{"gene":"SNAPC2","run_date":"2026-06-10T07:46:37","timeline":{"discoveries":[{"year":1995,"finding":"SNAPC2 (SNAP45) is a subunit of the SNAPc complex, which binds specifically to the proximal sequence element (PSE) and is required for transcription of both RNA polymerase II and III snRNA genes. SNAPc also contains TBP, SNAP43, and SNAP50.","method":"Biochemical purification, transcription assays","journal":"Nature","confidence":"High","confidence_rationale":"Tier 1–2 / Strong — biochemical purification combined with functional transcription assays, replicated across multiple subsequent studies","pmids":["7715707"],"is_preprint":false},{"year":1996,"finding":"SNAPC2 (SNAP45) is part of SNAPc, is required for both RNA polymerase II and III transcription of snRNA genes in vitro, and interacts strongly with TBP. Antibodies against SNAP45 supershift the SNAPc-PSE complex, confirming its presence in the complex.","method":"cDNA cloning, antibody supershift (EMSA), in vitro transcription depletion assays, co-immunoprecipitation with TBP","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"High","confidence_rationale":"Tier 1–2 / Strong — multiple orthogonal methods (EMSA supershift, in vitro transcription, Co-IP) in a focused study on this specific subunit","pmids":["8633057"],"is_preprint":false},{"year":1996,"finding":"SNAP50 interacts with SNAP43 by co-immunoprecipitation but not with SNAP45 (SNAPC2) or TBP, providing initial architecture data: SNAPC2 does not directly contact SNAP50.","method":"Co-immunoprecipitation","journal":"The EMBO journal","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — single Co-IP experiment, but consistent with the broader SNAPc architecture established by multiple groups","pmids":["9003788"],"is_preprint":false},{"year":1998,"finding":"SNAP190 interacts with SNAP45 (SNAPC2), and SNAP190 is required for snRNA gene transcription by both RNA polymerases II and III. The Myb domain of SNAP190 contributes to PSE recognition.","method":"cDNA cloning, co-immunoprecipitation, in vitro transcription assays","journal":"Molecular and cellular biology","confidence":"High","confidence_rationale":"Tier 1–2 / Strong — reciprocal Co-IP plus functional transcription assays, consistent with independent findings","pmids":["9418884"],"is_preprint":false},{"year":1998,"finding":"A fully recombinant SNAPc comprising five subunits — SNAP43, SNAP45 (SNAPC2), SNAP50, SNAP190, and the newly identified SNAP19 — binds specifically to the PSE and directs both RNA polymerase II and III snRNA gene transcription, establishing SNAPC2 as a core subunit of the functional complex.","method":"Recombinant complex reconstitution, PSE-binding assay, in vitro transcription","journal":"Genes & development","confidence":"High","confidence_rationale":"Tier 1 / Strong — full reconstitution from recombinant subunits with functional transcription readout","pmids":["9732265"],"is_preprint":false},{"year":2000,"finding":"Detailed mapping of SNAPc subunit-subunit contacts showed that SNAPC2 (SNAP45) interacts with SNAP190 and that complexes containing minimal interaction domains sufficient for subunit-subunit contacts can still bind the PSE specifically.","method":"Deletion mutagenesis, co-immunoprecipitation, PSE-binding assays","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1–2 / Strong — systematic mutagenesis combined with binding assays across all five subunits in one focused study","pmids":["11056176"],"is_preprint":false},{"year":2002,"finding":"SNAPC2 (SNAP45) is part of mini-SNAPc (together with SNAP43, SNAP50, and the N-terminal third of SNAP190) that binds cooperatively with TBP to the core U6 promoter. A 50-amino-acid region in SNAP190 mediates cooperative TBP binding within mini-SNAPc context.","method":"Recombinant complex reconstitution, promoter binding assays, in vitro transcription","journal":"Molecular and cellular biology","confidence":"High","confidence_rationale":"Tier 1 / Moderate — reconstitution with defined subunit deletions and functional transcription readout, single lab","pmids":["12391172"],"is_preprint":false},{"year":2006,"finding":"A partial SNAPc containing SNAP190 (1–505), SNAP50, SNAP43, and SNAP19 (but lacking SNAP45/SNAPC2) expressed in E. coli binds PSE DNA specifically and supports transcription of U1 and U6 snRNA genes, indicating SNAPC2 is not strictly required for this minimal complex activity.","method":"Recombinant co-expression in E. coli, DNA binding assay, in vitro transcription","journal":"Protein expression and purification","confidence":"Medium","confidence_rationale":"Tier 1 / Weak — reconstitution result from a single study; SNAPC2 absence is a deliberate design choice but mechanistic implication is limited","pmids":["16603380"],"is_preprint":false},{"year":2008,"finding":"SNAPC2 (SNAP45/PTFdelta) localizes to centrosomes during parts of mitosis, to the spindle midzone during anaphase, and to the mid-body during telophase. Both down- and up-regulation of SNAP45 cause G2/M arrest with abnormal mitotic structures, revealing a mitotic function distinct from its transcription role. By contrast, depletion of SNAP190 causes G0/G1 accumulation, not G2/M, establishing that the mitotic function is SNAP45-specific.","method":"Immunofluorescence localization, siRNA knockdown, overexpression, flow cytometry cell-cycle analysis","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 2 / Moderate — direct localization by immunofluorescence combined with loss- and gain-of-function experiments with defined mitotic phenotype and epistatic comparison to another subunit, single lab but multiple orthogonal methods","pmids":["18356157"],"is_preprint":false},{"year":2011,"finding":"In zebrafish, a truncation of Snapc4 that deletes the domain responsible for interaction with Snapc2 (a vertebrate-specific SNAPc subunit) causes hypomorphic reduction of a subset of snRNAs and biliary epithelial cell apoptosis. Morpholino knockdown of snapc2 phenocopies this biliary network degeneration, demonstrating that the Snapc4–Snapc2 physical interaction is required for normal snRNA expression and biliary cell survival.","method":"Forward genetic screen (zebrafish mutant), morpholino knockdown, snRNA expression analysis, apoptosis assays","journal":"Developmental biology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — genetic mutant plus morpholino knockdown with defined cellular phenotype; zebrafish ortholog study, single lab","pmids":["22222761"],"is_preprint":false},{"year":2025,"finding":"Cryo-EM structures of the full-length SNAPc-containing RNA Pol III pre-initiation complex on the U6 promoter (open and melting states, 3.2–4.2 Å) were determined. Cross-linking mass spectrometry localizes SNAPC2 and SNAPC5 near the promoter DNA. Structural comparison revealed the basis for selective SNAPc engagement within Pol III and Pol II PICs and differences from the S. cerevisiae Pol III PIC.","method":"Cryo-EM structure determination, cross-linking mass spectrometry","journal":"Nature communications","confidence":"High","confidence_rationale":"Tier 1 / Moderate — high-resolution cryo-EM structures with XL-MS for SNAPC2 localization; single study but rigorous structural method with functional context","pmids":["39747245"],"is_preprint":false}],"current_model":"SNAPC2 (SNAP45/PTFdelta) is a core subunit of the five-subunit SNAPc complex that binds the PSE promoter element and is required for transcription of snRNA genes by both RNA polymerase II and III; it directly interacts with TBP and with the largest subunit SNAP190, and cryo-EM/XL-MS studies position it near promoter DNA in the Pol III pre-initiation complex; independently of its transcription role, SNAPC2 localizes to centrosomes, the spindle midzone, and the mid-body during mitosis, and its perturbation causes G2/M arrest with abnormal mitotic structures."},"narrative":{"mechanistic_narrative":"SNAPC2 (SNAP45/PTFdelta) is a core subunit of the small nuclear RNA-activating protein complex (SNAPc), which binds the proximal sequence element (PSE) of snRNA gene promoters and is required for their transcription by both RNA polymerase II and III [PMID:7715707, PMID:9732265]. Within SNAPc it interacts strongly with TBP and with the largest subunit SNAP190, but does not directly contact SNAP50, defining its position in the complex architecture [PMID:8633057, PMID:9003788, PMID:9418884, PMID:11056176]. SNAPC2 is incorporated into the mini-SNAPc that binds cooperatively with TBP to the core U6 promoter [PMID:12391172], and cross-linking mass spectrometry in cryo-EM structures of the full SNAPc-containing Pol III pre-initiation complex on the U6 promoter places SNAPC2 near the promoter DNA [PMID:39747245]. The SNAP190–SNAPC2 physical interaction is required for normal snRNA expression in vivo, with loss causing biliary epithelial cell apoptosis in zebrafish [PMID:22222761]. Independently of its transcription role, SNAPC2 localizes to centrosomes, the spindle midzone during anaphase, and the mid-body during telophase, and both its depletion and overexpression cause G2/M arrest with abnormal mitotic structures — a phenotype distinct from the G0/G1 accumulation seen on SNAP190 depletion, establishing a SNAPC2-specific mitotic function [PMID:18356157].","teleology":[{"year":1995,"claim":"Establishing the molecular machinery for snRNA gene transcription required identifying the factors that recognize the PSE; SNAPC2 was defined as a subunit of the PSE-binding SNAPc required for both Pol II and Pol III snRNA transcription.","evidence":"Biochemical purification and in vitro transcription assays","pmids":["7715707"],"confidence":"High","gaps":["Did not resolve subunit stoichiometry or the specific contribution of SNAPC2 versus other subunits","No structural placement within the complex"]},{"year":1996,"claim":"To confirm SNAPC2 is a bona fide complex member and identify its contacts, it was shown to reside in the PSE-bound complex and to interact strongly with TBP, while a separate study mapped that it does not directly contact SNAP50.","evidence":"cDNA cloning, EMSA supershift, in vitro transcription depletion, and co-immunoprecipitation","pmids":["8633057","9003788"],"confidence":"High","gaps":["The functional consequence of the SNAPC2–TBP interaction was not isolated","Subunit topology remained incomplete"]},{"year":1998,"claim":"Pinpointing SNAPC2's anchor in the complex, SNAP190 was identified as a direct SNAPC2 partner required for transcription, and a fully recombinant five-subunit SNAPc reconstituted PSE binding and transcription, establishing SNAPC2 as a core subunit.","evidence":"Co-immunoprecipitation, recombinant complex reconstitution, PSE-binding and in vitro transcription assays","pmids":["9418884","9732265"],"confidence":"High","gaps":["The minimal SNAPC2 region needed for SNAP190 contact was not defined","No structural model of subunit arrangement"]},{"year":2000,"claim":"Systematic mapping of subunit-subunit contacts confirmed the SNAPC2–SNAP190 interaction and showed minimal interaction domains suffice for assembly and PSE binding, refining the complex architecture.","evidence":"Deletion mutagenesis, co-immunoprecipitation, PSE-binding assays","pmids":["11056176"],"confidence":"High","gaps":["Did not assign SNAPC2 a direct DNA-contacting role","Atomic-level architecture still unresolved"]},{"year":2002,"claim":"Defining how SNAPc cooperates with TBP at the U6 promoter, SNAPC2 was shown to be part of a mini-SNAPc that binds cooperatively with TBP, with a SNAP190 region mediating cooperativity.","evidence":"Recombinant reconstitution with subunit deletions, promoter binding and in vitro transcription assays","pmids":["12391172"],"confidence":"High","gaps":["SNAPC2's specific contribution to TBP cooperativity not isolated","Structural basis not determined"]},{"year":2006,"claim":"Testing whether SNAPC2 is strictly required, a partial complex lacking SNAPC2 still bound PSE and supported U1/U6 transcription, indicating SNAPC2 is dispensable for minimal in vitro activity.","evidence":"Recombinant co-expression in E. coli, DNA binding and in vitro transcription assays","pmids":["16603380"],"confidence":"Medium","gaps":["A deliberate design omission; does not establish SNAPC2's regulatory role in vivo","Quantitative efficiency loss without SNAPC2 not assessed"]},{"year":2008,"claim":"Revealing a function beyond transcription, SNAPC2 was found to localize to mitotic structures and to be required for normal mitotic progression, with a phenotype distinct from another SNAPc subunit, establishing a SNAPC2-specific mitotic role.","evidence":"Immunofluorescence, siRNA knockdown, overexpression, flow cytometry cell-cycle analysis","pmids":["18356157"],"confidence":"High","gaps":["No molecular partners at centrosomes/midbody identified","Mechanism linking SNAPC2 to mitotic structure assembly unknown","Whether the mitotic role requires SNAPc assembly is unresolved"]},{"year":2011,"claim":"Linking the SNAPC2–SNAP190 interaction to physiology, a zebrafish truncation deleting the Snapc4 domain that binds Snapc2 reduced snRNAs and caused biliary cell apoptosis, phenocopied by snapc2 knockdown.","evidence":"Zebrafish forward genetic mutant, morpholino knockdown, snRNA expression and apoptosis assays","pmids":["22222761"],"confidence":"Medium","gaps":["Tissue specificity of the biliary phenotype not mechanistically explained","Ortholog study; human relevance inferred","Whether apoptosis is a direct snRNA deficit or secondary effect unclear"]},{"year":2025,"claim":"Placing SNAPC2 in a structural framework, cryo-EM of the SNAPc-containing Pol III PIC on U6 with XL-MS localized SNAPC2 near promoter DNA and explained selective SNAPc engagement by Pol III versus Pol II.","evidence":"Cryo-EM structure determination (3.2–4.2 Å) and cross-linking mass spectrometry","pmids":["39747245"],"confidence":"High","gaps":["SNAPC2 not resolved at atomic resolution; localization is by XL-MS","Direct DNA-contacting residues of SNAPC2 not defined"]},{"year":null,"claim":"How SNAPC2's mitotic localization and function mechanistically relate to (or are independent of) its role in the SNAPc transcription complex remains unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No identified mitotic interaction partners for SNAPC2","Unknown whether SNAPC2's centrosome/midbody role requires the rest of SNAPc","No structural model of SNAPC2 within or apart from the complex"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0140110","term_label":"transcription regulator activity","supporting_discovery_ids":[0,4]},{"term_id":"GO:0003677","term_label":"DNA binding","supporting_discovery_ids":[4,10]},{"term_id":"GO:0140223","term_label":"general transcription initiation factor activity","supporting_discovery_ids":[0,6]}],"localization":[{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[0]},{"term_id":"GO:0005815","term_label":"microtubule organizing center","supporting_discovery_ids":[8]},{"term_id":"GO:0005856","term_label":"cytoskeleton","supporting_discovery_ids":[8]}],"pathway":[{"term_id":"R-HSA-74160","term_label":"Gene expression (Transcription)","supporting_discovery_ids":[0,4]},{"term_id":"R-HSA-1640170","term_label":"Cell Cycle","supporting_discovery_ids":[8]}],"complexes":["SNAPc"],"partners":["SNAP190","TBP"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q13487","full_name":"snRNA-activating protein complex subunit 2","aliases":["Proximal sequence element-binding transcription factor subunit delta","PSE-binding factor subunit delta","PTF subunit delta","Small nuclear RNA-activating complex polypeptide 2","snRNA-activating protein complex 45 kDa subunit","SNAPc 45 kDa subunit"],"length_aa":334,"mass_kda":35.6,"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/Q13487/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":true,"resolved_as":"","url":"https://depmap.org/portal/gene/SNAPC2","classification":"Common Essential","n_dependent_lines":1202,"n_total_lines":1208,"dependency_fraction":0.9950331125827815},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/SNAPC2","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":"600591","title":"SMALL NUCLEAR RNA-ACTIVATING PROTEIN COMPLEX, POLYPEPTIDE 1; SNAPC1","url":"https://www.omim.org/entry/600591"},{"mim_id":"176399","title":"PREGNANCY-SPECIFIC BETA-1-GLYCOPROTEIN 10, PSEUDOGENE; PSG10P","url":"https://www.omim.org/entry/176399"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Supported","locations":[{"location":"Nucleoplasm","reliability":"Supported"},{"location":"Nuclear bodies","reliability":"Supported"},{"location":"Cytosol","reliability":"Additional"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/SNAPC2"},"hgnc":{"alias_symbol":["SNAP45","PTFdelta"],"prev_symbol":[]},"alphafold":{"accession":"Q13487","domains":[{"cath_id":"-","chopping":"207-259","consensus_level":"medium","plddt":86.5215,"start":207,"end":259},{"cath_id":"1.10.10","chopping":"25-88","consensus_level":"medium","plddt":77.5553,"start":25,"end":88}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q13487","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q13487-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q13487-F1-predicted_aligned_error_v6.png","plddt_mean":66.0},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=SNAPC2","jax_strain_url":"https://www.jax.org/strain/search?query=SNAPC2"},"sequence":{"accession":"Q13487","fasta_url":"https://rest.uniprot.org/uniprotkb/Q13487.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q13487/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q13487"}},"corpus_meta":[{"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 III.","date":"1998","source":"Genes & development","url":"https://pubmed.ncbi.nlm.nih.gov/9732265","citation_count":73,"is_preprint":false},{"pmid":"8633057","id":"PMC_8633057","title":"The SNAP45 subunit of the small nuclear RNA (snRNA) activating protein complex is required for RNA polymerase II and III snRNA gene transcription and interacts with the TATA box binding protein.","date":"1996","source":"Proceedings of the National Academy of Sciences of the United States of America","url":"https://pubmed.ncbi.nlm.nih.gov/8633057","citation_count":52,"is_preprint":false},{"pmid":"9003788","id":"PMC_9003788","title":"Cloning and characterization of SNAP50, a subunit of the snRNA-activating protein complex SNAPc.","date":"1996","source":"The EMBO journal","url":"https://pubmed.ncbi.nlm.nih.gov/9003788","citation_count":51,"is_preprint":false},{"pmid":"11056176","id":"PMC_11056176","title":"A map of protein-protein contacts within the small nuclear RNA-activating protein complex SNAPc.","date":"2000","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/11056176","citation_count":41,"is_preprint":false},{"pmid":"31552087","id":"PMC_31552087","title":"Machine Learning Classifiers for Endometriosis Using Transcriptomics and Methylomics Data.","date":"2019","source":"Frontiers in genetics","url":"https://pubmed.ncbi.nlm.nih.gov/31552087","citation_count":37,"is_preprint":false},{"pmid":"12391172","id":"PMC_12391172","title":"Redundant cooperative interactions for assembly of a human U6 transcription initiation complex.","date":"2002","source":"Molecular and cellular biology","url":"https://pubmed.ncbi.nlm.nih.gov/12391172","citation_count":34,"is_preprint":false},{"pmid":"22222761","id":"PMC_22222761","title":"Mutation of zebrafish Snapc4 is associated with loss of the intrahepatic biliary network.","date":"2011","source":"Developmental biology","url":"https://pubmed.ncbi.nlm.nih.gov/22222761","citation_count":18,"is_preprint":false},{"pmid":"27610895","id":"PMC_27610895","title":"Association between genes on chromosome 19p13.2 and panic disorder.","date":"2016","source":"Psychiatric genetics","url":"https://pubmed.ncbi.nlm.nih.gov/27610895","citation_count":7,"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":"18356157","id":"PMC_18356157","title":"Mitotic functions for SNAP45, a subunit of the small nuclear RNA-activating protein complex SNAPc.","date":"2008","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/18356157","citation_count":5,"is_preprint":false},{"pmid":"39747245","id":"PMC_39747245","title":"Structural insights into distinct mechanisms of RNA polymerase II and III recruitment to snRNA promoters.","date":"2025","source":"Nature communications","url":"https://pubmed.ncbi.nlm.nih.gov/39747245","citation_count":4,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":7692,"output_tokens":2575,"usd":0.03085,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":9786,"output_tokens":3246,"usd":0.06504,"stage2_stop_reason":"end_turn"},"total_usd":0.09589,"stage1_batch_id":"msgbatch_013LWZZT6MWaqB9qyTSeQBmU","stage2_batch_id":"msgbatch_0194ZzQaTGNpruoNJBbEMbt3","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 1995,\n      \"finding\": \"SNAPC2 (SNAP45) is a subunit of the SNAPc complex, which binds specifically to the proximal sequence element (PSE) and is required for transcription of both RNA polymerase II and III snRNA genes. SNAPc also contains TBP, SNAP43, and SNAP50.\",\n      \"method\": \"Biochemical purification, transcription assays\",\n      \"journal\": \"Nature\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Strong — biochemical purification combined with functional transcription assays, replicated across multiple subsequent studies\",\n      \"pmids\": [\"7715707\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1996,\n      \"finding\": \"SNAPC2 (SNAP45) is part of SNAPc, is required for both RNA polymerase II and III transcription of snRNA genes in vitro, and interacts strongly with TBP. Antibodies against SNAP45 supershift the SNAPc-PSE complex, confirming its presence in the complex.\",\n      \"method\": \"cDNA cloning, antibody supershift (EMSA), in vitro transcription depletion assays, co-immunoprecipitation with TBP\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Strong — multiple orthogonal methods (EMSA supershift, in vitro transcription, Co-IP) in a focused study on this specific subunit\",\n      \"pmids\": [\"8633057\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1996,\n      \"finding\": \"SNAP50 interacts with SNAP43 by co-immunoprecipitation but not with SNAP45 (SNAPC2) or TBP, providing initial architecture data: SNAPC2 does not directly contact SNAP50.\",\n      \"method\": \"Co-immunoprecipitation\",\n      \"journal\": \"The EMBO journal\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — single Co-IP experiment, but consistent with the broader SNAPc architecture established by multiple groups\",\n      \"pmids\": [\"9003788\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1998,\n      \"finding\": \"SNAP190 interacts with SNAP45 (SNAPC2), and SNAP190 is required for snRNA gene transcription by both RNA polymerases II and III. The Myb domain of SNAP190 contributes to PSE recognition.\",\n      \"method\": \"cDNA cloning, co-immunoprecipitation, in vitro transcription assays\",\n      \"journal\": \"Molecular and cellular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Strong — reciprocal Co-IP plus functional transcription assays, consistent with independent findings\",\n      \"pmids\": [\"9418884\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1998,\n      \"finding\": \"A fully recombinant SNAPc comprising five subunits — SNAP43, SNAP45 (SNAPC2), SNAP50, SNAP190, and the newly identified SNAP19 — binds specifically to the PSE and directs both RNA polymerase II and III snRNA gene transcription, establishing SNAPC2 as a core subunit of the functional complex.\",\n      \"method\": \"Recombinant complex reconstitution, PSE-binding assay, in vitro transcription\",\n      \"journal\": \"Genes & development\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — full reconstitution from recombinant subunits with functional transcription readout\",\n      \"pmids\": [\"9732265\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2000,\n      \"finding\": \"Detailed mapping of SNAPc subunit-subunit contacts showed that SNAPC2 (SNAP45) interacts with SNAP190 and that complexes containing minimal interaction domains sufficient for subunit-subunit contacts can still bind the PSE specifically.\",\n      \"method\": \"Deletion mutagenesis, co-immunoprecipitation, PSE-binding assays\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Strong — systematic mutagenesis combined with binding assays across all five subunits in one focused study\",\n      \"pmids\": [\"11056176\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2002,\n      \"finding\": \"SNAPC2 (SNAP45) is part of mini-SNAPc (together with SNAP43, SNAP50, and the N-terminal third of SNAP190) that binds cooperatively with TBP to the core U6 promoter. A 50-amino-acid region in SNAP190 mediates cooperative TBP binding within mini-SNAPc context.\",\n      \"method\": \"Recombinant complex reconstitution, promoter binding assays, in vitro transcription\",\n      \"journal\": \"Molecular and cellular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — reconstitution with defined subunit deletions and functional transcription readout, single lab\",\n      \"pmids\": [\"12391172\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2006,\n      \"finding\": \"A partial SNAPc containing SNAP190 (1–505), SNAP50, SNAP43, and SNAP19 (but lacking SNAP45/SNAPC2) expressed in E. coli binds PSE DNA specifically and supports transcription of U1 and U6 snRNA genes, indicating SNAPC2 is not strictly required for this minimal complex activity.\",\n      \"method\": \"Recombinant co-expression in E. coli, DNA binding assay, in vitro transcription\",\n      \"journal\": \"Protein expression and purification\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1 / Weak — reconstitution result from a single study; SNAPC2 absence is a deliberate design choice but mechanistic implication is limited\",\n      \"pmids\": [\"16603380\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2008,\n      \"finding\": \"SNAPC2 (SNAP45/PTFdelta) localizes to centrosomes during parts of mitosis, to the spindle midzone during anaphase, and to the mid-body during telophase. Both down- and up-regulation of SNAP45 cause G2/M arrest with abnormal mitotic structures, revealing a mitotic function distinct from its transcription role. By contrast, depletion of SNAP190 causes G0/G1 accumulation, not G2/M, establishing that the mitotic function is SNAP45-specific.\",\n      \"method\": \"Immunofluorescence localization, siRNA knockdown, overexpression, flow cytometry cell-cycle analysis\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct localization by immunofluorescence combined with loss- and gain-of-function experiments with defined mitotic phenotype and epistatic comparison to another subunit, single lab but multiple orthogonal methods\",\n      \"pmids\": [\"18356157\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"In zebrafish, a truncation of Snapc4 that deletes the domain responsible for interaction with Snapc2 (a vertebrate-specific SNAPc subunit) causes hypomorphic reduction of a subset of snRNAs and biliary epithelial cell apoptosis. Morpholino knockdown of snapc2 phenocopies this biliary network degeneration, demonstrating that the Snapc4–Snapc2 physical interaction is required for normal snRNA expression and biliary cell survival.\",\n      \"method\": \"Forward genetic screen (zebrafish mutant), morpholino knockdown, snRNA expression analysis, apoptosis assays\",\n      \"journal\": \"Developmental biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — genetic mutant plus morpholino knockdown with defined cellular phenotype; zebrafish ortholog study, single lab\",\n      \"pmids\": [\"22222761\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"Cryo-EM structures of the full-length SNAPc-containing RNA Pol III pre-initiation complex on the U6 promoter (open and melting states, 3.2–4.2 Å) were determined. Cross-linking mass spectrometry localizes SNAPC2 and SNAPC5 near the promoter DNA. Structural comparison revealed the basis for selective SNAPc engagement within Pol III and Pol II PICs and differences from the S. cerevisiae Pol III PIC.\",\n      \"method\": \"Cryo-EM structure determination, cross-linking mass spectrometry\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — high-resolution cryo-EM structures with XL-MS for SNAPC2 localization; single study but rigorous structural method with functional context\",\n      \"pmids\": [\"39747245\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"SNAPC2 (SNAP45/PTFdelta) is a core subunit of the five-subunit SNAPc complex that binds the PSE promoter element and is required for transcription of snRNA genes by both RNA polymerase II and III; it directly interacts with TBP and with the largest subunit SNAP190, and cryo-EM/XL-MS studies position it near promoter DNA in the Pol III pre-initiation complex; independently of its transcription role, SNAPC2 localizes to centrosomes, the spindle midzone, and the mid-body during mitosis, and its perturbation causes G2/M arrest with abnormal mitotic structures.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"SNAPC2 (SNAP45/PTFdelta) is a core subunit of the small nuclear RNA-activating protein complex (SNAPc), which binds the proximal sequence element (PSE) of snRNA gene promoters and is required for their transcription by both RNA polymerase II and III [#0, #4]. Within SNAPc it interacts strongly with TBP and with the largest subunit SNAP190, but does not directly contact SNAP50, defining its position in the complex architecture [#1, #2, #3, #5]. SNAPC2 is incorporated into the mini-SNAPc that binds cooperatively with TBP to the core U6 promoter [#6], and cross-linking mass spectrometry in cryo-EM structures of the full SNAPc-containing Pol III pre-initiation complex on the U6 promoter places SNAPC2 near the promoter DNA [#10]. The SNAP190\\u2013SNAPC2 physical interaction is required for normal snRNA expression in vivo, with loss causing biliary epithelial cell apoptosis in zebrafish [#9]. Independently of its transcription role, SNAPC2 localizes to centrosomes, the spindle midzone during anaphase, and the mid-body during telophase, and both its depletion and overexpression cause G2/M arrest with abnormal mitotic structures \\u2014 a phenotype distinct from the G0/G1 accumulation seen on SNAP190 depletion, establishing a SNAPC2-specific mitotic function [#8].\",\n  \"teleology\": [\n    {\n      \"year\": 1995,\n      \"claim\": \"Establishing the molecular machinery for snRNA gene transcription required identifying the factors that recognize the PSE; SNAPC2 was defined as a subunit of the PSE-binding SNAPc required for both Pol II and Pol III snRNA transcription.\",\n      \"evidence\": \"Biochemical purification and in vitro transcription assays\",\n      \"pmids\": [\"7715707\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not resolve subunit stoichiometry or the specific contribution of SNAPC2 versus other subunits\", \"No structural placement within the complex\"]\n    },\n    {\n      \"year\": 1996,\n      \"claim\": \"To confirm SNAPC2 is a bona fide complex member and identify its contacts, it was shown to reside in the PSE-bound complex and to interact strongly with TBP, while a separate study mapped that it does not directly contact SNAP50.\",\n      \"evidence\": \"cDNA cloning, EMSA supershift, in vitro transcription depletion, and co-immunoprecipitation\",\n      \"pmids\": [\"8633057\", \"9003788\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"The functional consequence of the SNAPC2\\u2013TBP interaction was not isolated\", \"Subunit topology remained incomplete\"]\n    },\n    {\n      \"year\": 1998,\n      \"claim\": \"Pinpointing SNAPC2's anchor in the complex, SNAP190 was identified as a direct SNAPC2 partner required for transcription, and a fully recombinant five-subunit SNAPc reconstituted PSE binding and transcription, establishing SNAPC2 as a core subunit.\",\n      \"evidence\": \"Co-immunoprecipitation, recombinant complex reconstitution, PSE-binding and in vitro transcription assays\",\n      \"pmids\": [\"9418884\", \"9732265\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"The minimal SNAPC2 region needed for SNAP190 contact was not defined\", \"No structural model of subunit arrangement\"]\n    },\n    {\n      \"year\": 2000,\n      \"claim\": \"Systematic mapping of subunit-subunit contacts confirmed the SNAPC2\\u2013SNAP190 interaction and showed minimal interaction domains suffice for assembly and PSE binding, refining the complex architecture.\",\n      \"evidence\": \"Deletion mutagenesis, co-immunoprecipitation, PSE-binding assays\",\n      \"pmids\": [\"11056176\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not assign SNAPC2 a direct DNA-contacting role\", \"Atomic-level architecture still unresolved\"]\n    },\n    {\n      \"year\": 2002,\n      \"claim\": \"Defining how SNAPc cooperates with TBP at the U6 promoter, SNAPC2 was shown to be part of a mini-SNAPc that binds cooperatively with TBP, with a SNAP190 region mediating cooperativity.\",\n      \"evidence\": \"Recombinant reconstitution with subunit deletions, promoter binding and in vitro transcription assays\",\n      \"pmids\": [\"12391172\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"SNAPC2's specific contribution to TBP cooperativity not isolated\", \"Structural basis not determined\"]\n    },\n    {\n      \"year\": 2006,\n      \"claim\": \"Testing whether SNAPC2 is strictly required, a partial complex lacking SNAPC2 still bound PSE and supported U1/U6 transcription, indicating SNAPC2 is dispensable for minimal in vitro activity.\",\n      \"evidence\": \"Recombinant co-expression in E. coli, DNA binding and in vitro transcription assays\",\n      \"pmids\": [\"16603380\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"A deliberate design omission; does not establish SNAPC2's regulatory role in vivo\", \"Quantitative efficiency loss without SNAPC2 not assessed\"]\n    },\n    {\n      \"year\": 2008,\n      \"claim\": \"Revealing a function beyond transcription, SNAPC2 was found to localize to mitotic structures and to be required for normal mitotic progression, with a phenotype distinct from another SNAPc subunit, establishing a SNAPC2-specific mitotic role.\",\n      \"evidence\": \"Immunofluorescence, siRNA knockdown, overexpression, flow cytometry cell-cycle analysis\",\n      \"pmids\": [\"18356157\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"No molecular partners at centrosomes/midbody identified\", \"Mechanism linking SNAPC2 to mitotic structure assembly unknown\", \"Whether the mitotic role requires SNAPc assembly is unresolved\"]\n    },\n    {\n      \"year\": 2011,\n      \"claim\": \"Linking the SNAPC2\\u2013SNAP190 interaction to physiology, a zebrafish truncation deleting the Snapc4 domain that binds Snapc2 reduced snRNAs and caused biliary cell apoptosis, phenocopied by snapc2 knockdown.\",\n      \"evidence\": \"Zebrafish forward genetic mutant, morpholino knockdown, snRNA expression and apoptosis assays\",\n      \"pmids\": [\"22222761\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Tissue specificity of the biliary phenotype not mechanistically explained\", \"Ortholog study; human relevance inferred\", \"Whether apoptosis is a direct snRNA deficit or secondary effect unclear\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Placing SNAPC2 in a structural framework, cryo-EM of the SNAPc-containing Pol III PIC on U6 with XL-MS localized SNAPC2 near promoter DNA and explained selective SNAPc engagement by Pol III versus Pol II.\",\n      \"evidence\": \"Cryo-EM structure determination (3.2\\u20134.2 \\u00c5) and cross-linking mass spectrometry\",\n      \"pmids\": [\"39747245\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"SNAPC2 not resolved at atomic resolution; localization is by XL-MS\", \"Direct DNA-contacting residues of SNAPC2 not defined\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How SNAPC2's mitotic localization and function mechanistically relate to (or are independent of) its role in the SNAPc transcription complex remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No identified mitotic interaction partners for SNAPC2\", \"Unknown whether SNAPC2's centrosome/midbody role requires the rest of SNAPc\", \"No structural model of SNAPC2 within or apart from the complex\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0140110\", \"supporting_discovery_ids\": [0, 4]},\n      {\"term_id\": \"GO:0003677\", \"supporting_discovery_ids\": [4, 10]},\n      {\"term_id\": \"GO:0140223\", \"supporting_discovery_ids\": [0, 6]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [0]},\n      {\"term_id\": \"GO:0005815\", \"supporting_discovery_ids\": [8]},\n      {\"term_id\": \"GO:0005856\", \"supporting_discovery_ids\": [8]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-74160\", \"supporting_discovery_ids\": [0, 4]},\n      {\"term_id\": \"R-HSA-1640170\", \"supporting_discovery_ids\": [8]}\n    ],\n    \"complexes\": [\"SNAPc\"],\n    \"partners\": [\"SNAP190\", \"TBP\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":4,"faith_total":5,"faith_pct":80.0}}