{"gene":"GTF2F2","run_date":"2026-06-10T01:55:21","timeline":{"discoveries":[{"year":1988,"finding":"RAP30 binds RAP74 to form the RAP30/74 (TFIIF) heterodimer, which binds RNA polymerase II and is required for accurate transcription initiation by RNA pol II from multiple promoters (TATA-containing and TATA-less), but not by RNA pol III.","method":"Affinity chromatography, in vitro transcription assays with purified factors","journal":"Molecular and cellular biology","confidence":"High","confidence_rationale":"Tier 2 / Strong — affinity chromatography and functional reconstituted in vitro transcription, replicated across multiple promoters, foundational study","pmids":["3380090"],"is_preprint":false},{"year":1991,"finding":"The RAP30 subunit contains a region homologous to the RNA polymerase-binding domain of E. coli sigma70; RNA pol II specifically protected a serine residue in this sigma70-related region of RAP30 from phosphorylation in vitro, and RAP30/74 bound E. coli RNA polymerase and was displaced by sigma70, indicating functionally related RNA polymerase-binding regions.","method":"Sequence analysis, in vitro phosphorylation protection assay, competition binding assay with E. coli RNA polymerase and sigma70","journal":"Science (New York, N.Y.)","confidence":"High","confidence_rationale":"Tier 1 / Moderate — in vitro biochemical assay with mutagenesis-level specificity (phosphorylation protection) and competition experiment, single lab but two orthogonal methods","pmids":["1652156"],"is_preprint":false},{"year":1992,"finding":"Bacterially produced RAP30 alone binds RNA polymerase II in the absence of RAP74 and prevents RNA pol II from binding nonspecifically to DNA, thereby suppressing nonspecific transcription; the full RAP30/74 complex (but not RAP30 alone) can remove DNA-bound RNA pol II from DNA.","method":"Purified recombinant protein binding assay, in vitro transcription assay, DNA-binding competition assay","journal":"Molecular and cellular biology","confidence":"High","confidence_rationale":"Tier 1 / Moderate — reconstituted in vitro assays with recombinant proteins, multiple functional readouts in single study","pmids":["1729606"],"is_preprint":false},{"year":1992,"finding":"TBP, TFIIB, and RAP30 together constitute a minimal set of general transcription factors necessary and sufficient for specific, stable promoter binding by RNA pol II in vitro, requiring only the TATA box.","method":"Reconstituted in vitro transcription and promoter-binding assay with recombinant proteins purified from E. coli","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1 / Moderate — reconstitution with defined recombinant components, functional assay with clear minimal-set determination","pmids":["1577790"],"is_preprint":false},{"year":1992,"finding":"The carboxyl terminus of RAP30 shares sequence similarity with region 4 of bacterial sigma factors (particularly region 4.1 and 4.2 of B. subtilis sigma K); a mutant RAP30 lacking sequences similar to sigma homology region 4.2 assembles with RAP74 but has impaired ability to interact with RNA pol II.","method":"Deletion mutagenesis, biochemical interaction assays with purified factors","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1 / Moderate — mutagenesis with functional biochemical readout, two orthogonal methods (assembly assay + pol II interaction)","pmids":["1429731"],"is_preprint":false},{"year":1993,"finding":"RAP30 is required for formation of a Sarkosyl-resistant preinitiation complex (initiation function), while RAP74 is dispensable for initiation but required for very early elongation (promoter escape); RAP30 thus functions specifically as an initiation factor.","method":"In vitro transcription with Sarkosyl resistance assay, pulse-chase transcription assay using recombinant RAP30 and RAP74","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1 / Moderate — reconstituted in vitro transcription with mechanistic dissection of RAP30 vs RAP74 using two orthogonal assays","pmids":["8376403"],"is_preprint":false},{"year":1994,"finding":"The C terminus of RAP30 contains a cryptic DNA-binding domain homologous to the DNA-binding domain in conserved region 4 of sigma70 family sigma factors; this activity is masked in intact RAP30 but detectable as a fusion protein, and mutations abolishing DNA binding also abolish transcription.","method":"DNA-binding assay with fusion protein, deletion mutagenesis, in vitro transcription assay","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"High","confidence_rationale":"Tier 1 / Moderate — in vitro binding assays combined with mutagenesis and transcription functional readout, multiple orthogonal methods","pmids":["7937895"],"is_preprint":false},{"year":1994,"finding":"Both RAP30 and RAP74 subunits of TFIIF contribute to formation of stable preinitiation intermediates containing RNA pol II, to synthesis of first phosphodiester bonds, to formation of Sarkosyl-resistant preinitiation intermediates, and to stimulation of the rate of RNA chain elongation.","method":"Template competition experiments, in vitro transcription kinetics, Sarkosyl resistance assay with highly purified factors","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1 / Moderate — multiple distinct in vitro biochemical assays with highly purified reconstituted system","pmids":["7929273"],"is_preprint":false},{"year":1995,"finding":"The N-terminal domain of Drosophila TFIIF30 (RAP30 homolog) mediates interaction with TFIIF74 (RAP74), while the C-terminal domain (residues 119–276) can support approximately 50% of full transcriptional activity independently and mediates interaction with RNA pol II; a C-terminal fragment lacking the N-terminus does not assemble into a stable heterodimer with TFIIF74.","method":"Glycerol gradient sedimentation, reconstituted in vitro transcription with deletion mutants","journal":"The Journal of biological chemistry","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — functional domain mapping via deletion analysis and sedimentation in Drosophila ortholog, consistent with mammalian data","pmids":["7890767"],"is_preprint":false},{"year":1996,"finding":"RAP30 binds TFIIB through an N-terminal region (minimal binding region: amino acids 27–152), and RAP74 blocks TFIIB–RAP30 binding by both binding to TFIIB (via its C-terminal region, aa 358–517) and by binding RAP30; thus in the intact TFIIF complex, TFIIB–TFIIF contact is maintained through RAP74.","method":"Deletion mutagenesis, in vitro binding assays (GST pulldown/co-purification), in vitro transcription assay","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1 / Moderate — systematic deletion mapping with functional transcription assay and direct binding assays, multiple orthogonal methods in one study","pmids":["8662660"],"is_preprint":false},{"year":1996,"finding":"hTAFII100 (a TFIID component) directly interacts with RAP30 (the 30 kDa subunit of TFIIF) via the C-terminal WD-repeat domain of hTAFII100; an anti-hTAFII100 antibody that selectively inhibited this interaction also inhibited basal TFIID-dependent in vitro transcription; the hTAFII100–TFIIF interaction supports preinitiation complex formation in the presence of TFIID.","method":"Co-immunoprecipitation, antibody inhibition of in vitro transcription, interaction domain mapping","journal":"The EMBO journal","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — co-IP plus functional antibody inhibition and domain mapping, single lab with two orthogonal methods","pmids":["8758937"],"is_preprint":false},{"year":1998,"finding":"The three-dimensional structure of the human RAP30 DNA-binding domain (solved by NMR) reveals a winged helix-turn-helix fold structurally homologous to linker histone H5; the DNA-binding surface was identified, and the fold suggests RAP30 may act as a condensation factor for preinitiation complex assembly analogous to linker histones in chromatin.","method":"Multinuclear NMR spectroscopy, structural comparison, DNA-binding surface identification","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"High","confidence_rationale":"Tier 1 / Moderate — NMR structure with binding surface identification, structural homology with functional inference validated by domain-level data","pmids":["9689043"],"is_preprint":false},{"year":1998,"finding":"The N-terminal region (amino acids 1–29) of adenovirus E1A proteins from Ad12 and Ad2 binds RAP30 (TFIIF) in vitro; however, a mutant that failed to interact with RAP30 retained full transactivation activity, indicating RAP30 binding and transactivation are independent functions of this E1A domain.","method":"In vitro binding assay, mutagenesis, transactivation assay","journal":"Virus research","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — in vitro binding with mutagenesis but single lab and limited follow-up on mechanism","pmids":["9660075"],"is_preprint":false},{"year":1999,"finding":"Tat-SF1 associates specifically with RAP30 but not with the RAP74 subunit of TFIIF in nuclear extracts, as shown by co-immunoprecipitation; overexpression of Tat-SF1 and hSPT5 stimulates Tat-specific transcriptional activity in vivo, suggesting RAP30 participates in an elongation control complex.","method":"Co-immunoprecipitation from nuclear extracts, in vivo transcription assay with overexpression","journal":"Molecular and cellular biology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — reciprocal Co-IP combined with in vivo functional assay, single lab","pmids":["10454543"],"is_preprint":false},{"year":2000,"finding":"X-ray crystal structure of the RAP30/RAP74 interaction domains at 1.7 Å resolution reveals a novel 'triple barrel' dimerization fold; mutant data indicate that interactions with the transcription apparatus are mediated by this tripartite beta-barrel as well as by flexible loops and extending alpha/beta structures.","method":"X-ray crystallography at 1.7 Å, mutational analysis","journal":"Journal of molecular biology","confidence":"High","confidence_rationale":"Tier 1 / Moderate — high-resolution crystal structure combined with mutagenesis to validate functional interfaces","pmids":["11183778"],"is_preprint":false},{"year":2001,"finding":"RAP30 directly binds RNA pol II subunit RPB5 in vitro and in vivo; the RAP30-binding region on RPB5 maps to its central region (aa 47–120); within RAP30, the middle region (aa 101–170) contacts RPB5 in the context of the TFIIF complex (N-terminal region binds RPB5 in isolation but not within TFIIF); point mutations Y124A and Q131A in RAP30 abolish RPB5 binding and impair co-recovery of endogenous pol II with TFIIF, establishing RPB5 as a key contact for TFIIF–pol II association.","method":"In vitro pulldown with purified recombinant proteins, co-immunoprecipitation in COS1 cells, alanine-scanning mutagenesis, FLAG-affinity purification","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1 / Strong — in vitro reconstitution plus in vivo co-IP plus systematic mutagenesis identifying specific residues, multiple orthogonal methods","pmids":["11278533"],"is_preprint":false},{"year":2005,"finding":"Systematic alanine-scanning mutagenesis of RPB5 central region identified residues F76, I104, T111, and S113 as critical for RAP30 (TFIIF) binding, with T56 and L58 additionally required specifically for RAP30 binding; the overlapping nature of RAP30 and hepatitis B virus X protein binding sites on RPB5 was confirmed in both mammalian cells and in vitro.","method":"Two-step alanine scanning mutagenesis, in vitro binding assay, co-immunoprecipitation in mammalian cells","journal":"Journal of biochemistry","confidence":"High","confidence_rationale":"Tier 1 / Moderate — systematic mutagenesis with both in vitro and in vivo validation, two orthogonal methods","pmids":["16169872"],"is_preprint":false},{"year":2025,"finding":"GTF2F2 knockdown in the ovarian cancer cell line ES-2 significantly suppressed cell migration and invasion, and Western blot showed increased E-cadherin and decreased N-cadherin expression, indicating GTF2F2 promotes epithelial-mesenchymal transition (EMT) in this context.","method":"Gene knockdown (siRNA/shRNA), cell migration and invasion assays, Western blot for EMT markers","journal":"Journal of ovarian research","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single lab, single cell line, phenotypic readout without mechanistic pathway placement beyond EMT marker changes","pmids":["40442848"],"is_preprint":false}],"current_model":"GTF2F2 (RAP30) is the small subunit of the general transcription factor TFIIF (RAP30/74 heterodimer), which binds directly to RNA polymerase II (through contact with RPB5, critical residues Y124 and Q131) via a sigma70-homologous C-terminal domain; RAP30 suppresses non-specific pol II–DNA binding, is required for promoter-specific preinitiation complex assembly (together with TBP and TFIIB), drives formation of the first phosphodiester bonds, and stimulates elongation rate, while its winged-helix C-terminal DNA-binding domain and triple-barrel dimerization interface with RAP74 (solved by X-ray crystallography) mediate interactions with TFIIB, hTAFII100, and Tat-SF1 to coordinate both initiation and elongation stages of RNA pol II transcription."},"narrative":{"mechanistic_narrative":"GTF2F2 (RAP30) is the small subunit of the general transcription factor TFIIF, which it forms by heterodimerization with RAP74 to enable accurate, promoter-specific transcription initiation by RNA polymerase II from both TATA-containing and TATA-less promoters [PMID:3380090]. RAP30 carries the polymerase-binding activity of the complex: it contacts RNA pol II directly through subunit RPB5, an interaction mediated by its middle region and abolished by point mutations Y124A and Q131A [PMID:11278533], and it suppresses nonspecific pol II–DNA binding so that polymerase is delivered to promoters rather than bulk DNA [PMID:1729606]. Together with TBP and TFIIB, RAP30 constitutes the minimal set sufficient for stable promoter recognition by pol II [PMID:1577790], and it is specifically required for forming the Sarkosyl-resistant preinitiation complex, defining it as an initiation factor (whereas its RAP74 partner acts in promoter escape and elongation) [PMID:8376403]. RAP30 bridges the basal machinery through an N-terminal region that binds TFIIB [PMID:8662660] and through direct contact with the TFIID component hTAFII100 [PMID:8758937]. Its C-terminal domain is a cryptic winged helix-turn-helix DNA-binding module structurally homologous to linker histone H5 and to sigma70 region 4, with the DNA-binding surface required for transcription [PMID:7937895, PMID:9689043], while its dimerization interface with RAP74 adopts a triple-barrel fold [PMID:11183778]. Association with Tat-SF1 links RAP30 to elongation control as well [PMID:10454543]. A single low-confidence study reports that GTF2F2 promotes epithelial-mesenchymal transition in an ovarian cancer cell line [PMID:40442848].","teleology":[{"year":1988,"claim":"Established TFIIF as a RAP30/RAP74 heterodimer essential for accurate pol II initiation, answering what cellular activity these polymerase-associated proteins carry.","evidence":"Affinity chromatography and reconstituted in vitro transcription from multiple promoters","pmids":["3380090"],"confidence":"High","gaps":["Did not resolve which subunit contacts polymerase versus DNA","No structural information on the complex"]},{"year":1991,"claim":"Identified a sigma70-homologous polymerase-binding region in RAP30, explaining the molecular basis for its pol II association by analogy to bacterial sigma factors.","evidence":"Sequence analysis, in vitro phosphorylation protection, and competition binding against E. coli RNA polymerase/sigma70","pmids":["1652156"],"confidence":"High","gaps":["Functional analogy inferred from cross-species binding, not direct structural homology at the time","Did not map residues required for pol II contact"]},{"year":1992,"claim":"Showed RAP30 alone binds pol II and suppresses nonspecific DNA binding, and that TBP+TFIIB+RAP30 form the minimal promoter-recognition set, assigning RAP30 a defined role in directing polymerase to promoters.","evidence":"Recombinant protein binding, DNA-binding competition, and minimal-set reconstitution assays","pmids":["1729606","1577790"],"confidence":"High","gaps":["Mechanism of nonspecific-binding suppression not structurally defined","Did not separate initiation from elongation roles"]},{"year":1992,"claim":"Mapped the C-terminal sigma region 4.2-like sequence as required for pol II interaction, separating dimerization from polymerase contact.","evidence":"Deletion mutagenesis and biochemical interaction assays","pmids":["1429731"],"confidence":"High","gaps":["No high-resolution structure of the interaction surface","Did not identify pol II subunit contacted"]},{"year":1993,"claim":"Dissected the division of labor within TFIIF, defining RAP30 as an initiation factor required for the Sarkosyl-resistant preinitiation complex while RAP74 drives promoter escape.","evidence":"Sarkosyl-resistance and pulse-chase in vitro transcription with recombinant subunits","pmids":["8376403"],"confidence":"High","gaps":["1994 work later attributed elongation/PIC contributions to both subunits, partially refining this clean split","Molecular events distinguishing the two steps not resolved"]},{"year":1994,"claim":"Revealed a cryptic sigma70 region 4-like DNA-binding domain in the RAP30 C terminus whose DNA binding is required for transcription, linking a structural element to function.","evidence":"Fusion-protein DNA-binding assays, deletion mutagenesis, and in vitro transcription","pmids":["7937895","7929273"],"confidence":"High","gaps":["Why the activity is masked in intact RAP30 not explained","DNA target sequence specificity unresolved"]},{"year":1995,"claim":"Mapped RAP30 functional architecture in the Drosophila ortholog, assigning RAP74 dimerization to the N-terminus and pol II interaction/partial activity to the C-terminus.","evidence":"Glycerol gradient sedimentation and reconstituted transcription with deletion mutants (Drosophila ortholog)","pmids":["7890767"],"confidence":"Medium","gaps":["Domain assignments from ortholog require human confirmation","Basis of ~50% C-terminal activity not explained"]},{"year":1996,"claim":"Defined how RAP30 connects to the rest of the basal machinery, showing direct binding to TFIIB and to the TFIID subunit hTAFII100.","evidence":"Deletion mapping, GST pulldown/co-IP, antibody inhibition, and in vitro transcription","pmids":["8662660","8758937"],"confidence":"Medium","gaps":["hTAFII100 interaction supported by single-lab co-IP plus antibody inhibition","Stoichiometry of these contacts in the assembled PIC unknown"]},{"year":1998,"claim":"Solved the RAP30 DNA-binding domain structure as a winged helix homologous to linker histone H5, providing a structural rationale for a PIC condensation role.","evidence":"Multinuclear NMR with DNA-binding surface identification","pmids":["9689043"],"confidence":"High","gaps":["Condensation-factor model is structural inference, not directly demonstrated functionally","No DNA-bound complex structure"]},{"year":1999,"claim":"Linked RAP30 specifically to elongation control through subunit-selective association with Tat-SF1.","evidence":"Co-immunoprecipitation from nuclear extracts and in vivo overexpression transcription assay","pmids":["10454543"],"confidence":"Medium","gaps":["Single-lab co-IP; direct binding region not mapped","Functional consequence beyond Tat-specific transcription unclear"]},{"year":2001,"claim":"Identified RPB5 as the key pol II contact for TFIIF and pinpointed RAP30 residues Y124 and Q131 required for the interaction, defining the molecular interface for TFIIF–polymerase association.","evidence":"In vitro pulldown, co-IP in COS1 cells, and alanine-scanning mutagenesis","pmids":["11278533"],"confidence":"High","gaps":["Interface not resolved by structure","How RPB5 contact integrates with the C-terminal DNA-binding domain unknown"]},{"year":2005,"claim":"Mapped the reciprocal RPB5 residues critical for RAP30 binding and showed overlap with the hepatitis B X protein site, defining the contact from the polymerase side.","evidence":"Two-step alanine-scanning mutagenesis with in vitro binding and co-IP in mammalian cells","pmids":["16169872"],"confidence":"High","gaps":["Functional consequence of HBx competition for transcription not established here","No co-crystal of the RAP30–RPB5 interface"]},{"year":2025,"claim":"Tested a cellular phenotype, reporting that GTF2F2 promotes migration, invasion, and EMT in an ovarian cancer cell line.","evidence":"siRNA/shRNA knockdown, migration/invasion assays, and Western blot for EMT markers in ES-2 cells","pmids":["40442848"],"confidence":"Low","gaps":["Single cell line, single lab phenotype without mechanistic pathway placement","EMT effect not connected to RAP30's basal transcription function","No rescue or in vivo validation"]},{"year":null,"claim":"How RAP30's general transcription-initiation role is harnessed to regulate specific gene programs such as those driving EMT remains unresolved.","evidence":"","pmids":[],"confidence":"Low","gaps":["No structure of RAP30 within an assembled human PIC","No identification of target genes whose transcription depends on RAP30 in physiological contexts"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0140110","term_label":"transcription regulator activity","supporting_discovery_ids":[0,3,5]},{"term_id":"GO:0140223","term_label":"general transcription initiation factor activity","supporting_discovery_ids":[0,3]},{"term_id":"GO:0003677","term_label":"DNA binding","supporting_discovery_ids":[6,11]},{"term_id":"GO:0060090","term_label":"molecular adaptor activity","supporting_discovery_ids":[9,15]}],"localization":[{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[13]}],"pathway":[{"term_id":"R-HSA-74160","term_label":"Gene expression (Transcription)","supporting_discovery_ids":[0,3,5]}],"complexes":["TFIIF (RAP30/RAP74 heterodimer)"],"partners":["GTF2F1","POLR2E","GTF2B","TAF1C","TATSF1"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"P13984","full_name":"General transcription factor IIF subunit 2","aliases":["General transcription factor IIF 30 kDa subunit","Transcription initiation factor IIF subunit beta","TFIIF-beta","Transcription initiation factor RAP30"],"length_aa":249,"mass_kda":28.4,"function":"TFIIF is a general transcription initiation factor that binds to RNA polymerase II and helps to recruit it to the initiation complex in collaboration with TFIIB","subcellular_location":"Nucleus","url":"https://www.uniprot.org/uniprotkb/P13984/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":true,"resolved_as":"","url":"https://depmap.org/portal/gene/GTF2F2","classification":"Common Essential","n_dependent_lines":959,"n_total_lines":1208,"dependency_fraction":0.7938741721854304},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[{"gene":"POLR2B","stoichiometry":10.0},{"gene":"POLR2K","stoichiometry":4.0},{"gene":"POLR2E","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/search/GTF2F2","total_profiled":1310},"omim":[{"mim_id":"606485","title":"POLYMERASE II, RNA, SUBUNIT M; POLR2M","url":"https://www.omim.org/entry/606485"},{"mim_id":"604927","title":"C-TERMINAL DOMAIN OF RNA POLYMERASE II SUBUNIT A, PHOSPHATASE OF, SUBUNIT 1; CTDP1","url":"https://www.omim.org/entry/604927"},{"mim_id":"602955","title":"TAF6 RNA POLYMERASE II, TATA BOX-BINDING PROTEIN-ASSOCIATED FACTOR, 80-KD; TAF6","url":"https://www.omim.org/entry/602955"},{"mim_id":"189969","title":"GENERAL TRANSCRIPTION FACTOR IIF, POLYPEPTIDE 2, 30-KD; GTF2F2","url":"https://www.omim.org/entry/189969"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Supported","locations":[{"location":"Nucleoplasm","reliability":"Supported"},{"location":"Microtubules","reliability":"Additional"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/GTF2F2"},"hgnc":{"alias_symbol":["TFIIF","BTF4","RAP30"],"prev_symbol":[]},"alphafold":{"accession":"P13984","domains":[{"cath_id":"-","chopping":"7-133","consensus_level":"high","plddt":87.1647,"start":7,"end":133},{"cath_id":"1.10.10.10","chopping":"176-238","consensus_level":"high","plddt":87.8046,"start":176,"end":238}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/P13984","model_url":"https://alphafold.ebi.ac.uk/files/AF-P13984-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-P13984-F1-predicted_aligned_error_v6.png","plddt_mean":82.69},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=GTF2F2","jax_strain_url":"https://www.jax.org/strain/search?query=GTF2F2"},"sequence":{"accession":"P13984","fasta_url":"https://rest.uniprot.org/uniprotkb/P13984.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/P13984/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/P13984"}},"corpus_meta":[{"pmid":"3380090","id":"PMC_3380090","title":"RAP30/74: a general initiation factor that binds to RNA polymerase II.","date":"1988","source":"Molecular and cellular biology","url":"https://pubmed.ncbi.nlm.nih.gov/3380090","citation_count":111,"is_preprint":false},{"pmid":"1652156","id":"PMC_1652156","title":"Related RNA polymerase-binding regions in human RAP30/74 and Escherichia coli sigma 70.","date":"1991","source":"Science (New York, N.Y.)","url":"https://pubmed.ncbi.nlm.nih.gov/1652156","citation_count":93,"is_preprint":false},{"pmid":"7929273","id":"PMC_7929273","title":"Roles for both the RAP30 and RAP74 subunits of transcription factor IIF in transcription initiation and elongation by RNA polymerase II.","date":"1994","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/7929273","citation_count":87,"is_preprint":false},{"pmid":"1729606","id":"PMC_1729606","title":"The general transcription factor RAP30 binds to RNA polymerase II and prevents it from binding nonspecifically to DNA.","date":"1992","source":"Molecular and cellular biology","url":"https://pubmed.ncbi.nlm.nih.gov/1729606","citation_count":74,"is_preprint":false},{"pmid":"8758937","id":"PMC_8758937","title":"Distinct domains of hTAFII100 are required for functional interaction with transcription factor TFIIF beta (RAP30) and incorporation into the TFIID complex.","date":"1996","source":"The EMBO journal","url":"https://pubmed.ncbi.nlm.nih.gov/8758937","citation_count":74,"is_preprint":false},{"pmid":"11183778","id":"PMC_11183778","title":"Novel dimerization fold of RAP30/RAP74 in human TFIIF at 1.7 A resolution.","date":"2000","source":"Journal of molecular biology","url":"https://pubmed.ncbi.nlm.nih.gov/11183778","citation_count":72,"is_preprint":false},{"pmid":"9689043","id":"PMC_9689043","title":"Structural homology between the Rap30 DNA-binding domain and linker histone H5: implications for preinitiation complex assembly.","date":"1998","source":"Proceedings of the National Academy of Sciences of the United States of America","url":"https://pubmed.ncbi.nlm.nih.gov/9689043","citation_count":57,"is_preprint":false},{"pmid":"1577790","id":"PMC_1577790","title":"Recombinant TBP, transcription factor IIB, and RAP30 are sufficient for promoter recognition by mammalian RNA polymerase II.","date":"1992","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/1577790","citation_count":55,"is_preprint":false},{"pmid":"8390879","id":"PMC_8390879","title":"Production of human RAP30 and RAP74 in bacterial cells.","date":"1993","source":"Protein expression and purification","url":"https://pubmed.ncbi.nlm.nih.gov/8390879","citation_count":54,"is_preprint":false},{"pmid":"10454543","id":"PMC_10454543","title":"Tat-SF1 protein associates with RAP30 and human SPT5 proteins.","date":"1999","source":"Molecular and cellular biology","url":"https://pubmed.ncbi.nlm.nih.gov/10454543","citation_count":49,"is_preprint":false},{"pmid":"1429731","id":"PMC_1429731","title":"The carboxyl terminus of RAP30 is similar in sequence to region 4 of bacterial sigma factors and is required for function.","date":"1992","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/1429731","citation_count":48,"is_preprint":false},{"pmid":"8662660","id":"PMC_8662660","title":"RNA polymerase II-associated protein (RAP) 74 binds transcription factor (TF) IIB and blocks TFIIB-RAP30 binding.","date":"1996","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/8662660","citation_count":46,"is_preprint":false},{"pmid":"7937895","id":"PMC_7937895","title":"Cryptic DNA-binding domain in the C terminus of RNA polymerase II general transcription factor RAP30.","date":"1994","source":"Proceedings of the National Academy of Sciences of the United States of America","url":"https://pubmed.ncbi.nlm.nih.gov/7937895","citation_count":46,"is_preprint":false},{"pmid":"8376403","id":"PMC_8376403","title":"RAP30/74 (transcription factor IIF) is required for promoter escape by RNA polymerase II.","date":"1993","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/8376403","citation_count":41,"is_preprint":false},{"pmid":"11278533","id":"PMC_11278533","title":"Direct interaction between the subunit RAP30 of transcription factor IIF (TFIIF) and RNA polymerase subunit 5, which contributes to the association between TFIIF and RNA polymerase II.","date":"2001","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/11278533","citation_count":41,"is_preprint":false},{"pmid":"7827505","id":"PMC_7827505","title":"Importance of codon preference for production of human RAP74 and reconstitution of the RAP30/74 complex.","date":"1994","source":"Protein expression and purification","url":"https://pubmed.ncbi.nlm.nih.gov/7827505","citation_count":40,"is_preprint":false},{"pmid":"23921640","id":"PMC_23921640","title":"RNA polymerase III-specific general transcription factor IIIC contains a heterodimer resembling TFIIF Rap30/Rap74.","date":"2013","source":"Nucleic acids research","url":"https://pubmed.ncbi.nlm.nih.gov/23921640","citation_count":22,"is_preprint":false},{"pmid":"16169872","id":"PMC_16169872","title":"Mutational analysis of human RNA polymerase II subunit 5 (RPB5): the residues critical for interactions with TFIIF subunit RAP30 and hepatitis B virus X protein.","date":"2005","source":"Journal of biochemistry","url":"https://pubmed.ncbi.nlm.nih.gov/16169872","citation_count":20,"is_preprint":false},{"pmid":"9660075","id":"PMC_9660075","title":"Amino acids 1-29 of the adenovirus serotypes 12 and 2 E1A proteins interact with rap30 (TF(II)F) and TBP in vitro.","date":"1998","source":"Virus research","url":"https://pubmed.ncbi.nlm.nih.gov/9660075","citation_count":17,"is_preprint":false},{"pmid":"7890767","id":"PMC_7890767","title":"Structure and function of the small subunit of TFIIF (RAP30) from Drosophila melanogaster.","date":"1995","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/7890767","citation_count":8,"is_preprint":false},{"pmid":"10545274","id":"PMC_10545274","title":"Immunoaffinity purification of the RAP30 subunit of human transcription factor IIF.","date":"1999","source":"Protein expression and purification","url":"https://pubmed.ncbi.nlm.nih.gov/10545274","citation_count":7,"is_preprint":false},{"pmid":"29235836","id":"PMC_29235836","title":"Hypoxic regulation of MYBL1, MEST, TCF3, TCF8, GTF2B, GTF2F2 and SNAI2 genes expression in U87 glioma cells upon IRE1 inhibition.","date":"2016","source":"Ukrainian biochemical journal","url":"https://pubmed.ncbi.nlm.nih.gov/29235836","citation_count":4,"is_preprint":false},{"pmid":"40442848","id":"PMC_40442848","title":"Single-cell RNA sequencing reveals the role of GTF2F2 in ovarian cancer oncogenesis and progression.","date":"2025","source":"Journal of ovarian research","url":"https://pubmed.ncbi.nlm.nih.gov/40442848","citation_count":1,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":12115,"output_tokens":4269,"usd":0.05019,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":12208,"output_tokens":3768,"usd":0.07762,"stage2_stop_reason":"end_turn"},"total_usd":0.12781,"stage1_batch_id":"msgbatch_01DUPACZi7AAWwuZiUjseQF4","stage2_batch_id":"msgbatch_018yt7chE3f48PEFtDwtj6AE","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 1988,\n      \"finding\": \"RAP30 binds RAP74 to form the RAP30/74 (TFIIF) heterodimer, which binds RNA polymerase II and is required for accurate transcription initiation by RNA pol II from multiple promoters (TATA-containing and TATA-less), but not by RNA pol III.\",\n      \"method\": \"Affinity chromatography, in vitro transcription assays with purified factors\",\n      \"journal\": \"Molecular and cellular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — affinity chromatography and functional reconstituted in vitro transcription, replicated across multiple promoters, foundational study\",\n      \"pmids\": [\"3380090\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1991,\n      \"finding\": \"The RAP30 subunit contains a region homologous to the RNA polymerase-binding domain of E. coli sigma70; RNA pol II specifically protected a serine residue in this sigma70-related region of RAP30 from phosphorylation in vitro, and RAP30/74 bound E. coli RNA polymerase and was displaced by sigma70, indicating functionally related RNA polymerase-binding regions.\",\n      \"method\": \"Sequence analysis, in vitro phosphorylation protection assay, competition binding assay with E. coli RNA polymerase and sigma70\",\n      \"journal\": \"Science (New York, N.Y.)\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — in vitro biochemical assay with mutagenesis-level specificity (phosphorylation protection) and competition experiment, single lab but two orthogonal methods\",\n      \"pmids\": [\"1652156\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1992,\n      \"finding\": \"Bacterially produced RAP30 alone binds RNA polymerase II in the absence of RAP74 and prevents RNA pol II from binding nonspecifically to DNA, thereby suppressing nonspecific transcription; the full RAP30/74 complex (but not RAP30 alone) can remove DNA-bound RNA pol II from DNA.\",\n      \"method\": \"Purified recombinant protein binding assay, in vitro transcription assay, DNA-binding competition assay\",\n      \"journal\": \"Molecular and cellular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — reconstituted in vitro assays with recombinant proteins, multiple functional readouts in single study\",\n      \"pmids\": [\"1729606\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1992,\n      \"finding\": \"TBP, TFIIB, and RAP30 together constitute a minimal set of general transcription factors necessary and sufficient for specific, stable promoter binding by RNA pol II in vitro, requiring only the TATA box.\",\n      \"method\": \"Reconstituted in vitro transcription and promoter-binding assay with recombinant proteins purified from E. coli\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — reconstitution with defined recombinant components, functional assay with clear minimal-set determination\",\n      \"pmids\": [\"1577790\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1992,\n      \"finding\": \"The carboxyl terminus of RAP30 shares sequence similarity with region 4 of bacterial sigma factors (particularly region 4.1 and 4.2 of B. subtilis sigma K); a mutant RAP30 lacking sequences similar to sigma homology region 4.2 assembles with RAP74 but has impaired ability to interact with RNA pol II.\",\n      \"method\": \"Deletion mutagenesis, biochemical interaction assays with purified factors\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — mutagenesis with functional biochemical readout, two orthogonal methods (assembly assay + pol II interaction)\",\n      \"pmids\": [\"1429731\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1993,\n      \"finding\": \"RAP30 is required for formation of a Sarkosyl-resistant preinitiation complex (initiation function), while RAP74 is dispensable for initiation but required for very early elongation (promoter escape); RAP30 thus functions specifically as an initiation factor.\",\n      \"method\": \"In vitro transcription with Sarkosyl resistance assay, pulse-chase transcription assay using recombinant RAP30 and RAP74\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — reconstituted in vitro transcription with mechanistic dissection of RAP30 vs RAP74 using two orthogonal assays\",\n      \"pmids\": [\"8376403\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1994,\n      \"finding\": \"The C terminus of RAP30 contains a cryptic DNA-binding domain homologous to the DNA-binding domain in conserved region 4 of sigma70 family sigma factors; this activity is masked in intact RAP30 but detectable as a fusion protein, and mutations abolishing DNA binding also abolish transcription.\",\n      \"method\": \"DNA-binding assay with fusion protein, deletion mutagenesis, in vitro transcription assay\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — in vitro binding assays combined with mutagenesis and transcription functional readout, multiple orthogonal methods\",\n      \"pmids\": [\"7937895\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1994,\n      \"finding\": \"Both RAP30 and RAP74 subunits of TFIIF contribute to formation of stable preinitiation intermediates containing RNA pol II, to synthesis of first phosphodiester bonds, to formation of Sarkosyl-resistant preinitiation intermediates, and to stimulation of the rate of RNA chain elongation.\",\n      \"method\": \"Template competition experiments, in vitro transcription kinetics, Sarkosyl resistance assay with highly purified factors\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — multiple distinct in vitro biochemical assays with highly purified reconstituted system\",\n      \"pmids\": [\"7929273\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1995,\n      \"finding\": \"The N-terminal domain of Drosophila TFIIF30 (RAP30 homolog) mediates interaction with TFIIF74 (RAP74), while the C-terminal domain (residues 119–276) can support approximately 50% of full transcriptional activity independently and mediates interaction with RNA pol II; a C-terminal fragment lacking the N-terminus does not assemble into a stable heterodimer with TFIIF74.\",\n      \"method\": \"Glycerol gradient sedimentation, reconstituted in vitro transcription with deletion mutants\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — functional domain mapping via deletion analysis and sedimentation in Drosophila ortholog, consistent with mammalian data\",\n      \"pmids\": [\"7890767\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1996,\n      \"finding\": \"RAP30 binds TFIIB through an N-terminal region (minimal binding region: amino acids 27–152), and RAP74 blocks TFIIB–RAP30 binding by both binding to TFIIB (via its C-terminal region, aa 358–517) and by binding RAP30; thus in the intact TFIIF complex, TFIIB–TFIIF contact is maintained through RAP74.\",\n      \"method\": \"Deletion mutagenesis, in vitro binding assays (GST pulldown/co-purification), in vitro transcription assay\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — systematic deletion mapping with functional transcription assay and direct binding assays, multiple orthogonal methods in one study\",\n      \"pmids\": [\"8662660\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1996,\n      \"finding\": \"hTAFII100 (a TFIID component) directly interacts with RAP30 (the 30 kDa subunit of TFIIF) via the C-terminal WD-repeat domain of hTAFII100; an anti-hTAFII100 antibody that selectively inhibited this interaction also inhibited basal TFIID-dependent in vitro transcription; the hTAFII100–TFIIF interaction supports preinitiation complex formation in the presence of TFIID.\",\n      \"method\": \"Co-immunoprecipitation, antibody inhibition of in vitro transcription, interaction domain mapping\",\n      \"journal\": \"The EMBO journal\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — co-IP plus functional antibody inhibition and domain mapping, single lab with two orthogonal methods\",\n      \"pmids\": [\"8758937\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1998,\n      \"finding\": \"The three-dimensional structure of the human RAP30 DNA-binding domain (solved by NMR) reveals a winged helix-turn-helix fold structurally homologous to linker histone H5; the DNA-binding surface was identified, and the fold suggests RAP30 may act as a condensation factor for preinitiation complex assembly analogous to linker histones in chromatin.\",\n      \"method\": \"Multinuclear NMR spectroscopy, structural comparison, DNA-binding surface identification\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — NMR structure with binding surface identification, structural homology with functional inference validated by domain-level data\",\n      \"pmids\": [\"9689043\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1998,\n      \"finding\": \"The N-terminal region (amino acids 1–29) of adenovirus E1A proteins from Ad12 and Ad2 binds RAP30 (TFIIF) in vitro; however, a mutant that failed to interact with RAP30 retained full transactivation activity, indicating RAP30 binding and transactivation are independent functions of this E1A domain.\",\n      \"method\": \"In vitro binding assay, mutagenesis, transactivation assay\",\n      \"journal\": \"Virus research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — in vitro binding with mutagenesis but single lab and limited follow-up on mechanism\",\n      \"pmids\": [\"9660075\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1999,\n      \"finding\": \"Tat-SF1 associates specifically with RAP30 but not with the RAP74 subunit of TFIIF in nuclear extracts, as shown by co-immunoprecipitation; overexpression of Tat-SF1 and hSPT5 stimulates Tat-specific transcriptional activity in vivo, suggesting RAP30 participates in an elongation control complex.\",\n      \"method\": \"Co-immunoprecipitation from nuclear extracts, in vivo transcription assay with overexpression\",\n      \"journal\": \"Molecular and cellular biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal Co-IP combined with in vivo functional assay, single lab\",\n      \"pmids\": [\"10454543\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2000,\n      \"finding\": \"X-ray crystal structure of the RAP30/RAP74 interaction domains at 1.7 Å resolution reveals a novel 'triple barrel' dimerization fold; mutant data indicate that interactions with the transcription apparatus are mediated by this tripartite beta-barrel as well as by flexible loops and extending alpha/beta structures.\",\n      \"method\": \"X-ray crystallography at 1.7 Å, mutational analysis\",\n      \"journal\": \"Journal of molecular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — high-resolution crystal structure combined with mutagenesis to validate functional interfaces\",\n      \"pmids\": [\"11183778\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2001,\n      \"finding\": \"RAP30 directly binds RNA pol II subunit RPB5 in vitro and in vivo; the RAP30-binding region on RPB5 maps to its central region (aa 47–120); within RAP30, the middle region (aa 101–170) contacts RPB5 in the context of the TFIIF complex (N-terminal region binds RPB5 in isolation but not within TFIIF); point mutations Y124A and Q131A in RAP30 abolish RPB5 binding and impair co-recovery of endogenous pol II with TFIIF, establishing RPB5 as a key contact for TFIIF–pol II association.\",\n      \"method\": \"In vitro pulldown with purified recombinant proteins, co-immunoprecipitation in COS1 cells, alanine-scanning mutagenesis, FLAG-affinity purification\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — in vitro reconstitution plus in vivo co-IP plus systematic mutagenesis identifying specific residues, multiple orthogonal methods\",\n      \"pmids\": [\"11278533\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2005,\n      \"finding\": \"Systematic alanine-scanning mutagenesis of RPB5 central region identified residues F76, I104, T111, and S113 as critical for RAP30 (TFIIF) binding, with T56 and L58 additionally required specifically for RAP30 binding; the overlapping nature of RAP30 and hepatitis B virus X protein binding sites on RPB5 was confirmed in both mammalian cells and in vitro.\",\n      \"method\": \"Two-step alanine scanning mutagenesis, in vitro binding assay, co-immunoprecipitation in mammalian cells\",\n      \"journal\": \"Journal of biochemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — systematic mutagenesis with both in vitro and in vivo validation, two orthogonal methods\",\n      \"pmids\": [\"16169872\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"GTF2F2 knockdown in the ovarian cancer cell line ES-2 significantly suppressed cell migration and invasion, and Western blot showed increased E-cadherin and decreased N-cadherin expression, indicating GTF2F2 promotes epithelial-mesenchymal transition (EMT) in this context.\",\n      \"method\": \"Gene knockdown (siRNA/shRNA), cell migration and invasion assays, Western blot for EMT markers\",\n      \"journal\": \"Journal of ovarian research\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single lab, single cell line, phenotypic readout without mechanistic pathway placement beyond EMT marker changes\",\n      \"pmids\": [\"40442848\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"GTF2F2 (RAP30) is the small subunit of the general transcription factor TFIIF (RAP30/74 heterodimer), which binds directly to RNA polymerase II (through contact with RPB5, critical residues Y124 and Q131) via a sigma70-homologous C-terminal domain; RAP30 suppresses non-specific pol II–DNA binding, is required for promoter-specific preinitiation complex assembly (together with TBP and TFIIB), drives formation of the first phosphodiester bonds, and stimulates elongation rate, while its winged-helix C-terminal DNA-binding domain and triple-barrel dimerization interface with RAP74 (solved by X-ray crystallography) mediate interactions with TFIIB, hTAFII100, and Tat-SF1 to coordinate both initiation and elongation stages of RNA pol II transcription.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"GTF2F2 (RAP30) is the small subunit of the general transcription factor TFIIF, which it forms by heterodimerization with RAP74 to enable accurate, promoter-specific transcription initiation by RNA polymerase II from both TATA-containing and TATA-less promoters [#0]. RAP30 carries the polymerase-binding activity of the complex: it contacts RNA pol II directly through subunit RPB5, an interaction mediated by its middle region and abolished by point mutations Y124A and Q131A [#15], and it suppresses nonspecific pol II\\u2013DNA binding so that polymerase is delivered to promoters rather than bulk DNA [#2]. Together with TBP and TFIIB, RAP30 constitutes the minimal set sufficient for stable promoter recognition by pol II [#3], and it is specifically required for forming the Sarkosyl-resistant preinitiation complex, defining it as an initiation factor (whereas its RAP74 partner acts in promoter escape and elongation) [#5]. RAP30 bridges the basal machinery through an N-terminal region that binds TFIIB [#9] and through direct contact with the TFIID component hTAFII100 [#10]. Its C-terminal domain is a cryptic winged helix-turn-helix DNA-binding module structurally homologous to linker histone H5 and to sigma70 region 4, with the DNA-binding surface required for transcription [#6, #11], while its dimerization interface with RAP74 adopts a triple-barrel fold [#14]. Association with Tat-SF1 links RAP30 to elongation control as well [#13]. A single low-confidence study reports that GTF2F2 promotes epithelial-mesenchymal transition in an ovarian cancer cell line [#17].\",\n  \"teleology\": [\n    {\n      \"year\": 1988,\n      \"claim\": \"Established TFIIF as a RAP30/RAP74 heterodimer essential for accurate pol II initiation, answering what cellular activity these polymerase-associated proteins carry.\",\n      \"evidence\": \"Affinity chromatography and reconstituted in vitro transcription from multiple promoters\",\n      \"pmids\": [\"3380090\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not resolve which subunit contacts polymerase versus DNA\", \"No structural information on the complex\"]\n    },\n    {\n      \"year\": 1991,\n      \"claim\": \"Identified a sigma70-homologous polymerase-binding region in RAP30, explaining the molecular basis for its pol II association by analogy to bacterial sigma factors.\",\n      \"evidence\": \"Sequence analysis, in vitro phosphorylation protection, and competition binding against E. coli RNA polymerase/sigma70\",\n      \"pmids\": [\"1652156\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Functional analogy inferred from cross-species binding, not direct structural homology at the time\", \"Did not map residues required for pol II contact\"]\n    },\n    {\n      \"year\": 1992,\n      \"claim\": \"Showed RAP30 alone binds pol II and suppresses nonspecific DNA binding, and that TBP+TFIIB+RAP30 form the minimal promoter-recognition set, assigning RAP30 a defined role in directing polymerase to promoters.\",\n      \"evidence\": \"Recombinant protein binding, DNA-binding competition, and minimal-set reconstitution assays\",\n      \"pmids\": [\"1729606\", \"1577790\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Mechanism of nonspecific-binding suppression not structurally defined\", \"Did not separate initiation from elongation roles\"]\n    },\n    {\n      \"year\": 1992,\n      \"claim\": \"Mapped the C-terminal sigma region 4.2-like sequence as required for pol II interaction, separating dimerization from polymerase contact.\",\n      \"evidence\": \"Deletion mutagenesis and biochemical interaction assays\",\n      \"pmids\": [\"1429731\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"No high-resolution structure of the interaction surface\", \"Did not identify pol II subunit contacted\"]\n    },\n    {\n      \"year\": 1993,\n      \"claim\": \"Dissected the division of labor within TFIIF, defining RAP30 as an initiation factor required for the Sarkosyl-resistant preinitiation complex while RAP74 drives promoter escape.\",\n      \"evidence\": \"Sarkosyl-resistance and pulse-chase in vitro transcription with recombinant subunits\",\n      \"pmids\": [\"8376403\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"1994 work later attributed elongation/PIC contributions to both subunits, partially refining this clean split\", \"Molecular events distinguishing the two steps not resolved\"]\n    },\n    {\n      \"year\": 1994,\n      \"claim\": \"Revealed a cryptic sigma70 region 4-like DNA-binding domain in the RAP30 C terminus whose DNA binding is required for transcription, linking a structural element to function.\",\n      \"evidence\": \"Fusion-protein DNA-binding assays, deletion mutagenesis, and in vitro transcription\",\n      \"pmids\": [\"7937895\", \"7929273\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Why the activity is masked in intact RAP30 not explained\", \"DNA target sequence specificity unresolved\"]\n    },\n    {\n      \"year\": 1995,\n      \"claim\": \"Mapped RAP30 functional architecture in the Drosophila ortholog, assigning RAP74 dimerization to the N-terminus and pol II interaction/partial activity to the C-terminus.\",\n      \"evidence\": \"Glycerol gradient sedimentation and reconstituted transcription with deletion mutants (Drosophila ortholog)\",\n      \"pmids\": [\"7890767\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Domain assignments from ortholog require human confirmation\", \"Basis of ~50% C-terminal activity not explained\"]\n    },\n    {\n      \"year\": 1996,\n      \"claim\": \"Defined how RAP30 connects to the rest of the basal machinery, showing direct binding to TFIIB and to the TFIID subunit hTAFII100.\",\n      \"evidence\": \"Deletion mapping, GST pulldown/co-IP, antibody inhibition, and in vitro transcription\",\n      \"pmids\": [\"8662660\", \"8758937\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"hTAFII100 interaction supported by single-lab co-IP plus antibody inhibition\", \"Stoichiometry of these contacts in the assembled PIC unknown\"]\n    },\n    {\n      \"year\": 1998,\n      \"claim\": \"Solved the RAP30 DNA-binding domain structure as a winged helix homologous to linker histone H5, providing a structural rationale for a PIC condensation role.\",\n      \"evidence\": \"Multinuclear NMR with DNA-binding surface identification\",\n      \"pmids\": [\"9689043\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Condensation-factor model is structural inference, not directly demonstrated functionally\", \"No DNA-bound complex structure\"]\n    },\n    {\n      \"year\": 1999,\n      \"claim\": \"Linked RAP30 specifically to elongation control through subunit-selective association with Tat-SF1.\",\n      \"evidence\": \"Co-immunoprecipitation from nuclear extracts and in vivo overexpression transcription assay\",\n      \"pmids\": [\"10454543\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Single-lab co-IP; direct binding region not mapped\", \"Functional consequence beyond Tat-specific transcription unclear\"]\n    },\n    {\n      \"year\": 2001,\n      \"claim\": \"Identified RPB5 as the key pol II contact for TFIIF and pinpointed RAP30 residues Y124 and Q131 required for the interaction, defining the molecular interface for TFIIF\\u2013polymerase association.\",\n      \"evidence\": \"In vitro pulldown, co-IP in COS1 cells, and alanine-scanning mutagenesis\",\n      \"pmids\": [\"11278533\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Interface not resolved by structure\", \"How RPB5 contact integrates with the C-terminal DNA-binding domain unknown\"]\n    },\n    {\n      \"year\": 2005,\n      \"claim\": \"Mapped the reciprocal RPB5 residues critical for RAP30 binding and showed overlap with the hepatitis B X protein site, defining the contact from the polymerase side.\",\n      \"evidence\": \"Two-step alanine-scanning mutagenesis with in vitro binding and co-IP in mammalian cells\",\n      \"pmids\": [\"16169872\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Functional consequence of HBx competition for transcription not established here\", \"No co-crystal of the RAP30\\u2013RPB5 interface\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Tested a cellular phenotype, reporting that GTF2F2 promotes migration, invasion, and EMT in an ovarian cancer cell line.\",\n      \"evidence\": \"siRNA/shRNA knockdown, migration/invasion assays, and Western blot for EMT markers in ES-2 cells\",\n      \"pmids\": [\"40442848\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"Single cell line, single lab phenotype without mechanistic pathway placement\", \"EMT effect not connected to RAP30's basal transcription function\", \"No rescue or in vivo validation\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How RAP30's general transcription-initiation role is harnessed to regulate specific gene programs such as those driving EMT remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"No structure of RAP30 within an assembled human PIC\", \"No identification of target genes whose transcription depends on RAP30 in physiological contexts\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0140110\", \"supporting_discovery_ids\": [0, 3, 5]},\n      {\"term_id\": \"GO:0140223\", \"supporting_discovery_ids\": [0, 3]},\n      {\"term_id\": \"GO:0003677\", \"supporting_discovery_ids\": [6, 11]},\n      {\"term_id\": \"GO:0060090\", \"supporting_discovery_ids\": [9, 15]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [13]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-74160\", \"supporting_discovery_ids\": [0, 3, 5]}\n    ],\n    \"complexes\": [\"TFIIF (RAP30/RAP74 heterodimer)\"],\n    \"partners\": [\"GTF2F1\", \"POLR2E\", \"GTF2B\", \"TAF1C\", \"TATSF1\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":7,"faith_total":7,"faith_pct":100.0}}