{"gene":"SUPT3H","run_date":"2026-06-10T10:51:54","timeline":{"discoveries":[{"year":1992,"finding":"Yeast SPT3 physically associates with TFIID (TBP) in yeast cell extracts, as demonstrated by coimmunoprecipitation. Allele-specific suppression of spt15-21 (a TBP mutation) by spt3 mutations indicates a direct functional interaction between SPT3 and TBP required for transcription at particular promoters in vivo.","method":"Coimmunoprecipitation from yeast extracts; allele-specific extragenic suppressor genetics","journal":"Genes & development","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal genetic and biochemical evidence (Co-IP + allele-specific suppression), replicated and extended by multiple subsequent studies","pmids":["1628834"],"is_preprint":false},{"year":1984,"finding":"SPT3 is required for normal transcription initiation from delta (Ty LTR) sequences in S. cerevisiae; in spt3 null mutants, Ty delta-delta transcripts are absent and initiation shifts ~800 bp into the epsilon region, establishing SPT3 as a positive regulator of Ty element transcription.","method":"Genetic null mutant analysis; Northern blot / transcript mapping","journal":"Cell","confidence":"High","confidence_rationale":"Tier 2 / Strong — clean null mutant with defined transcriptional phenotype, foundational result replicated across many subsequent studies","pmids":["6096019"],"is_preprint":false},{"year":1998,"finding":"Human SUPT3H (hSPT3) is not associated in vivo with human TBP/TFIID or with a TBP-free TAFII complex; instead, hSPT3 co-purifies in vivo with TAFII31 and the long form of human GCN5 (hGCN5-L) in a novel complex (STAGA) that possesses histone acetyltransferase activity. This established STAGA as the human homologue of yeast SAGA.","method":"Immunoprecipitation from HeLa cell nuclear extracts; histone acetyltransferase activity assay; molecular cloning and sequence analysis","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal Co-IP with enzymatic activity assay, multiple orthogonal methods in one study, foundational paper for human STAGA/SAGA","pmids":["9726987"],"is_preprint":false},{"year":2000,"finding":"Within SAGA, Spt3 (and Spt8) inhibit TBP binding to the HIS3 promoter in vitro; SAGA lacking Spt3 or Spt8 loses this inhibitory activity. Two distinct forms of SAGA exist in cell extracts, one lacking Spt8, and conditions that induce transcription shift the balance toward the Spt8-lacking form, indicating that SAGA composition is dynamic and that Spt3/Spt8 function as inhibitory subunits for TBP recruitment under non-induced conditions.","method":"In vitro TBP-DNA binding assay with purified SAGA complexes; biochemical fractionation of SAGA isoforms; genetic analysis of spt3 and spt8 deletion effects on transcription","journal":"Molecular and cellular biology","confidence":"High","confidence_rationale":"Tier 1–2 / Moderate — in vitro binding assay with purified complex + genetic readout, multiple orthogonal methods in single study","pmids":["10611242"],"is_preprint":false},{"year":1997,"finding":"Genetic epistasis experiments show that SPT3 functionally interacts with MOT1 (an ATP-dependent TBP inhibitor) and TFIIA to regulate TBP-DNA interactions and TATA-box selection in vivo. Double mutant lethality (spt3Δ mot1) and suppression of spt3Δ by TFIIA overexpression define a cooperative pathway controlling TBP distribution at promoters.","method":"Synthetic lethality screen; genetic suppressor analysis; in vivo transcription assays","journal":"Molecular and cellular biology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — genetic epistasis with multiple allele combinations, single lab, no direct biochemical reconstitution of the three-way interaction","pmids":["8972209"],"is_preprint":false},{"year":1994,"finding":"Genetic analysis shows that spt8 null mutations are suppressed by particular spt3 alleles, suggesting that SPT8 promotes a functional SPT3–TBP interaction. Both SPT8 and SPT3 are required for TBP function at specific promoters.","method":"Genetic suppressor analysis; null mutant combination phenotyping","journal":"Genetics","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — allele-specific suppression genetics across multiple allele combinations, single lab","pmids":["8088510"],"is_preprint":false},{"year":2008,"finding":"Site-specific in vivo and in vitro cross-linking using the non-natural photoreactive amino acid BPA substituted onto TBP surface residues demonstrates a direct physical interaction between TBP and SAGA subunits Spt3 and Spt8. Mutations on the Spt3-interacting surface of TBP reduce TBP–SAGA interaction, decrease transcriptional activation, and impair TBP recruitment to a SAGA-dependent promoter, proving that a direct Spt3–TBP contact is required for activated transcription.","method":"Site-specific photocrosslinking with non-natural amino acid BPA in vivo and in vitro; chromatin immunoprecipitation; in vivo transcription assays; mutagenesis","journal":"Genes & development","confidence":"High","confidence_rationale":"Tier 1 / Strong — direct cross-linking with mutagenesis validation plus functional ChIP readout, multiple orthogonal methods demonstrating mechanistic direct interaction","pmids":["18981477"],"is_preprint":false},{"year":2004,"finding":"Spt3 (within SAGA) is required for nucleosome remodeling at the GAL1 promoter upon transcriptional induction, and this function is independent of TBP recruitment. Spt3 and Mot1 are both required for nucleosome remodeling and are recruited to GAL1 promoter (and a non-promoter nucleosome near an activator-binding site) in an interdependent manner, revealing a chromatin remodeling role for Spt3 distinct from its TBP-delivery role.","method":"Chromatin immunoprecipitation; nucleosome remodeling assays; genetic analysis of spt3 and mot1 mutants; synthetic promoter experiments","journal":"The EMBO journal","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — ChIP plus genetic dissection with multiple mutant combinations, single lab","pmids":["15057269"],"is_preprint":false},{"year":2007,"finding":"New dominant-negative spt3 mutations cluster in a conserved region of Spt3 and allele-specifically interact with spt15 (TBP) mutations, confirming a direct Spt3–TBP interface in vivo. One spt3 mutation (spt3-401) greatly increases SAGA–TBP physical association, while most spt3, spt8, and spt15 mutations do not alter bulk SAGA–TBP interaction, suggesting that direct Spt3–TBP contact is required for normal TBP levels at Spt3-dependent promoters.","method":"Dominant-negative overexpression genetics; extragenic suppressor isolation; TBP ChIP; SAGA–TBP co-immunoprecipitation","journal":"Genetics","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — allele-specific genetics combined with ChIP and Co-IP, single lab","pmids":["18073420"],"is_preprint":false},{"year":2007,"finding":"A SAGA-independent function of SPT3 is identified: deletion of SPT3, but not deletion of other SAGA subunits (SPT7), suppresses transcriptional defects of a not1-2 (Ccr4-Not scaffold) mutant, and spt3Δ shows synthetic phenotypes with spt7Δ. This indicates SPT3 has functions outside the SAGA complex that are functionally linked to the Ccr4-Not complex.","method":"Genetic suppressor analysis; transcriptional assays; genetic epistasis with SAGA and Ccr4-Not mutants","journal":"Genetics","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — genetic epistasis with multiple combinatorial mutants, single lab, no direct biochemical reconstitution of SAGA-independent SPT3 function","pmids":["17660549"],"is_preprint":false},{"year":1998,"finding":"The human SUPT3H cDNA encodes a protein sharing 30% identity with yeast Spt3 across three conserved domains. Full-length SUPT3H cannot complement yeast spt3Δ, but a human-yeast chimeric gene containing 42% human sequences can partially complement, indicating partial functional conservation of transcriptional control from yeast to human.","method":"Molecular cloning; yeast complementation assay with full-length and chimeric constructs","journal":"Genomics","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — functional complementation in yeast with chimeric gene approach, single lab","pmids":["9787080"],"is_preprint":false},{"year":2022,"finding":"In mammalian cells (human U2OS and mouse ESCs), SAGA can assemble without SUPT3H. Loss of SUPT3H does not cause major changes in TBP accumulation at gene promoters and does not globally impair RNA Pol II transcription; instead, SUPT3H affects transcription of only a specific gene subset and is required for mESC growth and self-renewal. This contrasts with yeast where Spt3 broadly controls TBP recruitment.","method":"Biochemical purification of SAGA from SUPT3H-knockout cells; ChIP for TBP; RNA-seq; mESC growth/self-renewal assays","journal":"Nucleic acids research","confidence":"High","confidence_rationale":"Tier 2 / Moderate — multiple orthogonal methods (complex purification, ChIP, RNA-seq, phenotypic assays) in one study demonstrating mammalian-specific mechanistic divergence","pmids":["35871303"],"is_preprint":false},{"year":2020,"finding":"The spliceosomal ATPase Prp5p directly interacts with SAGA subunit Spt8p (but not Spt3p) in vitro. However, both spt8Δ and spt3Δ rescue Prp5 splicing defects and restore Pol II recruitment to an intron-containing gene. This interaction mediates reciprocal coupling between transcription initiation/elongation (via the SAGA TBP-binding module containing Spt3/Spt8) and pre-spliceosome assembly.","method":"In vitro binding assay (Prp5–Spt8 direct interaction); genetic suppressor analysis; chromatin immunoprecipitation (ChIP and ChIP-seq)","journal":"Nucleic acids research","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — in vitro binding plus ChIP-seq plus genetic epistasis, but Spt3 itself does not directly bind Prp5; its role is inferred genetically","pmids":["32399566"],"is_preprint":false},{"year":2023,"finding":"In S. cerevisiae, Spt3 and Spt8 (SAGA subunits) block the spread of telomeric silencing regions at the right arm of chromosome III in a TBP-interaction-dependent manner; mutants altering the Spt3–TBP interaction impair boundary formation. Spt3 has a greater genome-wide transcriptional effect than Spt8, and boundary formation is DNA sequence-independent.","method":"Microarray transcriptome analysis; RT-qPCR of subtelomeric genes; genetic analysis of spt3–TBP interaction mutants","journal":"Biomolecules","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — genetic and transcriptomic analysis, single lab, no direct biochemical reconstitution of boundary mechanism","pmids":["37189367"],"is_preprint":false},{"year":2025,"finding":"ChIP-seq in amino acid-starved S. cerevisiae shows that deleting SPT3 or SPT8 (but not GCN5) reduces TBP binding at many Gcn4 target genes, while deleting GCN5 (but not SPT3 or SPT8) impairs promoter histone eviction. Nuclear depletion of TFIID subunit Taf1 further reduces TBP recruitment at SAGA-dependent genes only when Spt3 or Spt8 are absent, demonstrating that SAGA's TBP-recruitment function via Spt3/Spt8 is non-redundant with TFIID in the Gcn4 transcriptome.","method":"ChIP-seq for TBP and Pol II; auxin-inducible degron nuclear depletion of Taf1; genetic deletion of SPT3, SPT8, GCN5","journal":"Nucleic acids research","confidence":"High","confidence_rationale":"Tier 2 / Moderate — genome-wide ChIP-seq with multiple combinatorial mutants and orthogonal protein depletion, rigorous mechanistic dissection of SAGA TBP-delivery function","pmids":["40637224"],"is_preprint":false},{"year":2014,"finding":"In murine pre-osteoblastic MC3T3-E1 cells, the Supt3h promoter physically contacts the bone-specific Runx2-P1 promoter (located in the first intron of which Supt3h resides) with increased contact frequency during osteoblast differentiation. RUNX2 and CTCF bind the Supt3h promoter, and interplasmid-3C plus luciferase reporter assays show that the Supt3h promoter can modulate Runx2-P1 transcriptional activity via direct association.","method":"Chromosome conformation capture (3C); DNaseI hypersensitivity assay; ChIP for RUNX2 and CTCF; luciferase reporter assay","journal":"Nucleic acids research","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — 3C and reporter assays with ChIP, multiple methods, single lab; functional consequence of Supt3h promoter on Runx2-P1 activity established","pmids":["25120271"],"is_preprint":false}],"current_model":"SUPT3H/SPT3 is a conserved component of the SAGA (Spt-Ada-Gcn5-Acetyltransferase) coactivator complex that directly contacts TBP via a defined surface on both proteins to regulate TBP recruitment and transcription initiation at a subset of RNA Pol II promoters; in yeast, Spt3 (together with Spt8) can both promote and inhibit TBP-TATA interactions depending on promoter context, participates in nucleosome remodeling independently of TBP recruitment in cooperation with Mot1, and functions non-redundantly with TFIID for TBP delivery at Gcn4-induced genes; in mammalian cells, SUPT3H is dispensable for overall SAGA assembly and global TBP recruitment but is required for transcription of a specific gene subset and for mouse ESC growth and self-renewal, indicating that the TBP-delivery mechanism has diverged between yeast and mammals."},"narrative":{"mechanistic_narrative":"SUPT3H/Spt3 is a conserved subunit of the SAGA/STAGA transcriptional coactivator complex that governs TBP recruitment and transcription initiation at a subset of RNA Pol II promoters [PMID:9726987, PMID:18981477, PMID:40637224]. In yeast, Spt3 was first defined genetically as a positive regulator of Ty/delta element transcription [PMID:6096019] and shown to physically and functionally interact with TBP through allele-specific suppression of TBP mutations and coimmunoprecipitation [PMID:1628834]; this contact was later resolved as a direct Spt3–TBP interface by site-specific photocrosslinking, with mutations on the Spt3-interacting surface of TBP impairing TBP recruitment and activated transcription at SAGA-dependent promoters [PMID:18981477, PMID:18073420]. Within SAGA, Spt3 acts together with Spt8 as a context-dependent regulator of the TBP–TATA interaction — inhibiting TBP binding under non-induced conditions [PMID:10611242] — and operates within a cooperative network with the ATP-dependent TBP inhibitor Mot1 and TFIIA to control TBP distribution and TATA selection [PMID:8972209]. Spt3 additionally drives nucleosome remodeling at induced promoters in a manner separable from its TBP-delivery role [PMID:15057269] and contributes to functions outside SAGA linked to the Ccr4-Not complex [PMID:17660549]. Genome-wide, Spt3 (with Spt8) provides TBP recruitment at Gcn4 target genes that is non-redundant with TFIID [PMID:40637224]. The human orthologue SUPT3H is only partially functionally conserved [PMID:9787080] and resides in the histone-acetyltransferase-containing STAGA complex with GCN5-L and TAF31 [PMID:9726987]; in mammalian cells SAGA assembles without SUPT3H and global TBP recruitment and Pol II transcription are largely unaffected, yet SUPT3H is required for transcription of a specific gene subset and for mouse ESC growth and self-renewal, indicating divergence of the TBP-delivery mechanism between yeast and mammals [PMID:35871303].","teleology":[{"year":1984,"claim":"Established SPT3 as a functional regulator of transcription initiation before its molecular role was known, by showing it is required for proper start-site usage at Ty/delta elements.","evidence":"Genetic null mutant analysis with transcript mapping in S. cerevisiae","pmids":["6096019"],"confidence":"High","gaps":["No molecular partner or biochemical mechanism identified at this stage","Generality beyond Ty elements unaddressed"]},{"year":1992,"claim":"Connected SPT3 to the general transcription machinery by demonstrating physical and allele-specific genetic interaction with TBP, defining a functional Spt3–TBP relationship at specific promoters.","evidence":"Coimmunoprecipitation from yeast extracts plus allele-specific extragenic suppression of a TBP mutant","pmids":["1628834"],"confidence":"High","gaps":["Did not resolve whether the interaction is direct or bridged","Mechanism of promoter selectivity unknown"]},{"year":1994,"claim":"Implicated SPT8 as a promoter of the Spt3–TBP interaction, showing the two subunits act jointly on TBP function.","evidence":"Allele-specific suppressor genetics with spt3/spt8 mutant combinations in yeast","pmids":["8088510"],"confidence":"Medium","gaps":["Single lab, genetic inference without biochemical reconstitution","Molecular basis of SPT8 effect on Spt3 unclear"]},{"year":1997,"claim":"Placed SPT3 within a cooperative regulatory network controlling TBP distribution by defining genetic interactions with the TBP inhibitor MOT1 and with TFIIA.","evidence":"Synthetic lethality screen and genetic suppressor analysis with in vivo transcription assays","pmids":["8972209"],"confidence":"Medium","gaps":["No direct biochemical reconstitution of the three-way interaction","Mechanistic order of events not resolved"]},{"year":1998,"claim":"Identified the human orthologue and its complex context, showing hSPT3 resides in a HAT-containing STAGA complex with GCN5-L and TAF31 rather than with TBP/TFIID, establishing STAGA as the human SAGA counterpart.","evidence":"Immunoprecipitation from HeLa nuclear extracts, HAT activity assay, and molecular cloning","pmids":["9726987"],"confidence":"High","gaps":["Functional role of human SUPT3H in transcription not yet tested","Whether human SUPT3H contacts TBP unaddressed"]},{"year":1998,"claim":"Demonstrated partial functional conservation of SUPT3H from yeast to human via a chimeric complementation strategy.","evidence":"Yeast spt3Δ complementation with full-length and human-yeast chimeric constructs","pmids":["9787080"],"confidence":"Medium","gaps":["Full-length human protein cannot complement, leaving conserved versus divergent functions undefined","Single lab"]},{"year":2000,"claim":"Showed that Spt3/Spt8 act as inhibitory subunits for TBP recruitment under non-induced conditions and that SAGA composition is dynamic, reframing Spt3 as a context-dependent regulator rather than a purely positive factor.","evidence":"In vitro TBP-DNA binding with purified SAGA isoforms plus genetic analysis of deletions","pmids":["10611242"],"confidence":"High","gaps":["How induction switches SAGA composition mechanistically not resolved","In vitro inhibition versus in vivo activation reconciliation incomplete"]},{"year":2004,"claim":"Revealed a TBP-independent chromatin remodeling function of Spt3 at induced promoters, coordinated with Mot1, distinct from its TBP-delivery role.","evidence":"ChIP and nucleosome remodeling assays with spt3/mot1 mutants and synthetic promoters","pmids":["15057269"],"confidence":"Medium","gaps":["Molecular mechanism of remodeling by Spt3 not defined","Single lab"]},{"year":2007,"claim":"Defined a SAGA-independent function of SPT3 functionally linked to the Ccr4-Not complex, showing SPT3 acts outside the SAGA holocomplex.","evidence":"Genetic suppressor and epistasis analysis with SAGA and Ccr4-Not mutants","pmids":["17660549"],"confidence":"Medium","gaps":["No biochemical reconstitution of the SAGA-independent activity","Physical basis of SPT3–Ccr4-Not link unknown"]},{"year":2007,"claim":"Mapped a conserved Spt3 region as the TBP-contacting interface using dominant-negative mutations that allele-specifically interact with TBP and affect TBP levels at Spt3-dependent promoters.","evidence":"Dominant-negative genetics, suppressor isolation, TBP ChIP, and SAGA–TBP Co-IP","pmids":["18073420"],"confidence":"Medium","gaps":["Most mutations do not change bulk SAGA–TBP interaction, complicating interpretation","Single lab"]},{"year":2008,"claim":"Proved a direct physical Spt3–TBP contact required for activated transcription by mapping interacting surfaces and showing functional consequences for TBP recruitment.","evidence":"Site-specific BPA photocrosslinking in vivo and in vitro, mutagenesis, ChIP, and transcription assays","pmids":["18981477"],"confidence":"High","gaps":["Structural model of the contact not determined","Whether the same interface operates in mammals untested"]},{"year":2020,"claim":"Linked the SAGA TBP-binding module to pre-spliceosome assembly, with Spt3 contributing genetically though Spt8 is the direct Prp5 contact.","evidence":"In vitro binding, genetic suppressor analysis, and ChIP/ChIP-seq in yeast","pmids":["32399566"],"confidence":"Medium","gaps":["Spt3 itself does not directly bind Prp5; its role is inferred genetically","Mechanism of transcription-splicing coupling incompletely defined"]},{"year":2022,"claim":"Demonstrated mammalian divergence: SAGA assembles without SUPT3H and global TBP recruitment and Pol II transcription are largely intact, yet SUPT3H is required for a specific gene subset and for mESC self-renewal.","evidence":"SAGA purification from SUPT3H-knockout cells, TBP ChIP, RNA-seq, and mESC growth/self-renewal assays","pmids":["35871303"],"confidence":"High","gaps":["Identity and common features of the SUPT3H-dependent gene subset not defined","Mechanism replacing Spt3-mediated TBP delivery in mammals unknown"]},{"year":2023,"claim":"Extended Spt3 function to chromatin boundary control, showing Spt3/Spt8 block spread of telomeric silencing in a TBP-interaction-dependent, sequence-independent manner.","evidence":"Microarray transcriptomics, RT-qPCR, and analysis of spt3–TBP interaction mutants in yeast","pmids":["37189367"],"confidence":"Medium","gaps":["No direct biochemical reconstitution of the boundary mechanism","Single lab"]},{"year":2025,"claim":"Established that SAGA's Spt3/Spt8-mediated TBP recruitment is non-redundant with TFIID at Gcn4 target genes, separating Spt3-dependent TBP delivery from Gcn5-dependent histone eviction.","evidence":"TBP and Pol II ChIP-seq, auxin-inducible Taf1 depletion, and combinatorial SPT3/SPT8/GCN5 deletions in starved yeast","pmids":["40637224"],"confidence":"High","gaps":["Whether this non-redundancy is conserved in mammals untested","Quantitative contribution of Spt3 versus Spt8 not fully separated"]},{"year":null,"claim":"The mechanistic basis for the divergent, gene-subset-restricted role of mammalian SUPT3H — and how TBP delivery is achieved at SUPT3H-independent promoters in mammals — remains unresolved.","evidence":"","pmids":[],"confidence":"High","gaps":["No structural model of the SUPT3H–TBP interface in mammals","The shared regulatory logic of SUPT3H-dependent genes is undefined","Mechanism linking SUPT3H to mESC self-renewal unknown"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0140110","term_label":"transcription regulator activity","supporting_discovery_ids":[1,6,11,14]},{"term_id":"GO:0098772","term_label":"molecular function regulator activity","supporting_discovery_ids":[3,6,14]}],"localization":[{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[2,6,11]}],"pathway":[{"term_id":"R-HSA-74160","term_label":"Gene expression (Transcription)","supporting_discovery_ids":[1,2,6,14]},{"term_id":"R-HSA-4839726","term_label":"Chromatin organization","supporting_discovery_ids":[7,13]}],"complexes":["SAGA","STAGA"],"partners":["TBP","SPT8","GCN5","TAF31","MOT1"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"O75486","full_name":"Transcription initiation protein SPT3 homolog","aliases":["SPT3-like protein"],"length_aa":317,"mass_kda":35.8,"function":"Probable transcriptional activator","subcellular_location":"Nucleus","url":"https://www.uniprot.org/uniprotkb/O75486/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/SUPT3H","classification":"Not Classified","n_dependent_lines":89,"n_total_lines":1208,"dependency_fraction":0.07367549668874172},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[{"gene":"TAF12","stoichiometry":10.0},{"gene":"TRRAP","stoichiometry":10.0},{"gene":"SF3B3","stoichiometry":0.2},{"gene":"SF3B5","stoichiometry":0.2},{"gene":"USP22","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/search/SUPT3H","total_profiled":1310},"omim":[{"mim_id":"613374","title":"COILED-COIL DOMAIN-CONTAINING PROTEIN 101; CCDC101","url":"https://www.omim.org/entry/613374"},{"mim_id":"612762","title":"SPTY7-LIKE, STAGA COMPLEX SUBUNIT GAMMA; SUPT7L","url":"https://www.omim.org/entry/612762"},{"mim_id":"608790","title":"TRANSCRIPTIONAL ADAPTOR 2B; TADA2B","url":"https://www.omim.org/entry/608790"},{"mim_id":"607640","title":"ATAXIN 7; ATXN7","url":"https://www.omim.org/entry/607640"},{"mim_id":"602947","title":"SPT3 HOMOLOG, SAGA AND STAGA COMPLEX COMPONENT; SUPT3H","url":"https://www.omim.org/entry/602947"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Supported","locations":[{"location":"Nucleoplasm","reliability":"Supported"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in many","driving_tissues":[],"url":"https://www.proteinatlas.org/search/SUPT3H"},"hgnc":{"alias_symbol":["SPT3","SPT3L"],"prev_symbol":[]},"alphafold":{"accession":"O75486","domains":[{"cath_id":"-","chopping":"27-115_128-246_279-303","consensus_level":"medium","plddt":93.3984,"start":27,"end":303}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/O75486","model_url":"https://alphafold.ebi.ac.uk/files/AF-O75486-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-O75486-F1-predicted_aligned_error_v6.png","plddt_mean":80.38},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=SUPT3H","jax_strain_url":"https://www.jax.org/strain/search?query=SUPT3H"},"sequence":{"accession":"O75486","fasta_url":"https://rest.uniprot.org/uniprotkb/O75486.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/O75486/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/O75486"}},"corpus_meta":[{"pmid":"1628834","id":"PMC_1628834","title":"SPT3 interacts with TFIID to allow normal transcription in Saccharomyces cerevisiae.","date":"1992","source":"Genes & development","url":"https://pubmed.ncbi.nlm.nih.gov/1628834","citation_count":204,"is_preprint":false},{"pmid":"6096019","id":"PMC_6096019","title":"The SPT3 gene is required for normal transcription of Ty elements in S. cerevisiae.","date":"1984","source":"Cell","url":"https://pubmed.ncbi.nlm.nih.gov/6096019","citation_count":189,"is_preprint":false},{"pmid":"9726987","id":"PMC_9726987","title":"A human SPT3-TAFII31-GCN5-L acetylase complex distinct from transcription factor IID.","date":"1998","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/9726987","citation_count":166,"is_preprint":false},{"pmid":"10611242","id":"PMC_10611242","title":"Inhibition of TATA-binding protein function by SAGA subunits Spt3 and Spt8 at Gcn4-activated promoters.","date":"2000","source":"Molecular and cellular biology","url":"https://pubmed.ncbi.nlm.nih.gov/10611242","citation_count":114,"is_preprint":false},{"pmid":"3025601","id":"PMC_3025601","title":"Saccharomyces cerevisiae SPT3 gene is required for transposition and transpositional recombination of chromosomal Ty elements.","date":"1986","source":"Molecular and cellular biology","url":"https://pubmed.ncbi.nlm.nih.gov/3025601","citation_count":102,"is_preprint":false},{"pmid":"8972209","id":"PMC_8972209","title":"Evidence that Spt3 functionally interacts with Mot1, TFIIA, and TATA-binding protein to confer promoter-specific transcriptional control in Saccharomyces cerevisiae.","date":"1997","source":"Molecular and cellular biology","url":"https://pubmed.ncbi.nlm.nih.gov/8972209","citation_count":102,"is_preprint":false},{"pmid":"8943321","id":"PMC_8943321","title":"The NOT, SPT3, and MOT1 genes functionally interact to regulate transcription at core promoters.","date":"1996","source":"Molecular and cellular biology","url":"https://pubmed.ncbi.nlm.nih.gov/8943321","citation_count":102,"is_preprint":false},{"pmid":"8088510","id":"PMC_8088510","title":"The Saccharomyces cerevisiae SPT8 gene encodes a very acidic protein that is functionally related to SPT3 and TATA-binding protein.","date":"1994","source":"Genetics","url":"https://pubmed.ncbi.nlm.nih.gov/8088510","citation_count":82,"is_preprint":false},{"pmid":"18981477","id":"PMC_18981477","title":"Site-specific cross-linking of TBP in vivo and in vitro reveals a direct functional interaction with the SAGA subunit Spt3.","date":"2008","source":"Genes & development","url":"https://pubmed.ncbi.nlm.nih.gov/18981477","citation_count":80,"is_preprint":false},{"pmid":"22112214","id":"PMC_22112214","title":"Identification of pathogenesis-associated genes by T-DNA-mediated insertional mutagenesis in Botrytis cinerea: a type 2A phosphoprotein phosphatase and an SPT3 transcription factor have significant impact on virulence.","date":"2012","source":"Molecular plant-microbe interactions : MPMI","url":"https://pubmed.ncbi.nlm.nih.gov/22112214","citation_count":50,"is_preprint":false},{"pmid":"30562548","id":"PMC_30562548","title":"Parathyroid hormone-stimulation of Runx2 during osteoblast differentiation via the regulation of lnc-SUPT3H-1:16 (RUNX2-AS1:32) and miR-6797-5p.","date":"2018","source":"Biochimie","url":"https://pubmed.ncbi.nlm.nih.gov/30562548","citation_count":44,"is_preprint":false},{"pmid":"12072450","id":"PMC_12072450","title":"Spt3 plays opposite roles in filamentous growth in Saccharomyces cerevisiae and Candida albicans and is required for C. albicans virulence.","date":"2002","source":"Genetics","url":"https://pubmed.ncbi.nlm.nih.gov/12072450","citation_count":41,"is_preprint":false},{"pmid":"18073420","id":"PMC_18073420","title":"Characterization of new Spt3 and TATA-binding protein mutants of Saccharomyces cerevisiae: Spt3 TBP allele-specific interactions and bypass of Spt8.","date":"2007","source":"Genetics","url":"https://pubmed.ncbi.nlm.nih.gov/18073420","citation_count":37,"is_preprint":false},{"pmid":"15057269","id":"PMC_15057269","title":"Spt3 and Mot1 cooperate in nucleosome remodeling independently of TBP recruitment.","date":"2004","source":"The EMBO journal","url":"https://pubmed.ncbi.nlm.nih.gov/15057269","citation_count":32,"is_preprint":false},{"pmid":"3020500","id":"PMC_3020500","title":"Analysis of the yeast SPT3 gene and identification of its product, a positive regulator of Ty transcription.","date":"1986","source":"Nucleic acids research","url":"https://pubmed.ncbi.nlm.nih.gov/3020500","citation_count":30,"is_preprint":false},{"pmid":"25120271","id":"PMC_25120271","title":"The bone-specific Runx2-P1 promoter displays conserved three-dimensional chromatin structure with the syntenic Supt3h promoter.","date":"2014","source":"Nucleic acids research","url":"https://pubmed.ncbi.nlm.nih.gov/25120271","citation_count":27,"is_preprint":false},{"pmid":"3127692","id":"PMC_3127692","title":"SPT3 is required for normal levels of a-factor and alpha-factor expression in Saccharomyces cerevisiae.","date":"1988","source":"Molecular and cellular biology","url":"https://pubmed.ncbi.nlm.nih.gov/3127692","citation_count":25,"is_preprint":false},{"pmid":"9787080","id":"PMC_9787080","title":"Characterization of a human homologue of the Saccharomyces cerevisiae transcription factor spt3 (SUPT3H).","date":"1998","source":"Genomics","url":"https://pubmed.ncbi.nlm.nih.gov/9787080","citation_count":18,"is_preprint":false},{"pmid":"31025105","id":"PMC_31025105","title":"EDAR, LYPLAL1, PRDM16, PAX3, DKK1, TNFSF12, CACNA2D3, and SUPT3H gene variants influence facial morphology in a Eurasian population.","date":"2019","source":"Human genetics","url":"https://pubmed.ncbi.nlm.nih.gov/31025105","citation_count":17,"is_preprint":false},{"pmid":"17660549","id":"PMC_17660549","title":"A SAGA-independent function of SPT3 mediates transcriptional deregulation in a mutant of the Ccr4-not complex in Saccharomyces cerevisiae.","date":"2007","source":"Genetics","url":"https://pubmed.ncbi.nlm.nih.gov/17660549","citation_count":16,"is_preprint":false},{"pmid":"32399566","id":"PMC_32399566","title":"Prp5-Spt8/Spt3 interaction mediates a reciprocal coupling between splicing and transcription.","date":"2020","source":"Nucleic acids research","url":"https://pubmed.ncbi.nlm.nih.gov/32399566","citation_count":13,"is_preprint":false},{"pmid":"24289742","id":"PMC_24289742","title":"Transcription factors spt3 and spt8 are associated with conidiation, mycelium growth, and pathogenicity in Fusarium graminearum.","date":"2013","source":"FEMS microbiology letters","url":"https://pubmed.ncbi.nlm.nih.gov/24289742","citation_count":12,"is_preprint":false},{"pmid":"9559549","id":"PMC_9559549","title":"Identification and analysis of homologues of Saccharomyces cerevisiae Spt3 suggest conserved functional domains.","date":"1998","source":"Yeast (Chichester, England)","url":"https://pubmed.ncbi.nlm.nih.gov/9559549","citation_count":6,"is_preprint":false},{"pmid":"37189367","id":"PMC_37189367","title":"Spt3 and Spt8 Are Involved in the Formation of a Silencing Boundary by Interacting with TATA-Binding Protein.","date":"2023","source":"Biomolecules","url":"https://pubmed.ncbi.nlm.nih.gov/37189367","citation_count":5,"is_preprint":false},{"pmid":"35871303","id":"PMC_35871303","title":"SUPT3H-less SAGA coactivator can assemble and function without significantly perturbing RNA polymerase II transcription in mammalian cells.","date":"2022","source":"Nucleic acids research","url":"https://pubmed.ncbi.nlm.nih.gov/35871303","citation_count":5,"is_preprint":false},{"pmid":"20432932","id":"PMC_20432932","title":"[Improving ethanol tolerance of Saccharomyces cerevisiae industrial strain by directed evolution of SPT3].","date":"2010","source":"Sheng wu gong cheng xue bao = Chinese journal of biotechnology","url":"https://pubmed.ncbi.nlm.nih.gov/20432932","citation_count":4,"is_preprint":false},{"pmid":"28656551","id":"PMC_28656551","title":"Improvement of Lead Tolerance of Saccharomyces cerevisiae by Random Mutagenesis of Transcription Regulator SPT3.","date":"2017","source":"Applied biochemistry and biotechnology","url":"https://pubmed.ncbi.nlm.nih.gov/28656551","citation_count":3,"is_preprint":false},{"pmid":"8363741","id":"PMC_8363741","title":"[Effects of treatments (heat and fermentation by Rhizopus oligosporus sp-T3) of sweet white lupin seeds on certain factors of its nutritional use].","date":"1993","source":"Reproduction, nutrition, development","url":"https://pubmed.ncbi.nlm.nih.gov/8363741","citation_count":3,"is_preprint":false},{"pmid":"34849873","id":"PMC_34849873","title":"Functional characterization of the developmental genes asm2, asm3, and spt3 required for fruiting body formation in the filamentous ascomycete Sordaria macrospora.","date":"2021","source":"Genetics","url":"https://pubmed.ncbi.nlm.nih.gov/34849873","citation_count":2,"is_preprint":false},{"pmid":"40637224","id":"PMC_40637224","title":"SAGA subunits Spt3 and Spt8 act directly and non-redundantly with TFIID in TBP recruitment in the Gcn4 transcriptome.","date":"2025","source":"Nucleic acids research","url":"https://pubmed.ncbi.nlm.nih.gov/40637224","citation_count":1,"is_preprint":false},{"pmid":"32624556","id":"PMC_32624556","title":"The function of Spt3, a subunit of the SAGA complex, in PGK1 transcription is restored only partially when reintroduced by plasmid into taf1 spt3 double mutant yeast strains.","date":"2020","source":"Genes & genetic systems","url":"https://pubmed.ncbi.nlm.nih.gov/32624556","citation_count":1,"is_preprint":false},{"pmid":"36757926","id":"PMC_36757926","title":"TFIID dependency of steady-state mRNA transcription altered epigenetically by simultaneous functional loss of Taf1 and Spt3 is Hsp104-dependent.","date":"2023","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/36757926","citation_count":0,"is_preprint":false},{"pmid":null,"id":"bio_10.1101_2025.08.21.25334163","title":"Present-day admixed genomes reveal prehistoric adaptation to cold, maritime diet, and local pathogens in Patagonia","date":"2025-08-26","source":"bioRxiv","url":"https://doi.org/10.1101/2025.08.21.25334163","citation_count":0,"is_preprint":true}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":17142,"output_tokens":4370,"usd":0.058488,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":12301,"output_tokens":4412,"usd":0.085903,"stage2_stop_reason":"end_turn"},"total_usd":0.144391,"stage1_batch_id":"msgbatch_017qqVz33Ga63SCDwzb35XPb","stage2_batch_id":"msgbatch_01Scr2Ei9x4HJMiRGxwrmvLK","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 1992,\n      \"finding\": \"Yeast SPT3 physically associates with TFIID (TBP) in yeast cell extracts, as demonstrated by coimmunoprecipitation. Allele-specific suppression of spt15-21 (a TBP mutation) by spt3 mutations indicates a direct functional interaction between SPT3 and TBP required for transcription at particular promoters in vivo.\",\n      \"method\": \"Coimmunoprecipitation from yeast extracts; allele-specific extragenic suppressor genetics\",\n      \"journal\": \"Genes & development\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal genetic and biochemical evidence (Co-IP + allele-specific suppression), replicated and extended by multiple subsequent studies\",\n      \"pmids\": [\"1628834\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1984,\n      \"finding\": \"SPT3 is required for normal transcription initiation from delta (Ty LTR) sequences in S. cerevisiae; in spt3 null mutants, Ty delta-delta transcripts are absent and initiation shifts ~800 bp into the epsilon region, establishing SPT3 as a positive regulator of Ty element transcription.\",\n      \"method\": \"Genetic null mutant analysis; Northern blot / transcript mapping\",\n      \"journal\": \"Cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — clean null mutant with defined transcriptional phenotype, foundational result replicated across many subsequent studies\",\n      \"pmids\": [\"6096019\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1998,\n      \"finding\": \"Human SUPT3H (hSPT3) is not associated in vivo with human TBP/TFIID or with a TBP-free TAFII complex; instead, hSPT3 co-purifies in vivo with TAFII31 and the long form of human GCN5 (hGCN5-L) in a novel complex (STAGA) that possesses histone acetyltransferase activity. This established STAGA as the human homologue of yeast SAGA.\",\n      \"method\": \"Immunoprecipitation from HeLa cell nuclear extracts; histone acetyltransferase activity assay; molecular cloning and sequence analysis\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal Co-IP with enzymatic activity assay, multiple orthogonal methods in one study, foundational paper for human STAGA/SAGA\",\n      \"pmids\": [\"9726987\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2000,\n      \"finding\": \"Within SAGA, Spt3 (and Spt8) inhibit TBP binding to the HIS3 promoter in vitro; SAGA lacking Spt3 or Spt8 loses this inhibitory activity. Two distinct forms of SAGA exist in cell extracts, one lacking Spt8, and conditions that induce transcription shift the balance toward the Spt8-lacking form, indicating that SAGA composition is dynamic and that Spt3/Spt8 function as inhibitory subunits for TBP recruitment under non-induced conditions.\",\n      \"method\": \"In vitro TBP-DNA binding assay with purified SAGA complexes; biochemical fractionation of SAGA isoforms; genetic analysis of spt3 and spt8 deletion effects on transcription\",\n      \"journal\": \"Molecular and cellular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Moderate — in vitro binding assay with purified complex + genetic readout, multiple orthogonal methods in single study\",\n      \"pmids\": [\"10611242\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1997,\n      \"finding\": \"Genetic epistasis experiments show that SPT3 functionally interacts with MOT1 (an ATP-dependent TBP inhibitor) and TFIIA to regulate TBP-DNA interactions and TATA-box selection in vivo. Double mutant lethality (spt3Δ mot1) and suppression of spt3Δ by TFIIA overexpression define a cooperative pathway controlling TBP distribution at promoters.\",\n      \"method\": \"Synthetic lethality screen; genetic suppressor analysis; in vivo transcription assays\",\n      \"journal\": \"Molecular and cellular biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — genetic epistasis with multiple allele combinations, single lab, no direct biochemical reconstitution of the three-way interaction\",\n      \"pmids\": [\"8972209\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1994,\n      \"finding\": \"Genetic analysis shows that spt8 null mutations are suppressed by particular spt3 alleles, suggesting that SPT8 promotes a functional SPT3–TBP interaction. Both SPT8 and SPT3 are required for TBP function at specific promoters.\",\n      \"method\": \"Genetic suppressor analysis; null mutant combination phenotyping\",\n      \"journal\": \"Genetics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — allele-specific suppression genetics across multiple allele combinations, single lab\",\n      \"pmids\": [\"8088510\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2008,\n      \"finding\": \"Site-specific in vivo and in vitro cross-linking using the non-natural photoreactive amino acid BPA substituted onto TBP surface residues demonstrates a direct physical interaction between TBP and SAGA subunits Spt3 and Spt8. Mutations on the Spt3-interacting surface of TBP reduce TBP–SAGA interaction, decrease transcriptional activation, and impair TBP recruitment to a SAGA-dependent promoter, proving that a direct Spt3–TBP contact is required for activated transcription.\",\n      \"method\": \"Site-specific photocrosslinking with non-natural amino acid BPA in vivo and in vitro; chromatin immunoprecipitation; in vivo transcription assays; mutagenesis\",\n      \"journal\": \"Genes & development\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — direct cross-linking with mutagenesis validation plus functional ChIP readout, multiple orthogonal methods demonstrating mechanistic direct interaction\",\n      \"pmids\": [\"18981477\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2004,\n      \"finding\": \"Spt3 (within SAGA) is required for nucleosome remodeling at the GAL1 promoter upon transcriptional induction, and this function is independent of TBP recruitment. Spt3 and Mot1 are both required for nucleosome remodeling and are recruited to GAL1 promoter (and a non-promoter nucleosome near an activator-binding site) in an interdependent manner, revealing a chromatin remodeling role for Spt3 distinct from its TBP-delivery role.\",\n      \"method\": \"Chromatin immunoprecipitation; nucleosome remodeling assays; genetic analysis of spt3 and mot1 mutants; synthetic promoter experiments\",\n      \"journal\": \"The EMBO journal\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — ChIP plus genetic dissection with multiple mutant combinations, single lab\",\n      \"pmids\": [\"15057269\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2007,\n      \"finding\": \"New dominant-negative spt3 mutations cluster in a conserved region of Spt3 and allele-specifically interact with spt15 (TBP) mutations, confirming a direct Spt3–TBP interface in vivo. One spt3 mutation (spt3-401) greatly increases SAGA–TBP physical association, while most spt3, spt8, and spt15 mutations do not alter bulk SAGA–TBP interaction, suggesting that direct Spt3–TBP contact is required for normal TBP levels at Spt3-dependent promoters.\",\n      \"method\": \"Dominant-negative overexpression genetics; extragenic suppressor isolation; TBP ChIP; SAGA–TBP co-immunoprecipitation\",\n      \"journal\": \"Genetics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — allele-specific genetics combined with ChIP and Co-IP, single lab\",\n      \"pmids\": [\"18073420\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2007,\n      \"finding\": \"A SAGA-independent function of SPT3 is identified: deletion of SPT3, but not deletion of other SAGA subunits (SPT7), suppresses transcriptional defects of a not1-2 (Ccr4-Not scaffold) mutant, and spt3Δ shows synthetic phenotypes with spt7Δ. This indicates SPT3 has functions outside the SAGA complex that are functionally linked to the Ccr4-Not complex.\",\n      \"method\": \"Genetic suppressor analysis; transcriptional assays; genetic epistasis with SAGA and Ccr4-Not mutants\",\n      \"journal\": \"Genetics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — genetic epistasis with multiple combinatorial mutants, single lab, no direct biochemical reconstitution of SAGA-independent SPT3 function\",\n      \"pmids\": [\"17660549\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1998,\n      \"finding\": \"The human SUPT3H cDNA encodes a protein sharing 30% identity with yeast Spt3 across three conserved domains. Full-length SUPT3H cannot complement yeast spt3Δ, but a human-yeast chimeric gene containing 42% human sequences can partially complement, indicating partial functional conservation of transcriptional control from yeast to human.\",\n      \"method\": \"Molecular cloning; yeast complementation assay with full-length and chimeric constructs\",\n      \"journal\": \"Genomics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — functional complementation in yeast with chimeric gene approach, single lab\",\n      \"pmids\": [\"9787080\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"In mammalian cells (human U2OS and mouse ESCs), SAGA can assemble without SUPT3H. Loss of SUPT3H does not cause major changes in TBP accumulation at gene promoters and does not globally impair RNA Pol II transcription; instead, SUPT3H affects transcription of only a specific gene subset and is required for mESC growth and self-renewal. This contrasts with yeast where Spt3 broadly controls TBP recruitment.\",\n      \"method\": \"Biochemical purification of SAGA from SUPT3H-knockout cells; ChIP for TBP; RNA-seq; mESC growth/self-renewal assays\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple orthogonal methods (complex purification, ChIP, RNA-seq, phenotypic assays) in one study demonstrating mammalian-specific mechanistic divergence\",\n      \"pmids\": [\"35871303\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"The spliceosomal ATPase Prp5p directly interacts with SAGA subunit Spt8p (but not Spt3p) in vitro. However, both spt8Δ and spt3Δ rescue Prp5 splicing defects and restore Pol II recruitment to an intron-containing gene. This interaction mediates reciprocal coupling between transcription initiation/elongation (via the SAGA TBP-binding module containing Spt3/Spt8) and pre-spliceosome assembly.\",\n      \"method\": \"In vitro binding assay (Prp5–Spt8 direct interaction); genetic suppressor analysis; chromatin immunoprecipitation (ChIP and ChIP-seq)\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — in vitro binding plus ChIP-seq plus genetic epistasis, but Spt3 itself does not directly bind Prp5; its role is inferred genetically\",\n      \"pmids\": [\"32399566\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"In S. cerevisiae, Spt3 and Spt8 (SAGA subunits) block the spread of telomeric silencing regions at the right arm of chromosome III in a TBP-interaction-dependent manner; mutants altering the Spt3–TBP interaction impair boundary formation. Spt3 has a greater genome-wide transcriptional effect than Spt8, and boundary formation is DNA sequence-independent.\",\n      \"method\": \"Microarray transcriptome analysis; RT-qPCR of subtelomeric genes; genetic analysis of spt3–TBP interaction mutants\",\n      \"journal\": \"Biomolecules\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — genetic and transcriptomic analysis, single lab, no direct biochemical reconstitution of boundary mechanism\",\n      \"pmids\": [\"37189367\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"ChIP-seq in amino acid-starved S. cerevisiae shows that deleting SPT3 or SPT8 (but not GCN5) reduces TBP binding at many Gcn4 target genes, while deleting GCN5 (but not SPT3 or SPT8) impairs promoter histone eviction. Nuclear depletion of TFIID subunit Taf1 further reduces TBP recruitment at SAGA-dependent genes only when Spt3 or Spt8 are absent, demonstrating that SAGA's TBP-recruitment function via Spt3/Spt8 is non-redundant with TFIID in the Gcn4 transcriptome.\",\n      \"method\": \"ChIP-seq for TBP and Pol II; auxin-inducible degron nuclear depletion of Taf1; genetic deletion of SPT3, SPT8, GCN5\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — genome-wide ChIP-seq with multiple combinatorial mutants and orthogonal protein depletion, rigorous mechanistic dissection of SAGA TBP-delivery function\",\n      \"pmids\": [\"40637224\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"In murine pre-osteoblastic MC3T3-E1 cells, the Supt3h promoter physically contacts the bone-specific Runx2-P1 promoter (located in the first intron of which Supt3h resides) with increased contact frequency during osteoblast differentiation. RUNX2 and CTCF bind the Supt3h promoter, and interplasmid-3C plus luciferase reporter assays show that the Supt3h promoter can modulate Runx2-P1 transcriptional activity via direct association.\",\n      \"method\": \"Chromosome conformation capture (3C); DNaseI hypersensitivity assay; ChIP for RUNX2 and CTCF; luciferase reporter assay\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — 3C and reporter assays with ChIP, multiple methods, single lab; functional consequence of Supt3h promoter on Runx2-P1 activity established\",\n      \"pmids\": [\"25120271\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"SUPT3H/SPT3 is a conserved component of the SAGA (Spt-Ada-Gcn5-Acetyltransferase) coactivator complex that directly contacts TBP via a defined surface on both proteins to regulate TBP recruitment and transcription initiation at a subset of RNA Pol II promoters; in yeast, Spt3 (together with Spt8) can both promote and inhibit TBP-TATA interactions depending on promoter context, participates in nucleosome remodeling independently of TBP recruitment in cooperation with Mot1, and functions non-redundantly with TFIID for TBP delivery at Gcn4-induced genes; in mammalian cells, SUPT3H is dispensable for overall SAGA assembly and global TBP recruitment but is required for transcription of a specific gene subset and for mouse ESC growth and self-renewal, indicating that the TBP-delivery mechanism has diverged between yeast and mammals.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"SUPT3H/Spt3 is a conserved subunit of the SAGA/STAGA transcriptional coactivator complex that governs TBP recruitment and transcription initiation at a subset of RNA Pol II promoters [#2, #6, #14]. In yeast, Spt3 was first defined genetically as a positive regulator of Ty/delta element transcription [#1] and shown to physically and functionally interact with TBP through allele-specific suppression of TBP mutations and coimmunoprecipitation [#0]; this contact was later resolved as a direct Spt3–TBP interface by site-specific photocrosslinking, with mutations on the Spt3-interacting surface of TBP impairing TBP recruitment and activated transcription at SAGA-dependent promoters [#6, #8]. Within SAGA, Spt3 acts together with Spt8 as a context-dependent regulator of the TBP–TATA interaction — inhibiting TBP binding under non-induced conditions [#3] — and operates within a cooperative network with the ATP-dependent TBP inhibitor Mot1 and TFIIA to control TBP distribution and TATA selection [#4]. Spt3 additionally drives nucleosome remodeling at induced promoters in a manner separable from its TBP-delivery role [#7] and contributes to functions outside SAGA linked to the Ccr4-Not complex [#9]. Genome-wide, Spt3 (with Spt8) provides TBP recruitment at Gcn4 target genes that is non-redundant with TFIID [#14]. The human orthologue SUPT3H is only partially functionally conserved [#10] and resides in the histone-acetyltransferase-containing STAGA complex with GCN5-L and TAF31 [#2]; in mammalian cells SAGA assembles without SUPT3H and global TBP recruitment and Pol II transcription are largely unaffected, yet SUPT3H is required for transcription of a specific gene subset and for mouse ESC growth and self-renewal, indicating divergence of the TBP-delivery mechanism between yeast and mammals [#11].\",\n  \"teleology\": [\n    {\n      \"year\": 1984,\n      \"claim\": \"Established SPT3 as a functional regulator of transcription initiation before its molecular role was known, by showing it is required for proper start-site usage at Ty/delta elements.\",\n      \"evidence\": \"Genetic null mutant analysis with transcript mapping in S. cerevisiae\",\n      \"pmids\": [\"6096019\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"No molecular partner or biochemical mechanism identified at this stage\", \"Generality beyond Ty elements unaddressed\"]\n    },\n    {\n      \"year\": 1992,\n      \"claim\": \"Connected SPT3 to the general transcription machinery by demonstrating physical and allele-specific genetic interaction with TBP, defining a functional Spt3–TBP relationship at specific promoters.\",\n      \"evidence\": \"Coimmunoprecipitation from yeast extracts plus allele-specific extragenic suppression of a TBP mutant\",\n      \"pmids\": [\"1628834\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not resolve whether the interaction is direct or bridged\", \"Mechanism of promoter selectivity unknown\"]\n    },\n    {\n      \"year\": 1994,\n      \"claim\": \"Implicated SPT8 as a promoter of the Spt3–TBP interaction, showing the two subunits act jointly on TBP function.\",\n      \"evidence\": \"Allele-specific suppressor genetics with spt3/spt8 mutant combinations in yeast\",\n      \"pmids\": [\"8088510\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Single lab, genetic inference without biochemical reconstitution\", \"Molecular basis of SPT8 effect on Spt3 unclear\"]\n    },\n    {\n      \"year\": 1997,\n      \"claim\": \"Placed SPT3 within a cooperative regulatory network controlling TBP distribution by defining genetic interactions with the TBP inhibitor MOT1 and with TFIIA.\",\n      \"evidence\": \"Synthetic lethality screen and genetic suppressor analysis with in vivo transcription assays\",\n      \"pmids\": [\"8972209\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No direct biochemical reconstitution of the three-way interaction\", \"Mechanistic order of events not resolved\"]\n    },\n    {\n      \"year\": 1998,\n      \"claim\": \"Identified the human orthologue and its complex context, showing hSPT3 resides in a HAT-containing STAGA complex with GCN5-L and TAF31 rather than with TBP/TFIID, establishing STAGA as the human SAGA counterpart.\",\n      \"evidence\": \"Immunoprecipitation from HeLa nuclear extracts, HAT activity assay, and molecular cloning\",\n      \"pmids\": [\"9726987\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Functional role of human SUPT3H in transcription not yet tested\", \"Whether human SUPT3H contacts TBP unaddressed\"]\n    },\n    {\n      \"year\": 1998,\n      \"claim\": \"Demonstrated partial functional conservation of SUPT3H from yeast to human via a chimeric complementation strategy.\",\n      \"evidence\": \"Yeast spt3Δ complementation with full-length and human-yeast chimeric constructs\",\n      \"pmids\": [\"9787080\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Full-length human protein cannot complement, leaving conserved versus divergent functions undefined\", \"Single lab\"]\n    },\n    {\n      \"year\": 2000,\n      \"claim\": \"Showed that Spt3/Spt8 act as inhibitory subunits for TBP recruitment under non-induced conditions and that SAGA composition is dynamic, reframing Spt3 as a context-dependent regulator rather than a purely positive factor.\",\n      \"evidence\": \"In vitro TBP-DNA binding with purified SAGA isoforms plus genetic analysis of deletions\",\n      \"pmids\": [\"10611242\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"How induction switches SAGA composition mechanistically not resolved\", \"In vitro inhibition versus in vivo activation reconciliation incomplete\"]\n    },\n    {\n      \"year\": 2004,\n      \"claim\": \"Revealed a TBP-independent chromatin remodeling function of Spt3 at induced promoters, coordinated with Mot1, distinct from its TBP-delivery role.\",\n      \"evidence\": \"ChIP and nucleosome remodeling assays with spt3/mot1 mutants and synthetic promoters\",\n      \"pmids\": [\"15057269\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Molecular mechanism of remodeling by Spt3 not defined\", \"Single lab\"]\n    },\n    {\n      \"year\": 2007,\n      \"claim\": \"Defined a SAGA-independent function of SPT3 functionally linked to the Ccr4-Not complex, showing SPT3 acts outside the SAGA holocomplex.\",\n      \"evidence\": \"Genetic suppressor and epistasis analysis with SAGA and Ccr4-Not mutants\",\n      \"pmids\": [\"17660549\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No biochemical reconstitution of the SAGA-independent activity\", \"Physical basis of SPT3–Ccr4-Not link unknown\"]\n    },\n    {\n      \"year\": 2007,\n      \"claim\": \"Mapped a conserved Spt3 region as the TBP-contacting interface using dominant-negative mutations that allele-specifically interact with TBP and affect TBP levels at Spt3-dependent promoters.\",\n      \"evidence\": \"Dominant-negative genetics, suppressor isolation, TBP ChIP, and SAGA–TBP Co-IP\",\n      \"pmids\": [\"18073420\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Most mutations do not change bulk SAGA–TBP interaction, complicating interpretation\", \"Single lab\"]\n    },\n    {\n      \"year\": 2008,\n      \"claim\": \"Proved a direct physical Spt3–TBP contact required for activated transcription by mapping interacting surfaces and showing functional consequences for TBP recruitment.\",\n      \"evidence\": \"Site-specific BPA photocrosslinking in vivo and in vitro, mutagenesis, ChIP, and transcription assays\",\n      \"pmids\": [\"18981477\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Structural model of the contact not determined\", \"Whether the same interface operates in mammals untested\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Linked the SAGA TBP-binding module to pre-spliceosome assembly, with Spt3 contributing genetically though Spt8 is the direct Prp5 contact.\",\n      \"evidence\": \"In vitro binding, genetic suppressor analysis, and ChIP/ChIP-seq in yeast\",\n      \"pmids\": [\"32399566\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Spt3 itself does not directly bind Prp5; its role is inferred genetically\", \"Mechanism of transcription-splicing coupling incompletely defined\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Demonstrated mammalian divergence: SAGA assembles without SUPT3H and global TBP recruitment and Pol II transcription are largely intact, yet SUPT3H is required for a specific gene subset and for mESC self-renewal.\",\n      \"evidence\": \"SAGA purification from SUPT3H-knockout cells, TBP ChIP, RNA-seq, and mESC growth/self-renewal assays\",\n      \"pmids\": [\"35871303\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Identity and common features of the SUPT3H-dependent gene subset not defined\", \"Mechanism replacing Spt3-mediated TBP delivery in mammals unknown\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Extended Spt3 function to chromatin boundary control, showing Spt3/Spt8 block spread of telomeric silencing in a TBP-interaction-dependent, sequence-independent manner.\",\n      \"evidence\": \"Microarray transcriptomics, RT-qPCR, and analysis of spt3–TBP interaction mutants in yeast\",\n      \"pmids\": [\"37189367\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No direct biochemical reconstitution of the boundary mechanism\", \"Single lab\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Established that SAGA's Spt3/Spt8-mediated TBP recruitment is non-redundant with TFIID at Gcn4 target genes, separating Spt3-dependent TBP delivery from Gcn5-dependent histone eviction.\",\n      \"evidence\": \"TBP and Pol II ChIP-seq, auxin-inducible Taf1 depletion, and combinatorial SPT3/SPT8/GCN5 deletions in starved yeast\",\n      \"pmids\": [\"40637224\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether this non-redundancy is conserved in mammals untested\", \"Quantitative contribution of Spt3 versus Spt8 not fully separated\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"The mechanistic basis for the divergent, gene-subset-restricted role of mammalian SUPT3H — and how TBP delivery is achieved at SUPT3H-independent promoters in mammals — remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"High\",\n      \"gaps\": [\"No structural model of the SUPT3H–TBP interface in mammals\", \"The shared regulatory logic of SUPT3H-dependent genes is undefined\", \"Mechanism linking SUPT3H to mESC self-renewal unknown\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0140110\", \"supporting_discovery_ids\": [1, 6, 11, 14]},\n      {\"term_id\": \"GO:0098772\", \"supporting_discovery_ids\": [3, 6, 14]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [2, 6, 11]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-74160\", \"supporting_discovery_ids\": [1, 2, 6, 14]},\n      {\"term_id\": \"R-HSA-4839726\", \"supporting_discovery_ids\": [7, 13]}\n    ],\n    \"complexes\": [\"SAGA\", \"STAGA\"],\n    \"partners\": [\"TBP\", \"SPT8\", \"GCN5\", \"TAF31\", \"MOT1\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"faith_supported":6,"faith_total":6,"faith_pct":100.0}}