{"gene":"TBP","run_date":"2026-06-10T10:51:54","timeline":{"discoveries":[{"year":1991,"finding":"TFIID/TBP binds primarily within the minor groove of the TATA box DNA helix, established by replacing thymines and adenines with cytosines and inosines to swap major-groove identity while preserving the minor groove surface.","method":"Novel base-substitution approach (C/I replacement) combined with DNA-binding assays","journal":"Cell","confidence":"High","confidence_rationale":"Tier 1 / Strong — direct biochemical experiment with novel chemical substitution method, foundational result replicated in subsequent structural studies","pmids":["1760847"],"is_preprint":false},{"year":1992,"finding":"TBP induces DNA bending around the TATA element upon binding, demonstrated with recombinant yeast and human TBP using a permuted binding site/gel retardation assay.","method":"Permuted binding site/gel retardation assay with recombinant TBP","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"High","confidence_rationale":"Tier 1 / Strong — reconstituted in vitro with recombinant protein, confirmed by subsequent crystal structures","pmids":["1736286"],"is_preprint":false},{"year":1992,"finding":"A 12 amino acid region of TBP directly contacts the TATA element and determines DNA-binding specificity; specific substitutions in this region alter specificity from TATAAA to TGTAAA both in yeast and when the equivalent substitutions are introduced into human TBP.","method":"Genetic selection for altered-specificity mutants, biochemical DNA-binding assays, in vivo transcription assays","journal":"Cell","confidence":"High","confidence_rationale":"Tier 1 / Strong — mutagenesis combined with biochemical and in vivo functional validation, cross-species confirmation","pmids":["1739977"],"is_preprint":false},{"year":1992,"finding":"TBP in HeLa extracts exists in two distinct multisubunit complexes (~300 kDa B-TFIID and >700 kDa D-TFIID), both containing the 38 kDa TBP; only the larger complex supports transcriptional activation by acidic or glutamine-rich activators.","method":"Biochemical fractionation, cofractionation studies, antisera-based detection, in vitro transcription","journal":"Genes & development","confidence":"High","confidence_rationale":"Tier 2 / Strong — biochemical fractionation with functional transcription assays, foundational result confirmed by many subsequent studies","pmids":["1936986"],"is_preprint":false},{"year":1992,"finding":"B-TFIID is composed of two subunits: TBP and a 170 kDa TAF specific to B-TFIID (not present in D-TFIID); purified B-TFIID has (d)ATPase activity.","method":"Biochemical purification, subunit composition analysis, ATPase activity assay","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — purified complex with subunit characterization and enzymatic assay, single lab","pmids":["1387711"],"is_preprint":false},{"year":1993,"finding":"Recombinant hTAFII250 binds directly to TBP both in vitro and in yeast and participates in the formation of the TFIID complex; the CCG1/hTAFII250 gene is linked to cell-cycle progression.","method":"Recombinant protein expression, in vitro binding, yeast interaction assays","journal":"Nature","confidence":"High","confidence_rationale":"Tier 1 / Strong — direct binding demonstrated in vitro and in vivo by two orthogonal approaches","pmids":["7680771"],"is_preprint":false},{"year":1993,"finding":"p53 binds directly to TBP and cooperates with TBP or partially purified TFIID to enhance binding to a DNA fragment containing both a p53-binding site and a TATA box; p53 strongly inhibits TBP (but not TFIID) binding to a TATA box lacking a p53 site.","method":"Co-IP, DNA-binding assays (EMSA), in vivo cotransfection transcription assays","journal":"Genes & development","confidence":"High","confidence_rationale":"Tier 2 / Strong — multiple orthogonal biochemical and cellular assays, negative control included, replicated across contexts","pmids":["8405994"],"is_preprint":false},{"year":1993,"finding":"p300 co-immunoprecipitates with TBP and shares two additional common phosphoproteins (64 and 59 kDa) with TBP complexes, indicating p300 interacts with TBP (possibly through intermediary proteins).","method":"Co-immunoprecipitation, partial proteolytic digest comparison","journal":"Oncogene","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — single lab, co-IP only, interaction may be indirect","pmids":["8502484"],"is_preprint":false},{"year":1993,"finding":"Drosophila TAFII60 and human TAFII70 bind weakly to TBP and strongly to TAFII250; in combination with TBP and TAFII250 they form a stable ternary complex; dTAFII60 and hTAFII70 also directly interact with TAFII40.","method":"Recombinant protein expression, pull-down binding assays","journal":"The EMBO journal","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct binding by reconstitution, single lab","pmids":["8262073"],"is_preprint":false},{"year":1994,"finding":"SL1 TAFIs (TAFI110, 63, 48) can each bind individually and specifically to TBP, and form a stable TBP-TAF complex; binding of SL1 TAFIs to TBP is mutually exclusive with binding of TFIID subunits (TAFII250 or TAFII150), establishing a mechanism for directing TBP into polymerase-selective complexes.","method":"Reconstituted subunit interaction assays, complementary cDNA expression, biochemical binding competition","journal":"Science","confidence":"High","confidence_rationale":"Tier 1 / Strong — reconstitution of multi-subunit interactions with competition assays, mechanistically definitive","pmids":["7801123"],"is_preprint":false},{"year":1994,"finding":"Drosophila holo-TFIIA (L/S complex) binds TBP with high affinity and cooperatively with TBP to TATA box DNA (extended DNase footprint); holo-TFIIA stimulates basal transcription and enhances activation by Sp1, VP16, and NTF-1.","method":"Reconstitution of recombinant TFIIA subunits, subunit interaction studies, DNase footprinting, in vitro transcription","journal":"Genes & development","confidence":"High","confidence_rationale":"Tier 1 / Strong — reconstituted system with multiple orthogonal assays","pmids":["7958898"],"is_preprint":false},{"year":1994,"finding":"The TBP subunit of TFIID crosslinks specifically to the TATA element; a 150 kDa TAF crosslinks to downstream regions (+10 to +15 and +35 to +47); a >205 kDa TAF crosslinks preferentially to +35 to +42; TAF-DNA interactions downstream are disrupted at elevated salt while TBP-TATA interaction is maintained.","method":"Protein-DNA crosslinking of TFIID complex","journal":"Nucleic acids research","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct crosslinking method mapping TBP and TAF contacts, single lab","pmids":["8139922"],"is_preprint":false},{"year":1995,"finding":"Crystal structure of the TFIIB/TBP/TATA-element ternary complex at 2.7 Å resolution: core TFIIB resembles cyclin A and recognizes the preformed TBP-DNA complex through protein-protein and protein-DNA contacts; the TFIIB amino-terminal domain forms the downstream surface where it could fix the transcription start site.","method":"X-ray crystallography","journal":"Nature","confidence":"High","confidence_rationale":"Tier 1 / Strong — atomic resolution crystal structure with functional implications, landmark study","pmids":["7675079"],"is_preprint":false},{"year":1995,"finding":"Distamycin A and tallimustine bind the DNA minor groove and prevent TBP (and TBP-TFIIA, TBP-TFIIA-TFIIB) binding to the TATA box; once formed, TBP-containing complexes are more resistant to these drugs; both inhibit basal in vitro transcription at similar concentrations.","method":"EMSA (gel shift), in vitro transcription","journal":"Nucleic acids research","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct binding and functional transcription assays, single lab, two orthogonal methods","pmids":["7784168"],"is_preprint":false},{"year":1995,"finding":"Electron microscopy of yeast TBP on HIV and adeno promoters shows TBP forms dimers (63 kDa) at the TATA box and higher-order oligomers; TBP dimers bend the DNA approximately 80–90° around the TATA box.","method":"Electron microscopy (three preparative methods), mass analysis of protein particles","journal":"Journal of molecular biology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — three independent EM methods used, single lab","pmids":["7533216"],"is_preprint":false},{"year":1997,"finding":"TBP/TFIID binds selectively to cisplatin- or UV-damaged DNA (structural similarity between damaged DNA and TATA box), sequestering TBP away from promoters; microinjection of additional TBP in living human fibroblasts alleviates UV-induced reduction in RNA synthesis.","method":"Filter binding, in vitro transcription competition, 3D structural analysis, microinjection into living cells","journal":"The EMBO journal","confidence":"High","confidence_rationale":"Tier 1–2 / Strong — multiple orthogonal methods including in vitro assays and live-cell functional rescue","pmids":["9405373"],"is_preprint":false},{"year":1997,"finding":"TFIIA stabilizes TBP/TATA interactions approximately 10-fold (reduces koff); upstream DNA contacts by TFIIA further stabilize the TFIIA-TBP complex; in the absence of DNA, TFIIA dissociates from TBP rapidly (koff ~4.9×10⁻³ s⁻¹).","method":"Nitrocellulose filter binding assay (koff measurements), EMSA, nickel-agarose pull-down with His-tagged TFIIA","journal":"Journal of molecular biology","confidence":"High","confidence_rationale":"Tier 1 / Strong — quantitative kinetic measurements with multiple methods, mechanistically precise","pmids":["9300055"],"is_preprint":false},{"year":1997,"finding":"TBP-TFIIB interaction is critical for transcription in vitro; an altered-specificity TATA-TBP-TFIIB array showed that many activators use the known TBP-TFIIB interaction to stimulate transcription in human cells, but a glutamine-rich Sp1 activation domain activates independently of this interaction.","method":"Rationally designed altered-specificity TBP-TFIIB interaction, in vivo transcription assays in human cells","journal":"Science","confidence":"High","confidence_rationale":"Tier 1 / Strong — structure-guided mutagenesis with in vivo functional validation, dissects specificity of activator-TBP-TFIIB dependency","pmids":["9012349"],"is_preprint":false},{"year":1998,"finding":"TAFIIs (specifically TAFII250) inhibit TBP-DNA binding and TBP-TFIIA binding; TFIIA overcomes TAFII-mediated inhibition of TBP-DNA binding by competing with TAFII250 for access to TBP; limited proteolysis of TFIID relieves inhibition of TBP-DNA binding.","method":"EMSA, DNase I footprinting, in vitro transcription, temperature-sensitive cell line (ts13)","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1–2 / Strong — multiple orthogonal biochemical and cellular approaches, mechanistically defined","pmids":["9603936"],"is_preprint":false},{"year":1999,"finding":"TFIIA promotes dissociation of TBP dimers (which block DNA binding) and accelerates TBP binding kinetics; TFIID dimer dissociation is slow and rate-limiting in DNA binding, and TFIIA induces rapid dissociation of TFIID dimers to facilitate promoter loading.","method":"Biochemical dimerization assays, kinetic DNA-binding assays","journal":"Molecular cell","confidence":"High","confidence_rationale":"Tier 1 / Strong — quantitative kinetic biochemistry demonstrating novel regulatory mechanism for TBP dimer/TFIID dimer dissociation by TFIIA","pmids":["10518227"],"is_preprint":false},{"year":1999,"finding":"TBP binding in vivo is regulated: Mot1 prevents TBP binding to inactive promoters, and activator-mediated stimulation of TBP binding requires TFIIB and Srb4; TBP binding generally correlates with transcriptional activity across endogenous yeast genes.","method":"DNA-crosslinking/immunoprecipitation (in vivo), mutant yeast strains (genetic epistasis)","journal":"Nature","confidence":"High","confidence_rationale":"Tier 2 / Strong — in vivo crosslinking-IP with genetic epistasis across multiple genes, replicated at endogenous loci","pmids":["10376604"],"is_preprint":false},{"year":1999,"finding":"TBP-related factor TRF2 (TBPL1) binds TFIIA and TFIIB but does not bind canonical TATA boxes; TRF2 is associated with distinct chromosomal loci from TBP in Drosophila, suggesting different promoter specificity.","method":"Protein interaction assays, Drosophila polytene chromosome staining","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct binding assays and chromosomal localization, single lab","pmids":["10220372"],"is_preprint":false},{"year":2000,"finding":"In vivo, TBP exists in at least two transcriptionally active forms: a TAF-containing form (TFIID) and a TAF-independent form; promoter occupancy by TAFs does not universally correlate with transcriptional activity, unlike TBP, TFIIA, and TFIIB occupancy.","method":"Chromatin immunoprecipitation (ChIP) at yeast promoters, genome-wide expression analysis","journal":"Science","confidence":"High","confidence_rationale":"Tier 2 / Strong — ChIP across many promoters, two orthogonal approaches (expression + occupancy), independently confirmed","pmids":["10818000"],"is_preprint":false},{"year":2000,"finding":"TBP-related factor TRF1 preferentially binds and directs transcription from the tudor gene promoter in Drosophila, a TRF1-responsive promoter distinct from TBP-regulated promoters.","method":"Polytene chromosome staining, ChIP, mRNA analysis, cotransfection assays, in vitro transcription reconstitution, DNase I footprinting","journal":"Science","confidence":"High","confidence_rationale":"Tier 1 / Strong — reconstituted in vitro transcription plus multiple in vivo validations, multiple orthogonal methods","pmids":["10797011"],"is_preprint":false},{"year":2001,"finding":"MOT1 uses ATP hydrolysis to remove TBP from DNA; MOT1 requires a 17 bp double-stranded DNA 'handle' upstream of the TATA box; TBP-DNA disruption does not require DNA strand separation, bending, or helix twisting, suggesting translocation along the handle drives disruption.","method":"In vitro ATPase/disruption assays with template variants, mutant DNA substrates","journal":"The EMBO journal","confidence":"High","confidence_rationale":"Tier 1 / Strong — detailed mechanistic dissection with multiple substrate variants, single lab but rigorous","pmids":["11296235"],"is_preprint":false},{"year":2002,"finding":"GFP-TBP stably associates with condensed mitotic chromosomes (no FRAP signal during mitosis); in interphase cells, GFP-TBP shows ~100-fold slower FRAP than TFIIB; endogenous TBP and TAFs cofractionate with mitotic chromatin, suggesting TBP-TAF complexes remain promoter-bound for multiple rounds of transcription.","method":"FRAP of GFP-TBP in live HeLa cells, chromatin fractionation","journal":"Molecular biology of the cell","confidence":"High","confidence_rationale":"Tier 2 / Strong — live-cell FRAP combined with biochemical fractionation, quantitative comparison with control factor (TFIIB)","pmids":["11809839"],"is_preprint":false},{"year":2003,"finding":"p53 represses RNA polymerase III transcription through direct interaction with TBP; overexpressing TBP reverses p53-mediated inhibition of tRNA gene transcription; p53 does not disrupt TBP-Brf1 interaction but prevents Brf1 complexes from associating with TFIIIC2 and RNA pol III; ChIP shows TFIIIB occupancy decreases upon p53 induction.","method":"In vitro transcription, overexpression rescue, chromatin immunoprecipitation (ChIP), co-immunoprecipitation","journal":"The EMBO journal","confidence":"High","confidence_rationale":"Tier 2 / Strong — multiple orthogonal methods including ChIP, functional rescue, and interaction assays, mechanistically precise","pmids":["12773395"],"is_preprint":false},{"year":2004,"finding":"RNA aptamers generated against yeast TBP bind TBP competitively with TATA-DNA and some actively disrupt preformed TBP-TATA complexes even in the context of TFIIB and TFIIA; aptamers inhibit transcription in crude extracts, revealing dynamic TBP interactions during initiation and reinitiation.","method":"SELEX, aptamer binding assays, in vitro transcription with crude extracts","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct binding and functional assays in multiple contexts, single lab","pmids":["15103022"],"is_preprint":false},{"year":2004,"finding":"Immunomapping of yeast TFIID by EM revealed TBP is located in the linker domain between lobes A and C of the trilobed TFIID structure, with the N-terminal 100 residues of TAF1 spanning over TBP.","method":"Electron microscopy, immunomapping with antibodies against TFIID subunits","journal":"The EMBO journal","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — EM-based immunomapping, single lab, limited resolution","pmids":["14765106"],"is_preprint":false},{"year":2006,"finding":"SAGA binds TBP directly via its Spt8 subunit (and Ada1); Spt8 and SAGA compete with DNA (rather than forming a triple complex) to bind TBP, supporting a handoff model where SAGA transfers TBP to the TATA box rather than binding together with TBP at the promoter.","method":"Chemical crosslinking to identify SAGA-TBP contacts, direct binding assays (competition with DNA and TBP dimer)","journal":"The EMBO journal","confidence":"High","confidence_rationale":"Tier 1 / Strong — direct binding competition assays with multiple substrates, mechanistically clear model","pmids":["16888622"],"is_preprint":false},{"year":2006,"finding":"The Med8 N-terminal domain of the Mediator head subcomplex Med8-Med18-Med20 binds TBP in vitro and is essential in vivo; the Med8/18/20 subcomplex contains a putative multipartite TBP-binding site in the Mediator head.","method":"X-ray crystallography of Med8C/18/20 submodule, in vitro TBP-binding assays, genetic complementation","journal":"Nature structural & molecular biology","confidence":"High","confidence_rationale":"Tier 1 / Strong — crystal structure plus direct binding assay and genetic validation","pmids":["16964259"],"is_preprint":false},{"year":2006,"finding":"Brd2 is a TBP-associated protein; a 26 amino acid peptide in the first bromodomain of Brd2 mediates Brd2-TBP interaction; serum stimulation induces formation of a Brd2-E2F-1-TBP complex in vivo, with Brd2 recruiting TBP into the E2F-1 transcriptional complex.","method":"Co-immunoprecipitation, domain mapping, overexpression assays, luciferase reporter assays","journal":"Molecular and cellular biochemistry","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — co-IP and functional reporter assays, single lab, domain mapped","pmids":["17111193"],"is_preprint":false},{"year":2008,"finding":"During mitosis, TBP recruits PP2A to active gene promoters; the TBP-PP2A complex dephosphorylates and inactivates condensin at these promoters to prevent chromatin compaction, thereby bookmarking previously active genes for re-activation in daughter cells.","method":"Co-immunoprecipitation, ChIP-on-chip, functional assays for condensin inactivation","journal":"Nature cell biology","confidence":"High","confidence_rationale":"Tier 2 / Strong — co-IP for complex, ChIP-on-chip for genome-wide binding, functional condensin dephosphorylation assay, multiple orthogonal methods","pmids":["18931662"],"is_preprint":false},{"year":2010,"finding":"TFIIA and the transactivator Rap1 cooperate to commit TFIID for transcription initiation; cryo-EM structures reveal Rap1 and TFIIA bind TFIID simultaneously, TFIIA undergoes a Rap1-induced conformational change that increases exposure of TBP within TFIID; a large DNA loop forms between the activator site and proximal promoter, locked by a TFIIA-Rap1 protein bridge.","method":"Cryo-electron microscopy, structural reconstruction of TFIID-TFIIA-Rap1-DNA complexes","journal":"Nature","confidence":"High","confidence_rationale":"Tier 1 / Strong — cryo-EM structural analysis of full complex, mechanistically defines how activator exposes TBP for promoter binding","pmids":["20559389"],"is_preprint":false},{"year":2013,"finding":"Human TFIID exists in two predominant structural states differing by ~100 Å translocation of lobe A; TFIIA and promoter DNA together facilitate transition to a rearranged state that enables promoter recognition; TATA, Inr, MTE, and DPE promoter motifs were mapped within the TFIID-TFIIA-DNA structure.","method":"Single-particle electron microscopy (cryo-EM), DNA labeling, DNase footprinting","journal":"Cell","confidence":"High","confidence_rationale":"Tier 1 / Strong — cryo-EM with functional footprinting validation, multiple promoter elements mapped","pmids":["23332750"],"is_preprint":false},{"year":2014,"finding":"TRF2 (TBPL1/TRF2), not TBP, is required for transcription of TCT-dependent ribosomal protein genes in Drosophila and humans; TBP depletion does not affect TCT-dependent transcription, while TRF2 depletion does; purified TRF2 activates TCT but not TATA promoters in vitro.","method":"Overexpression and depletion of TBP/TRF2, in vitro transcription with purified TRF2, ChIP-seq","journal":"Genes & development","confidence":"High","confidence_rationale":"Tier 1 / Strong — in vitro reconstitution plus depletion experiments and ChIP-seq, negative result for TBP and positive for TRF2 mechanistically decisive","pmids":["24958592"],"is_preprint":false},{"year":2014,"finding":"Age-related decline in Hsc70 chaperone activity leads to increased mutant TBP accumulation in SCA17 mice; mutant TBP shows decreased association with XBP1s, resulting in reduced transcription of MANF; expression of Hsc70 improves TBP-XBP1s interaction and MANF transcription.","method":"Inducible knock-in mouse model, co-immunoprecipitation, gene expression analysis, MANF overexpression rescue","journal":"Neuron","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — in vivo mouse model with co-IP and functional rescue, single lab","pmids":["24462098"],"is_preprint":false},{"year":2015,"finding":"TBP interacts with the Cnd2 kleisin subunit of condensin and recruits condensin onto RNA polymerase III-transcribed genes and highly transcribed Pol II genes in fission yeast; disruption of the Cnd2-TBP interaction causes defects in condensin localization, mitotic chromosome assembly, chromosome segregation, and cellular lethality.","method":"Co-immunoprecipitation, ChIP, genetic analysis with interaction-disrupting mutants","journal":"Molecular cell","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal co-IP, genome-wide ChIP, loss-of-function with defined mechanistic and phenotypic readout","pmids":["26257282"],"is_preprint":false},{"year":2015,"finding":"TBP protein levels are regulated by the ubiquitin-proteasome system; E3 ligase Huwe1 targets TBP for K48-linked ubiquitination and proteasomal degradation; deubiquitinase USP10 antagonizes Huwe1 and protects TBP from degradation; upregulation of Huwe1 during myogenesis induces TBP degradation and drives myotube differentiation.","method":"In vitro ubiquitination assay with biochemical fractionation, mass spectrometry identification of Huwe1, cell-based functional assays","journal":"eLife","confidence":"High","confidence_rationale":"Tier 1 / Strong — in vitro reconstitution of ubiquitination plus cellular functional assays with identified E3 and DUB, multiple orthogonal methods","pmids":["26393420"],"is_preprint":false},{"year":2016,"finding":"Cryo-EM structure of human TFIID with TFIIA and core promoter DNA at sub-nanometre resolution shows TAF1 and TAF2 mediate major interactions with the downstream promoter; TFIIA bridges the TBP-TATA complex with lobe B of TFIID; all core promoter elements are contacted by TFIID subunits.","method":"Single-particle cryo-electron microscopy, structural analysis","journal":"Nature","confidence":"High","confidence_rationale":"Tier 1 / Strong — sub-nanometre cryo-EM structure of complete TFIID-TFIIA-DNA complex","pmids":["27007846"],"is_preprint":false},{"year":2017,"finding":"TAF11 and TAF13 form a ternary complex with TBP via the TAF11/TAF13 histone-fold domains; TAF11/TAF13 competes with TATA-box DNA and with the TAF1 N-terminal domain (TAND1) for TBP binding; the highly conserved C-terminal TBP-interaction domain (CTID) of TAF13 is essential for cell growth; TAF11/TAF13 interacts with the DNA-binding surface of TBP.","method":"Crystal structure of TAF11/TAF13/TBP complex (2.4 Å), cross-linking mass spectrometry, biochemical competition assays, genetic complementation","journal":"eLife","confidence":"High","confidence_rationale":"Tier 1 / Strong — crystal structure plus biochemical competition and genetic essentiality, multiple orthogonal methods in single rigorous study","pmids":["29111974"],"is_preprint":false},{"year":2018,"finding":"Cryo-EM of human TFIID with TFIIA and promoter DNA reveals five structural states; initial TFIID binding to the downstream promoter positions upstream DNA and facilitates scanning of TBP for a TATA box, followed by engagement of the promoter — defining a mechanism for TBP loading onto promoter DNA by TFIID.","method":"Cryo-electron microscopy, chemical cross-linking mass spectrometry, biochemical reconstitution","journal":"Science","confidence":"High","confidence_rationale":"Tier 1 / Strong — cryo-EM at multiple states combined with biochemical reconstitution, mechanistically defines TBP loading pathway","pmids":["30442764"],"is_preprint":false},{"year":2018,"finding":"TBP remains stably bound to active gene promoters on mitotic chromosomes in mouse ES cells (average residence time of minutes vs. seconds for typical TFs, by single-molecule live imaging); acute TBP degradation reduces RNA Pol II association with mitotic chromosomes and impairs transcriptional reactivation after mitosis.","method":"Live-cell single-molecule imaging, drug-inducible degron system, ChIP","journal":"eLife","confidence":"High","confidence_rationale":"Tier 2 / Strong — single-molecule live imaging plus inducible degron with functional readout, multiple orthogonal approaches","pmids":["29939130"],"is_preprint":false},{"year":2018,"finding":"Chaperonin CCT specifically associates with nascent TAF5 and hands it off to TAF6-TAF9, acting as a checkpoint for TFIID assembly; TAF5-TAF6-TAF9 form a cytoplasmic submodule with novel interactions essential for TFIID integrity; TAF9 allocation between TFIID and SAGA is regulated by these submodule interactions.","method":"Quantitative proteomics, structural analysis, mutational analysis, mass spectrometry of submodules","journal":"Nature structural & molecular biology","confidence":"High","confidence_rationale":"Tier 1 / Strong — structural and mutational analysis combined with quantitative proteomics, multiple orthogonal methods","pmids":["30510221"],"is_preprint":false},{"year":2019,"finding":"H3K4me3Q5ser (combinatorial serotonylation and methylation on histone H3) potentiates TFIID binding to H3K4me3 nucleosomes; tissue transglutaminase 2 serotonylates H3 at Q5 on H3K4me3-marked nucleosomes; ectopic expression of a H3 mutant that cannot be serotonylated alters H3K4me3Q5ser-target gene expression and impairs differentiation.","method":"In vitro enzyme assay (transglutaminase), genome-wide chromatin analysis, TFIID binding assay, H3 mutant cell lines","journal":"Nature","confidence":"High","confidence_rationale":"Tier 1 / Strong — enzymatic reconstitution, direct TFIID binding assay, genome-wide mapping, and mutant cell functional validation","pmids":["30867594"],"is_preprint":false},{"year":2019,"finding":"Two discrete regions of MYC (amino acids 98–111 and 115–124) interact with TBP; a crystal structure (2.4 Å) shows MYC aa 98–111 interacts with TBP in the presence of TAF1 TAND1; MYC aa 115–124 resembles a TBP anchor motif; MYC mutants that abrogate TBP interaction compromise MYC transcriptional activity.","method":"2.4 Å crystal structure, biochemical binding assays, site-specific MYC mutagenesis with functional assays","journal":"Nature structural & molecular biology","confidence":"High","confidence_rationale":"Tier 1 / Strong — crystal structure plus mutagenesis with functional consequences, multiple orthogonal methods","pmids":["31686052"],"is_preprint":false},{"year":2020,"finding":"Cryo-EM structure of yeast SAGA with bound TBP reveals an octamer of histone-fold domains in the SAGA core that forms a peripheral site for TBP where steric hindrance represses spurious DNA binding; biochemical analysis shows TBP delivery from SAGA to promoter DNA requires TFIIA and correlates with TBP-DNA affinity, supporting a handoff mechanism.","method":"Cryo-electron microscopy (3.5 Å core resolution), biochemical TBP delivery assays","journal":"Nature","confidence":"High","confidence_rationale":"Tier 1 / Strong — near-atomic resolution cryo-EM plus biochemical mechanistic validation","pmids":["31969704"],"is_preprint":false},{"year":2020,"finding":"TFIID is required for RNA Polymerase II promoter-proximal pausing; replacement of TFIID with TBP alone in a purified reconstituted in vitro transcription system abolishes pausing; acute depletion of TFIID subunits in human and Drosophila cells disrupts genome-wide RNAPII pausing.","method":"Reconstituted in vitro transcription with purified factors, drug-inducible TFIID subunit depletion, PRO-seq","journal":"Molecular cell","confidence":"High","confidence_rationale":"Tier 1 / Strong — reconstituted in vitro assay plus genome-wide in vivo validation, multiple orthogonal methods","pmids":["32229306"],"is_preprint":false},{"year":2021,"finding":"TBP can bind to a nucleosome containing the Widom-601 sequence; TFIIA stabilizes TBP-nucleosome binding; cryo-EM structures show TBP binds at SHL -6 (TATA-like, TFIIA-independent) and SHL +2 (GC-rich, TFIIA-dependent, with detachment of upstream terminal DNA from histone octamer); TBP-nucleosome complexes are sterically incompatible with PIC assembly.","method":"Cryo-electron microscopy (three structures), biochemical binding assays","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"High","confidence_rationale":"Tier 1 / Strong — multiple cryo-EM structures plus biochemical validation, mechanistically explains nucleosome barrier to transcription","pmids":["34301908"],"is_preprint":false},{"year":2022,"finding":"TIF1γ binds TBP in competition with TAF15, displacing TAF15 from the TAF15/TBP complex; TIF1γ also multi-mono-ubiquitylates TAF15 and drives its nuclear export; the TAF15/TBP complex is required for IL-6 transactivation-induced EMT in lung adenocarcinoma cells.","method":"Co-immunoprecipitation, competition binding assays, ubiquitylation assays, nuclear export assays, cell functional assays","journal":"Cell reports","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — co-IP plus ubiquitylation and functional assays, single lab, multiple orthogonal methods","pmids":["36261009"],"is_preprint":false},{"year":2023,"finding":"Human TFIID biogenesis occurs co-translationally; all protein heterodimerization steps occur during protein synthesis; TAF1 acts as a flexible scaffold that drives co-translational recruitment of TFIID submodules preassembled in the cytoplasm onto the nascent TAF1 polypeptide.","method":"RNA-immunoprecipitation (RIP), single-molecule imaging, proteomics, structure-function analyses","journal":"Nature structural & molecular biology","confidence":"High","confidence_rationale":"Tier 2 / Strong — multiple orthogonal methods (RIP, single-molecule imaging, proteomics, mutagenesis), mechanistically defines TFIID assembly pathway","pmids":["37386215"],"is_preprint":false},{"year":2015,"finding":"Large polyQ repeats (105Q) in TBP preferentially cause muscle degeneration and reduce expression of muscle-specific genes by decreasing the association of MyoD with TBP and with DNA promoters; smaller polyQ repeats do not show this effect, demonstrating polyQ length-dependent differential protein interactions.","method":"Knockin mouse models, co-immunoprecipitation, ChIP, direct muscle expression of TBP with different polyQ lengths","journal":"Cell reports","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — co-IP and ChIP with functional mouse model, single lab, length-dependent comparison","pmids":["26387956"],"is_preprint":false}],"current_model":"TBP is a highly conserved TATA box-binding protein that binds the DNA minor groove, bends DNA ~80–90°, and nucleates RNA polymerase II (and I/III) preinitiation complex assembly as a subunit of TFIID (with TAFs) or other TBP-containing complexes (SL1, TFIIIB, SAGA); its promoter loading is controlled by TFIIA (which dissociates inhibitory TBP/TFIID dimers and stabilizes TBP-DNA binding), by TAF-mediated inhibition of TBP-DNA binding (relieved by TFIIA), by MOT1-catalyzed ATP-dependent removal of TBP from DNA, and by Huwe1/USP10-mediated ubiquitination/deubiquitination that controls TBP protein levels; TBP stably occupies active promoters on mitotic chromosomes to bookmark genes for post-mitotic reactivation via a TBP-PP2A complex that inactivates condensin; TBP interacts with multiple regulators including p53, MYC, Mediator (via Med8), Rap1-TFIIA, and condensin (via Cnd2), with structures of TFIID-TFIIA-DNA, TFIIB-TBP-TATA, and SAGA-TBP complexes providing atomic-level mechanisms for TBP delivery and promoter engagement."},"narrative":{"mechanistic_narrative":"TBP is the core promoter recognition factor that nucleates RNA polymerase preinitiation complex assembly by engaging the TATA element through the DNA minor groove [PMID:1760847] and bending the duplex ~80–90° around the TATA box [PMID:1736286, PMID:7533216]; a discrete 12-residue surface determines its sequence specificity [PMID:1739977]. TBP partitions into multiple multisubunit complexes—TAF-containing TFIID forms and TAF-independent forms in vivo [PMID:1936986, PMID:10818000]—and is directed into polymerase-selective complexes through mutually exclusive TAF binding, where SL1 TAFs and TFIID TAFs (TAF1/TAF250, TAF11/TAF13) compete for the same TBP surfaces [PMID:7801123, PMID:29111974]. Within TFIID, TBP occupies the linker between lobes, and cryo-EM has resolved how downstream-promoter engagement by TAF1/TAF2 positions DNA so TBP scans for and loads onto the TATA box, a transition driven by TFIIA and promoter DNA [PMID:14765106, PMID:27007846, PMID:30442764]. TBP delivery is tightly regulated: TFIIA dissociates inhibitory TBP/TFIID dimers and stabilizes TBP–DNA binding while relieving TAF-mediated autoinhibition [PMID:9300055, PMID:9603936, PMID:10518227], MOT1 uses ATP hydrolysis and a DNA handle to strip TBP from DNA [PMID:11296235], and SAGA hands TBP off to the promoter through a steric, TFIIA-dependent mechanism rather than co-binding [PMID:16888622, PMID:31969704]. Once loaded, TBP–DNA is recognized by TFIIB to build the start-site-defining complex [PMID:7675079, PMID:9012349], and TFIID—but not TBP alone—is required for RNA Pol II promoter-proximal pausing [PMID:32229306]. Beyond initiation, TBP is a transcriptional and regulatory hub: it is bound and modulated by p53, MYC, Mediator (via Med8), Brd2, and TAF15 [PMID:8405994, PMID:31686052, PMID:16964259, PMID:17111193, PMID:36261009], its protein levels are set by Huwe1-mediated K48 ubiquitination opposed by USP10 [PMID:26393420], and it stably bookmarks active promoters on mitotic chromosomes—recruiting PP2A to inactivate condensin and sustaining Pol II occupancy for post-mitotic transcriptional reactivation [PMID:11809839, PMID:18931662, PMID:26257282, PMID:29939130]. Polyglutamine-expanded TBP causes the neurodegenerative disorder SCA17, where mutant TBP loses interactions with partners such as XBP1s and MyoD to alter target gene transcription [PMID:24462098, PMID:26387956].","teleology":[{"year":1991,"claim":"Established the physical basis of promoter recognition by showing TBP reads the TATA box through the DNA minor groove rather than the major groove, defining an unusual mode of sequence-specific DNA binding.","evidence":"Base-substitution (C/I replacement) chemistry combined with DNA-binding assays","pmids":["1760847"],"confidence":"High","gaps":["Did not resolve the atomic contacts or the protein surface mediating recognition","Did not address regulation of binding in vivo"]},{"year":1992,"claim":"Defined TBP's mechanical action on DNA and the protein determinant of specificity, showing TBP bends the helix and that a 12-residue region sets sequence preference.","evidence":"Permuted-site gel retardation with recombinant TBP; altered-specificity mutagenesis with biochemical and in vivo transcription assays","pmids":["1736286","1739977"],"confidence":"High","gaps":["Bend angle quantified more precisely only later by EM","Did not connect bending to downstream PIC assembly"]},{"year":1992,"claim":"Revealed that TBP is not a free factor but resides in distinct multisubunit complexes with different functional capacities, only the larger of which supports activated transcription.","evidence":"Biochemical fractionation of HeLa extracts, cofractionation, in vitro transcription; B-TFIID subunit composition and ATPase assay","pmids":["1936986","1387711"],"confidence":"High","gaps":["Full TAF composition of D-TFIID not enumerated","Functional role of B-TFIID ATPase unresolved"]},{"year":1993,"claim":"Identified direct TAF and regulator contacts on TBP, establishing TFIID architecture and linking TBP to oncogenic/tumor-suppressor regulation via TAF250, p53, and p300.","evidence":"Recombinant binding and yeast interaction (TAF250); Co-IP and EMSA (p53, p300); reconstitution of TAF60/70 ternary complexes","pmids":["7680771","8405994","8502484","8262073"],"confidence":"High","gaps":["p300–TBP interaction may be indirect (Co-IP only)","Stoichiometry and assembly order of TAF subcomplexes not yet defined"]},{"year":1994,"claim":"Explained how TBP is sorted among polymerase systems and how cofactors modulate its DNA engagement, showing SL1 TAFs bind TBP mutually exclusively with TFIID TAFs and that TFIIA cooperatively enhances TBP–TATA binding.","evidence":"Reconstituted subunit competition assays (SL1); recombinant TFIIA reconstitution with DNase footprinting and in vitro transcription","pmids":["7801123","7958898"],"confidence":"High","gaps":["Kinetics of TFIIA stabilization quantified only later","Mechanism of dimer/oligomer interplay not yet addressed"]},{"year":1995,"claim":"Provided atomic and structural mechanism for promoter engagement, showing TFIIB recognizes the preformed TBP–DNA complex and that TBP forms DNA-bending dimers/oligomers at the TATA box.","evidence":"X-ray crystallography of TFIIB/TBP/TATA; electron microscopy and mass analysis of TBP particles","pmids":["7675079","7533216"],"confidence":"High","gaps":["Functional role of TBP oligomers in vivo unresolved","Did not capture the full PIC"]},{"year":1995,"claim":"Connected TBP availability to genome integrity and to small-molecule control, showing TBP is sequestered by damaged DNA and that minor-groove ligands block TBP loading.","evidence":"Filter binding, in vitro transcription competition, structural analysis, microinjection rescue; EMSA with distamycin/tallimustine","pmids":["9405373","7784168"],"confidence":"High","gaps":["Physiological extent of TBP sequestration by lesions unquantified","Drug specificity for TBP versus general minor-groove occupancy unclear"]},{"year":1997,"claim":"Quantified and dissected TFIIA's role and the activator dependence on the TBP–TFIIB interface, showing TFIIA stabilizes TBP–DNA ~10-fold and that most but not all activators route through TBP–TFIIB contacts.","evidence":"Filter-binding koff measurements and EMSA (TFIIA); altered-specificity TBP–TFIIB array in human cells","pmids":["9300055","9012349"],"confidence":"High","gaps":["Sp1 glutamine-rich domain's alternative path not mapped","In vivo kinetics on chromatin not addressed"]},{"year":1998,"claim":"Defined a regulatory logic of autoinhibition within TFIID, showing TAF250 inhibits TBP–DNA binding and TFIIA relieves this by competing for TBP.","evidence":"EMSA, DNase I footprinting, in vitro transcription, ts13 cell line","pmids":["9603936"],"confidence":"High","gaps":["Structural basis of TAF250 occlusion resolved only later","In vivo balance of inhibition versus relief not quantified"]},{"year":1999,"claim":"Resolved how inhibitory TBP/TFIID dimers are cleared and how TBP loading is controlled in cells, showing TFIIA dissociates dimers and that Mot1, TFIIB, and Srb4 gate TBP occupancy at promoters.","evidence":"Kinetic dimerization/DNA-binding biochemistry; in vivo crosslinking-IP with yeast genetic epistasis","pmids":["10518227","10376604"],"confidence":"High","gaps":["Mechanism of Mot1 action not yet biochemically dissected","Generality across promoter classes incompletely sampled"]},{"year":1999,"claim":"Distinguished TBP from paralogous TBP-related factors, showing TRF2 binds TFIIA/TFIIB but not canonical TATA boxes and localizes to distinct loci.","evidence":"Protein interaction assays and Drosophila polytene chromosome staining","pmids":["10220372"],"confidence":"Medium","gaps":["TRF2 promoter specificity not yet defined (single-lab, descriptive)","Functional target genes not identified at this stage"]},{"year":2000,"claim":"Established in vivo that TBP occupancy, not TAF occupancy, tracks transcription, and that TBP exists in both TAF-dependent and TAF-independent active forms; in parallel, TRF1 was shown to direct a dedicated promoter class.","evidence":"ChIP at yeast promoters with genome-wide expression; reconstituted TRF1-directed transcription with multiple in vivo validations","pmids":["10818000","10797011"],"confidence":"High","gaps":["Identity of the TAF-independent TBP form not biochemically defined","Mechanism of TAF-free TBP recruitment unclear"]},{"year":2001,"claim":"Solved the mechanism of MOT1-driven TBP removal, showing ATP hydrolysis and translocation along an upstream DNA handle strips TBP without strand separation or unbending.","evidence":"In vitro ATPase/disruption assays with template and substrate variants","pmids":["11296235"],"confidence":"High","gaps":["Structural snapshot of MOT1–TBP–DNA not obtained","In vivo redistribution consequences not directly measured here"]},{"year":2002,"claim":"Revealed a non-canonical role of TBP in mitotic gene memory, showing TBP–TAF complexes remain stably promoter-bound on condensed mitotic chromosomes.","evidence":"FRAP of GFP-TBP in live HeLa cells and chromatin fractionation","pmids":["11809839"],"confidence":"High","gaps":["Functional consequence of mitotic retention not yet established","Mechanism enforcing stable binding unknown at this point"]},{"year":2003,"claim":"Extended TBP regulation to Pol III, showing p53 represses tRNA gene transcription by acting on TBP-containing TFIIIB assembly.","evidence":"In vitro transcription, overexpression rescue, ChIP, Co-IP","pmids":["12773395"],"confidence":"High","gaps":["Structural basis of p53–TBP modulation not resolved","Whether the same axis operates at Pol I unaddressed here"]},{"year":2004,"claim":"Demonstrated that TBP–TATA complexes are dynamic and disruptable during initiation/reinitiation using engineered RNA aptamers that compete with DNA even in the presence of TFIIA/TFIIB; EM placed TBP in the TFIID linker domain.","evidence":"SELEX aptamer binding and in vitro transcription; EM immunomapping of yeast TFIID","pmids":["15103022","14765106"],"confidence":"Medium","gaps":["Aptamer relevance to physiological regulators uncertain (single lab)","TFIID immunomap limited in resolution"]},{"year":2006,"claim":"Defined a handoff mechanism for TBP delivery by SAGA and additional regulatory contacts, showing SAGA (via Spt8/Ada1) competes with DNA for TBP and that Med8 and Brd2 provide further TBP-binding interfaces.","evidence":"Crosslinking and competition binding (SAGA); crystallography plus binding and genetics (Med8); Co-IP and reporter assays (Brd2)","pmids":["16888622","16964259","17111193"],"confidence":"High","gaps":["Brd2–TBP interaction supported by single-lab Co-IP","Structural picture of SAGA–TBP completed only later"]},{"year":2008,"claim":"Provided the functional mechanism of mitotic bookmarking, showing TBP recruits PP2A to dephosphorylate and inactivate condensin at active promoters, preventing compaction and enabling reactivation in daughter cells.","evidence":"Co-IP, ChIP-on-chip, condensin inactivation assays","pmids":["18931662"],"confidence":"High","gaps":["How TBP selects which promoters to bookmark not defined","Direct structural basis of TBP–PP2A–condensin axis unresolved"]},{"year":2010,"claim":"Captured how an activator licenses TBP for promoter binding, showing Rap1 and TFIIA cooperatively commit TFIID via a conformational change that exposes TBP and a locked DNA loop.","evidence":"Cryo-EM of TFIID–TFIIA–Rap1–DNA complexes","pmids":["20559389"],"confidence":"High","gaps":["Generality of the Rap1 mechanism to other activators not established","Resolution limited details of TBP–DNA contacts"]},{"year":2013,"claim":"Resolved the conformational gating of human TFIID, showing a large lobe-A translocation driven by TFIIA and DNA that enables promoter recognition, with all core promoter motifs mapped.","evidence":"Single-particle cryo-EM, DNA labeling, DNase footprinting","pmids":["23332750"],"confidence":"High","gaps":["Kinetics of the conformational transition not measured","How modifications/regulators bias states unaddressed"]},{"year":2014,"claim":"Sharpened the TBP/TRF division of labor and connected TBP misfolding to disease, showing TRF2 (not TBP) drives TCT/ribosomal protein gene transcription and that Hsc70 decline worsens mutant TBP in SCA17 by impairing TBP–XBP1s-driven MANF expression.","evidence":"Depletion/overexpression with in vitro transcription and ChIP-seq (TRF2); SCA17 knock-in mouse with Co-IP and rescue (Hsc70/MANF)","pmids":["24958592","24462098"],"confidence":"Medium","gaps":["SCA17 chaperone-MANF axis from single-lab mouse model","Direct structural basis of mutant TBP–partner loss not defined"]},{"year":2015,"claim":"Linked TBP to chromosome architecture and to its own turnover, showing TBP recruits condensin via Cnd2 to highly transcribed genes and that Huwe1/USP10 set TBP protein levels to control differentiation; polyQ expansion impairs MyoD–TBP coupling in muscle.","evidence":"Co-IP, ChIP, interaction-disrupting mutants (Cnd2); in vitro ubiquitination, MS, cellular assays (Huwe1/USP10); knockin mice with Co-IP/ChIP (polyQ)","pmids":["26257282","26393420","26387956"],"confidence":"High","gaps":["polyQ–MyoD effects from single-lab model (Medium)","Coordination between TBP turnover and condensin recruitment unexplored"]},{"year":2016,"claim":"Achieved sub-nanometre definition of the promoter-engaged TFIID, showing TAF1/TAF2 dominate downstream-promoter contacts and TFIIA bridges TBP–TATA to lobe B.","evidence":"Single-particle cryo-EM of human TFIID–TFIIA–DNA","pmids":["27007846"],"confidence":"High","gaps":["Dynamic loading pathway not yet resolved as discrete states","Side-by-side comparison with non-TATA promoters limited"]},{"year":2017,"claim":"Defined a further layer of TBP autoinhibition within TFIID, showing TAF11/TAF13 occupy the DNA-binding surface of TBP and compete with both TATA-DNA and the TAF1 TAND1 domain.","evidence":"Crystal structure of TAF11/TAF13/TBP, XL-MS, competition assays, genetic complementation","pmids":["29111974"],"confidence":"High","gaps":["How TAF11/13 release is triggered during loading unclear","Interplay with TFIIA-mediated relief not fully integrated"]},{"year":2018,"claim":"Defined the TBP-loading pathway and the functional importance of mitotic retention, showing TFIID scans for the TATA box through multiple states and that TBP residency on mitotic chromosomes is required for post-mitotic transcriptional reactivation.","evidence":"Cryo-EM of five states with XL-MS (loading); single-molecule imaging and degron with ChIP (mitotic retention)","pmids":["30442764","29939130"],"confidence":"High","gaps":["Determinants of which promoters retain TBP through mitosis unresolved","Timing relative to PP2A–condensin axis not directly linked"]},{"year":2018,"claim":"Revealed a cytoplasmic, chaperone-gated TFIID assembly route, showing CCT hands nascent TAF5 to TAF6-TAF9 to form a submodule and partition TAF9 between TFIID and SAGA.","evidence":"Quantitative proteomics, structural and mutational analysis, MS of submodules","pmids":["30510221"],"confidence":"High","gaps":["Where TBP enters this assembly hierarchy not pinpointed here","Regulation of submodule flux unknown"]},{"year":2019,"claim":"Connected TFIID recruitment to chromatin modifications and to oncogenic activators, showing serotonylated H3K4me3 (H3K4me3Q5ser) potentiates TFIID binding and that MYC directly contacts TBP to drive its transcriptional activity.","evidence":"Transglutaminase enzyme assay, genome-wide chromatin analysis, TFIID binding (serotonylation); crystal structure and MYC mutagenesis (MYC–TBP)","pmids":["30867594","31686052"],"confidence":"High","gaps":["How serotonylation alters TBP positioning structurally not resolved","MYC–TBP contribution relative to other MYC cofactors unquantified"]},{"year":2020,"claim":"Completed the structural mechanism of SAGA-mediated TBP delivery and revealed TFIID's role beyond initiation, showing SAGA's histone-fold octamer represses spurious TBP–DNA binding and hands TBP off via TFIIA, and that TFIID (not TBP alone) is required for Pol II pausing.","evidence":"Cryo-EM of SAGA–TBP with delivery assays; reconstituted in vitro transcription, TFIID depletion, PRO-seq","pmids":["31969704","32229306"],"confidence":"High","gaps":["Which TAF subunit mediates the pausing function not pinpointed","How SAGA and TFIID delivery routes are coordinated in cells unclear"]},{"year":2021,"claim":"Explained the nucleosome barrier to TBP, showing TBP can bind nucleosomal DNA at defined superhelical locations (TFIIA-dependent and -independent) but in configurations incompatible with PIC assembly.","evidence":"Cryo-EM of three TBP–nucleosome structures and biochemical binding assays","pmids":["34301908"],"confidence":"High","gaps":["In vivo relevance of nucleosomal TBP binding not established","How chromatin remodelers convert these states to active PIC unknown"]},{"year":2022,"claim":"Identified a competitive regulatory exchange on TBP linked to cancer phenotypes, showing TIF1γ displaces and ubiquitylates TAF15 from a TAF15/TBP complex required for IL-6-driven EMT.","evidence":"Co-IP, competition binding, ubiquitylation and nuclear-export assays, cellular functional assays","pmids":["36261009"],"confidence":"Medium","gaps":["Single-lab mechanism; structural basis of TAF15/TBP not resolved","Generality beyond lung adenocarcinoma context untested"]},{"year":2023,"claim":"Defined how the TBP-containing TFIID is built, showing co-translational, TAF1-scaffolded assembly of cytoplasmic submodules onto the nascent TAF1 polypeptide.","evidence":"RNA-immunoprecipitation, single-molecule imaging, proteomics, structure-function analyses","pmids":["37386215"],"confidence":"High","gaps":["Timing of TBP incorporation into the co-translational pathway not pinpointed","How assembly errors are corrected or degraded unaddressed"]},{"year":null,"claim":"How the many competing TBP interfaces—TAF autoinhibition, TFIIA relief, MOT1 removal, SAGA handoff, chromatin-mark sensing, and Huwe1/USP10 turnover—are integrated in real time at individual promoters to set transcriptional output remains unresolved.","evidence":"","pmids":[],"confidence":"High","gaps":["No unified kinetic model linking TBP delivery, removal, and degradation at native loci","Determinants of promoter-specific TBP retention through mitosis undefined","Structural basis of disease-causing polyQ expansion's altered interactions not solved"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0003677","term_label":"DNA binding","supporting_discovery_ids":[0,1,2,11,48]},{"term_id":"GO:0140110","term_label":"transcription regulator activity","supporting_discovery_ids":[3,17,20,22,47]},{"term_id":"GO:0140223","term_label":"general transcription initiation factor activity","supporting_discovery_ids":[3,12,39]},{"term_id":"GO:0042393","term_label":"histone binding","supporting_discovery_ids":[44,48]}],"localization":[{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[25,32,42]},{"term_id":"GO:0005654","term_label":"nucleoplasm","supporting_discovery_ids":[20,22,32]},{"term_id":"GO:0000228","term_label":"nuclear chromosome","supporting_discovery_ids":[25,32,42]},{"term_id":"GO:0005829","term_label":"cytosol","supporting_discovery_ids":[43,50]}],"pathway":[{"term_id":"R-HSA-74160","term_label":"Gene expression (Transcription)","supporting_discovery_ids":[3,12,20,39,47]},{"term_id":"R-HSA-1640170","term_label":"Cell Cycle","supporting_discovery_ids":[25,32,37,42]},{"term_id":"R-HSA-4839726","term_label":"Chromatin organization","supporting_discovery_ids":[44,48]},{"term_id":"R-HSA-392499","term_label":"Metabolism of proteins","supporting_discovery_ids":[38,49,50]}],"complexes":["TFIID","SL1","TFIIIB","SAGA"],"partners":["TFIIA","TFIIB","TAF1","MOT1","P53","MYC","TAF13","CND2"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"P20226","full_name":"TATA-box-binding protein","aliases":["TATA sequence-binding protein","TATA-binding factor","TATA-box factor","Transcription initiation factor TFIID TBP subunit"],"length_aa":339,"mass_kda":37.7,"function":"The TFIID basal transcription factor complex plays a major role in the initiation of RNA polymerase II (Pol II)-dependent transcription (PubMed:33795473). TFIID recognizes and binds promoters with or without a TATA box via its subunit TBP, a TATA-box-binding protein, and promotes assembly of the pre-initiation complex (PIC) (PubMed:2194289, PubMed:2363050, PubMed:2374612, PubMed:27193682, PubMed:33795473). The TFIID complex consists of TBP and TBP-associated factors (TAFs), including TAF1, TAF2, TAF3, TAF4, TAF5, TAF6, TAF7, TAF8, TAF9, TAF10, TAF11, TAF12 and TAF13 (PubMed:27007846, PubMed:33795473). The TFIID complex structure can be divided into 3 modules TFIID-A, TFIID-B, and TFIID-C (PubMed:33795473). TBP forms the TFIID-A module together with TAF3 and TAF5 (PubMed:33795473). TBP is a general transcription factor that functions at the core of the TFIID complex (PubMed:2194289, PubMed:2363050, PubMed:2374612, PubMed:27193682, PubMed:33795473, PubMed:9836642). During assembly of the core PIC on the promoter, as part of TFIID, TBP binds to and also bends promoter DNA, irrespective of whether the promoter contains a TATA box (PubMed:33795473). Component of a BRF2-containing transcription factor complex that regulates transcription mediated by RNA polymerase III (PubMed:26638071). Component of the transcription factor SL1/TIF-IB complex, which is involved in the assembly of the PIC during RNA polymerase I-dependent transcription (PubMed:15970593). The rate of PIC formation probably is primarily dependent on the rate of association of SL1 with the rDNA promoter (PubMed:15970593). SL1 is involved in stabilization of nucleolar transcription factor 1/UBTF on rDNA (PubMed:15970593)","subcellular_location":"Nucleus","url":"https://www.uniprot.org/uniprotkb/P20226/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":true,"resolved_as":"","url":"https://depmap.org/portal/gene/TBP","classification":"Common Essential","n_dependent_lines":996,"n_total_lines":1208,"dependency_fraction":0.8245033112582781},"opencell":{"profiled":true,"resolved_as":"","ensg_id":"ENSG00000112592","cell_line_id":"CID000847","localizations":[{"compartment":"nucleoplasm","grade":3},{"compartment":"nuclear_punctae","grade":2}],"interactors":[{"gene":"GTF2A1","stoichiometry":10.0},{"gene":"TAF5","stoichiometry":10.0},{"gene":"BRF1","stoichiometry":10.0},{"gene":"BTAF1","stoichiometry":10.0},{"gene":"TAF12","stoichiometry":4.0},{"gene":"POLR2K","stoichiometry":4.0},{"gene":"TAF7","stoichiometry":4.0},{"gene":"TAF4","stoichiometry":4.0},{"gene":"TAF6","stoichiometry":4.0},{"gene":"TAF3","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/target/CID000847","total_profiled":1310},"omim":[{"mim_id":"621494","title":"RNA, U6 SMALL NUCLEAR 9; RNU6-9","url":"https://www.omim.org/entry/621494"},{"mim_id":"621493","title":"RNA, U6 SMALL NUCLEAR 8; RNU6-8","url":"https://www.omim.org/entry/621493"},{"mim_id":"621492","title":"RNA, U6 SMALL NUCLEAR 7; RNU6-7","url":"https://www.omim.org/entry/621492"},{"mim_id":"621491","title":"RNA, U6 SMALL NUCLEAR 2; RNU6-2","url":"https://www.omim.org/entry/621491"},{"mim_id":"618765","title":"ESF1 NUCLEOLAR PRE-rRNA-PROCESSING PROTEIN; ESF1","url":"https://www.omim.org/entry/618765"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Supported","locations":[{"location":"Nucleoplasm","reliability":"Supported"},{"location":"Cytosol","reliability":"Additional"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/TBP"},"hgnc":{"alias_symbol":["TFIID","TBP1"],"prev_symbol":["GTF2D1","SCA17"]},"alphafold":{"accession":"P20226","domains":[{"cath_id":"3.30.310.10","chopping":"171-256","consensus_level":"high","plddt":96.5564,"start":171,"end":256},{"cath_id":"3.30.310.10","chopping":"265-336","consensus_level":"high","plddt":95.9636,"start":265,"end":336}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/P20226","model_url":"https://alphafold.ebi.ac.uk/files/AF-P20226-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-P20226-F1-predicted_aligned_error_v6.png","plddt_mean":77.12},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=TBP","jax_strain_url":"https://www.jax.org/strain/search?query=TBP"},"sequence":{"accession":"P20226","fasta_url":"https://rest.uniprot.org/uniprotkb/P20226.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/P20226/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/P20226"}},"corpus_meta":[{"pmid":"8811195","id":"PMC_8811195","title":"Biochemistry and structural biology of transcription factor IID (TFIID).","date":"1996","source":"Annual review of biochemistry","url":"https://pubmed.ncbi.nlm.nih.gov/8811195","citation_count":628,"is_preprint":false},{"pmid":"7675079","id":"PMC_7675079","title":"Crystal structure of a TFIIB-TBP-TATA-element ternary complex.","date":"1995","source":"Nature","url":"https://pubmed.ncbi.nlm.nih.gov/7675079","citation_count":483,"is_preprint":false},{"pmid":"30867594","id":"PMC_30867594","title":"Histone serotonylation is a permissive modification that enhances TFIID binding to H3K4me3.","date":"2019","source":"Nature","url":"https://pubmed.ncbi.nlm.nih.gov/30867594","citation_count":369,"is_preprint":false},{"pmid":"10864329","id":"PMC_10864329","title":"Redundant roles for the TFIID and SAGA complexes in global 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international journal of clinical chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/20004653","citation_count":25,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":40781,"output_tokens":11315,"usd":0.146034,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":22076,"output_tokens":8880,"usd":0.16619,"stage2_stop_reason":"end_turn"},"total_usd":0.312224,"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\": 1991,\n      \"finding\": \"TFIID/TBP binds primarily within the minor groove of the TATA box DNA helix, established by replacing thymines and adenines with cytosines and inosines to swap major-groove identity while preserving the minor groove surface.\",\n      \"method\": \"Novel base-substitution approach (C/I replacement) combined with DNA-binding assays\",\n      \"journal\": \"Cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — direct biochemical experiment with novel chemical substitution method, foundational result replicated in subsequent structural studies\",\n      \"pmids\": [\"1760847\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1992,\n      \"finding\": \"TBP induces DNA bending around the TATA element upon binding, demonstrated with recombinant yeast and human TBP using a permuted binding site/gel retardation assay.\",\n      \"method\": \"Permuted binding site/gel retardation assay with recombinant TBP\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — reconstituted in vitro with recombinant protein, confirmed by subsequent crystal structures\",\n      \"pmids\": [\"1736286\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1992,\n      \"finding\": \"A 12 amino acid region of TBP directly contacts the TATA element and determines DNA-binding specificity; specific substitutions in this region alter specificity from TATAAA to TGTAAA both in yeast and when the equivalent substitutions are introduced into human TBP.\",\n      \"method\": \"Genetic selection for altered-specificity mutants, biochemical DNA-binding assays, in vivo transcription assays\",\n      \"journal\": \"Cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — mutagenesis combined with biochemical and in vivo functional validation, cross-species confirmation\",\n      \"pmids\": [\"1739977\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1992,\n      \"finding\": \"TBP in HeLa extracts exists in two distinct multisubunit complexes (~300 kDa B-TFIID and >700 kDa D-TFIID), both containing the 38 kDa TBP; only the larger complex supports transcriptional activation by acidic or glutamine-rich activators.\",\n      \"method\": \"Biochemical fractionation, cofractionation studies, antisera-based detection, in vitro transcription\",\n      \"journal\": \"Genes & development\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — biochemical fractionation with functional transcription assays, foundational result confirmed by many subsequent studies\",\n      \"pmids\": [\"1936986\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1992,\n      \"finding\": \"B-TFIID is composed of two subunits: TBP and a 170 kDa TAF specific to B-TFIID (not present in D-TFIID); purified B-TFIID has (d)ATPase activity.\",\n      \"method\": \"Biochemical purification, subunit composition analysis, ATPase activity assay\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — purified complex with subunit characterization and enzymatic assay, single lab\",\n      \"pmids\": [\"1387711\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1993,\n      \"finding\": \"Recombinant hTAFII250 binds directly to TBP both in vitro and in yeast and participates in the formation of the TFIID complex; the CCG1/hTAFII250 gene is linked to cell-cycle progression.\",\n      \"method\": \"Recombinant protein expression, in vitro binding, yeast interaction assays\",\n      \"journal\": \"Nature\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — direct binding demonstrated in vitro and in vivo by two orthogonal approaches\",\n      \"pmids\": [\"7680771\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1993,\n      \"finding\": \"p53 binds directly to TBP and cooperates with TBP or partially purified TFIID to enhance binding to a DNA fragment containing both a p53-binding site and a TATA box; p53 strongly inhibits TBP (but not TFIID) binding to a TATA box lacking a p53 site.\",\n      \"method\": \"Co-IP, DNA-binding assays (EMSA), in vivo cotransfection transcription assays\",\n      \"journal\": \"Genes & development\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — multiple orthogonal biochemical and cellular assays, negative control included, replicated across contexts\",\n      \"pmids\": [\"8405994\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1993,\n      \"finding\": \"p300 co-immunoprecipitates with TBP and shares two additional common phosphoproteins (64 and 59 kDa) with TBP complexes, indicating p300 interacts with TBP (possibly through intermediary proteins).\",\n      \"method\": \"Co-immunoprecipitation, partial proteolytic digest comparison\",\n      \"journal\": \"Oncogene\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — single lab, co-IP only, interaction may be indirect\",\n      \"pmids\": [\"8502484\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1993,\n      \"finding\": \"Drosophila TAFII60 and human TAFII70 bind weakly to TBP and strongly to TAFII250; in combination with TBP and TAFII250 they form a stable ternary complex; dTAFII60 and hTAFII70 also directly interact with TAFII40.\",\n      \"method\": \"Recombinant protein expression, pull-down binding assays\",\n      \"journal\": \"The EMBO journal\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct binding by reconstitution, single lab\",\n      \"pmids\": [\"8262073\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1994,\n      \"finding\": \"SL1 TAFIs (TAFI110, 63, 48) can each bind individually and specifically to TBP, and form a stable TBP-TAF complex; binding of SL1 TAFIs to TBP is mutually exclusive with binding of TFIID subunits (TAFII250 or TAFII150), establishing a mechanism for directing TBP into polymerase-selective complexes.\",\n      \"method\": \"Reconstituted subunit interaction assays, complementary cDNA expression, biochemical binding competition\",\n      \"journal\": \"Science\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — reconstitution of multi-subunit interactions with competition assays, mechanistically definitive\",\n      \"pmids\": [\"7801123\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1994,\n      \"finding\": \"Drosophila holo-TFIIA (L/S complex) binds TBP with high affinity and cooperatively with TBP to TATA box DNA (extended DNase footprint); holo-TFIIA stimulates basal transcription and enhances activation by Sp1, VP16, and NTF-1.\",\n      \"method\": \"Reconstitution of recombinant TFIIA subunits, subunit interaction studies, DNase footprinting, in vitro transcription\",\n      \"journal\": \"Genes & development\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — reconstituted system with multiple orthogonal assays\",\n      \"pmids\": [\"7958898\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1994,\n      \"finding\": \"The TBP subunit of TFIID crosslinks specifically to the TATA element; a 150 kDa TAF crosslinks to downstream regions (+10 to +15 and +35 to +47); a >205 kDa TAF crosslinks preferentially to +35 to +42; TAF-DNA interactions downstream are disrupted at elevated salt while TBP-TATA interaction is maintained.\",\n      \"method\": \"Protein-DNA crosslinking of TFIID complex\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct crosslinking method mapping TBP and TAF contacts, single lab\",\n      \"pmids\": [\"8139922\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1995,\n      \"finding\": \"Crystal structure of the TFIIB/TBP/TATA-element ternary complex at 2.7 Å resolution: core TFIIB resembles cyclin A and recognizes the preformed TBP-DNA complex through protein-protein and protein-DNA contacts; the TFIIB amino-terminal domain forms the downstream surface where it could fix the transcription start site.\",\n      \"method\": \"X-ray crystallography\",\n      \"journal\": \"Nature\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — atomic resolution crystal structure with functional implications, landmark study\",\n      \"pmids\": [\"7675079\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1995,\n      \"finding\": \"Distamycin A and tallimustine bind the DNA minor groove and prevent TBP (and TBP-TFIIA, TBP-TFIIA-TFIIB) binding to the TATA box; once formed, TBP-containing complexes are more resistant to these drugs; both inhibit basal in vitro transcription at similar concentrations.\",\n      \"method\": \"EMSA (gel shift), in vitro transcription\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct binding and functional transcription assays, single lab, two orthogonal methods\",\n      \"pmids\": [\"7784168\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1995,\n      \"finding\": \"Electron microscopy of yeast TBP on HIV and adeno promoters shows TBP forms dimers (63 kDa) at the TATA box and higher-order oligomers; TBP dimers bend the DNA approximately 80–90° around the TATA box.\",\n      \"method\": \"Electron microscopy (three preparative methods), mass analysis of protein particles\",\n      \"journal\": \"Journal of molecular biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — three independent EM methods used, single lab\",\n      \"pmids\": [\"7533216\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1997,\n      \"finding\": \"TBP/TFIID binds selectively to cisplatin- or UV-damaged DNA (structural similarity between damaged DNA and TATA box), sequestering TBP away from promoters; microinjection of additional TBP in living human fibroblasts alleviates UV-induced reduction in RNA synthesis.\",\n      \"method\": \"Filter binding, in vitro transcription competition, 3D structural analysis, microinjection into living cells\",\n      \"journal\": \"The EMBO journal\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Strong — multiple orthogonal methods including in vitro assays and live-cell functional rescue\",\n      \"pmids\": [\"9405373\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1997,\n      \"finding\": \"TFIIA stabilizes TBP/TATA interactions approximately 10-fold (reduces koff); upstream DNA contacts by TFIIA further stabilize the TFIIA-TBP complex; in the absence of DNA, TFIIA dissociates from TBP rapidly (koff ~4.9×10⁻³ s⁻¹).\",\n      \"method\": \"Nitrocellulose filter binding assay (koff measurements), EMSA, nickel-agarose pull-down with His-tagged TFIIA\",\n      \"journal\": \"Journal of molecular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — quantitative kinetic measurements with multiple methods, mechanistically precise\",\n      \"pmids\": [\"9300055\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1997,\n      \"finding\": \"TBP-TFIIB interaction is critical for transcription in vitro; an altered-specificity TATA-TBP-TFIIB array showed that many activators use the known TBP-TFIIB interaction to stimulate transcription in human cells, but a glutamine-rich Sp1 activation domain activates independently of this interaction.\",\n      \"method\": \"Rationally designed altered-specificity TBP-TFIIB interaction, in vivo transcription assays in human cells\",\n      \"journal\": \"Science\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — structure-guided mutagenesis with in vivo functional validation, dissects specificity of activator-TBP-TFIIB dependency\",\n      \"pmids\": [\"9012349\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1998,\n      \"finding\": \"TAFIIs (specifically TAFII250) inhibit TBP-DNA binding and TBP-TFIIA binding; TFIIA overcomes TAFII-mediated inhibition of TBP-DNA binding by competing with TAFII250 for access to TBP; limited proteolysis of TFIID relieves inhibition of TBP-DNA binding.\",\n      \"method\": \"EMSA, DNase I footprinting, in vitro transcription, temperature-sensitive cell line (ts13)\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Strong — multiple orthogonal biochemical and cellular approaches, mechanistically defined\",\n      \"pmids\": [\"9603936\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1999,\n      \"finding\": \"TFIIA promotes dissociation of TBP dimers (which block DNA binding) and accelerates TBP binding kinetics; TFIID dimer dissociation is slow and rate-limiting in DNA binding, and TFIIA induces rapid dissociation of TFIID dimers to facilitate promoter loading.\",\n      \"method\": \"Biochemical dimerization assays, kinetic DNA-binding assays\",\n      \"journal\": \"Molecular cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — quantitative kinetic biochemistry demonstrating novel regulatory mechanism for TBP dimer/TFIID dimer dissociation by TFIIA\",\n      \"pmids\": [\"10518227\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1999,\n      \"finding\": \"TBP binding in vivo is regulated: Mot1 prevents TBP binding to inactive promoters, and activator-mediated stimulation of TBP binding requires TFIIB and Srb4; TBP binding generally correlates with transcriptional activity across endogenous yeast genes.\",\n      \"method\": \"DNA-crosslinking/immunoprecipitation (in vivo), mutant yeast strains (genetic epistasis)\",\n      \"journal\": \"Nature\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — in vivo crosslinking-IP with genetic epistasis across multiple genes, replicated at endogenous loci\",\n      \"pmids\": [\"10376604\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1999,\n      \"finding\": \"TBP-related factor TRF2 (TBPL1) binds TFIIA and TFIIB but does not bind canonical TATA boxes; TRF2 is associated with distinct chromosomal loci from TBP in Drosophila, suggesting different promoter specificity.\",\n      \"method\": \"Protein interaction assays, Drosophila polytene chromosome staining\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct binding assays and chromosomal localization, single lab\",\n      \"pmids\": [\"10220372\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2000,\n      \"finding\": \"In vivo, TBP exists in at least two transcriptionally active forms: a TAF-containing form (TFIID) and a TAF-independent form; promoter occupancy by TAFs does not universally correlate with transcriptional activity, unlike TBP, TFIIA, and TFIIB occupancy.\",\n      \"method\": \"Chromatin immunoprecipitation (ChIP) at yeast promoters, genome-wide expression analysis\",\n      \"journal\": \"Science\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — ChIP across many promoters, two orthogonal approaches (expression + occupancy), independently confirmed\",\n      \"pmids\": [\"10818000\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2000,\n      \"finding\": \"TBP-related factor TRF1 preferentially binds and directs transcription from the tudor gene promoter in Drosophila, a TRF1-responsive promoter distinct from TBP-regulated promoters.\",\n      \"method\": \"Polytene chromosome staining, ChIP, mRNA analysis, cotransfection assays, in vitro transcription reconstitution, DNase I footprinting\",\n      \"journal\": \"Science\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — reconstituted in vitro transcription plus multiple in vivo validations, multiple orthogonal methods\",\n      \"pmids\": [\"10797011\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2001,\n      \"finding\": \"MOT1 uses ATP hydrolysis to remove TBP from DNA; MOT1 requires a 17 bp double-stranded DNA 'handle' upstream of the TATA box; TBP-DNA disruption does not require DNA strand separation, bending, or helix twisting, suggesting translocation along the handle drives disruption.\",\n      \"method\": \"In vitro ATPase/disruption assays with template variants, mutant DNA substrates\",\n      \"journal\": \"The EMBO journal\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — detailed mechanistic dissection with multiple substrate variants, single lab but rigorous\",\n      \"pmids\": [\"11296235\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2002,\n      \"finding\": \"GFP-TBP stably associates with condensed mitotic chromosomes (no FRAP signal during mitosis); in interphase cells, GFP-TBP shows ~100-fold slower FRAP than TFIIB; endogenous TBP and TAFs cofractionate with mitotic chromatin, suggesting TBP-TAF complexes remain promoter-bound for multiple rounds of transcription.\",\n      \"method\": \"FRAP of GFP-TBP in live HeLa cells, chromatin fractionation\",\n      \"journal\": \"Molecular biology of the cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — live-cell FRAP combined with biochemical fractionation, quantitative comparison with control factor (TFIIB)\",\n      \"pmids\": [\"11809839\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2003,\n      \"finding\": \"p53 represses RNA polymerase III transcription through direct interaction with TBP; overexpressing TBP reverses p53-mediated inhibition of tRNA gene transcription; p53 does not disrupt TBP-Brf1 interaction but prevents Brf1 complexes from associating with TFIIIC2 and RNA pol III; ChIP shows TFIIIB occupancy decreases upon p53 induction.\",\n      \"method\": \"In vitro transcription, overexpression rescue, chromatin immunoprecipitation (ChIP), co-immunoprecipitation\",\n      \"journal\": \"The EMBO journal\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — multiple orthogonal methods including ChIP, functional rescue, and interaction assays, mechanistically precise\",\n      \"pmids\": [\"12773395\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2004,\n      \"finding\": \"RNA aptamers generated against yeast TBP bind TBP competitively with TATA-DNA and some actively disrupt preformed TBP-TATA complexes even in the context of TFIIB and TFIIA; aptamers inhibit transcription in crude extracts, revealing dynamic TBP interactions during initiation and reinitiation.\",\n      \"method\": \"SELEX, aptamer binding assays, in vitro transcription with crude extracts\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct binding and functional assays in multiple contexts, single lab\",\n      \"pmids\": [\"15103022\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2004,\n      \"finding\": \"Immunomapping of yeast TFIID by EM revealed TBP is located in the linker domain between lobes A and C of the trilobed TFIID structure, with the N-terminal 100 residues of TAF1 spanning over TBP.\",\n      \"method\": \"Electron microscopy, immunomapping with antibodies against TFIID subunits\",\n      \"journal\": \"The EMBO journal\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — EM-based immunomapping, single lab, limited resolution\",\n      \"pmids\": [\"14765106\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2006,\n      \"finding\": \"SAGA binds TBP directly via its Spt8 subunit (and Ada1); Spt8 and SAGA compete with DNA (rather than forming a triple complex) to bind TBP, supporting a handoff model where SAGA transfers TBP to the TATA box rather than binding together with TBP at the promoter.\",\n      \"method\": \"Chemical crosslinking to identify SAGA-TBP contacts, direct binding assays (competition with DNA and TBP dimer)\",\n      \"journal\": \"The EMBO journal\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — direct binding competition assays with multiple substrates, mechanistically clear model\",\n      \"pmids\": [\"16888622\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2006,\n      \"finding\": \"The Med8 N-terminal domain of the Mediator head subcomplex Med8-Med18-Med20 binds TBP in vitro and is essential in vivo; the Med8/18/20 subcomplex contains a putative multipartite TBP-binding site in the Mediator head.\",\n      \"method\": \"X-ray crystallography of Med8C/18/20 submodule, in vitro TBP-binding assays, genetic complementation\",\n      \"journal\": \"Nature structural & molecular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — crystal structure plus direct binding assay and genetic validation\",\n      \"pmids\": [\"16964259\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2006,\n      \"finding\": \"Brd2 is a TBP-associated protein; a 26 amino acid peptide in the first bromodomain of Brd2 mediates Brd2-TBP interaction; serum stimulation induces formation of a Brd2-E2F-1-TBP complex in vivo, with Brd2 recruiting TBP into the E2F-1 transcriptional complex.\",\n      \"method\": \"Co-immunoprecipitation, domain mapping, overexpression assays, luciferase reporter assays\",\n      \"journal\": \"Molecular and cellular biochemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — co-IP and functional reporter assays, single lab, domain mapped\",\n      \"pmids\": [\"17111193\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2008,\n      \"finding\": \"During mitosis, TBP recruits PP2A to active gene promoters; the TBP-PP2A complex dephosphorylates and inactivates condensin at these promoters to prevent chromatin compaction, thereby bookmarking previously active genes for re-activation in daughter cells.\",\n      \"method\": \"Co-immunoprecipitation, ChIP-on-chip, functional assays for condensin inactivation\",\n      \"journal\": \"Nature cell biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — co-IP for complex, ChIP-on-chip for genome-wide binding, functional condensin dephosphorylation assay, multiple orthogonal methods\",\n      \"pmids\": [\"18931662\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2010,\n      \"finding\": \"TFIIA and the transactivator Rap1 cooperate to commit TFIID for transcription initiation; cryo-EM structures reveal Rap1 and TFIIA bind TFIID simultaneously, TFIIA undergoes a Rap1-induced conformational change that increases exposure of TBP within TFIID; a large DNA loop forms between the activator site and proximal promoter, locked by a TFIIA-Rap1 protein bridge.\",\n      \"method\": \"Cryo-electron microscopy, structural reconstruction of TFIID-TFIIA-Rap1-DNA complexes\",\n      \"journal\": \"Nature\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — cryo-EM structural analysis of full complex, mechanistically defines how activator exposes TBP for promoter binding\",\n      \"pmids\": [\"20559389\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"Human TFIID exists in two predominant structural states differing by ~100 Å translocation of lobe A; TFIIA and promoter DNA together facilitate transition to a rearranged state that enables promoter recognition; TATA, Inr, MTE, and DPE promoter motifs were mapped within the TFIID-TFIIA-DNA structure.\",\n      \"method\": \"Single-particle electron microscopy (cryo-EM), DNA labeling, DNase footprinting\",\n      \"journal\": \"Cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — cryo-EM with functional footprinting validation, multiple promoter elements mapped\",\n      \"pmids\": [\"23332750\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"TRF2 (TBPL1/TRF2), not TBP, is required for transcription of TCT-dependent ribosomal protein genes in Drosophila and humans; TBP depletion does not affect TCT-dependent transcription, while TRF2 depletion does; purified TRF2 activates TCT but not TATA promoters in vitro.\",\n      \"method\": \"Overexpression and depletion of TBP/TRF2, in vitro transcription with purified TRF2, ChIP-seq\",\n      \"journal\": \"Genes & development\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — in vitro reconstitution plus depletion experiments and ChIP-seq, negative result for TBP and positive for TRF2 mechanistically decisive\",\n      \"pmids\": [\"24958592\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"Age-related decline in Hsc70 chaperone activity leads to increased mutant TBP accumulation in SCA17 mice; mutant TBP shows decreased association with XBP1s, resulting in reduced transcription of MANF; expression of Hsc70 improves TBP-XBP1s interaction and MANF transcription.\",\n      \"method\": \"Inducible knock-in mouse model, co-immunoprecipitation, gene expression analysis, MANF overexpression rescue\",\n      \"journal\": \"Neuron\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — in vivo mouse model with co-IP and functional rescue, single lab\",\n      \"pmids\": [\"24462098\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"TBP interacts with the Cnd2 kleisin subunit of condensin and recruits condensin onto RNA polymerase III-transcribed genes and highly transcribed Pol II genes in fission yeast; disruption of the Cnd2-TBP interaction causes defects in condensin localization, mitotic chromosome assembly, chromosome segregation, and cellular lethality.\",\n      \"method\": \"Co-immunoprecipitation, ChIP, genetic analysis with interaction-disrupting mutants\",\n      \"journal\": \"Molecular cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal co-IP, genome-wide ChIP, loss-of-function with defined mechanistic and phenotypic readout\",\n      \"pmids\": [\"26257282\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"TBP protein levels are regulated by the ubiquitin-proteasome system; E3 ligase Huwe1 targets TBP for K48-linked ubiquitination and proteasomal degradation; deubiquitinase USP10 antagonizes Huwe1 and protects TBP from degradation; upregulation of Huwe1 during myogenesis induces TBP degradation and drives myotube differentiation.\",\n      \"method\": \"In vitro ubiquitination assay with biochemical fractionation, mass spectrometry identification of Huwe1, cell-based functional assays\",\n      \"journal\": \"eLife\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — in vitro reconstitution of ubiquitination plus cellular functional assays with identified E3 and DUB, multiple orthogonal methods\",\n      \"pmids\": [\"26393420\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"Cryo-EM structure of human TFIID with TFIIA and core promoter DNA at sub-nanometre resolution shows TAF1 and TAF2 mediate major interactions with the downstream promoter; TFIIA bridges the TBP-TATA complex with lobe B of TFIID; all core promoter elements are contacted by TFIID subunits.\",\n      \"method\": \"Single-particle cryo-electron microscopy, structural analysis\",\n      \"journal\": \"Nature\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — sub-nanometre cryo-EM structure of complete TFIID-TFIIA-DNA complex\",\n      \"pmids\": [\"27007846\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"TAF11 and TAF13 form a ternary complex with TBP via the TAF11/TAF13 histone-fold domains; TAF11/TAF13 competes with TATA-box DNA and with the TAF1 N-terminal domain (TAND1) for TBP binding; the highly conserved C-terminal TBP-interaction domain (CTID) of TAF13 is essential for cell growth; TAF11/TAF13 interacts with the DNA-binding surface of TBP.\",\n      \"method\": \"Crystal structure of TAF11/TAF13/TBP complex (2.4 Å), cross-linking mass spectrometry, biochemical competition assays, genetic complementation\",\n      \"journal\": \"eLife\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — crystal structure plus biochemical competition and genetic essentiality, multiple orthogonal methods in single rigorous study\",\n      \"pmids\": [\"29111974\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"Cryo-EM of human TFIID with TFIIA and promoter DNA reveals five structural states; initial TFIID binding to the downstream promoter positions upstream DNA and facilitates scanning of TBP for a TATA box, followed by engagement of the promoter — defining a mechanism for TBP loading onto promoter DNA by TFIID.\",\n      \"method\": \"Cryo-electron microscopy, chemical cross-linking mass spectrometry, biochemical reconstitution\",\n      \"journal\": \"Science\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — cryo-EM at multiple states combined with biochemical reconstitution, mechanistically defines TBP loading pathway\",\n      \"pmids\": [\"30442764\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"TBP remains stably bound to active gene promoters on mitotic chromosomes in mouse ES cells (average residence time of minutes vs. seconds for typical TFs, by single-molecule live imaging); acute TBP degradation reduces RNA Pol II association with mitotic chromosomes and impairs transcriptional reactivation after mitosis.\",\n      \"method\": \"Live-cell single-molecule imaging, drug-inducible degron system, ChIP\",\n      \"journal\": \"eLife\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — single-molecule live imaging plus inducible degron with functional readout, multiple orthogonal approaches\",\n      \"pmids\": [\"29939130\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"Chaperonin CCT specifically associates with nascent TAF5 and hands it off to TAF6-TAF9, acting as a checkpoint for TFIID assembly; TAF5-TAF6-TAF9 form a cytoplasmic submodule with novel interactions essential for TFIID integrity; TAF9 allocation between TFIID and SAGA is regulated by these submodule interactions.\",\n      \"method\": \"Quantitative proteomics, structural analysis, mutational analysis, mass spectrometry of submodules\",\n      \"journal\": \"Nature structural & molecular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — structural and mutational analysis combined with quantitative proteomics, multiple orthogonal methods\",\n      \"pmids\": [\"30510221\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"H3K4me3Q5ser (combinatorial serotonylation and methylation on histone H3) potentiates TFIID binding to H3K4me3 nucleosomes; tissue transglutaminase 2 serotonylates H3 at Q5 on H3K4me3-marked nucleosomes; ectopic expression of a H3 mutant that cannot be serotonylated alters H3K4me3Q5ser-target gene expression and impairs differentiation.\",\n      \"method\": \"In vitro enzyme assay (transglutaminase), genome-wide chromatin analysis, TFIID binding assay, H3 mutant cell lines\",\n      \"journal\": \"Nature\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — enzymatic reconstitution, direct TFIID binding assay, genome-wide mapping, and mutant cell functional validation\",\n      \"pmids\": [\"30867594\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"Two discrete regions of MYC (amino acids 98–111 and 115–124) interact with TBP; a crystal structure (2.4 Å) shows MYC aa 98–111 interacts with TBP in the presence of TAF1 TAND1; MYC aa 115–124 resembles a TBP anchor motif; MYC mutants that abrogate TBP interaction compromise MYC transcriptional activity.\",\n      \"method\": \"2.4 Å crystal structure, biochemical binding assays, site-specific MYC mutagenesis with functional assays\",\n      \"journal\": \"Nature structural & molecular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — crystal structure plus mutagenesis with functional consequences, multiple orthogonal methods\",\n      \"pmids\": [\"31686052\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"Cryo-EM structure of yeast SAGA with bound TBP reveals an octamer of histone-fold domains in the SAGA core that forms a peripheral site for TBP where steric hindrance represses spurious DNA binding; biochemical analysis shows TBP delivery from SAGA to promoter DNA requires TFIIA and correlates with TBP-DNA affinity, supporting a handoff mechanism.\",\n      \"method\": \"Cryo-electron microscopy (3.5 Å core resolution), biochemical TBP delivery assays\",\n      \"journal\": \"Nature\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — near-atomic resolution cryo-EM plus biochemical mechanistic validation\",\n      \"pmids\": [\"31969704\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"TFIID is required for RNA Polymerase II promoter-proximal pausing; replacement of TFIID with TBP alone in a purified reconstituted in vitro transcription system abolishes pausing; acute depletion of TFIID subunits in human and Drosophila cells disrupts genome-wide RNAPII pausing.\",\n      \"method\": \"Reconstituted in vitro transcription with purified factors, drug-inducible TFIID subunit depletion, PRO-seq\",\n      \"journal\": \"Molecular cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — reconstituted in vitro assay plus genome-wide in vivo validation, multiple orthogonal methods\",\n      \"pmids\": [\"32229306\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"TBP can bind to a nucleosome containing the Widom-601 sequence; TFIIA stabilizes TBP-nucleosome binding; cryo-EM structures show TBP binds at SHL -6 (TATA-like, TFIIA-independent) and SHL +2 (GC-rich, TFIIA-dependent, with detachment of upstream terminal DNA from histone octamer); TBP-nucleosome complexes are sterically incompatible with PIC assembly.\",\n      \"method\": \"Cryo-electron microscopy (three structures), biochemical binding assays\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — multiple cryo-EM structures plus biochemical validation, mechanistically explains nucleosome barrier to transcription\",\n      \"pmids\": [\"34301908\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"TIF1γ binds TBP in competition with TAF15, displacing TAF15 from the TAF15/TBP complex; TIF1γ also multi-mono-ubiquitylates TAF15 and drives its nuclear export; the TAF15/TBP complex is required for IL-6 transactivation-induced EMT in lung adenocarcinoma cells.\",\n      \"method\": \"Co-immunoprecipitation, competition binding assays, ubiquitylation assays, nuclear export assays, cell functional assays\",\n      \"journal\": \"Cell reports\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — co-IP plus ubiquitylation and functional assays, single lab, multiple orthogonal methods\",\n      \"pmids\": [\"36261009\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"Human TFIID biogenesis occurs co-translationally; all protein heterodimerization steps occur during protein synthesis; TAF1 acts as a flexible scaffold that drives co-translational recruitment of TFIID submodules preassembled in the cytoplasm onto the nascent TAF1 polypeptide.\",\n      \"method\": \"RNA-immunoprecipitation (RIP), single-molecule imaging, proteomics, structure-function analyses\",\n      \"journal\": \"Nature structural & molecular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — multiple orthogonal methods (RIP, single-molecule imaging, proteomics, mutagenesis), mechanistically defines TFIID assembly pathway\",\n      \"pmids\": [\"37386215\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"Large polyQ repeats (105Q) in TBP preferentially cause muscle degeneration and reduce expression of muscle-specific genes by decreasing the association of MyoD with TBP and with DNA promoters; smaller polyQ repeats do not show this effect, demonstrating polyQ length-dependent differential protein interactions.\",\n      \"method\": \"Knockin mouse models, co-immunoprecipitation, ChIP, direct muscle expression of TBP with different polyQ lengths\",\n      \"journal\": \"Cell reports\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — co-IP and ChIP with functional mouse model, single lab, length-dependent comparison\",\n      \"pmids\": [\"26387956\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"TBP is a highly conserved TATA box-binding protein that binds the DNA minor groove, bends DNA ~80–90°, and nucleates RNA polymerase II (and I/III) preinitiation complex assembly as a subunit of TFIID (with TAFs) or other TBP-containing complexes (SL1, TFIIIB, SAGA); its promoter loading is controlled by TFIIA (which dissociates inhibitory TBP/TFIID dimers and stabilizes TBP-DNA binding), by TAF-mediated inhibition of TBP-DNA binding (relieved by TFIIA), by MOT1-catalyzed ATP-dependent removal of TBP from DNA, and by Huwe1/USP10-mediated ubiquitination/deubiquitination that controls TBP protein levels; TBP stably occupies active promoters on mitotic chromosomes to bookmark genes for post-mitotic reactivation via a TBP-PP2A complex that inactivates condensin; TBP interacts with multiple regulators including p53, MYC, Mediator (via Med8), Rap1-TFIIA, and condensin (via Cnd2), with structures of TFIID-TFIIA-DNA, TFIIB-TBP-TATA, and SAGA-TBP complexes providing atomic-level mechanisms for TBP delivery and promoter engagement.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"TBP is the core promoter recognition factor that nucleates RNA polymerase preinitiation complex assembly by engaging the TATA element through the DNA minor groove [#0] and bending the duplex ~80–90° around the TATA box [#1, #14]; a discrete 12-residue surface determines its sequence specificity [#2]. TBP partitions into multiple multisubunit complexes—TAF-containing TFIID forms and TAF-independent forms in vivo [#3, #22]—and is directed into polymerase-selective complexes through mutually exclusive TAF binding, where SL1 TAFs and TFIID TAFs (TAF1/TAF250, TAF11/TAF13) compete for the same TBP surfaces [#9, #40]. Within TFIID, TBP occupies the linker between lobes, and cryo-EM has resolved how downstream-promoter engagement by TAF1/TAF2 positions DNA so TBP scans for and loads onto the TATA box, a transition driven by TFIIA and promoter DNA [#28, #39, #41]. TBP delivery is tightly regulated: TFIIA dissociates inhibitory TBP/TFIID dimers and stabilizes TBP–DNA binding while relieving TAF-mediated autoinhibition [#16, #18, #19], MOT1 uses ATP hydrolysis and a DNA handle to strip TBP from DNA [#24], and SAGA hands TBP off to the promoter through a steric, TFIIA-dependent mechanism rather than co-binding [#29, #46]. Once loaded, TBP–DNA is recognized by TFIIB to build the start-site-defining complex [#12, #17], and TFIID—but not TBP alone—is required for RNA Pol II promoter-proximal pausing [#47]. Beyond initiation, TBP is a transcriptional and regulatory hub: it is bound and modulated by p53, MYC, Mediator (via Med8), Brd2, and TAF15 [#6, #45, #30, #31, #49], its protein levels are set by Huwe1-mediated K48 ubiquitination opposed by USP10 [#38], and it stably bookmarks active promoters on mitotic chromosomes—recruiting PP2A to inactivate condensin and sustaining Pol II occupancy for post-mitotic transcriptional reactivation [#25, #32, #37, #42]. Polyglutamine-expanded TBP causes the neurodegenerative disorder SCA17, where mutant TBP loses interactions with partners such as XBP1s and MyoD to alter target gene transcription [#36, #51].\",\n  \"teleology\": [\n    {\n      \"year\": 1991,\n      \"claim\": \"Established the physical basis of promoter recognition by showing TBP reads the TATA box through the DNA minor groove rather than the major groove, defining an unusual mode of sequence-specific DNA binding.\",\n      \"evidence\": \"Base-substitution (C/I replacement) chemistry combined with DNA-binding assays\",\n      \"pmids\": [\"1760847\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not resolve the atomic contacts or the protein surface mediating recognition\", \"Did not address regulation of binding in vivo\"]\n    },\n    {\n      \"year\": 1992,\n      \"claim\": \"Defined TBP's mechanical action on DNA and the protein determinant of specificity, showing TBP bends the helix and that a 12-residue region sets sequence preference.\",\n      \"evidence\": \"Permuted-site gel retardation with recombinant TBP; altered-specificity mutagenesis with biochemical and in vivo transcription assays\",\n      \"pmids\": [\"1736286\", \"1739977\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Bend angle quantified more precisely only later by EM\", \"Did not connect bending to downstream PIC assembly\"]\n    },\n    {\n      \"year\": 1992,\n      \"claim\": \"Revealed that TBP is not a free factor but resides in distinct multisubunit complexes with different functional capacities, only the larger of which supports activated transcription.\",\n      \"evidence\": \"Biochemical fractionation of HeLa extracts, cofractionation, in vitro transcription; B-TFIID subunit composition and ATPase assay\",\n      \"pmids\": [\"1936986\", \"1387711\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Full TAF composition of D-TFIID not enumerated\", \"Functional role of B-TFIID ATPase unresolved\"]\n    },\n    {\n      \"year\": 1993,\n      \"claim\": \"Identified direct TAF and regulator contacts on TBP, establishing TFIID architecture and linking TBP to oncogenic/tumor-suppressor regulation via TAF250, p53, and p300.\",\n      \"evidence\": \"Recombinant binding and yeast interaction (TAF250); Co-IP and EMSA (p53, p300); reconstitution of TAF60/70 ternary complexes\",\n      \"pmids\": [\"7680771\", \"8405994\", \"8502484\", \"8262073\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"p300–TBP interaction may be indirect (Co-IP only)\", \"Stoichiometry and assembly order of TAF subcomplexes not yet defined\"]\n    },\n    {\n      \"year\": 1994,\n      \"claim\": \"Explained how TBP is sorted among polymerase systems and how cofactors modulate its DNA engagement, showing SL1 TAFs bind TBP mutually exclusively with TFIID TAFs and that TFIIA cooperatively enhances TBP–TATA binding.\",\n      \"evidence\": \"Reconstituted subunit competition assays (SL1); recombinant TFIIA reconstitution with DNase footprinting and in vitro transcription\",\n      \"pmids\": [\"7801123\", \"7958898\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Kinetics of TFIIA stabilization quantified only later\", \"Mechanism of dimer/oligomer interplay not yet addressed\"]\n    },\n    {\n      \"year\": 1995,\n      \"claim\": \"Provided atomic and structural mechanism for promoter engagement, showing TFIIB recognizes the preformed TBP–DNA complex and that TBP forms DNA-bending dimers/oligomers at the TATA box.\",\n      \"evidence\": \"X-ray crystallography of TFIIB/TBP/TATA; electron microscopy and mass analysis of TBP particles\",\n      \"pmids\": [\"7675079\", \"7533216\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Functional role of TBP oligomers in vivo unresolved\", \"Did not capture the full PIC\"]\n    },\n    {\n      \"year\": 1995,\n      \"claim\": \"Connected TBP availability to genome integrity and to small-molecule control, showing TBP is sequestered by damaged DNA and that minor-groove ligands block TBP loading.\",\n      \"evidence\": \"Filter binding, in vitro transcription competition, structural analysis, microinjection rescue; EMSA with distamycin/tallimustine\",\n      \"pmids\": [\"9405373\", \"7784168\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Physiological extent of TBP sequestration by lesions unquantified\", \"Drug specificity for TBP versus general minor-groove occupancy unclear\"]\n    },\n    {\n      \"year\": 1997,\n      \"claim\": \"Quantified and dissected TFIIA's role and the activator dependence on the TBP–TFIIB interface, showing TFIIA stabilizes TBP–DNA ~10-fold and that most but not all activators route through TBP–TFIIB contacts.\",\n      \"evidence\": \"Filter-binding koff measurements and EMSA (TFIIA); altered-specificity TBP–TFIIB array in human cells\",\n      \"pmids\": [\"9300055\", \"9012349\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Sp1 glutamine-rich domain's alternative path not mapped\", \"In vivo kinetics on chromatin not addressed\"]\n    },\n    {\n      \"year\": 1998,\n      \"claim\": \"Defined a regulatory logic of autoinhibition within TFIID, showing TAF250 inhibits TBP–DNA binding and TFIIA relieves this by competing for TBP.\",\n      \"evidence\": \"EMSA, DNase I footprinting, in vitro transcription, ts13 cell line\",\n      \"pmids\": [\"9603936\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Structural basis of TAF250 occlusion resolved only later\", \"In vivo balance of inhibition versus relief not quantified\"]\n    },\n    {\n      \"year\": 1999,\n      \"claim\": \"Resolved how inhibitory TBP/TFIID dimers are cleared and how TBP loading is controlled in cells, showing TFIIA dissociates dimers and that Mot1, TFIIB, and Srb4 gate TBP occupancy at promoters.\",\n      \"evidence\": \"Kinetic dimerization/DNA-binding biochemistry; in vivo crosslinking-IP with yeast genetic epistasis\",\n      \"pmids\": [\"10518227\", \"10376604\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Mechanism of Mot1 action not yet biochemically dissected\", \"Generality across promoter classes incompletely sampled\"]\n    },\n    {\n      \"year\": 1999,\n      \"claim\": \"Distinguished TBP from paralogous TBP-related factors, showing TRF2 binds TFIIA/TFIIB but not canonical TATA boxes and localizes to distinct loci.\",\n      \"evidence\": \"Protein interaction assays and Drosophila polytene chromosome staining\",\n      \"pmids\": [\"10220372\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"TRF2 promoter specificity not yet defined (single-lab, descriptive)\", \"Functional target genes not identified at this stage\"]\n    },\n    {\n      \"year\": 2000,\n      \"claim\": \"Established in vivo that TBP occupancy, not TAF occupancy, tracks transcription, and that TBP exists in both TAF-dependent and TAF-independent active forms; in parallel, TRF1 was shown to direct a dedicated promoter class.\",\n      \"evidence\": \"ChIP at yeast promoters with genome-wide expression; reconstituted TRF1-directed transcription with multiple in vivo validations\",\n      \"pmids\": [\"10818000\", \"10797011\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Identity of the TAF-independent TBP form not biochemically defined\", \"Mechanism of TAF-free TBP recruitment unclear\"]\n    },\n    {\n      \"year\": 2001,\n      \"claim\": \"Solved the mechanism of MOT1-driven TBP removal, showing ATP hydrolysis and translocation along an upstream DNA handle strips TBP without strand separation or unbending.\",\n      \"evidence\": \"In vitro ATPase/disruption assays with template and substrate variants\",\n      \"pmids\": [\"11296235\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Structural snapshot of MOT1–TBP–DNA not obtained\", \"In vivo redistribution consequences not directly measured here\"]\n    },\n    {\n      \"year\": 2002,\n      \"claim\": \"Revealed a non-canonical role of TBP in mitotic gene memory, showing TBP–TAF complexes remain stably promoter-bound on condensed mitotic chromosomes.\",\n      \"evidence\": \"FRAP of GFP-TBP in live HeLa cells and chromatin fractionation\",\n      \"pmids\": [\"11809839\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Functional consequence of mitotic retention not yet established\", \"Mechanism enforcing stable binding unknown at this point\"]\n    },\n    {\n      \"year\": 2003,\n      \"claim\": \"Extended TBP regulation to Pol III, showing p53 represses tRNA gene transcription by acting on TBP-containing TFIIIB assembly.\",\n      \"evidence\": \"In vitro transcription, overexpression rescue, ChIP, Co-IP\",\n      \"pmids\": [\"12773395\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Structural basis of p53–TBP modulation not resolved\", \"Whether the same axis operates at Pol I unaddressed here\"]\n    },\n    {\n      \"year\": 2004,\n      \"claim\": \"Demonstrated that TBP–TATA complexes are dynamic and disruptable during initiation/reinitiation using engineered RNA aptamers that compete with DNA even in the presence of TFIIA/TFIIB; EM placed TBP in the TFIID linker domain.\",\n      \"evidence\": \"SELEX aptamer binding and in vitro transcription; EM immunomapping of yeast TFIID\",\n      \"pmids\": [\"15103022\", \"14765106\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Aptamer relevance to physiological regulators uncertain (single lab)\", \"TFIID immunomap limited in resolution\"]\n    },\n    {\n      \"year\": 2006,\n      \"claim\": \"Defined a handoff mechanism for TBP delivery by SAGA and additional regulatory contacts, showing SAGA (via Spt8/Ada1) competes with DNA for TBP and that Med8 and Brd2 provide further TBP-binding interfaces.\",\n      \"evidence\": \"Crosslinking and competition binding (SAGA); crystallography plus binding and genetics (Med8); Co-IP and reporter assays (Brd2)\",\n      \"pmids\": [\"16888622\", \"16964259\", \"17111193\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Brd2–TBP interaction supported by single-lab Co-IP\", \"Structural picture of SAGA–TBP completed only later\"]\n    },\n    {\n      \"year\": 2008,\n      \"claim\": \"Provided the functional mechanism of mitotic bookmarking, showing TBP recruits PP2A to dephosphorylate and inactivate condensin at active promoters, preventing compaction and enabling reactivation in daughter cells.\",\n      \"evidence\": \"Co-IP, ChIP-on-chip, condensin inactivation assays\",\n      \"pmids\": [\"18931662\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"How TBP selects which promoters to bookmark not defined\", \"Direct structural basis of TBP–PP2A–condensin axis unresolved\"]\n    },\n    {\n      \"year\": 2010,\n      \"claim\": \"Captured how an activator licenses TBP for promoter binding, showing Rap1 and TFIIA cooperatively commit TFIID via a conformational change that exposes TBP and a locked DNA loop.\",\n      \"evidence\": \"Cryo-EM of TFIID–TFIIA–Rap1–DNA complexes\",\n      \"pmids\": [\"20559389\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Generality of the Rap1 mechanism to other activators not established\", \"Resolution limited details of TBP–DNA contacts\"]\n    },\n    {\n      \"year\": 2013,\n      \"claim\": \"Resolved the conformational gating of human TFIID, showing a large lobe-A translocation driven by TFIIA and DNA that enables promoter recognition, with all core promoter motifs mapped.\",\n      \"evidence\": \"Single-particle cryo-EM, DNA labeling, DNase footprinting\",\n      \"pmids\": [\"23332750\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Kinetics of the conformational transition not measured\", \"How modifications/regulators bias states unaddressed\"]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"Sharpened the TBP/TRF division of labor and connected TBP misfolding to disease, showing TRF2 (not TBP) drives TCT/ribosomal protein gene transcription and that Hsc70 decline worsens mutant TBP in SCA17 by impairing TBP–XBP1s-driven MANF expression.\",\n      \"evidence\": \"Depletion/overexpression with in vitro transcription and ChIP-seq (TRF2); SCA17 knock-in mouse with Co-IP and rescue (Hsc70/MANF)\",\n      \"pmids\": [\"24958592\", \"24462098\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"SCA17 chaperone-MANF axis from single-lab mouse model\", \"Direct structural basis of mutant TBP–partner loss not defined\"]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"Linked TBP to chromosome architecture and to its own turnover, showing TBP recruits condensin via Cnd2 to highly transcribed genes and that Huwe1/USP10 set TBP protein levels to control differentiation; polyQ expansion impairs MyoD–TBP coupling in muscle.\",\n      \"evidence\": \"Co-IP, ChIP, interaction-disrupting mutants (Cnd2); in vitro ubiquitination, MS, cellular assays (Huwe1/USP10); knockin mice with Co-IP/ChIP (polyQ)\",\n      \"pmids\": [\"26257282\", \"26393420\", \"26387956\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"polyQ–MyoD effects from single-lab model (Medium)\", \"Coordination between TBP turnover and condensin recruitment unexplored\"]\n    },\n    {\n      \"year\": 2016,\n      \"claim\": \"Achieved sub-nanometre definition of the promoter-engaged TFIID, showing TAF1/TAF2 dominate downstream-promoter contacts and TFIIA bridges TBP–TATA to lobe B.\",\n      \"evidence\": \"Single-particle cryo-EM of human TFIID–TFIIA–DNA\",\n      \"pmids\": [\"27007846\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Dynamic loading pathway not yet resolved as discrete states\", \"Side-by-side comparison with non-TATA promoters limited\"]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"Defined a further layer of TBP autoinhibition within TFIID, showing TAF11/TAF13 occupy the DNA-binding surface of TBP and compete with both TATA-DNA and the TAF1 TAND1 domain.\",\n      \"evidence\": \"Crystal structure of TAF11/TAF13/TBP, XL-MS, competition assays, genetic complementation\",\n      \"pmids\": [\"29111974\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"How TAF11/13 release is triggered during loading unclear\", \"Interplay with TFIIA-mediated relief not fully integrated\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Defined the TBP-loading pathway and the functional importance of mitotic retention, showing TFIID scans for the TATA box through multiple states and that TBP residency on mitotic chromosomes is required for post-mitotic transcriptional reactivation.\",\n      \"evidence\": \"Cryo-EM of five states with XL-MS (loading); single-molecule imaging and degron with ChIP (mitotic retention)\",\n      \"pmids\": [\"30442764\", \"29939130\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Determinants of which promoters retain TBP through mitosis unresolved\", \"Timing relative to PP2A–condensin axis not directly linked\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Revealed a cytoplasmic, chaperone-gated TFIID assembly route, showing CCT hands nascent TAF5 to TAF6-TAF9 to form a submodule and partition TAF9 between TFIID and SAGA.\",\n      \"evidence\": \"Quantitative proteomics, structural and mutational analysis, MS of submodules\",\n      \"pmids\": [\"30510221\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Where TBP enters this assembly hierarchy not pinpointed here\", \"Regulation of submodule flux unknown\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Connected TFIID recruitment to chromatin modifications and to oncogenic activators, showing serotonylated H3K4me3 (H3K4me3Q5ser) potentiates TFIID binding and that MYC directly contacts TBP to drive its transcriptional activity.\",\n      \"evidence\": \"Transglutaminase enzyme assay, genome-wide chromatin analysis, TFIID binding (serotonylation); crystal structure and MYC mutagenesis (MYC–TBP)\",\n      \"pmids\": [\"30867594\", \"31686052\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"How serotonylation alters TBP positioning structurally not resolved\", \"MYC–TBP contribution relative to other MYC cofactors unquantified\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Completed the structural mechanism of SAGA-mediated TBP delivery and revealed TFIID's role beyond initiation, showing SAGA's histone-fold octamer represses spurious TBP–DNA binding and hands TBP off via TFIIA, and that TFIID (not TBP alone) is required for Pol II pausing.\",\n      \"evidence\": \"Cryo-EM of SAGA–TBP with delivery assays; reconstituted in vitro transcription, TFIID depletion, PRO-seq\",\n      \"pmids\": [\"31969704\", \"32229306\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Which TAF subunit mediates the pausing function not pinpointed\", \"How SAGA and TFIID delivery routes are coordinated in cells unclear\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Explained the nucleosome barrier to TBP, showing TBP can bind nucleosomal DNA at defined superhelical locations (TFIIA-dependent and -independent) but in configurations incompatible with PIC assembly.\",\n      \"evidence\": \"Cryo-EM of three TBP–nucleosome structures and biochemical binding assays\",\n      \"pmids\": [\"34301908\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"In vivo relevance of nucleosomal TBP binding not established\", \"How chromatin remodelers convert these states to active PIC unknown\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Identified a competitive regulatory exchange on TBP linked to cancer phenotypes, showing TIF1γ displaces and ubiquitylates TAF15 from a TAF15/TBP complex required for IL-6-driven EMT.\",\n      \"evidence\": \"Co-IP, competition binding, ubiquitylation and nuclear-export assays, cellular functional assays\",\n      \"pmids\": [\"36261009\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Single-lab mechanism; structural basis of TAF15/TBP not resolved\", \"Generality beyond lung adenocarcinoma context untested\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Defined how the TBP-containing TFIID is built, showing co-translational, TAF1-scaffolded assembly of cytoplasmic submodules onto the nascent TAF1 polypeptide.\",\n      \"evidence\": \"RNA-immunoprecipitation, single-molecule imaging, proteomics, structure-function analyses\",\n      \"pmids\": [\"37386215\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Timing of TBP incorporation into the co-translational pathway not pinpointed\", \"How assembly errors are corrected or degraded unaddressed\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How the many competing TBP interfaces—TAF autoinhibition, TFIIA relief, MOT1 removal, SAGA handoff, chromatin-mark sensing, and Huwe1/USP10 turnover—are integrated in real time at individual promoters to set transcriptional output remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"High\",\n      \"gaps\": [\"No unified kinetic model linking TBP delivery, removal, and degradation at native loci\", \"Determinants of promoter-specific TBP retention through mitosis undefined\", \"Structural basis of disease-causing polyQ expansion's altered interactions not solved\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0003677\", \"supporting_discovery_ids\": [0, 1, 2, 11, 48]},\n      {\"term_id\": \"GO:0140110\", \"supporting_discovery_ids\": [3, 17, 20, 22, 47]},\n      {\"term_id\": \"GO:0140223\", \"supporting_discovery_ids\": [3, 12, 39]},\n      {\"term_id\": \"GO:0042393\", \"supporting_discovery_ids\": [44, 48]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [25, 32, 42]},\n      {\"term_id\": \"GO:0005654\", \"supporting_discovery_ids\": [20, 22, 32]},\n      {\"term_id\": \"GO:0000228\", \"supporting_discovery_ids\": [25, 32, 42]},\n      {\"term_id\": \"GO:0005829\", \"supporting_discovery_ids\": [43, 50]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-74160\", \"supporting_discovery_ids\": [3, 12, 20, 39, 47]},\n      {\"term_id\": \"R-HSA-1640170\", \"supporting_discovery_ids\": [25, 32, 37, 42]},\n      {\"term_id\": \"R-HSA-4839726\", \"supporting_discovery_ids\": [44, 48]},\n      {\"term_id\": \"R-HSA-392499\", \"supporting_discovery_ids\": [38, 49, 50]}\n    ],\n    \"complexes\": [\"TFIID\", \"SL1\", \"TFIIIB\", \"SAGA\"],\n    \"partners\": [\"TFIIA\", \"TFIIB\", \"TAF1\", \"MOT1\", \"p53\", \"MYC\", \"TAF13\", \"Cnd2\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":7,"faith_total":7,"faith_pct":100.0}}