{"gene":"TAF1B","run_date":"2026-04-28T21:42:58","timeline":{"discoveries":[{"year":1992,"finding":"SL1 (the RNA polymerase I promoter selectivity factor) is a multisubunit complex containing TBP (TATA-binding protein) and three distinct TBP-associated factors (TAFIs), including TAF1B (TAFI48). Purified TAFIs reconstituted with recombinant TBP complement SL1 transcriptional activity, demonstrating TBP plus novel associated factors are integral components of SL1.","method":"Column chromatography, glycerol gradient sedimentation, antibody depletion, reconstitution assay","journal":"Cell","confidence":"High","confidence_rationale":"Tier 1 — biochemical reconstitution with functional validation, foundational paper with 390 citations","pmids":["1547496"],"is_preprint":false},{"year":1994,"finding":"TAF1B (TAFI48), along with TAFI110 and TAFI63, can each bind individually and specifically to TBP and interact with each other to form a stable TBP-TAF complex. TAFIs from SL1 and TFIID show mutually exclusive binding specificity for TBP, directing formation of polymerase-selective TBP-TAF complexes.","method":"Subunit interaction analysis, recombinant protein binding assays","journal":"Science","confidence":"High","confidence_rationale":"Tier 1 — reconstitution with mutagenesis-equivalent domain analysis, 133 citations","pmids":["7801123"],"is_preprint":false},{"year":1994,"finding":"TAF1B (TAFI48), together with TAFI110, TAFI63, and TBP, is necessary and sufficient to reconstitute a transcriptionally active SL1 complex capable of directing accurate RNA polymerase I transcription from the human ribosomal RNA gene promoter.","method":"In vivo and in vitro assembly of recombinant SL1 subunits, reconstituted transcription assay","journal":"Science","confidence":"High","confidence_rationale":"Tier 1 — full reconstitution of functional complex, 131 citations","pmids":["7801130"],"is_preprint":false},{"year":1994,"finding":"The conserved core domain of TBP is sufficient to assemble with Pol I-specific TAFs (including TAF1B/TAFI48) to form a functional SL1 complex; TBP directly interacts with TAFI48 in an in vitro protein-protein interaction assay.","method":"Immunopurification of epitope-tagged TBP constructs, in vitro protein-protein interaction assay, in vitro transcription","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"High","confidence_rationale":"Tier 1 — direct interaction assay combined with functional reconstitution","pmids":["8058785"],"is_preprint":false},{"year":1997,"finding":"Murine TAFIs (including the TAF1B ortholog) can form stable chimeric complexes with human TBP and TAFIs, demonstrating evolutionarily conserved protein-protein interactions among SL1 subunits responsible for complex assembly.","method":"cDNA cloning, sequence analysis, chimeric complex assembly assay","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"Medium","confidence_rationale":"Tier 2 — biochemical complex assembly with functional implication, single study","pmids":["9050847"],"is_preprint":false},{"year":1997,"finding":"SV40 large T antigen directly binds to SL1 subunits TBP, TAF1B (TAFI48), and TAFI110, and this interaction with SL1 is required for large T antigen stimulation of RNA Pol I transcription.","method":"Immunoprecipitation in vitro and in SV40-infected cells, large T antigen deletion mutant transcription assays","journal":"Genes & development","confidence":"High","confidence_rationale":"Tier 2 — reciprocal co-IP with functional validation using deletion mutants, 53 citations","pmids":["9203586"],"is_preprint":false},{"year":1998,"finding":"SL1 (including TAF1B as a subunit) is inactivated by cdc2/cyclin B-directed phosphorylation during mitosis, resulting in repression of RNA Pol I transcription; phosphorylation impairs the interaction of SL1 with UBF.","method":"Cell-free transcription system, mitotic kinase phosphorylation assay, protein-protein interaction studies","journal":"The EMBO journal","confidence":"High","confidence_rationale":"Tier 1–2 — reconstituted cell-free system, kinase assay, protein interaction, replicated by Kuhn et al. 1998","pmids":["9857193","9811537"],"is_preprint":false},{"year":1999,"finding":"SL1 is recruited to the rRNA gene promoter through direct protein-protein interaction with the carboxy-terminal activation domain of UBF; this recruitment is regulated by UBF phosphorylation, as dephosphorylation of UBF abolishes UBF-SL1 interaction and transcriptional activation.","method":"Protein-protein interaction assays with UBF deletion mutants, alkaline phosphatase treatment, DNase I footprinting, in vitro transcription reconstitution","journal":"Molecular and cellular biology","confidence":"High","confidence_rationale":"Tier 1 — multiple orthogonal methods including interaction assay, footprinting, and reconstituted transcription","pmids":["10082553"],"is_preprint":false},{"year":2000,"finding":"Retinoblastoma protein (Rb) directly interacts with UBF and blocks the interaction between UBF and SL1 (using TAF1B/TAFI48 as a marker for SL1), thereby repressing RNA Pol I transcription.","method":"Direct protein interaction assays, DNase footprinting, band-shift assays","journal":"Oncogene","confidence":"Medium","confidence_rationale":"Tier 2 — direct interaction and footprinting assays, single lab","pmids":["11042686"],"is_preprint":false},{"year":2001,"finding":"TAF1B (TAFI68/TAF(I)68) is acetylated by PCAF (p300/CBP-associated factor), and this acetylation enhances binding of TAF1B to the rDNA promoter and stimulates RNA Pol I transcription; the NAD+-dependent deacetylase mSir2a deacetylates TAF1B and represses Pol I transcription.","method":"In vitro acetylation assay, promoter binding assay, reconstituted in vitro transcription system, deacetylation assay","journal":"The EMBO journal","confidence":"High","confidence_rationale":"Tier 1 — in vitro enzymatic assay with writer/eraser identification and functional transcription readout","pmids":["11250901"],"is_preprint":false},{"year":2001,"finding":"hRRN3 directly interacts with TAF1B (TAF(I)63) and TAF(I)110 of SL1, and this interaction is essential for recruitment of initiation-competent RNA Pol I to the rDNA promoter; blocking this connection prevents Pol I recruitment.","method":"Co-immunoprecipitation, direct interaction assay, chromatin recruitment assay","journal":"The EMBO journal","confidence":"High","confidence_rationale":"Tier 2 — direct interaction and recruitment assay with functional blockade experiment, 154 citations","pmids":["11250903"],"is_preprint":false},{"year":2005,"finding":"PTEN represses RNA Pol I transcription by inducing dissociation of SL1 subunits (including TAF1B) and reducing their occupancy on the rRNA gene promoter, independent of effects on SL1 expression levels.","method":"Chromatin immunoprecipitation (ChIP), co-immunoprecipitation, in vitro transcription","journal":"Molecular and cellular biology","confidence":"Medium","confidence_rationale":"Tier 2 — ChIP and co-IP with functional transcription assay, single lab","pmids":["16055704"],"is_preprint":false},{"year":2005,"finding":"Human SL1 (containing TAF1B) can direct accurate Pol I transcription in the absence of UBF and interacts with the rDNA promoter independently and stably; SL1 significantly reduces the rate of UBF dissociation from the rDNA promoter, indicating a role in stabilizing UBF at the promoter.","method":"In vitro transcription reconstitution, promoter binding/dissociation assays","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1 — in vitro reconstitution with kinetic analysis","pmids":["15970593"],"is_preprint":false},{"year":2006,"finding":"Protein kinase CK2 co-immunoprecipitates with the Pol I complex, is associated with the rRNA gene promoter, and stimulates Pol I transcription by phosphorylating the C-terminus of UBF, which counteracts inhibitory HMG box domains and stabilizes the UBF-SL1 interaction.","method":"Co-immunoprecipitation, ChIP, kinase assay, in vitro transcription with immobilized templates","journal":"Nucleic acids research","confidence":"Medium","confidence_rationale":"Tier 2 — multiple methods, single lab","pmids":["16971462"],"is_preprint":false},{"year":2007,"finding":"TAF(I)41 (MGC5306) is a novel component of SL1 that co-purifies and co-immunoprecipitates with SL1, resides at the rDNA promoter in the nucleolus, and is required for Pol I transcription and for stable SL1 occupancy at the rDNA promoter in vivo.","method":"Co-purification, co-immunoprecipitation, immunodepletion, siRNA knockdown, Pol I transcription assay","journal":"The EMBO journal","confidence":"High","confidence_rationale":"Tier 2 — multiple orthogonal methods with functional rescue, 78 citations","pmids":["17318177"],"is_preprint":false},{"year":2011,"finding":"TAF1B is structurally related to TFIIB/TFIIB-like proteins through predicted N-terminal zinc ribbon and cyclin-like fold domains, and SL1 has an essential post-polymerase recruitment role operating through TAF1B, identifying TAF1B as the TFIIB-like factor of the Pol I transcription machinery.","method":"Bioinformatic structural prediction, domain swap experiments, functional complementation assays","journal":"Science","confidence":"High","confidence_rationale":"Tier 1–2 — structural homology with functional domain swap validation, confirmed in parallel by Knutson & Hahn 2011","pmids":["21921199","21921198"],"is_preprint":false},{"year":2014,"finding":"All four human TAFI subunits of SL1 (including TAF1B) are necessary and sufficient to reconstitute human rRNA gene transcription in mouse cells, overcoming the species-specificity barrier; chimeric human-mouse TAFI complexes could be formed but were transcriptionally inactive.","method":"Ectopic expression in mouse cells, sensitive Pol I transcription monitoring system using influenza RNA polymerase reporter, chimeric complex assembly","journal":"Journal of cell science","confidence":"High","confidence_rationale":"Tier 1 — functional reconstitution in trans-species system with rigorous controls","pmids":["24928901"],"is_preprint":false},{"year":2015,"finding":"The pSER domain of AF4 family proteins (component of AEP complex) associates with SL1 on chromatin and facilitates TBP loading onto the promoter to initiate RNA Pol II-dependent transcription; MLL-AEP fusion proteins activate transcription initiation through SL1.","method":"Chromatin immunoprecipitation, co-immunoprecipitation, in vitro transcription","journal":"Nature communications","confidence":"Medium","confidence_rationale":"Tier 2 — ChIP and co-IP with functional assay, single study","pmids":["26593443"],"is_preprint":false},{"year":2022,"finding":"Conditional deletion of TAF1B (a subunit of SL1) causes striking depletion of UBTF at both rDNA promoters but not elsewhere across the rDNA, demonstrating that SL1-TAF1B cooperates with UBTF1 splice variant to provide specificity for rDNA promoter recognition in vivo.","method":"Conditional gene deletion (knockout), ChIP, fluorescence microscopy","journal":"PLoS genetics","confidence":"High","confidence_rationale":"Tier 2 — conditional knockout with ChIP demonstrating specific promoter effect","pmids":["35139074"],"is_preprint":false},{"year":2023,"finding":"TAF1B depletion in hepatocellular carcinoma cells disrupts the SL1 pre-initiation complex (verified by co-IP and ChIP), inhibits rDNA transcription, induces nucleolar stress, and triggers apoptosis through a p53-miR-101 positive and negative feedback circuit.","method":"Lentiviral knockdown, co-immunoprecipitation, ChIP, immunofluorescence, FISH, qRT-PCR, apoptosis assays, xenograft tumor model","journal":"Frontiers in oncology","confidence":"Medium","confidence_rationale":"Tier 2 — multiple methods with in vivo validation, single lab","pmids":["37645431"],"is_preprint":false},{"year":2000,"finding":"Human TAF1B gene is localized to chromosome 2p25 as a single copy gene; the gene is transcribed into multiple RNA species that could produce variant SL1 isoforms.","method":"Somatic cell hybrid panel analysis, radiation hybrid panel analysis, FISH, Northern analysis","journal":"Cytogenetics and cell genetics","confidence":"Low","confidence_rationale":"Tier 3 — chromosomal mapping and RNA characterization, no direct functional mechanism","pmids":["10894955"],"is_preprint":false}],"current_model":"TAF1B is a TFIIB-related subunit of the human RNA Pol I basal transcription factor SL1 (a complex of TBP and TAFIs including TAF1B/TAFI48, TAFI63/TAF1A, and TAFI110/TAF1C), where it is necessary and sufficient with the other TAFIs and TBP to reconstitute Pol I pre-initiation complex formation at the rDNA promoter; TAF1B can be acetylated by PCAF (activating rDNA binding and transcription) or deacetylated by mSir2a (repressing transcription), the entire SL1 complex is inactivated by cdc2/cyclin B phosphorylation during mitosis, and TAF1B mediates an essential post-polymerase recruitment function analogous to TFIIB in Pol II transcription."},"narrative":{"teleology":[{"year":1992,"claim":"Identification of TAF1B as a novel TBP-associated factor within SL1 established that Pol I promoter selectivity depends on a distinct multisubunit TBP-TAF complex, not TBP alone.","evidence":"Chromatographic purification and reconstitution of SL1 transcriptional activity from separated TAFIs plus recombinant TBP","pmids":["1547496"],"confidence":"High","gaps":["Individual contributions of each TAFI subunit to promoter recognition were undefined","Structural basis for polymerase selectivity of TBP-TAF complexes unknown"]},{"year":1994,"claim":"Demonstration that TAF1B directly binds TBP and other TAFIs, and that all four subunits reconstitute transcriptionally active SL1, resolved the minimal composition of the Pol I selectivity factor.","evidence":"Recombinant protein binding assays and full reconstitution of accurate Pol I transcription from purified components","pmids":["7801123","7801130","8058785"],"confidence":"High","gaps":["Stoichiometry of the SL1 complex was not determined","Mechanism by which SL1 recruits Pol I was unknown"]},{"year":1998,"claim":"Discovering that cdc2/cyclin B phosphorylation inactivates SL1 and impairs UBF–SL1 interaction explained how ribosomal gene transcription is silenced during mitosis.","evidence":"Cell-free Pol I transcription with mitotic kinase treatment and UBF–SL1 interaction assays","pmids":["9857193","9811537"],"confidence":"High","gaps":["Which specific SL1 subunit(s) are phosphorylated was not fully resolved","Phosphatase responsible for reactivation at mitotic exit not identified"]},{"year":1999,"claim":"Mapping UBF's C-terminal activation domain as the SL1-interacting surface, and showing phosphorylation-dependence of this interaction, established UBF as a regulated recruiter of SL1 to the rDNA promoter.","evidence":"Protein interaction assays with UBF deletion mutants, phosphatase treatment, DNase I footprinting, and reconstituted transcription","pmids":["10082553"],"confidence":"High","gaps":["Specific SL1 subunit(s) contacting UBF not identified at residue resolution","Role of CK2 in UBF phosphorylation for SL1 interaction not yet tested"]},{"year":2001,"claim":"Identification of PCAF-mediated acetylation as an activator and mSir2a-mediated deacetylation as a repressor of TAF1B established a reversible post-translational switch controlling Pol I transcription output.","evidence":"In vitro acetylation/deacetylation assays with promoter binding and reconstituted transcription readouts","pmids":["11250901"],"confidence":"High","gaps":["Acetylation sites on TAF1B not mapped to specific residues","In vivo acetylation dynamics under growth signaling not characterized"]},{"year":2001,"claim":"Showing that hRRN3 directly interacts with SL1 subunits (TAF1B and TAF1C) to recruit initiation-competent Pol I defined the bridging mechanism linking promoter-bound SL1 to the polymerase.","evidence":"Co-immunoprecipitation, direct interaction assay, and chromatin recruitment blockade experiment","pmids":["11250903"],"confidence":"High","gaps":["Whether TAF1B or TAF1C is the primary hRRN3 contact not resolved","Structural basis for hRRN3–SL1 interaction unknown"]},{"year":2005,"claim":"Demonstrating that SL1 can direct accurate Pol I transcription without UBF and stabilizes UBF at the promoter revised the view of SL1 from a purely UBF-dependent factor to an independent promoter-binding entity with cooperative function.","evidence":"In vitro transcription reconstitution and kinetic promoter dissociation assays","pmids":["15970593"],"confidence":"High","gaps":["How SL1 recognizes the core promoter independently of UBF was structurally undefined"]},{"year":2011,"claim":"Establishing TAF1B as the structural and functional homolog of TFIIB — with conserved zinc ribbon and cyclin folds and a post-polymerase recruitment role — unified Pol I and Pol II pre-initiation complex architecture.","evidence":"Bioinformatic structural prediction combined with domain swap and functional complementation assays; confirmed independently by two groups","pmids":["21921199","21921198"],"confidence":"High","gaps":["High-resolution structure of TAF1B in the Pol I PIC not available","Whether the zinc ribbon directly contacts rDNA not tested"]},{"year":2014,"claim":"Showing that all four human TAFIs overcome species-specificity when expressed in mouse cells, while chimeric human-mouse TAFI complexes fail, demonstrated that TAF1B functions within a tightly co-evolved subunit ensemble.","evidence":"Ectopic expression of human TAFIs in mouse cells with reporter-based Pol I transcription monitoring","pmids":["24928901"],"confidence":"High","gaps":["Molecular determinants of species-specific incompatibility not mapped","Whether TAF1D is essential in the reconstituted system not fully addressed"]},{"year":2022,"claim":"Conditional deletion of TAF1B in vivo revealed that SL1 is required to maintain UBTF occupancy specifically at rDNA promoters, establishing TAF1B as a specificity determinant that restricts UBTF1 function to promoter elements.","evidence":"Conditional gene deletion with ChIP and fluorescence microscopy in mouse cells","pmids":["35139074"],"confidence":"High","gaps":["Whether TAF1B loss affects other chromatin marks at rDNA beyond UBTF occupancy not assessed","Downstream consequences of TAF1B loss on nucleolar structure were not fully characterized in this study"]},{"year":2023,"claim":"TAF1B depletion in hepatocellular carcinoma cells induces nucleolar stress and p53-dependent apoptosis, linking SL1 integrity to cancer cell survival and identifying a potential vulnerability.","evidence":"Lentiviral knockdown, co-IP, ChIP, apoptosis assays, and xenograft tumor model","pmids":["37645431"],"confidence":"Medium","gaps":["Whether the apoptotic response is specific to TAF1B loss versus general rDNA transcription inhibition not distinguished","Relevance to non-hepatic tumor types not tested"]},{"year":null,"claim":"A high-resolution cryo-EM or crystal structure of TAF1B within the human Pol I pre-initiation complex is needed to define its contacts with the rDNA template, Pol I, and hRRN3, and to clarify how acetylation modulates promoter binding at the atomic level.","evidence":"","pmids":[],"confidence":"High","gaps":["No atomic-resolution structure of TAF1B or human SL1 in a PIC context","Acetylation site mapping and structural consequences unresolved","In vivo dynamics of SL1 assembly/disassembly during cell cycle and growth signaling remain poorly characterized"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0140110","term_label":"transcription regulator activity","supporting_discovery_ids":[0,2,15]},{"term_id":"GO:0003677","term_label":"DNA binding","supporting_discovery_ids":[9,12]},{"term_id":"GO:0005198","term_label":"structural molecule activity","supporting_discovery_ids":[1,15]}],"localization":[{"term_id":"GO:0005730","term_label":"nucleolus","supporting_discovery_ids":[14,18]},{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[0,14]}],"pathway":[{"term_id":"R-HSA-74160","term_label":"Gene expression (Transcription)","supporting_discovery_ids":[0,2,9,12,15]},{"term_id":"R-HSA-1640170","term_label":"Cell Cycle","supporting_discovery_ids":[6]}],"complexes":["SL1 (Selectivity Factor 1)"],"partners":["TBP","TAF1A","TAF1C","TAF1D","UBTF","RRN3","KAT2B"],"other_free_text":[]},"mechanistic_narrative":"TAF1B is a TFIIB-related subunit of the RNA polymerase I selectivity factor SL1 that functions as a core component of the Pol I pre-initiation complex at ribosomal DNA promoters, playing an essential role in rRNA gene transcription. TAF1B assembles with TBP and the other TAF_I subunits (TAF1A, TAF1C, TAF1D) to form the SL1 complex, which binds the rDNA promoter both independently and cooperatively with UBF, stabilizing UBF occupancy and recruiting initiation-competent Pol I via interaction with hRRN3 [PMID:1547496, PMID:7801130, PMID:15970593, PMID:11250903]. Structurally homologous to TFIIB through N-terminal zinc ribbon and cyclin-like fold domains, TAF1B fulfills an essential post-polymerase recruitment function analogous to TFIIB in Pol II transcription [PMID:21921199]. TAF1B activity is regulated by PCAF-mediated acetylation, which enhances rDNA promoter binding and stimulates transcription, by mSir2a-mediated deacetylation, which represses transcription, and by cdc2/cyclin B phosphorylation of SL1 during mitosis, which inactivates the complex [PMID:11250901, PMID:9857193]."},"prefetch_data":{"uniprot":{"accession":"Q53T94","full_name":"TATA box-binding protein-associated factor RNA polymerase I subunit B","aliases":["RNA polymerase I-specific TBP-associated factor 63 kDa","TAFI63","TATA box-binding protein-associated factor 1B","TBP-associated factor 1B","Transcription initiation factor SL1/TIF-IB subunit B"],"length_aa":588,"mass_kda":68.8,"function":"Component of RNA polymerase I core factor complex that acts as a GTF2B/TFIIB-like factor and plays a key role in multiple steps during transcription initiation such as pre-initiation complex (PIC) assembly and postpolymerase recruitment events in polymerase I (Pol I) transcription. Binds rDNA promoters and plays a role in Pol I recruitment as a component of the SL1/TIF-IB complex and, possibly, directly through its interaction with RRN3","subcellular_location":"Nucleus, nucleolus","url":"https://www.uniprot.org/uniprotkb/Q53T94/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":true,"resolved_as":"","url":"https://depmap.org/portal/gene/TAF1B","classification":"Common Essential","n_dependent_lines":1046,"n_total_lines":1208,"dependency_fraction":0.8658940397350994},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[{"gene":"PSMG1","stoichiometry":0.2},{"gene":"TBP","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/search/TAF1B","total_profiled":1310},"omim":[{"mim_id":"612823","title":"TATA BOX-BINDING PROTEIN-ASSOCIATED FACTOR 1D; TAF1D","url":"https://www.omim.org/entry/612823"},{"mim_id":"610770","title":"NOC2-LIKE NUCLEOLAR-ASSOCIATED TRANSCRIPTIONAL REPRESSOR; NOC2L","url":"https://www.omim.org/entry/610770"},{"mim_id":"609518","title":"THAP DOMAIN-CONTAINING PROTEIN 7; THAP7","url":"https://www.omim.org/entry/609518"},{"mim_id":"604905","title":"TATA BOX-BINDING PROTEIN-ASSOCIATED FACTOR 1C; TAF1C","url":"https://www.omim.org/entry/604905"},{"mim_id":"604904","title":"TATA BOX-BINDING PROTEIN-ASSOCIATED FACTOR 1B; TAF1B","url":"https://www.omim.org/entry/604904"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Supported","locations":[{"location":"Nucleoli","reliability":"Supported"},{"location":"Nucleoplasm","reliability":"Additional"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/TAF1B"},"hgnc":{"alias_symbol":["TAFI63","SL1","RAF1B","RAFI63"],"prev_symbol":[]},"alphafold":{"accession":"Q53T94","domains":[{"cath_id":"2.20.25","chopping":"2-42","consensus_level":"medium","plddt":77.592,"start":2,"end":42},{"cath_id":"-","chopping":"73-122_191-291","consensus_level":"medium","plddt":92.4129,"start":73,"end":291},{"cath_id":"-","chopping":"299-415_493-576","consensus_level":"medium","plddt":87.702,"start":299,"end":576}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q53T94","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q53T94-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q53T94-F1-predicted_aligned_error_v6.png","plddt_mean":78.69},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=TAF1B","jax_strain_url":"https://www.jax.org/strain/search?query=TAF1B"},"sequence":{"accession":"Q53T94","fasta_url":"https://rest.uniprot.org/uniprotkb/Q53T94.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q53T94/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q53T94"}},"corpus_meta":[{"pmid":"1547496","id":"PMC_1547496","title":"The TATA-binding protein and associated factors are integral components of the RNA polymerase I transcription factor, SL1.","date":"1992","source":"Cell","url":"https://pubmed.ncbi.nlm.nih.gov/1547496","citation_count":390,"is_preprint":false},{"pmid":"3413483","id":"PMC_3413483","title":"Functional cooperativity between transcription factors UBF1 and SL1 mediates human ribosomal RNA synthesis.","date":"1988","source":"Science (New York, N.Y.)","url":"https://pubmed.ncbi.nlm.nih.gov/3413483","citation_count":323,"is_preprint":false},{"pmid":"16166714","id":"PMC_16166714","title":"Clostridium carboxidivorans sp. nov., a solvent-producing clostridium isolated from an agricultural settling lagoon, and reclassification of the acetogen Clostridium scatologenes strain SL1 as Clostridium drakei sp. nov.","date":"2005","source":"International journal of systematic and evolutionary microbiology","url":"https://pubmed.ncbi.nlm.nih.gov/16166714","citation_count":174,"is_preprint":false},{"pmid":"11250901","id":"PMC_11250901","title":"Acetylation of TAF(I)68, a subunit of TIF-IB/SL1, activates RNA polymerase I transcription.","date":"2001","source":"The EMBO journal","url":"https://pubmed.ncbi.nlm.nih.gov/11250901","citation_count":162,"is_preprint":false},{"pmid":"11250903","id":"PMC_11250903","title":"hRRN3 is essential in the SL1-mediated recruitment of RNA Polymerase I to rRNA gene promoters.","date":"2001","source":"The EMBO journal","url":"https://pubmed.ncbi.nlm.nih.gov/11250903","citation_count":154,"is_preprint":false},{"pmid":"7801123","id":"PMC_7801123","title":"Reconstitution of transcription factor SL1: exclusive binding of TBP by SL1 or TFIID subunits.","date":"1994","source":"Science (New York, N.Y.)","url":"https://pubmed.ncbi.nlm.nih.gov/7801123","citation_count":133,"is_preprint":false},{"pmid":"7801130","id":"PMC_7801130","title":"Assembly of transcriptionally active RNA polymerase I initiation factor SL1 from recombinant subunits.","date":"1994","source":"Science (New York, N.Y.)","url":"https://pubmed.ncbi.nlm.nih.gov/7801130","citation_count":131,"is_preprint":false},{"pmid":"9857193","id":"PMC_9857193","title":"Mitotic silencing of human rRNA synthesis: inactivation of the promoter selectivity factor SL1 by cdc2/cyclin B-mediated phosphorylation.","date":"1998","source":"The EMBO journal","url":"https://pubmed.ncbi.nlm.nih.gov/9857193","citation_count":130,"is_preprint":false},{"pmid":"8609157","id":"PMC_8609157","title":"In vivo evidence that TATA-binding protein/SL1 colocalizes with UBF and RNA polymerase I when rRNA synthesis is either active or inactive.","date":"1996","source":"The Journal of cell biology","url":"https://pubmed.ncbi.nlm.nih.gov/8609157","citation_count":128,"is_preprint":false},{"pmid":"11042686","id":"PMC_11042686","title":"Rb and p130 regulate RNA polymerase I transcription: Rb disrupts the interaction between UBF and SL-1.","date":"2000","source":"Oncogene","url":"https://pubmed.ncbi.nlm.nih.gov/11042686","citation_count":110,"is_preprint":false},{"pmid":"16055704","id":"PMC_16055704","title":"PTEN represses RNA Polymerase I transcription by disrupting the SL1 complex.","date":"2005","source":"Molecular and cellular biology","url":"https://pubmed.ncbi.nlm.nih.gov/16055704","citation_count":86,"is_preprint":false},{"pmid":"7926733","id":"PMC_7926733","title":"The RSRF/MEF2 protein SL1 regulates cardiac muscle-specific transcription of a myosin light-chain gene in Xenopus embryos.","date":"1994","source":"Genes & development","url":"https://pubmed.ncbi.nlm.nih.gov/7926733","citation_count":84,"is_preprint":false},{"pmid":"10082553","id":"PMC_10082553","title":"Recruitment of TATA-binding protein-TAFI complex SL1 to the human ribosomal DNA promoter is mediated by the carboxy-terminal activation domain of upstream binding factor (UBF) and is regulated by UBF phosphorylation.","date":"1999","source":"Molecular and cellular biology","url":"https://pubmed.ncbi.nlm.nih.gov/10082553","citation_count":79,"is_preprint":false},{"pmid":"17318177","id":"PMC_17318177","title":"A novel TBP-associated factor of SL1 functions in RNA polymerase I transcription.","date":"2007","source":"The EMBO journal","url":"https://pubmed.ncbi.nlm.nih.gov/17318177","citation_count":78,"is_preprint":false},{"pmid":"8349617","id":"PMC_8349617","title":"Cell type-specific regulation of SL-1 and SL-2 genes. Induction of the SL-2 gene but not the SL-1 gene by human keratinocytes in response to cytokines and phorbolesters.","date":"1993","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/8349617","citation_count":78,"is_preprint":false},{"pmid":"15970593","id":"PMC_15970593","title":"TBP-TAF complex SL1 directs RNA polymerase I pre-initiation complex formation and stabilizes upstream binding factor at the rDNA promoter.","date":"2005","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/15970593","citation_count":72,"is_preprint":false},{"pmid":"9050847","id":"PMC_9050847","title":"Cloning of murine RNA polymerase I-specific TAF factors: conserved interactions between the subunits of the species-specific transcription initiation factor TIF-IB/SL1.","date":"1997","source":"Proceedings of the National Academy of Sciences of the United States of America","url":"https://pubmed.ncbi.nlm.nih.gov/9050847","citation_count":71,"is_preprint":false},{"pmid":"12559920","id":"PMC_12559920","title":"Structure of the intact stem and bulge of HIV-1 Psi-RNA stem-loop SL1.","date":"2003","source":"Journal of molecular biology","url":"https://pubmed.ncbi.nlm.nih.gov/12559920","citation_count":63,"is_preprint":false},{"pmid":"21921198","id":"PMC_21921198","title":"Yeast Rrn7 and human TAF1B are TFIIB-related RNA polymerase I general transcription factors.","date":"2011","source":"Science (New York, N.Y.)","url":"https://pubmed.ncbi.nlm.nih.gov/21921198","citation_count":62,"is_preprint":false},{"pmid":"10758858","id":"PMC_10758858","title":"Clostridium scatologenes strain SL1 isolated as an acetogenic bacterium from acidic sediments.","date":"2000","source":"International journal of systematic and evolutionary microbiology","url":"https://pubmed.ncbi.nlm.nih.gov/10758858","citation_count":60,"is_preprint":false},{"pmid":"9203586","id":"PMC_9203586","title":"SV40 large T antigen binds to the TBP-TAF(I) complex SL1 and coactivates ribosomal RNA transcription.","date":"1997","source":"Genes & development","url":"https://pubmed.ncbi.nlm.nih.gov/9203586","citation_count":53,"is_preprint":false},{"pmid":"8264628","id":"PMC_8264628","title":"TATA box-binding protein (TBP) is a constituent of the polymerase I-specific transcription initiation factor TIF-IB (SL1) bound to the rRNA promoter and shows differential sensitivity to TBP-directed reagents in polymerase I, II, and III transcription factors.","date":"1994","source":"Molecular and cellular biology","url":"https://pubmed.ncbi.nlm.nih.gov/8264628","citation_count":52,"is_preprint":false},{"pmid":"12225748","id":"PMC_12225748","title":"Structure and stability of wild-type and mutant RNA internal loops from the SL-1 domain of the HIV-1 packaging signal.","date":"2002","source":"Journal of molecular biology","url":"https://pubmed.ncbi.nlm.nih.gov/12225748","citation_count":51,"is_preprint":false},{"pmid":"8552083","id":"PMC_8552083","title":"The species-specific RNA polymerase I transcription factor SL-1 binds to upstream binding factor.","date":"1996","source":"Molecular and cellular biology","url":"https://pubmed.ncbi.nlm.nih.gov/8552083","citation_count":50,"is_preprint":false},{"pmid":"21921199","id":"PMC_21921199","title":"TAF1B is a TFIIB-like component of the basal transcription machinery for RNA polymerase I.","date":"2011","source":"Science (New York, N.Y.)","url":"https://pubmed.ncbi.nlm.nih.gov/21921199","citation_count":49,"is_preprint":false},{"pmid":"12140758","id":"PMC_12140758","title":"Identification of MARCKS, FLJ11383 and TAF1B as putative novel target genes in colorectal carcinomas with microsatellite instability.","date":"2002","source":"Oncogene","url":"https://pubmed.ncbi.nlm.nih.gov/12140758","citation_count":47,"is_preprint":false},{"pmid":"8666237","id":"PMC_8666237","title":"The SL1 trans-spliced leader RNA performs an essential embryonic function in Caenorhabditis elegans that can also be supplied by SL2 RNA.","date":"1996","source":"Genes & development","url":"https://pubmed.ncbi.nlm.nih.gov/8666237","citation_count":46,"is_preprint":false},{"pmid":"9811537","id":"PMC_9811537","title":"Mitotic phosphorylation of the TBP-containing factor SL1 represses ribosomal gene transcription.","date":"1998","source":"Journal of molecular biology","url":"https://pubmed.ncbi.nlm.nih.gov/9811537","citation_count":45,"is_preprint":false},{"pmid":"16950265","id":"PMC_16950265","title":"SL1 RNA gene recovery from Enterobius vermicularis ancient DNA in pre-Columbian human coprolites.","date":"2006","source":"International journal for parasitology","url":"https://pubmed.ncbi.nlm.nih.gov/16950265","citation_count":45,"is_preprint":false},{"pmid":"26593443","id":"PMC_26593443","title":"AF4 uses the SL1 components of RNAP1 machinery to initiate MLL fusion- and AEP-dependent transcription.","date":"2015","source":"Nature communications","url":"https://pubmed.ncbi.nlm.nih.gov/26593443","citation_count":44,"is_preprint":false},{"pmid":"16410614","id":"PMC_16410614","title":"A new NMR solution structure of the SL1 HIV-1Lai loop-loop dimer.","date":"2006","source":"Nucleic acids research","url":"https://pubmed.ncbi.nlm.nih.gov/16410614","citation_count":44,"is_preprint":false},{"pmid":"16971462","id":"PMC_16971462","title":"CK2-mediated stimulation of Pol I transcription by stabilization of UBF-SL1 interaction.","date":"2006","source":"Nucleic acids research","url":"https://pubmed.ncbi.nlm.nih.gov/16971462","citation_count":43,"is_preprint":false},{"pmid":"7585246","id":"PMC_7585246","title":"SL1 trans-splicing specified by AU-rich synthetic RNA inserted at the 5' end of Caenorhabditis elegans pre-mRNA.","date":"1995","source":"RNA (New York, N.Y.)","url":"https://pubmed.ncbi.nlm.nih.gov/7585246","citation_count":38,"is_preprint":false},{"pmid":"8418050","id":"PMC_8418050","title":"Effects of N-acetylglucosamine on carbohydrate fermentation by Streptococcus mutans NCTC 10449 and Streptococcus sobrinus SL-1.","date":"1993","source":"Infection and immunity","url":"https://pubmed.ncbi.nlm.nih.gov/8418050","citation_count":38,"is_preprint":false},{"pmid":"12851400","id":"PMC_12851400","title":"Rev binds specifically to a purine loop in the SL1 region of the HIV-1 leader RNA.","date":"2003","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/12851400","citation_count":37,"is_preprint":false},{"pmid":"12731867","id":"PMC_12731867","title":"Stem of SL1 RNA in HIV-1: structure and nucleocapsid protein binding for a 1 x 3 internal loop.","date":"2003","source":"Biochemistry","url":"https://pubmed.ncbi.nlm.nih.gov/12731867","citation_count":37,"is_preprint":false},{"pmid":"15338281","id":"PMC_15338281","title":"A survey of SL1-spliced transcripts from the root-lesion nematode Pratylenchus penetrans.","date":"2004","source":"Molecular genetics and genomics : MGG","url":"https://pubmed.ncbi.nlm.nih.gov/15338281","citation_count":33,"is_preprint":false},{"pmid":"23555693","id":"PMC_23555693","title":"RNAi-mediated knockdown of catalase causes cell cycle arrest in SL-1 cells and results in low survival rate of Spodoptera litura (Fabricius).","date":"2013","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/23555693","citation_count":31,"is_preprint":false},{"pmid":"10082545","id":"PMC_10082545","title":"A kinase activity associated with simian virus 40 large T antigen phosphorylates upstream binding factor (UBF) and promotes formation of a stable initiation complex between UBF and SL1.","date":"1999","source":"Molecular and cellular biology","url":"https://pubmed.ncbi.nlm.nih.gov/10082545","citation_count":27,"is_preprint":false},{"pmid":"17341460","id":"PMC_17341460","title":"Nucleocapsid protein-mediated maturation of dimer initiation complex of full-length SL1 stemloop of HIV-1: sequence effects and mechanism of RNA refolding.","date":"2007","source":"Nucleic acids research","url":"https://pubmed.ncbi.nlm.nih.gov/17341460","citation_count":25,"is_preprint":false},{"pmid":"27564129","id":"PMC_27564129","title":"TBP loading by AF4 through SL1 is the major rate-limiting step in MLL fusion-dependent transcription.","date":"2016","source":"Cell cycle (Georgetown, Tex.)","url":"https://pubmed.ncbi.nlm.nih.gov/27564129","citation_count":22,"is_preprint":false},{"pmid":"30353654","id":"PMC_30353654","title":"Targeting c-met receptor tyrosine kinase by the DNA aptamer SL1 as a potential novel therapeutic option for myeloma.","date":"2018","source":"Journal of cellular and molecular medicine","url":"https://pubmed.ncbi.nlm.nih.gov/30353654","citation_count":22,"is_preprint":false},{"pmid":"8058785","id":"PMC_8058785","title":"The conserved core domain of the human TATA binding protein is sufficient to assemble the multisubunit RNA polymerase I-specific transcription factor SL1.","date":"1994","source":"Proceedings of the National Academy of Sciences of the United States of America","url":"https://pubmed.ncbi.nlm.nih.gov/8058785","citation_count":19,"is_preprint":false},{"pmid":"27614183","id":"PMC_27614183","title":"Biodegradation of phenanthrene by Rhizobium petrolearium SL-1.","date":"2016","source":"Journal of applied microbiology","url":"https://pubmed.ncbi.nlm.nih.gov/27614183","citation_count":19,"is_preprint":false},{"pmid":"7959796","id":"PMC_7959796","title":"Physical mapping at 6q27 of the locus for the TATA box-binding protein, the DNA-binding subunit of TFIID and a component of SL1 and TFIIIB, strongly suggests that it is single copy in the human genome.","date":"1994","source":"Genomics","url":"https://pubmed.ncbi.nlm.nih.gov/7959796","citation_count":19,"is_preprint":false},{"pmid":"35326106","id":"PMC_35326106","title":"The E3 Ubiquitin Ligase Gene Sl1 Is Critical for Cadmium Tolerance in Solanum lycopersicum L.","date":"2022","source":"Antioxidants (Basel, Switzerland)","url":"https://pubmed.ncbi.nlm.nih.gov/35326106","citation_count":18,"is_preprint":false},{"pmid":"16023135","id":"PMC_16023135","title":"Conformational pathway for the kissing complex-->extended dimer transition of the SL1 stem-loop from genomic HIV-1 RNA as monitored by targeted molecular dynamics techniques.","date":"2005","source":"Journal of molecular biology","url":"https://pubmed.ncbi.nlm.nih.gov/16023135","citation_count":18,"is_preprint":false},{"pmid":"35139074","id":"PMC_35139074","title":"Ribosomal DNA promoter recognition is determined in vivo by cooperation between UBTF1 and SL1 and is compromised in the UBTF-E210K neuroregression syndrome.","date":"2022","source":"PLoS genetics","url":"https://pubmed.ncbi.nlm.nih.gov/35139074","citation_count":18,"is_preprint":false},{"pmid":"10022876","id":"PMC_10022876","title":"Alterations in the conserved SL1 trans-spliced leader of Caenorhabditis elegans demonstrate flexibility in length and sequence requirements in vivo.","date":"1999","source":"Molecular and cellular biology","url":"https://pubmed.ncbi.nlm.nih.gov/10022876","citation_count":17,"is_preprint":false},{"pmid":"22405626","id":"PMC_22405626","title":"Cis-acting element (SL1) of Potato virus X controls viral movement by interacting with the NbMPB2Cb and viral proteins.","date":"2012","source":"Virology","url":"https://pubmed.ncbi.nlm.nih.gov/22405626","citation_count":17,"is_preprint":false},{"pmid":"16984912","id":"PMC_16984912","title":"The SL1-SL2 (stem-loop) domain is the primary determinant for stability of the gamma retroviral genomic RNA dimer.","date":"2006","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/16984912","citation_count":16,"is_preprint":false},{"pmid":"1820572","id":"PMC_1820572","title":"Chain formation and de-chaining in Streptococcus sobrinus SL-1.","date":"1991","source":"Oral microbiology and immunology","url":"https://pubmed.ncbi.nlm.nih.gov/1820572","citation_count":14,"is_preprint":false},{"pmid":"16511348","id":"PMC_16511348","title":"The SL1 stem-loop structure at the 5'-end of potato virus X RNA is required for efficient binding to host proteins and for viral infectivity.","date":"2006","source":"Molecules and cells","url":"https://pubmed.ncbi.nlm.nih.gov/16511348","citation_count":14,"is_preprint":false},{"pmid":"7563053","id":"PMC_7563053","title":"Determination of the folding topology of the SL1 RNA from Caenorhabditis elegans by multidimensional heteronuclear NMR.","date":"1995","source":"Journal of molecular biology","url":"https://pubmed.ncbi.nlm.nih.gov/7563053","citation_count":14,"is_preprint":false},{"pmid":"9361004","id":"PMC_9361004","title":"The fundamental ribosomal RNA transcription initiation factor-IB (TIF-IB, SL1, factor D) binds to the rRNA core promoter primarily by minor groove contacts.","date":"1997","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/9361004","citation_count":14,"is_preprint":false},{"pmid":"6254885","id":"PMC_6254885","title":"Partial purification and properties of a mannofructokinase from Streptococcus mutans SL-1.","date":"1980","source":"Infection and immunity","url":"https://pubmed.ncbi.nlm.nih.gov/6254885","citation_count":13,"is_preprint":false},{"pmid":"12451421","id":"PMC_12451421","title":"HIV-1(Lai) genomic RNA: combined used of NMR and molecular dynamics simulation for studying the structure and internal dynamics of a mutated SL1 hairpin.","date":"2002","source":"European biophysics journal : EBJ","url":"https://pubmed.ncbi.nlm.nih.gov/12451421","citation_count":12,"is_preprint":false},{"pmid":"15150793","id":"PMC_15150793","title":"On the stability of different experimental dimeric structures of the SL1 sequence from the genomic RNA of HIV-1 in solution: a molecular dynamics simulation and electrophoresis study.","date":"2004","source":"Biopolymers","url":"https://pubmed.ncbi.nlm.nih.gov/15150793","citation_count":11,"is_preprint":false},{"pmid":"21718714","id":"PMC_21718714","title":"Toxicity and differential protein analysis following destruxin A treatment of Spodoptera litura (Lepidoptera: Noctuidae) SL-1 cells.","date":"2011","source":"Toxicon : official journal of the International Society on Toxinology","url":"https://pubmed.ncbi.nlm.nih.gov/21718714","citation_count":11,"is_preprint":false},{"pmid":"24928901","id":"PMC_24928901","title":"Reconstitution of human rRNA gene transcription in mouse cells by a complete SL1 complex.","date":"2014","source":"Journal of cell science","url":"https://pubmed.ncbi.nlm.nih.gov/24928901","citation_count":10,"is_preprint":false},{"pmid":"7357011","id":"PMC_7357011","title":"Partial purification and properties of a specific glucokinase from Streptococcus mutans SL-1.","date":"1980","source":"Biochimica et biophysica acta","url":"https://pubmed.ncbi.nlm.nih.gov/7357011","citation_count":10,"is_preprint":false},{"pmid":"38283228","id":"PMC_38283228","title":"NMR 1H,19F-based screening of the four stem-looped structure 5_SL1-SL4 located in the 5'-untranslated region of SARS-CoV 2 RNA.","date":"2023","source":"RSC medicinal chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/38283228","citation_count":10,"is_preprint":false},{"pmid":"9765308","id":"PMC_9765308","title":"A novel transcription initiation factor (TIF), TIF-IE, is required for homogeneous Acanthamoeba castellanii TIF-IB (SL1) to form a committed complex.","date":"1998","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/9765308","citation_count":10,"is_preprint":false},{"pmid":"28988960","id":"PMC_28988960","title":"PDIM and SL1 accumulation in Mycobacterium tuberculosis is associated with mce4A expression.","date":"2017","source":"Gene","url":"https://pubmed.ncbi.nlm.nih.gov/28988960","citation_count":9,"is_preprint":false},{"pmid":"27835956","id":"PMC_27835956","title":"SL1 revisited: functional analysis of the structure and conformation of HIV-1 genome RNA.","date":"2016","source":"Retrovirology","url":"https://pubmed.ncbi.nlm.nih.gov/27835956","citation_count":9,"is_preprint":false},{"pmid":"7966304","id":"PMC_7966304","title":"Yeast TBP can replace its human homologue in the RNA polymerase I-specific multisubunit factor SL1.","date":"1994","source":"Journal of molecular biology","url":"https://pubmed.ncbi.nlm.nih.gov/7966304","citation_count":8,"is_preprint":false},{"pmid":"26071815","id":"PMC_26071815","title":"The cytotoxicology of momordicins I and II on Spodoptera litura cultured cell line SL-1.","date":"2014","source":"Pesticide biochemistry and physiology","url":"https://pubmed.ncbi.nlm.nih.gov/26071815","citation_count":8,"is_preprint":false},{"pmid":"35736244","id":"PMC_35736244","title":"A novel, essential trans-splicing protein connects the nematode SL1 snRNP to the CBC-ARS2 complex.","date":"2022","source":"Nucleic acids research","url":"https://pubmed.ncbi.nlm.nih.gov/35736244","citation_count":7,"is_preprint":false},{"pmid":"26610737","id":"PMC_26610737","title":"Elevated sL1-CAM levels in BALF and serum of IPF patients.","date":"2015","source":"Respirology (Carlton, Vic.)","url":"https://pubmed.ncbi.nlm.nih.gov/26610737","citation_count":7,"is_preprint":false},{"pmid":"10894955","id":"PMC_10894955","title":"Genomic localization of the human genes TAF1A, TAF1B and TAF1C, encoding TAF(I)48, TAF(I)63 and TAF(I)110 subunits of class I general transcription initiation factor SL1.","date":"2000","source":"Cytogenetics and cell genetics","url":"https://pubmed.ncbi.nlm.nih.gov/10894955","citation_count":7,"is_preprint":false},{"pmid":"17313192","id":"PMC_17313192","title":"Molecular dynamics simulation for probing the flexibility of the 35 nucleotide SL1 sequence kissing complex from HIV-1Lai genomic RNA.","date":"2007","source":"Journal of biomolecular structure & dynamics","url":"https://pubmed.ncbi.nlm.nih.gov/17313192","citation_count":7,"is_preprint":false},{"pmid":"34453696","id":"PMC_34453696","title":"1H, 13C and 15N assignment of stem-loop SL1 from the 5'-UTR of SARS-CoV-2.","date":"2021","source":"Biomolecular NMR assignments","url":"https://pubmed.ncbi.nlm.nih.gov/34453696","citation_count":6,"is_preprint":false},{"pmid":"29463404","id":"PMC_29463404","title":"Cytotoxicity of chemical constituents from Torricellia tiliifolia DC. on Spodoptera litura (SL-1) cells.","date":"2017","source":"Pesticide biochemistry and physiology","url":"https://pubmed.ncbi.nlm.nih.gov/29463404","citation_count":6,"is_preprint":false},{"pmid":"30718603","id":"PMC_30718603","title":"Heterodera glycines utilizes promiscuous spliced leaders and demonstrates a unique preference for a species-specific spliced leader over C. elegans SL1.","date":"2019","source":"Scientific reports","url":"https://pubmed.ncbi.nlm.nih.gov/30718603","citation_count":6,"is_preprint":false},{"pmid":"37658190","id":"PMC_37658190","title":"The Synergic Effect of Gut-Derived Probiotic Bacillus cereus SL1 And Ocimum sanctum on Growth, Intestinal Histopathology, Innate Immunity, and Expression of Enzymatic Antioxidant Genes in Fish, Cirrhinus mrigala (Hamilton, 1822).","date":"2023","source":"Probiotics and antimicrobial proteins","url":"https://pubmed.ncbi.nlm.nih.gov/37658190","citation_count":6,"is_preprint":false},{"pmid":"15107005","id":"PMC_15107005","title":"Base pairing at the stem-loop junction in the SL1 kissing complex of HIV-1 RNA: a thermodynamic study probed by molecular dynamics simulation.","date":"2004","source":"Journal of biomolecular structure & dynamics","url":"https://pubmed.ncbi.nlm.nih.gov/15107005","citation_count":5,"is_preprint":false},{"pmid":"35876068","id":"PMC_35876068","title":"Spliceosomal SL1 RNA binding to U1-70K: the role of the extended RRM.","date":"2022","source":"Nucleic acids research","url":"https://pubmed.ncbi.nlm.nih.gov/35876068","citation_count":4,"is_preprint":false},{"pmid":"9450246","id":"PMC_9450246","title":"Characteristics of nucleotide sequences flanking the trans-spliced leader SL1 exon in Dirofilaria immitis, Brugia malayi, and Brugia pahangi.","date":"1997","source":"The Journal of veterinary medical science","url":"https://pubmed.ncbi.nlm.nih.gov/9450246","citation_count":4,"is_preprint":false},{"pmid":"11563557","id":"PMC_11563557","title":"Modeling the dynamics of a mutated stem-loop in the SL1 domain of HIV-1Lai genomic RNA by 1H-NOESY spectra.","date":"2001","source":"Journal of biomolecular NMR","url":"https://pubmed.ncbi.nlm.nih.gov/11563557","citation_count":4,"is_preprint":false},{"pmid":"37645431","id":"PMC_37645431","title":"TAF1B depletion leads to apoptotic cell death by inducing nucleolar stress and activating p53-miR-101 circuit in hepatocellular carcinoma.","date":"2023","source":"Frontiers in oncology","url":"https://pubmed.ncbi.nlm.nih.gov/37645431","citation_count":3,"is_preprint":false},{"pmid":"38340823","id":"PMC_38340823","title":"Changes of MRGs and ARGs in Acinetobacter sp. SL-1 used for treatment of Cr(VI)-contaminated wastewater with waste molasses as carbon source.","date":"2024","source":"The Science of the total environment","url":"https://pubmed.ncbi.nlm.nih.gov/38340823","citation_count":3,"is_preprint":false},{"pmid":"12717718","id":"PMC_12717718","title":"Modeling the dynamics of the solvated SL1 domain of HIV-1 genomic RNA.","date":"2003","source":"Biopolymers","url":"https://pubmed.ncbi.nlm.nih.gov/12717718","citation_count":3,"is_preprint":false},{"pmid":"8789420","id":"PMC_8789420","title":"Mechanical and electrophysiological effects of a hydroxyphenyl-substituted tetrahydroisoquinoline, SL-1, on isolated rat cardiac tissues.","date":"1995","source":"Canadian journal of physiology and pharmacology","url":"https://pubmed.ncbi.nlm.nih.gov/8789420","citation_count":3,"is_preprint":false},{"pmid":"11259308","id":"PMC_11259308","title":"Solution structure of the SL1 RNA of the M1 double-stranded RNA virus of Saccharomyces cerevisiae.","date":"2001","source":"Biophysical journal","url":"https://pubmed.ncbi.nlm.nih.gov/11259308","citation_count":2,"is_preprint":false},{"pmid":"40305098","id":"PMC_40305098","title":"M. tuberculosis surface sulfoglycolipid SL-1 activates the mechanosensitive channel TRPV4 to enhance lysosomal biogenesis and exocytosis in macrophages.","date":"2025","source":"Molecular biology of the cell","url":"https://pubmed.ncbi.nlm.nih.gov/40305098","citation_count":2,"is_preprint":false},{"pmid":"18008323","id":"PMC_18008323","title":"Insight into the intrinsic flexibility of the SL1 stem-loop from genomic RNA of HIV-1 as probed by molecular dynamics simulation.","date":"2008","source":"Biopolymers","url":"https://pubmed.ncbi.nlm.nih.gov/18008323","citation_count":2,"is_preprint":false},{"pmid":"39930702","id":"PMC_39930702","title":"Preclinical Evaluation of 68Ga-Labeled SL1 Aptamer for c-Met Targeted PET Imaging.","date":"2025","source":"Molecular pharmaceutics","url":"https://pubmed.ncbi.nlm.nih.gov/39930702","citation_count":1,"is_preprint":false},{"pmid":"40001439","id":"PMC_40001439","title":"In Vitro Antiviral Activity of a Silydianin-Rich Extract from Silybum marianum Seeds Against Four Strains of Enteroviruses: EV71, Coxsackievirus B2, Coxsackievirus A10, and Poliovirus SL-1 and Its Impact on Improving Delayed Gastric Emptying in Mice.","date":"2025","source":"Antibiotics (Basel, Switzerland)","url":"https://pubmed.ncbi.nlm.nih.gov/40001439","citation_count":1,"is_preprint":false},{"pmid":"40666927","id":"PMC_40666927","title":"Mycobacterium tuberculosis sulfolipid-1 (Sl-1) increases the excitability of mouse and human TRPV1-positive sensory neurons in a YM254890-reversible fashion.","date":"2025","source":"bioRxiv : the preprint server for biology","url":"https://pubmed.ncbi.nlm.nih.gov/40666927","citation_count":1,"is_preprint":false},{"pmid":"1213052","id":"PMC_1213052","title":"Invertase in cell-free culture fluids of Streptococcus mutans strain SL-1.","date":"1975","source":"Experientia","url":"https://pubmed.ncbi.nlm.nih.gov/1213052","citation_count":1,"is_preprint":false},{"pmid":"40758647","id":"PMC_40758647","title":"Targeting the SARS-CoV-2 RNA Translation Initiation Element SL1 by Molecules of Low Molecular Weight.","date":"2025","source":"Journal of the American Chemical Society","url":"https://pubmed.ncbi.nlm.nih.gov/40758647","citation_count":0,"is_preprint":false},{"pmid":"38169774","id":"PMC_38169774","title":"Inhibition of TAF1B impairs ribosome biosynthesis and suppresses cell proliferation in stomach adenocarcinoma through promoting c-MYC mRNA degradation.","date":"2023","source":"Heliyon","url":"https://pubmed.ncbi.nlm.nih.gov/38169774","citation_count":0,"is_preprint":false},{"pmid":"41995017","id":"PMC_41995017","title":"Interacting with GUN1 and MORF2, SL1 modulates plastid RNA editing during norflurazon-induced retrograde signaling.","date":"2026","source":"Plant physiology","url":"https://pubmed.ncbi.nlm.nih.gov/41995017","citation_count":0,"is_preprint":false},{"pmid":"40348322","id":"PMC_40348322","title":"The impact of the novel σ1 receptor ligand (S)-L1 on brain endothelial cells and cerebrovascular reactivity challenged by ischemia.","date":"2025","source":"European journal of pharmacology","url":"https://pubmed.ncbi.nlm.nih.gov/40348322","citation_count":0,"is_preprint":false},{"pmid":null,"id":"bio_10.1101_2025.09.12.675721","title":"Mechanism of SARS-CoV-2 Nucleocapsid Protein Phosphorylation-induced Functional Switch","date":"2025-09-12","source":"bioRxiv","url":"https://doi.org/10.1101/2025.09.12.675721","citation_count":0,"is_preprint":true},{"pmid":null,"id":"bio_10.1101_2025.08.29.672993","title":"Development of LYTACs via incorporating a nucleolin-targeting and lysosome-directed aptamer","date":"2025-09-02","source":"bioRxiv","url":"https://doi.org/10.1101/2025.08.29.672993","citation_count":0,"is_preprint":true}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":44759,"output_tokens":4367,"usd":0.099891},"stage2":{"model":"claude-opus-4-6","input_tokens":7880,"output_tokens":2771,"usd":0.163013},"total_usd":0.262904,"stage1_batch_id":"msgbatch_01RPbVc9PDH9zQmYK5Hs6srm","stage2_batch_id":"msgbatch_01JVbVLzeKN2yVrsGp3zC8aM","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 1992,\n      \"finding\": \"SL1 (the RNA polymerase I promoter selectivity factor) is a multisubunit complex containing TBP (TATA-binding protein) and three distinct TBP-associated factors (TAFIs), including TAF1B (TAFI48). Purified TAFIs reconstituted with recombinant TBP complement SL1 transcriptional activity, demonstrating TBP plus novel associated factors are integral components of SL1.\",\n      \"method\": \"Column chromatography, glycerol gradient sedimentation, antibody depletion, reconstitution assay\",\n      \"journal\": \"Cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — biochemical reconstitution with functional validation, foundational paper with 390 citations\",\n      \"pmids\": [\"1547496\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1994,\n      \"finding\": \"TAF1B (TAFI48), along with TAFI110 and TAFI63, can each bind individually and specifically to TBP and interact with each other to form a stable TBP-TAF complex. TAFIs from SL1 and TFIID show mutually exclusive binding specificity for TBP, directing formation of polymerase-selective TBP-TAF complexes.\",\n      \"method\": \"Subunit interaction analysis, recombinant protein binding assays\",\n      \"journal\": \"Science\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — reconstitution with mutagenesis-equivalent domain analysis, 133 citations\",\n      \"pmids\": [\"7801123\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1994,\n      \"finding\": \"TAF1B (TAFI48), together with TAFI110, TAFI63, and TBP, is necessary and sufficient to reconstitute a transcriptionally active SL1 complex capable of directing accurate RNA polymerase I transcription from the human ribosomal RNA gene promoter.\",\n      \"method\": \"In vivo and in vitro assembly of recombinant SL1 subunits, reconstituted transcription assay\",\n      \"journal\": \"Science\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — full reconstitution of functional complex, 131 citations\",\n      \"pmids\": [\"7801130\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1994,\n      \"finding\": \"The conserved core domain of TBP is sufficient to assemble with Pol I-specific TAFs (including TAF1B/TAFI48) to form a functional SL1 complex; TBP directly interacts with TAFI48 in an in vitro protein-protein interaction assay.\",\n      \"method\": \"Immunopurification of epitope-tagged TBP constructs, in vitro protein-protein interaction assay, in vitro transcription\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — direct interaction assay combined with functional reconstitution\",\n      \"pmids\": [\"8058785\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1997,\n      \"finding\": \"Murine TAFIs (including the TAF1B ortholog) can form stable chimeric complexes with human TBP and TAFIs, demonstrating evolutionarily conserved protein-protein interactions among SL1 subunits responsible for complex assembly.\",\n      \"method\": \"cDNA cloning, sequence analysis, chimeric complex assembly assay\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — biochemical complex assembly with functional implication, single study\",\n      \"pmids\": [\"9050847\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1997,\n      \"finding\": \"SV40 large T antigen directly binds to SL1 subunits TBP, TAF1B (TAFI48), and TAFI110, and this interaction with SL1 is required for large T antigen stimulation of RNA Pol I transcription.\",\n      \"method\": \"Immunoprecipitation in vitro and in SV40-infected cells, large T antigen deletion mutant transcription assays\",\n      \"journal\": \"Genes & development\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — reciprocal co-IP with functional validation using deletion mutants, 53 citations\",\n      \"pmids\": [\"9203586\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1998,\n      \"finding\": \"SL1 (including TAF1B as a subunit) is inactivated by cdc2/cyclin B-directed phosphorylation during mitosis, resulting in repression of RNA Pol I transcription; phosphorylation impairs the interaction of SL1 with UBF.\",\n      \"method\": \"Cell-free transcription system, mitotic kinase phosphorylation assay, protein-protein interaction studies\",\n      \"journal\": \"The EMBO journal\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 — reconstituted cell-free system, kinase assay, protein interaction, replicated by Kuhn et al. 1998\",\n      \"pmids\": [\"9857193\", \"9811537\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1999,\n      \"finding\": \"SL1 is recruited to the rRNA gene promoter through direct protein-protein interaction with the carboxy-terminal activation domain of UBF; this recruitment is regulated by UBF phosphorylation, as dephosphorylation of UBF abolishes UBF-SL1 interaction and transcriptional activation.\",\n      \"method\": \"Protein-protein interaction assays with UBF deletion mutants, alkaline phosphatase treatment, DNase I footprinting, in vitro transcription reconstitution\",\n      \"journal\": \"Molecular and cellular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — multiple orthogonal methods including interaction assay, footprinting, and reconstituted transcription\",\n      \"pmids\": [\"10082553\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2000,\n      \"finding\": \"Retinoblastoma protein (Rb) directly interacts with UBF and blocks the interaction between UBF and SL1 (using TAF1B/TAFI48 as a marker for SL1), thereby repressing RNA Pol I transcription.\",\n      \"method\": \"Direct protein interaction assays, DNase footprinting, band-shift assays\",\n      \"journal\": \"Oncogene\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — direct interaction and footprinting assays, single lab\",\n      \"pmids\": [\"11042686\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2001,\n      \"finding\": \"TAF1B (TAFI68/TAF(I)68) is acetylated by PCAF (p300/CBP-associated factor), and this acetylation enhances binding of TAF1B to the rDNA promoter and stimulates RNA Pol I transcription; the NAD+-dependent deacetylase mSir2a deacetylates TAF1B and represses Pol I transcription.\",\n      \"method\": \"In vitro acetylation assay, promoter binding assay, reconstituted in vitro transcription system, deacetylation assay\",\n      \"journal\": \"The EMBO journal\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — in vitro enzymatic assay with writer/eraser identification and functional transcription readout\",\n      \"pmids\": [\"11250901\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2001,\n      \"finding\": \"hRRN3 directly interacts with TAF1B (TAF(I)63) and TAF(I)110 of SL1, and this interaction is essential for recruitment of initiation-competent RNA Pol I to the rDNA promoter; blocking this connection prevents Pol I recruitment.\",\n      \"method\": \"Co-immunoprecipitation, direct interaction assay, chromatin recruitment assay\",\n      \"journal\": \"The EMBO journal\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — direct interaction and recruitment assay with functional blockade experiment, 154 citations\",\n      \"pmids\": [\"11250903\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2005,\n      \"finding\": \"PTEN represses RNA Pol I transcription by inducing dissociation of SL1 subunits (including TAF1B) and reducing their occupancy on the rRNA gene promoter, independent of effects on SL1 expression levels.\",\n      \"method\": \"Chromatin immunoprecipitation (ChIP), co-immunoprecipitation, in vitro transcription\",\n      \"journal\": \"Molecular and cellular biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — ChIP and co-IP with functional transcription assay, single lab\",\n      \"pmids\": [\"16055704\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2005,\n      \"finding\": \"Human SL1 (containing TAF1B) can direct accurate Pol I transcription in the absence of UBF and interacts with the rDNA promoter independently and stably; SL1 significantly reduces the rate of UBF dissociation from the rDNA promoter, indicating a role in stabilizing UBF at the promoter.\",\n      \"method\": \"In vitro transcription reconstitution, promoter binding/dissociation assays\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — in vitro reconstitution with kinetic analysis\",\n      \"pmids\": [\"15970593\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2006,\n      \"finding\": \"Protein kinase CK2 co-immunoprecipitates with the Pol I complex, is associated with the rRNA gene promoter, and stimulates Pol I transcription by phosphorylating the C-terminus of UBF, which counteracts inhibitory HMG box domains and stabilizes the UBF-SL1 interaction.\",\n      \"method\": \"Co-immunoprecipitation, ChIP, kinase assay, in vitro transcription with immobilized templates\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — multiple methods, single lab\",\n      \"pmids\": [\"16971462\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2007,\n      \"finding\": \"TAF(I)41 (MGC5306) is a novel component of SL1 that co-purifies and co-immunoprecipitates with SL1, resides at the rDNA promoter in the nucleolus, and is required for Pol I transcription and for stable SL1 occupancy at the rDNA promoter in vivo.\",\n      \"method\": \"Co-purification, co-immunoprecipitation, immunodepletion, siRNA knockdown, Pol I transcription assay\",\n      \"journal\": \"The EMBO journal\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — multiple orthogonal methods with functional rescue, 78 citations\",\n      \"pmids\": [\"17318177\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"TAF1B is structurally related to TFIIB/TFIIB-like proteins through predicted N-terminal zinc ribbon and cyclin-like fold domains, and SL1 has an essential post-polymerase recruitment role operating through TAF1B, identifying TAF1B as the TFIIB-like factor of the Pol I transcription machinery.\",\n      \"method\": \"Bioinformatic structural prediction, domain swap experiments, functional complementation assays\",\n      \"journal\": \"Science\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 — structural homology with functional domain swap validation, confirmed in parallel by Knutson & Hahn 2011\",\n      \"pmids\": [\"21921199\", \"21921198\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"All four human TAFI subunits of SL1 (including TAF1B) are necessary and sufficient to reconstitute human rRNA gene transcription in mouse cells, overcoming the species-specificity barrier; chimeric human-mouse TAFI complexes could be formed but were transcriptionally inactive.\",\n      \"method\": \"Ectopic expression in mouse cells, sensitive Pol I transcription monitoring system using influenza RNA polymerase reporter, chimeric complex assembly\",\n      \"journal\": \"Journal of cell science\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — functional reconstitution in trans-species system with rigorous controls\",\n      \"pmids\": [\"24928901\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"The pSER domain of AF4 family proteins (component of AEP complex) associates with SL1 on chromatin and facilitates TBP loading onto the promoter to initiate RNA Pol II-dependent transcription; MLL-AEP fusion proteins activate transcription initiation through SL1.\",\n      \"method\": \"Chromatin immunoprecipitation, co-immunoprecipitation, in vitro transcription\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — ChIP and co-IP with functional assay, single study\",\n      \"pmids\": [\"26593443\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"Conditional deletion of TAF1B (a subunit of SL1) causes striking depletion of UBTF at both rDNA promoters but not elsewhere across the rDNA, demonstrating that SL1-TAF1B cooperates with UBTF1 splice variant to provide specificity for rDNA promoter recognition in vivo.\",\n      \"method\": \"Conditional gene deletion (knockout), ChIP, fluorescence microscopy\",\n      \"journal\": \"PLoS genetics\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — conditional knockout with ChIP demonstrating specific promoter effect\",\n      \"pmids\": [\"35139074\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"TAF1B depletion in hepatocellular carcinoma cells disrupts the SL1 pre-initiation complex (verified by co-IP and ChIP), inhibits rDNA transcription, induces nucleolar stress, and triggers apoptosis through a p53-miR-101 positive and negative feedback circuit.\",\n      \"method\": \"Lentiviral knockdown, co-immunoprecipitation, ChIP, immunofluorescence, FISH, qRT-PCR, apoptosis assays, xenograft tumor model\",\n      \"journal\": \"Frontiers in oncology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — multiple methods with in vivo validation, single lab\",\n      \"pmids\": [\"37645431\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2000,\n      \"finding\": \"Human TAF1B gene is localized to chromosome 2p25 as a single copy gene; the gene is transcribed into multiple RNA species that could produce variant SL1 isoforms.\",\n      \"method\": \"Somatic cell hybrid panel analysis, radiation hybrid panel analysis, FISH, Northern analysis\",\n      \"journal\": \"Cytogenetics and cell genetics\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 — chromosomal mapping and RNA characterization, no direct functional mechanism\",\n      \"pmids\": [\"10894955\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"TAF1B is a TFIIB-related subunit of the human RNA Pol I basal transcription factor SL1 (a complex of TBP and TAFIs including TAF1B/TAFI48, TAFI63/TAF1A, and TAFI110/TAF1C), where it is necessary and sufficient with the other TAFIs and TBP to reconstitute Pol I pre-initiation complex formation at the rDNA promoter; TAF1B can be acetylated by PCAF (activating rDNA binding and transcription) or deacetylated by mSir2a (repressing transcription), the entire SL1 complex is inactivated by cdc2/cyclin B phosphorylation during mitosis, and TAF1B mediates an essential post-polymerase recruitment function analogous to TFIIB in Pol II transcription.\"\n}\n```","stage2_raw":"```json\n{\n  \"mechanistic_narrative\": \"TAF1B is a TFIIB-related subunit of the RNA polymerase I selectivity factor SL1 that functions as a core component of the Pol I pre-initiation complex at ribosomal DNA promoters, playing an essential role in rRNA gene transcription. TAF1B assembles with TBP and the other TAF_I subunits (TAF1A, TAF1C, TAF1D) to form the SL1 complex, which binds the rDNA promoter both independently and cooperatively with UBF, stabilizing UBF occupancy and recruiting initiation-competent Pol I via interaction with hRRN3 [PMID:1547496, PMID:7801130, PMID:15970593, PMID:11250903]. Structurally homologous to TFIIB through N-terminal zinc ribbon and cyclin-like fold domains, TAF1B fulfills an essential post-polymerase recruitment function analogous to TFIIB in Pol II transcription [PMID:21921199]. TAF1B activity is regulated by PCAF-mediated acetylation, which enhances rDNA promoter binding and stimulates transcription, by mSir2a-mediated deacetylation, which represses transcription, and by cdc2/cyclin B phosphorylation of SL1 during mitosis, which inactivates the complex [PMID:11250901, PMID:9857193].\",\n  \"teleology\": [\n    {\n      \"year\": 1992,\n      \"claim\": \"Identification of TAF1B as a novel TBP-associated factor within SL1 established that Pol I promoter selectivity depends on a distinct multisubunit TBP-TAF complex, not TBP alone.\",\n      \"evidence\": \"Chromatographic purification and reconstitution of SL1 transcriptional activity from separated TAFIs plus recombinant TBP\",\n      \"pmids\": [\"1547496\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Individual contributions of each TAFI subunit to promoter recognition were undefined\", \"Structural basis for polymerase selectivity of TBP-TAF complexes unknown\"]\n    },\n    {\n      \"year\": 1994,\n      \"claim\": \"Demonstration that TAF1B directly binds TBP and other TAFIs, and that all four subunits reconstitute transcriptionally active SL1, resolved the minimal composition of the Pol I selectivity factor.\",\n      \"evidence\": \"Recombinant protein binding assays and full reconstitution of accurate Pol I transcription from purified components\",\n      \"pmids\": [\"7801123\", \"7801130\", \"8058785\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Stoichiometry of the SL1 complex was not determined\", \"Mechanism by which SL1 recruits Pol I was unknown\"]\n    },\n    {\n      \"year\": 1998,\n      \"claim\": \"Discovering that cdc2/cyclin B phosphorylation inactivates SL1 and impairs UBF–SL1 interaction explained how ribosomal gene transcription is silenced during mitosis.\",\n      \"evidence\": \"Cell-free Pol I transcription with mitotic kinase treatment and UBF–SL1 interaction assays\",\n      \"pmids\": [\"9857193\", \"9811537\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Which specific SL1 subunit(s) are phosphorylated was not fully resolved\", \"Phosphatase responsible for reactivation at mitotic exit not identified\"]\n    },\n    {\n      \"year\": 1999,\n      \"claim\": \"Mapping UBF's C-terminal activation domain as the SL1-interacting surface, and showing phosphorylation-dependence of this interaction, established UBF as a regulated recruiter of SL1 to the rDNA promoter.\",\n      \"evidence\": \"Protein interaction assays with UBF deletion mutants, phosphatase treatment, DNase I footprinting, and reconstituted transcription\",\n      \"pmids\": [\"10082553\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Specific SL1 subunit(s) contacting UBF not identified at residue resolution\", \"Role of CK2 in UBF phosphorylation for SL1 interaction not yet tested\"]\n    },\n    {\n      \"year\": 2001,\n      \"claim\": \"Identification of PCAF-mediated acetylation as an activator and mSir2a-mediated deacetylation as a repressor of TAF1B established a reversible post-translational switch controlling Pol I transcription output.\",\n      \"evidence\": \"In vitro acetylation/deacetylation assays with promoter binding and reconstituted transcription readouts\",\n      \"pmids\": [\"11250901\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Acetylation sites on TAF1B not mapped to specific residues\", \"In vivo acetylation dynamics under growth signaling not characterized\"]\n    },\n    {\n      \"year\": 2001,\n      \"claim\": \"Showing that hRRN3 directly interacts with SL1 subunits (TAF1B and TAF1C) to recruit initiation-competent Pol I defined the bridging mechanism linking promoter-bound SL1 to the polymerase.\",\n      \"evidence\": \"Co-immunoprecipitation, direct interaction assay, and chromatin recruitment blockade experiment\",\n      \"pmids\": [\"11250903\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether TAF1B or TAF1C is the primary hRRN3 contact not resolved\", \"Structural basis for hRRN3–SL1 interaction unknown\"]\n    },\n    {\n      \"year\": 2005,\n      \"claim\": \"Demonstrating that SL1 can direct accurate Pol I transcription without UBF and stabilizes UBF at the promoter revised the view of SL1 from a purely UBF-dependent factor to an independent promoter-binding entity with cooperative function.\",\n      \"evidence\": \"In vitro transcription reconstitution and kinetic promoter dissociation assays\",\n      \"pmids\": [\"15970593\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"How SL1 recognizes the core promoter independently of UBF was structurally undefined\"]\n    },\n    {\n      \"year\": 2011,\n      \"claim\": \"Establishing TAF1B as the structural and functional homolog of TFIIB — with conserved zinc ribbon and cyclin folds and a post-polymerase recruitment role — unified Pol I and Pol II pre-initiation complex architecture.\",\n      \"evidence\": \"Bioinformatic structural prediction combined with domain swap and functional complementation assays; confirmed independently by two groups\",\n      \"pmids\": [\"21921199\", \"21921198\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"High-resolution structure of TAF1B in the Pol I PIC not available\", \"Whether the zinc ribbon directly contacts rDNA not tested\"]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"Showing that all four human TAFIs overcome species-specificity when expressed in mouse cells, while chimeric human-mouse TAFI complexes fail, demonstrated that TAF1B functions within a tightly co-evolved subunit ensemble.\",\n      \"evidence\": \"Ectopic expression of human TAFIs in mouse cells with reporter-based Pol I transcription monitoring\",\n      \"pmids\": [\"24928901\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Molecular determinants of species-specific incompatibility not mapped\", \"Whether TAF1D is essential in the reconstituted system not fully addressed\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Conditional deletion of TAF1B in vivo revealed that SL1 is required to maintain UBTF occupancy specifically at rDNA promoters, establishing TAF1B as a specificity determinant that restricts UBTF1 function to promoter elements.\",\n      \"evidence\": \"Conditional gene deletion with ChIP and fluorescence microscopy in mouse cells\",\n      \"pmids\": [\"35139074\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether TAF1B loss affects other chromatin marks at rDNA beyond UBTF occupancy not assessed\", \"Downstream consequences of TAF1B loss on nucleolar structure were not fully characterized in this study\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"TAF1B depletion in hepatocellular carcinoma cells induces nucleolar stress and p53-dependent apoptosis, linking SL1 integrity to cancer cell survival and identifying a potential vulnerability.\",\n      \"evidence\": \"Lentiviral knockdown, co-IP, ChIP, apoptosis assays, and xenograft tumor model\",\n      \"pmids\": [\"37645431\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Whether the apoptotic response is specific to TAF1B loss versus general rDNA transcription inhibition not distinguished\", \"Relevance to non-hepatic tumor types not tested\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"A high-resolution cryo-EM or crystal structure of TAF1B within the human Pol I pre-initiation complex is needed to define its contacts with the rDNA template, Pol I, and hRRN3, and to clarify how acetylation modulates promoter binding at the atomic level.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"High\",\n      \"gaps\": [\"No atomic-resolution structure of TAF1B or human SL1 in a PIC context\", \"Acetylation site mapping and structural consequences unresolved\", \"In vivo dynamics of SL1 assembly/disassembly during cell cycle and growth signaling remain poorly characterized\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0140110\", \"supporting_discovery_ids\": [0, 2, 15]},\n      {\"term_id\": \"GO:0003677\", \"supporting_discovery_ids\": [9, 12]},\n      {\"term_id\": \"GO:0005198\", \"supporting_discovery_ids\": [1, 15]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005730\", \"supporting_discovery_ids\": [14, 18]},\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [0, 14]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-74160\", \"supporting_discovery_ids\": [0, 2, 9, 12, 15]},\n      {\"term_id\": \"R-HSA-1640170\", \"supporting_discovery_ids\": [6]}\n    ],\n    \"complexes\": [\n      \"SL1 (Selectivity Factor 1)\"\n    ],\n    \"partners\": [\n      \"TBP\",\n      \"TAF1A\",\n      \"TAF1C\",\n      \"TAF1D\",\n      \"UBTF\",\n      \"RRN3\",\n      \"KAT2B\"\n    ],\n    \"other_free_text\": []\n  }\n}\n```"}