lines, RT-PCR of transcript ratios, infectivity assay\",\n      \"pmids\": [\"19479034\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Contradicts earlier in vitro elongation reconstitution\", \"Direct splicing mechanism on HIV RNA not mapped\"]\n    },\n    {\n      \"year\": 2009,\n      \"claim\": \"Defined HTATSF1's non-redundant cooperation with DSIF and Paf1C and dependence on P-TEFb, integrating it into the elongation control circuit at a model gene.\",\n      \"evidence\": \"activity-based fractionation, ChIP at FOS, in vitro elongation, P-TEFb inhibition\",\n      \"pmids\": [\"19952111\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Generality beyond FOS not established here\", \"Order of recruitment events partly inferred\"]\n    },\n    {\n      \"year\": 2011,\n      \"claim\": \"Genome-wide analysis showed transcription-activating and alternative-splicing functions are largely separable, arguing HTATSF1 does not obligately couple the two processes cellularly.\",\n      \"evidence\": \"RNAi knockdown, exon-array, bioinformatics\",\n      \"pmids\": [\"21282347\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Mechanistic basis for two separable functions unexplained\", \"Single primary method\"]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"In vivo Drosophila genetics defined the splicing substrate class (short, GC-rich, weak 3' splice site introns) and a developmental requirement in neural progenitors.\",\n      \"evidence\": \"Drosophila loss-of-function, co-IP with U2 snRNP, RNA-seq splicing analysis\",\n      \"pmids\": [\"28935704\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether human introns share the same features not directly tested\", \"Direct vs indirect splicing effects not fully separated\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Provided the structural basis for U2 snRNP engagement, defining the UHM–ULM interface with SF3b1 at atomic resolution and mutual regulation of protein levels.\",\n      \"evidence\": \"X-ray crystallography (1.1–2.1 Å), UHM mutagenesis, binding affinity, RNAi\",\n      \"pmids\": [\"30567737\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Functional consequence of disrupting interface in cells not exhaustively tested\", \"Role within the assembling spliceosome not visualized\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Uncovered a DNA repair function: CK2 phosphorylation at Ser748 recruits TOPBP1 to load RAD51 and promote homologous recombination.\",\n      \"evidence\": \"phosphorylation assay, co-IP, HR repair assay, mutant cells, tumor data\",\n      \"pmids\": [\"38762174\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"How a splicing/transcription factor accesses damage sites unclear\", \"Single lab\"]\n    },\n    {\n      \"year\": 2026,\n      \"claim\": \"Defined the structural basis of TOPBP1 recognition, showing cooperative BRCT1/BRCT2 binding of phospho-HTATSF1 with V158 conferring ligand specificity.\",\n      \"evidence\": \"X-ray crystallography (1.9 Å), mutagenesis, binding assays, AlphaFold3 modeling\",\n      \"pmids\": [\"42251821\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"In-cell validation of V158-dependent specificity limited\", \"Integration with full HR machinery not shown\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Established HTATSF1 as a positive regulator of innate antiviral immunity via HECTD3-dependent K63-ubiquitination of TRAF3 and TAK1-TRAF6 signaling, with an in vivo survival phenotype.\",\n      \"evidence\": \"co-IP, ubiquitination assays, mouse and cell knockouts, cytokine and viral infection models\",\n      \"pmids\": [\"41466838\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Relationship between immune role and nuclear RNA functions unclear\", \"Direct vs scaffolding role in ubiquitination not fully separated\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How HTATSF1's distinct activities — elongation, U2-dependent splicing, HR repair, and antiviral signaling — are coordinated or partitioned within a single protein remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No unified model linking nuclear RNA roles to repair and immune functions\", \"Domain-level partitioning of the four activities undefined\", \"Regulatory cues switching between functions unknown\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0003723\", \"supporting_discovery_ids\": [0, 2]},\n      {\"term_id\": \"GO:0060090\", \"supporting_discovery_ids\": [3, 9]},\n      {\"term_id\": \"GO:0140110\", \"supporting_discovery_ids\": [0, 6]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [6, 8]},\n      {\"term_id\": \"GO:0000228\", \"supporting_discovery_ids\": [6]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-74160\", \"supporting_discovery_ids\": [0, 6]},\n      {\"term_id\": \"R-HSA-8953854\", \"supporting_discovery_ids\": [2, 9]},\n      {\"term_id\": \"R-HSA-73894\", \"supporting_discovery_ids\": [10, 12]},\n      {\"term_id\": \"R-HSA-168256\", \"supporting_discovery_ids\": [11]}\n    ],\n    \"complexes\": [\"U2 snRNP\", \"P-TEFb-associated elongation complex\"],\n    \"partners\": [\"SF3B1\", \"SUPT5H\", \"GTF2F2\", \"TOPBP1\", \"HECTD3\", \"TRAF3\", \"TRAF6\", \"PRPF11\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":8,"faith_total":8,"faith_pct":100.0}}