{"gene":"SNAPC1","run_date":"2026-04-28T20:42:08","timeline":{"discoveries":[{"year":1995,"finding":"SNAPc (containing SNAP43/SNAPC1, SNAP45, SNAP50, and TBP) is a TBP-TAF complex required for transcription of both RNA polymerase II and III snRNA genes; it binds specifically to the proximal sequence element (PSE), a non-TATA-box basal promoter element common to both gene types.","method":"Biochemical purification, EMSA, in vitro transcription assay","journal":"Nature","confidence":"High","confidence_rationale":"Tier 1 — original reconstitution and functional characterization with multiple orthogonal methods","pmids":["7715707"],"is_preprint":false},{"year":1996,"finding":"SNAP43 (SNAPC1) is a subunit of SNAPc that is required for both RNA polymerase II and III transcription of snRNA genes; antibodies against SNAP45 (which interacts with SNAP43) retard SNAPc-PSE complex mobility, confirming subunit composition.","method":"Immunodepletion, EMSA, in vitro transcription assay, co-immunoprecipitation","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"High","confidence_rationale":"Tier 1 — in vitro transcription with immunodepletion and EMSA, replicated across subunit studies","pmids":["8633057"],"is_preprint":false},{"year":1996,"finding":"SNAP50 contacts DNA within the SNAP complex (UV cross-linking) and interacts with SNAP43 (SNAPC1) by co-immunoprecipitation, but not with SNAP45 or TBP, defining initial SNAPc architecture.","method":"UV cross-linking, co-immunoprecipitation, in vitro transcription assay","journal":"The EMBO journal","confidence":"High","confidence_rationale":"Tier 1 — direct DNA contact shown by UV cross-linking; protein interactions by co-IP with functional transcription readout","pmids":["9003788"],"is_preprint":false},{"year":1998,"finding":"SNAP19 is a fifth SNAPc subunit that, together with SNAP43, SNAP45, SNAP50, and SNAP190, assembles a recombinant SNAPc that binds the PSE and directs both RNA polymerase II and III snRNA gene transcription, demonstrating that the same core SNAPc nucleates two classes of initiation complexes.","method":"Recombinant protein reconstitution, EMSA, in vitro transcription assay","journal":"Genes & development","confidence":"High","confidence_rationale":"Tier 1 — full reconstitution from defined recombinant subunits with functional transcription validation","pmids":["9732265"],"is_preprint":false},{"year":1998,"finding":"SNAP190, the largest SNAPc subunit, contains a Myb DNA-binding domain (four complete repeats plus a half repeat) that contributes to PSE recognition; SNAP190 interacts with SNAP45 and with the Oct-1 activator, and is required for snRNA gene transcription by both RNA polymerases II and III.","method":"cDNA cloning, EMSA with truncation mutants, co-immunoprecipitation, in vitro transcription assay","journal":"Molecular and cellular biology","confidence":"High","confidence_rationale":"Tier 1 — domain mapping with truncation mutants, functional transcription assay, and protein interaction studies","pmids":["9418884"],"is_preprint":false},{"year":2000,"finding":"A detailed map of protein-protein contacts within SNAPc was established: specific subunit domains required for subunit-subunit association were defined, and complexes containing only those interaction domains retain specific PSE binding, indicating that direct subunit contacts are sufficient for DNA recognition.","method":"Co-immunoprecipitation with deletion/truncation mutants, EMSA","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 2 — systematic domain mapping with reciprocal co-IP and DNA binding assays","pmids":["11056176"],"is_preprint":false},{"year":2002,"finding":"A 50-amino-acid region within SNAP190 mediates cooperative binding with TBP in the context of mini-SNAPc (SNAP43, SNAP50, and N-terminal SNAP190); mini-SNAPc derivatives lacking this region remain transcriptionally active because TBP can still be recruited via cooperative interactions with Brf2, revealing redundant mechanisms for TBP recruitment to the U6 promoter.","method":"Promoter binding assays with truncation mutants, in vitro transcription assay, recombinant protein reconstitution","journal":"Molecular and cellular biology","confidence":"High","confidence_rationale":"Tier 1 — domain mapping with defined recombinant complexes and functional transcription readout","pmids":["12391172"],"is_preprint":false},{"year":2003,"finding":"Two SNAPc subunits, SNAP43 (SNAPC1) and SNAP190, directly interact with the TBP DNA-binding domain; the SNAP190 Myb domain is sufficient to recruit TBP to the U6 TATA box and stimulates SNAP190-TBP-Brf2 complex assembly, defining the assembly pathway of the RNA polymerase III-specific preinitiation complex.","method":"TBP recruitment assays, co-immunoprecipitation, EMSA with truncation mutants","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1-2 — direct interaction mapping with functional recruitment assays and multiple protein combinations","pmids":["12621023"],"is_preprint":false},{"year":2004,"finding":"In Drosophila, the SNAPC1 ortholog DmPBP45 (identified by sequence similarity to human SNAP43) contacts DNA differentially depending on PSE sequence: it cross-links strongly for two turns downstream of the U1 PSE but only a half turn downstream of the U6 PSE, consistent with a model in which PSE-dependent conformational differences in the DmPBP complex determine RNA polymerase specificity.","method":"Photo-cross-linking, S2 cell expression, EMSA","journal":"Molecular and cellular biology","confidence":"Medium","confidence_rationale":"Tier 2 — direct DNA contact mapping with photo-cross-linking; single lab, Drosophila ortholog","pmids":["14966271"],"is_preprint":false},{"year":2006,"finding":"The SNAP50 zinc finger domain (eight cysteine/histidine residues identified by alanine scanning) plays an important role in PSE DNA binding by SNAPc; metal binding studies revealed a single zinc atom, indicating one functional coordination site; four cysteine residues essential for DNA binding were also required for both U1 (Pol II) and U6 (Pol III) transcription, while the remaining four residues showed differential effects on Pol II vs Pol III transcription.","method":"Alanine scanning mutagenesis, metal binding assays, EMSA, in vitro transcription assay","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1 — systematic mutagenesis combined with metal binding and functional transcription assays","pmids":["16901896"],"is_preprint":false},{"year":2006,"finding":"A partial SNAPc (SNAP190[1-505], SNAP50, SNAP43/SNAPC1, and SNAP19) co-expressed in E. coli binds PSE DNA specifically, recruits TBP to U6 promoter DNA, and supports transcription of both human U1 and U6 snRNA genes by RNA polymerases II and III, respectively.","method":"Recombinant co-expression in E. coli, EMSA, TBP recruitment assay, reconstituted in vitro transcription","journal":"Protein expression and purification","confidence":"High","confidence_rationale":"Tier 1 — reconstituted complex from defined subunits with multiple functional readouts","pmids":["16603380"],"is_preprint":false},{"year":2012,"finding":"ChIP-seq revealed that SNAPC1 occupancy extends beyond snRNA genes to include a large number of transcriptionally active protein-coding genes, co-localizing with elongating RNA polymerase II; inhibition of transcriptional elongation caused loss of SNAPC1 from gene 3' ends; depletion of SNAPC1 specifically diminished transcriptional responsiveness of many genes to EGF and retinoic acid stimulation, identifying SNAPC1 as a general transcriptional coactivator functioning through elongating RNAPII.","method":"ChIP-seq, RNA interference/depletion, transcriptional elongation inhibition, gene expression analysis","journal":"Molecular and cellular biology","confidence":"High","confidence_rationale":"Tier 2 — genome-wide ChIP-seq with functional KD and mechanistic dissection across two signaling pathways","pmids":["22966203"],"is_preprint":false},{"year":2022,"finding":"Cryo-EM structure of human SNAPc (SNAP190 N-terminal domain, SNAP50, and SNAP43/SNAPC1) bound to the U6-1 PSE at 3.49 Å resolution revealed a 'wrap-around' assembly mode; three SNAP50 motifs contact both major and minor grooves of PSE in coordination with the SNAP190 Myb domain, explaining PSE sequence conservation and SNAPc recognition specificity.","method":"Cryo-electron microscopy structural determination","journal":"Nature communications","confidence":"High","confidence_rationale":"Tier 1 — high-resolution cryo-EM structure with identification of specific DNA-protein contacts","pmids":["36369505"],"is_preprint":false},{"year":2025,"finding":"SNAPC1 is SUMOylated at lysine residues K245 and K333; a SUMOylation-deficient mutant (SNAPC1 2KR) cannot sustain basal snRNA transcription despite being recruited to the PSE; SNAPC1 SUMOylation is required for its interaction with SNAPC4 but not SNAPC3, indicating that SUMO modification controls SNAPc complex assembly and snRNA transcriptional activity.","method":"CRISPR/dCas9-SENP1 targeting, site-directed mutagenesis, inducible degron depletion system, co-immunoprecipitation, in vivo transcription assay","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"High","confidence_rationale":"Tier 1-2 — identification of SUMO sites by mutagenesis, rescue experiments with degron system, and protein interaction mapping with orthogonal methods","pmids":["40956881"],"is_preprint":false}],"current_model":"SNAPC1 (SNAP43) is a core subunit of the five-subunit SNAPc complex that binds the proximal sequence element (PSE) of snRNA gene promoters via a 'wrap-around' mechanism (cryo-EM structure), directly contacts TBP and SNAP190 to nucleate RNA polymerase II and III preinitiation complexes, and is SUMOylated at K245/K333—a modification required for interaction with SNAPC4 and for sustaining basal snRNA transcription; additionally, SNAPC1 associates with elongating RNA polymerase II at protein-coding genes genome-wide and is required for transcriptional responsiveness to extracellular signals such as EGF and retinoic acid."},"narrative":{"teleology":[{"year":1995,"claim":"Identification of SNAPC1 as a subunit of a novel TBP-containing complex (SNAPc) that binds the PSE and is required for both Pol II and Pol III snRNA transcription established the fundamental biochemical framework for understanding snRNA promoter recognition.","evidence":"Biochemical purification, EMSA, and in vitro transcription from human cell extracts","pmids":["7715707","8633057"],"confidence":"High","gaps":["Structural basis of PSE recognition unknown","No information on in vivo relevance or genome-wide occupancy","Role of individual subunits in DNA contact not resolved"]},{"year":1996,"claim":"Mapping of direct subunit contacts — SNAP50 interacts with SNAP43 but not SNAP45 or TBP — provided the first internal architecture of SNAPc and defined SNAPC1 as a central bridging subunit.","evidence":"UV cross-linking to DNA and co-immunoprecipitation of recombinant subunits","pmids":["9003788"],"confidence":"High","gaps":["Full five-subunit interaction network not yet mapped","DNA contacts by SNAPC1 itself not assessed"]},{"year":1998,"claim":"Reconstitution of a complete five-subunit recombinant SNAPc (SNAP19, SNAP43, SNAP45, SNAP50, SNAP190) that binds the PSE and directs both Pol II and Pol III snRNA transcription demonstrated that no additional factors are needed for SNAPc function and confirmed SNAPC1 as an essential structural component.","evidence":"Recombinant protein co-expression, EMSA, in vitro transcription","pmids":["9732265","9418884"],"confidence":"High","gaps":["How the same complex directs two different polymerases remained unclear","Contribution of individual subunit domains to transcription not delineated"]},{"year":2000,"claim":"Systematic domain-mapping of all pairwise subunit contacts within SNAPc, including SNAPC1, showed that minimal interaction domains are sufficient for PSE binding, establishing that direct protein–protein contacts underpin DNA recognition.","evidence":"Co-immunoprecipitation of truncation/deletion mutants combined with EMSA","pmids":["11056176"],"confidence":"High","gaps":["No high-resolution structural information","Post-translational modifications not explored"]},{"year":2003,"claim":"Demonstration that both SNAPC1 and SNAP190 directly contact the TBP DNA-binding domain defined the assembly pathway for the Pol III preinitiation complex and established SNAPC1's role in TBP recruitment.","evidence":"TBP recruitment assays, co-immunoprecipitation, and EMSA with truncation mutants","pmids":["12621023","12391172"],"confidence":"High","gaps":["Structural details of TBP–SNAPC1 interface unknown","Whether SNAPC1–TBP contact is required for Pol II snRNA transcription not tested"]},{"year":2004,"claim":"Photo-cross-linking of the Drosophila SNAPC1 ortholog to PSE DNA revealed polymerase-specific differences in DNA contacts, supporting a model in which PSE-dependent conformational changes in SNAPc determine Pol II vs. Pol III recruitment.","evidence":"Photo-cross-linking and EMSA in Drosophila S2 cells","pmids":["14966271"],"confidence":"Medium","gaps":["Observation in Drosophila; relevance to human SNAPC1 not confirmed","Conformational change inferred indirectly from cross-linking pattern"]},{"year":2012,"claim":"ChIP-seq discovery that SNAPC1 occupies protein-coding genes genome-wide and tracks with elongating Pol II, combined with depletion experiments showing impaired EGF and retinoic acid transcriptional responses, revealed an unexpected second role for SNAPC1 as a general transcriptional coactivator beyond snRNA genes.","evidence":"ChIP-seq, RNAi depletion, elongation inhibition, and gene expression profiling in human cells","pmids":["22966203"],"confidence":"High","gaps":["Mechanism by which SNAPC1 promotes elongation unknown","Whether this function requires other SNAPc subunits not established","Direct protein–protein contacts linking SNAPC1 to the elongation machinery not identified"]},{"year":2022,"claim":"A 3.49 Å cryo-EM structure of the SNAP190–SNAP50–SNAP43 sub-complex bound to the U6-1 PSE resolved the 'wrap-around' DNA recognition mode, explaining PSE sequence conservation and providing the first high-resolution view of SNAPC1 within the assembled complex.","evidence":"Cryo-electron microscopy of reconstituted human SNAPc–PSE complex","pmids":["36369505"],"confidence":"High","gaps":["Structure lacks SNAP19 and SNAP45 subunits","No structure of full preinitiation complex with TBP or polymerase","SNAPC1 DNA contacts not individually resolved in this structure"]},{"year":2025,"claim":"Identification of K245 and K333 as SUMOylation sites on SNAPC1, with demonstration that SUMOylation is required for SNAPC4 interaction and for sustaining basal snRNA transcription, established post-translational modification as a regulatory layer controlling SNAPc assembly and activity.","evidence":"CRISPR/dCas9-SENP1 targeting, site-directed mutagenesis, inducible degron depletion, co-immunoprecipitation, in vivo transcription assays","pmids":["40956881"],"confidence":"High","gaps":["Whether SUMOylation affects SNAPC1 function at protein-coding genes is unknown","SUMO E3 ligase responsible for SNAPC1 modification not identified","Dynamics of SUMOylation during the cell cycle or signaling not explored"]},{"year":null,"claim":"Key unresolved questions include how SNAPC1 mechanistically promotes transcriptional elongation at protein-coding genes, whether it functions independently of other SNAPc subunits in that context, and how its SUMOylation is regulated in response to physiological signals.","evidence":"","pmids":[],"confidence":"High","gaps":["No reconstituted elongation assay with SNAPC1","Full SNAPc structure with all five subunits and bound polymerase not available","Relationship between SNAPc-dependent and SNAPc-independent functions of SNAPC1 unresolved"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0003677","term_label":"DNA binding","supporting_discovery_ids":[0,8,12]},{"term_id":"GO:0140110","term_label":"transcription regulator activity","supporting_discovery_ids":[11]},{"term_id":"GO:0060090","term_label":"molecular adaptor activity","supporting_discovery_ids":[5,7]}],"localization":[{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[0,11,12]}],"pathway":[{"term_id":"R-HSA-8953854","term_label":"Metabolism of RNA","supporting_discovery_ids":[0,3,13]}],"complexes":["SNAPc"],"partners":["SNAPC2","SNAPC3","SNAPC4","SNAPC5","TBP"],"other_free_text":[]},"mechanistic_narrative":"SNAPC1 (SNAP43) is a core subunit of the five-subunit SNAPc complex that binds the proximal sequence element (PSE) of snRNA gene promoters and nucleates preinitiation complex assembly for both RNA polymerase II and RNA polymerase III transcription. Within SNAPc, SNAPC1 directly contacts SNAP50, SNAP190, and TBP, contributing to a 'wrap-around' DNA-binding architecture resolved by cryo-EM, and its SUMOylation at K245 and K333 is required for interaction with SNAPC4 and for sustaining basal snRNA transcription [PMID:7715707, PMID:36369505, PMID:40956881]. Beyond snRNA genes, SNAPC1 associates with elongating RNA polymerase II at protein-coding genes genome-wide and is required for transcriptional responsiveness to extracellular signals such as EGF and retinoic acid, establishing it as a general transcriptional coactivator [PMID:22966203]. SNAPC1 thus operates at two levels: as a PSE-recognition scaffold essential for snRNA gene expression, and as an elongation-associated factor modulating signal-dependent transcription of mRNA genes."},"prefetch_data":{"uniprot":{"accession":"Q16533","full_name":"snRNA-activating protein complex subunit 1","aliases":["Proximal sequence element-binding transcription factor subunit gamma","PSE-binding factor subunit gamma","PTF subunit gamma","Small nuclear RNA-activating complex polypeptide 1","snRNA-activating protein complex 43 kDa subunit","SNAPc 43 kDa subunit"],"length_aa":368,"mass_kda":43.0,"function":"Part of the SNAPc complex required for the transcription of both RNA polymerase II and III small-nuclear RNA genes. Binds to the proximal sequence element (PSE), a non-TATA-box basal promoter element common to these 2 types of genes. Recruits TBP and BRF2 to the U6 snRNA TATA box","subcellular_location":"Nucleus","url":"https://www.uniprot.org/uniprotkb/Q16533/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":true,"resolved_as":"","url":"https://depmap.org/portal/gene/SNAPC1","classification":"Common Essential","n_dependent_lines":1205,"n_total_lines":1208,"dependency_fraction":0.9975165562913907},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/SNAPC1","total_profiled":1310},"omim":[{"mim_id":"605979","title":"SMALL NUCLEAR RNA-ACTIVATING PROTEIN COMPLEX, POLYPEPTIDE 5; SNAPC5","url":"https://www.omim.org/entry/605979"},{"mim_id":"605076","title":"SMALL NUCLEAR RNA-ACTIVATING PROTEIN COMPLEX, POLYPEPTIDE 2; SNAPC2","url":"https://www.omim.org/entry/605076"},{"mim_id":"602777","title":"SMALL NUCLEAR RNA-ACTIVATING PROTEIN COMPLEX, POLYPEPTIDE 4; SNAPC4","url":"https://www.omim.org/entry/602777"},{"mim_id":"602348","title":"SMALL NUCLEAR RNA-ACTIVATING PROTEIN COMPLEX, POLYPEPTIDE 3; SNAPC3","url":"https://www.omim.org/entry/602348"},{"mim_id":"600591","title":"SMALL NUCLEAR RNA-ACTIVATING PROTEIN COMPLEX, POLYPEPTIDE 1; SNAPC1","url":"https://www.omim.org/entry/600591"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Enhanced","locations":[{"location":"Nucleoli","reliability":"Enhanced"},{"location":"Nucleoplasm","reliability":"Additional"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/SNAPC1"},"hgnc":{"alias_symbol":["SNAP43","PTFgamma"],"prev_symbol":[]},"alphafold":{"accession":"Q16533","domains":[{"cath_id":"-","chopping":"6-162","consensus_level":"high","plddt":89.7238,"start":6,"end":162},{"cath_id":"-","chopping":"166-232","consensus_level":"medium","plddt":80.4357,"start":166,"end":232}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q16533","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q16533-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q16533-F1-predicted_aligned_error_v6.png","plddt_mean":71.12},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=SNAPC1","jax_strain_url":"https://www.jax.org/strain/search?query=SNAPC1"},"sequence":{"accession":"Q16533","fasta_url":"https://rest.uniprot.org/uniprotkb/Q16533.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q16533/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q16533"}},"corpus_meta":[{"pmid":"17079134","id":"PMC_17079134","title":"Identification of differentially expressed genes in HPV-positive and HPV-negative oropharyngeal squamous cell carcinomas.","date":"2006","source":"European journal of cancer (Oxford, England : 1990)","url":"https://pubmed.ncbi.nlm.nih.gov/17079134","citation_count":150,"is_preprint":false},{"pmid":"7715707","id":"PMC_7715707","title":"A TBP-TAF complex required for transcription of human snRNA genes by RNA polymerase II and III.","date":"1995","source":"Nature","url":"https://pubmed.ncbi.nlm.nih.gov/7715707","citation_count":128,"is_preprint":false},{"pmid":"9418884","id":"PMC_9418884","title":"The large subunit of basal transcription factor SNAPc is a Myb domain protein that interacts with Oct-1.","date":"1998","source":"Molecular and cellular biology","url":"https://pubmed.ncbi.nlm.nih.gov/9418884","citation_count":82,"is_preprint":false},{"pmid":"9732265","id":"PMC_9732265","title":"SNAP19 mediates the assembly of a functional core promoter complex (SNAPc) shared by RNA polymerases II and 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Part B, Neuropsychiatric genetics : the official publication of the International Society of Psychiatric Genetics","url":"https://pubmed.ncbi.nlm.nih.gov/34042246","citation_count":17,"is_preprint":false},{"pmid":"16901896","id":"PMC_16901896","title":"The unorthodox SNAP50 zinc finger domain contributes to cooperative promoter recognition by human SNAPC.","date":"2006","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/16901896","citation_count":16,"is_preprint":false},{"pmid":"22966203","id":"PMC_22966203","title":"Requirement for SNAPC1 in transcriptional responsiveness to diverse extracellular signals.","date":"2012","source":"Molecular and cellular biology","url":"https://pubmed.ncbi.nlm.nih.gov/22966203","citation_count":15,"is_preprint":false},{"pmid":"36369505","id":"PMC_36369505","title":"Structural basis of human SNAPc recognizing proximal sequence element of snRNA promoter.","date":"2022","source":"Nature communications","url":"https://pubmed.ncbi.nlm.nih.gov/36369505","citation_count":11,"is_preprint":false},{"pmid":"16603380","id":"PMC_16603380","title":"Co-expression of multiple subunits enables recombinant SNAPC assembly and function for transcription by human RNA polymerases II and III.","date":"2006","source":"Protein expression and purification","url":"https://pubmed.ncbi.nlm.nih.gov/16603380","citation_count":6,"is_preprint":false},{"pmid":"25111050","id":"PMC_25111050","title":"Mapping of a chromosome 12 region associated with airway hyperresponsiveness in a recombinant congenic mouse strain and selection of potential candidate genes by expression and sequence variation analyses.","date":"2014","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/25111050","citation_count":6,"is_preprint":false},{"pmid":"9644240","id":"PMC_9644240","title":"The human PTFgamma/SNAP43 gene: structure, chromosomal location, and identification of a VNTR in 5'-UTR.","date":"1998","source":"Journal of biochemistry","url":"https://pubmed.ncbi.nlm.nih.gov/9644240","citation_count":2,"is_preprint":false},{"pmid":"37042131","id":"PMC_37042131","title":"[Read-through circular RNA rt-circ-HS promotes hypoxia inducible factor 1α expression and renal carcinoma cell proliferation, migration and invasiveness].","date":"2023","source":"Beijing da xue xue bao. 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Health sciences","url":"https://pubmed.ncbi.nlm.nih.gov/37042131","citation_count":2,"is_preprint":false},{"pmid":"40956881","id":"PMC_40956881","title":"SUMO conjugation to promoter-proximal sequence elements-associated proteins impacts on snRNA transcription.","date":"2025","source":"Proceedings of the National Academy of Sciences of the United States of America","url":"https://pubmed.ncbi.nlm.nih.gov/40956881","citation_count":0,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":13149,"output_tokens":3256,"usd":0.044144},"stage2":{"model":"claude-opus-4-6","input_tokens":6642,"output_tokens":2401,"usd":0.139852},"total_usd":0.183996,"stage1_batch_id":"msgbatch_011rkcQdVV1RaFq9XhcG6df6","stage2_batch_id":"msgbatch_01RzgrJafdF4EWHhj5mNi6dh","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 1995,\n      \"finding\": \"SNAPc (containing SNAP43/SNAPC1, SNAP45, SNAP50, and TBP) is a TBP-TAF complex required for transcription of both RNA polymerase II and III snRNA genes; it binds specifically to the proximal sequence element (PSE), a non-TATA-box basal promoter element common to both gene types.\",\n      \"method\": \"Biochemical purification, EMSA, in vitro transcription assay\",\n      \"journal\": \"Nature\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — original reconstitution and functional characterization with multiple orthogonal methods\",\n      \"pmids\": [\"7715707\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1996,\n      \"finding\": \"SNAP43 (SNAPC1) is a subunit of SNAPc that is required for both RNA polymerase II and III transcription of snRNA genes; antibodies against SNAP45 (which interacts with SNAP43) retard SNAPc-PSE complex mobility, confirming subunit composition.\",\n      \"method\": \"Immunodepletion, EMSA, in vitro transcription assay, co-immunoprecipitation\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — in vitro transcription with immunodepletion and EMSA, replicated across subunit studies\",\n      \"pmids\": [\"8633057\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1996,\n      \"finding\": \"SNAP50 contacts DNA within the SNAP complex (UV cross-linking) and interacts with SNAP43 (SNAPC1) by co-immunoprecipitation, but not with SNAP45 or TBP, defining initial SNAPc architecture.\",\n      \"method\": \"UV cross-linking, co-immunoprecipitation, in vitro transcription assay\",\n      \"journal\": \"The EMBO journal\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — direct DNA contact shown by UV cross-linking; protein interactions by co-IP with functional transcription readout\",\n      \"pmids\": [\"9003788\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1998,\n      \"finding\": \"SNAP19 is a fifth SNAPc subunit that, together with SNAP43, SNAP45, SNAP50, and SNAP190, assembles a recombinant SNAPc that binds the PSE and directs both RNA polymerase II and III snRNA gene transcription, demonstrating that the same core SNAPc nucleates two classes of initiation complexes.\",\n      \"method\": \"Recombinant protein reconstitution, EMSA, in vitro transcription assay\",\n      \"journal\": \"Genes & development\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — full reconstitution from defined recombinant subunits with functional transcription validation\",\n      \"pmids\": [\"9732265\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1998,\n      \"finding\": \"SNAP190, the largest SNAPc subunit, contains a Myb DNA-binding domain (four complete repeats plus a half repeat) that contributes to PSE recognition; SNAP190 interacts with SNAP45 and with the Oct-1 activator, and is required for snRNA gene transcription by both RNA polymerases II and III.\",\n      \"method\": \"cDNA cloning, EMSA with truncation mutants, co-immunoprecipitation, in vitro transcription assay\",\n      \"journal\": \"Molecular and cellular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — domain mapping with truncation mutants, functional transcription assay, and protein interaction studies\",\n      \"pmids\": [\"9418884\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2000,\n      \"finding\": \"A detailed map of protein-protein contacts within SNAPc was established: specific subunit domains required for subunit-subunit association were defined, and complexes containing only those interaction domains retain specific PSE binding, indicating that direct subunit contacts are sufficient for DNA recognition.\",\n      \"method\": \"Co-immunoprecipitation with deletion/truncation mutants, EMSA\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — systematic domain mapping with reciprocal co-IP and DNA binding assays\",\n      \"pmids\": [\"11056176\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2002,\n      \"finding\": \"A 50-amino-acid region within SNAP190 mediates cooperative binding with TBP in the context of mini-SNAPc (SNAP43, SNAP50, and N-terminal SNAP190); mini-SNAPc derivatives lacking this region remain transcriptionally active because TBP can still be recruited via cooperative interactions with Brf2, revealing redundant mechanisms for TBP recruitment to the U6 promoter.\",\n      \"method\": \"Promoter binding assays with truncation mutants, in vitro transcription assay, recombinant protein reconstitution\",\n      \"journal\": \"Molecular and cellular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — domain mapping with defined recombinant complexes and functional transcription readout\",\n      \"pmids\": [\"12391172\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2003,\n      \"finding\": \"Two SNAPc subunits, SNAP43 (SNAPC1) and SNAP190, directly interact with the TBP DNA-binding domain; the SNAP190 Myb domain is sufficient to recruit TBP to the U6 TATA box and stimulates SNAP190-TBP-Brf2 complex assembly, defining the assembly pathway of the RNA polymerase III-specific preinitiation complex.\",\n      \"method\": \"TBP recruitment assays, co-immunoprecipitation, EMSA with truncation mutants\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 — direct interaction mapping with functional recruitment assays and multiple protein combinations\",\n      \"pmids\": [\"12621023\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2004,\n      \"finding\": \"In Drosophila, the SNAPC1 ortholog DmPBP45 (identified by sequence similarity to human SNAP43) contacts DNA differentially depending on PSE sequence: it cross-links strongly for two turns downstream of the U1 PSE but only a half turn downstream of the U6 PSE, consistent with a model in which PSE-dependent conformational differences in the DmPBP complex determine RNA polymerase specificity.\",\n      \"method\": \"Photo-cross-linking, S2 cell expression, EMSA\",\n      \"journal\": \"Molecular and cellular biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — direct DNA contact mapping with photo-cross-linking; single lab, Drosophila ortholog\",\n      \"pmids\": [\"14966271\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2006,\n      \"finding\": \"The SNAP50 zinc finger domain (eight cysteine/histidine residues identified by alanine scanning) plays an important role in PSE DNA binding by SNAPc; metal binding studies revealed a single zinc atom, indicating one functional coordination site; four cysteine residues essential for DNA binding were also required for both U1 (Pol II) and U6 (Pol III) transcription, while the remaining four residues showed differential effects on Pol II vs Pol III transcription.\",\n      \"method\": \"Alanine scanning mutagenesis, metal binding assays, EMSA, in vitro transcription assay\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — systematic mutagenesis combined with metal binding and functional transcription assays\",\n      \"pmids\": [\"16901896\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2006,\n      \"finding\": \"A partial SNAPc (SNAP190[1-505], SNAP50, SNAP43/SNAPC1, and SNAP19) co-expressed in E. coli binds PSE DNA specifically, recruits TBP to U6 promoter DNA, and supports transcription of both human U1 and U6 snRNA genes by RNA polymerases II and III, respectively.\",\n      \"method\": \"Recombinant co-expression in E. coli, EMSA, TBP recruitment assay, reconstituted in vitro transcription\",\n      \"journal\": \"Protein expression and purification\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — reconstituted complex from defined subunits with multiple functional readouts\",\n      \"pmids\": [\"16603380\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"ChIP-seq revealed that SNAPC1 occupancy extends beyond snRNA genes to include a large number of transcriptionally active protein-coding genes, co-localizing with elongating RNA polymerase II; inhibition of transcriptional elongation caused loss of SNAPC1 from gene 3' ends; depletion of SNAPC1 specifically diminished transcriptional responsiveness of many genes to EGF and retinoic acid stimulation, identifying SNAPC1 as a general transcriptional coactivator functioning through elongating RNAPII.\",\n      \"method\": \"ChIP-seq, RNA interference/depletion, transcriptional elongation inhibition, gene expression analysis\",\n      \"journal\": \"Molecular and cellular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — genome-wide ChIP-seq with functional KD and mechanistic dissection across two signaling pathways\",\n      \"pmids\": [\"22966203\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"Cryo-EM structure of human SNAPc (SNAP190 N-terminal domain, SNAP50, and SNAP43/SNAPC1) bound to the U6-1 PSE at 3.49 Å resolution revealed a 'wrap-around' assembly mode; three SNAP50 motifs contact both major and minor grooves of PSE in coordination with the SNAP190 Myb domain, explaining PSE sequence conservation and SNAPc recognition specificity.\",\n      \"method\": \"Cryo-electron microscopy structural determination\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — high-resolution cryo-EM structure with identification of specific DNA-protein contacts\",\n      \"pmids\": [\"36369505\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"SNAPC1 is SUMOylated at lysine residues K245 and K333; a SUMOylation-deficient mutant (SNAPC1 2KR) cannot sustain basal snRNA transcription despite being recruited to the PSE; SNAPC1 SUMOylation is required for its interaction with SNAPC4 but not SNAPC3, indicating that SUMO modification controls SNAPc complex assembly and snRNA transcriptional activity.\",\n      \"method\": \"CRISPR/dCas9-SENP1 targeting, site-directed mutagenesis, inducible degron depletion system, co-immunoprecipitation, in vivo transcription assay\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 — identification of SUMO sites by mutagenesis, rescue experiments with degron system, and protein interaction mapping with orthogonal methods\",\n      \"pmids\": [\"40956881\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"SNAPC1 (SNAP43) is a core subunit of the five-subunit SNAPc complex that binds the proximal sequence element (PSE) of snRNA gene promoters via a 'wrap-around' mechanism (cryo-EM structure), directly contacts TBP and SNAP190 to nucleate RNA polymerase II and III preinitiation complexes, and is SUMOylated at K245/K333—a modification required for interaction with SNAPC4 and for sustaining basal snRNA transcription; additionally, SNAPC1 associates with elongating RNA polymerase II at protein-coding genes genome-wide and is required for transcriptional responsiveness to extracellular signals such as EGF and retinoic acid.\"\n}\n```","stage2_raw":"```json\n{\n  \"mechanistic_narrative\": \"SNAPC1 (SNAP43) is a core subunit of the five-subunit SNAPc complex that binds the proximal sequence element (PSE) of snRNA gene promoters and nucleates preinitiation complex assembly for both RNA polymerase II and RNA polymerase III transcription. Within SNAPc, SNAPC1 directly contacts SNAP50, SNAP190, and TBP, contributing to a 'wrap-around' DNA-binding architecture resolved by cryo-EM, and its SUMOylation at K245 and K333 is required for interaction with SNAPC4 and for sustaining basal snRNA transcription [PMID:7715707, PMID:36369505, PMID:40956881]. Beyond snRNA genes, SNAPC1 associates with elongating RNA polymerase II at protein-coding genes genome-wide and is required for transcriptional responsiveness to extracellular signals such as EGF and retinoic acid, establishing it as a general transcriptional coactivator [PMID:22966203]. SNAPC1 thus operates at two levels: as a PSE-recognition scaffold essential for snRNA gene expression, and as an elongation-associated factor modulating signal-dependent transcription of mRNA genes.\",\n  \"teleology\": [\n    {\n      \"year\": 1995,\n      \"claim\": \"Identification of SNAPC1 as a subunit of a novel TBP-containing complex (SNAPc) that binds the PSE and is required for both Pol II and Pol III snRNA transcription established the fundamental biochemical framework for understanding snRNA promoter recognition.\",\n      \"evidence\": \"Biochemical purification, EMSA, and in vitro transcription from human cell extracts\",\n      \"pmids\": [\"7715707\", \"8633057\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Structural basis of PSE recognition unknown\", \"No information on in vivo relevance or genome-wide occupancy\", \"Role of individual subunits in DNA contact not resolved\"]\n    },\n    {\n      \"year\": 1996,\n      \"claim\": \"Mapping of direct subunit contacts — SNAP50 interacts with SNAP43 but not SNAP45 or TBP — provided the first internal architecture of SNAPc and defined SNAPC1 as a central bridging subunit.\",\n      \"evidence\": \"UV cross-linking to DNA and co-immunoprecipitation of recombinant subunits\",\n      \"pmids\": [\"9003788\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Full five-subunit interaction network not yet mapped\", \"DNA contacts by SNAPC1 itself not assessed\"]\n    },\n    {\n      \"year\": 1998,\n      \"claim\": \"Reconstitution of a complete five-subunit recombinant SNAPc (SNAP19, SNAP43, SNAP45, SNAP50, SNAP190) that binds the PSE and directs both Pol II and Pol III snRNA transcription demonstrated that no additional factors are needed for SNAPc function and confirmed SNAPC1 as an essential structural component.\",\n      \"evidence\": \"Recombinant protein co-expression, EMSA, in vitro transcription\",\n      \"pmids\": [\"9732265\", \"9418884\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"How the same complex directs two different polymerases remained unclear\", \"Contribution of individual subunit domains to transcription not delineated\"]\n    },\n    {\n      \"year\": 2000,\n      \"claim\": \"Systematic domain-mapping of all pairwise subunit contacts within SNAPc, including SNAPC1, showed that minimal interaction domains are sufficient for PSE binding, establishing that direct protein–protein contacts underpin DNA recognition.\",\n      \"evidence\": \"Co-immunoprecipitation of truncation/deletion mutants combined with EMSA\",\n      \"pmids\": [\"11056176\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"No high-resolution structural information\", \"Post-translational modifications not explored\"]\n    },\n    {\n      \"year\": 2003,\n      \"claim\": \"Demonstration that both SNAPC1 and SNAP190 directly contact the TBP DNA-binding domain defined the assembly pathway for the Pol III preinitiation complex and established SNAPC1's role in TBP recruitment.\",\n      \"evidence\": \"TBP recruitment assays, co-immunoprecipitation, and EMSA with truncation mutants\",\n      \"pmids\": [\"12621023\", \"12391172\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Structural details of TBP–SNAPC1 interface unknown\", \"Whether SNAPC1–TBP contact is required for Pol II snRNA transcription not tested\"]\n    },\n    {\n      \"year\": 2004,\n      \"claim\": \"Photo-cross-linking of the Drosophila SNAPC1 ortholog to PSE DNA revealed polymerase-specific differences in DNA contacts, supporting a model in which PSE-dependent conformational changes in SNAPc determine Pol II vs. Pol III recruitment.\",\n      \"evidence\": \"Photo-cross-linking and EMSA in Drosophila S2 cells\",\n      \"pmids\": [\"14966271\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Observation in Drosophila; relevance to human SNAPC1 not confirmed\", \"Conformational change inferred indirectly from cross-linking pattern\"]\n    },\n    {\n      \"year\": 2012,\n      \"claim\": \"ChIP-seq discovery that SNAPC1 occupies protein-coding genes genome-wide and tracks with elongating Pol II, combined with depletion experiments showing impaired EGF and retinoic acid transcriptional responses, revealed an unexpected second role for SNAPC1 as a general transcriptional coactivator beyond snRNA genes.\",\n      \"evidence\": \"ChIP-seq, RNAi depletion, elongation inhibition, and gene expression profiling in human cells\",\n      \"pmids\": [\"22966203\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Mechanism by which SNAPC1 promotes elongation unknown\", \"Whether this function requires other SNAPc subunits not established\", \"Direct protein–protein contacts linking SNAPC1 to the elongation machinery not identified\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"A 3.49 Å cryo-EM structure of the SNAP190–SNAP50–SNAP43 sub-complex bound to the U6-1 PSE resolved the 'wrap-around' DNA recognition mode, explaining PSE sequence conservation and providing the first high-resolution view of SNAPC1 within the assembled complex.\",\n      \"evidence\": \"Cryo-electron microscopy of reconstituted human SNAPc–PSE complex\",\n      \"pmids\": [\"36369505\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Structure lacks SNAP19 and SNAP45 subunits\", \"No structure of full preinitiation complex with TBP or polymerase\", \"SNAPC1 DNA contacts not individually resolved in this structure\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Identification of K245 and K333 as SUMOylation sites on SNAPC1, with demonstration that SUMOylation is required for SNAPC4 interaction and for sustaining basal snRNA transcription, established post-translational modification as a regulatory layer controlling SNAPc assembly and activity.\",\n      \"evidence\": \"CRISPR/dCas9-SENP1 targeting, site-directed mutagenesis, inducible degron depletion, co-immunoprecipitation, in vivo transcription assays\",\n      \"pmids\": [\"40956881\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether SUMOylation affects SNAPC1 function at protein-coding genes is unknown\", \"SUMO E3 ligase responsible for SNAPC1 modification not identified\", \"Dynamics of SUMOylation during the cell cycle or signaling not explored\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"Key unresolved questions include how SNAPC1 mechanistically promotes transcriptional elongation at protein-coding genes, whether it functions independently of other SNAPc subunits in that context, and how its SUMOylation is regulated in response to physiological signals.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"High\",\n      \"gaps\": [\"No reconstituted elongation assay with SNAPC1\", \"Full SNAPc structure with all five subunits and bound polymerase not available\", \"Relationship between SNAPc-dependent and SNAPc-independent functions of SNAPC1 unresolved\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0003677\", \"supporting_discovery_ids\": [0, 8, 12]},\n      {\"term_id\": \"GO:0140110\", \"supporting_discovery_ids\": [11]},\n      {\"term_id\": \"GO:0060090\", \"supporting_discovery_ids\": [5, 7]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [0, 11, 12]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"GO:0074160\", \"supporting_discovery_ids\": [0, 1, 3, 11]},\n      {\"term_id\": \"R-HSA-8953854\", \"supporting_discovery_ids\": [0, 3, 13]}\n    ],\n    \"complexes\": [\"SNAPc\"],\n    \"partners\": [\"SNAPC2\", \"SNAPC3\", \"SNAPC4\", \"SNAPC5\", \"TBP\"],\n    \"other_free_text\": []\n  }\n}\n```"}