{"gene":"INTS5","run_date":"2026-06-10T01:55:23","timeline":{"discoveries":[{"year":2021,"finding":"INTS5 forms a stable subcomplex with INTS8 (INTS5/8 subcomplex) within the Integrator complex, biochemically characterized as a distinct module separate from the INTS10/13/14 subcomplex and the INTS4/9/11 catalytic core.","method":"Biochemical fractionation and subcomplex reconstitution; cryo-EM structural determination of the catalytic core","journal":"Molecular cell","confidence":"High","confidence_rationale":"Tier 1 / Moderate — biochemical reconstitution of subcomplexes with cryo-EM structural validation, single lab but multiple orthogonal methods","pmids":["33548203"],"is_preprint":false},{"year":2024,"finding":"INTS5 forms a structural subcomplex with INTS8, INTS10, and INTS15 (INTS5/8/10/15), as determined by cryo-EM; this subcomplex is positioned within the fully assembled Integrator bound to the paused RNA Polymerase II elongation complex (PEC), defining the architectural role of INTS5 in Integrator assembly.","method":"Cryo-EM structure determination of INTS5/8/10/15 subcomplex and integrative modeling of the full Integrator-PEC","journal":"Molecular cell","confidence":"High","confidence_rationale":"Tier 1 / Moderate — cryo-EM structure with integrative modeling, single lab, multiple orthogonal structural and biochemical methods","pmids":["38823386"],"is_preprint":false},{"year":2009,"finding":"Antisense morpholino knockdown of zebrafish Ints5 disrupts U1 and U2 snRNA 3' end processing, leading to aberrant splicing of smad1 and smad5 mRNAs, reduced expression of hematopoietic genes scl and gata1, and arrested red blood cell differentiation, placing INTS5 function upstream of BMP/Smad signaling in hematopoiesis.","method":"Antisense morpholino knockdown in zebrafish embryos; RT-PCR analysis of snRNA processing and smad splicing; blood smear analysis","journal":"Development (Cambridge, England)","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — clean morpholino KD with defined cellular and molecular phenotypes (snRNA processing, splicing, hematopoiesis) and genetic epistasis placement, single lab","pmids":["19605500"],"is_preprint":false},{"year":2019,"finding":"Loss of Drosophila intS5 (ortholog of INTS5) in neuroblast lineages causes dedifferentiation of intermediate neural progenitors (INPs) into ectopic type II neuroblasts; cell-type-specific DamID identified 1413 IntS5-binding sites in INPs including the earmuff (erm) transcription factor locus, and erm expression is lost in intS5 mutants, placing Integrator/INTS5 upstream of Erm in suppressing INP dedifferentiation.","method":"Drosophila genetics (loss-of-function mutants and INP-specific RNAi knockdown); cell-type-specific DamID chromatin binding analysis; genetic interaction (intS8 × erm double mutants)","journal":"Cell reports","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — genetic loss-of-function with defined cellular phenotype, DamID binding data, and epistasis analysis; single lab, Drosophila ortholog","pmids":["31018143"],"is_preprint":false}],"current_model":"INTS5 is a structural subunit of the Integrator complex that forms a dedicated INTS5/INTS8 subcomplex (and a larger INTS5/8/10/15 module) positioned within the fully assembled Integrator bound to paused RNA Polymerase II; it is required for proper 3' end processing of snRNAs, and loss of INTS5 function disrupts snRNA processing, causes aberrant splicing of downstream signaling transcripts (e.g., smad1/5), and leads to failure of transcriptional regulation at specific genomic loci, resulting in hematopoietic defects in zebrafish and neural progenitor dedifferentiation in Drosophila."},"narrative":{"mechanistic_narrative":"INTS5 is a structural subunit of the Integrator complex that contributes to the 3' end processing of small nuclear RNAs and to Integrator-dependent transcriptional regulation at RNA Polymerase II [PMID:33548203, PMID:19605500]. Within Integrator it nucleates a dedicated module, forming a stable subcomplex with INTS8 that is biochemically distinct from the INTS10/13/14 subcomplex and the INTS4/9/11 catalytic core [PMID:33548203]; this module expands into an INTS5/8/10/15 assembly that cryo-EM and integrative modeling place within the fully assembled Integrator bound to the paused RNA Polymerase II elongation complex, defining INTS5's architectural role in Integrator organization [PMID:38823386]. Functionally, loss of INTS5 disrupts U1 and U2 snRNA 3' end processing, which in zebrafish causes aberrant splicing of smad1 and smad5, reduced expression of the hematopoietic genes scl and gata1, and arrested erythroid differentiation, placing INTS5 upstream of BMP/Smad signaling in hematopoiesis [PMID:19605500]. In Drosophila neuroblast lineages, intS5 binds thousands of genomic sites including the earmuff transcription factor locus and is required for earmuff expression, so that its loss leads to dedifferentiation of intermediate neural progenitors into ectopic neuroblasts [PMID:31018143].","teleology":[{"year":2009,"claim":"Established that INTS5 is functionally required for snRNA 3' end processing and links this activity to a developmental signaling and differentiation program, defining its biological role before its structural place in Integrator was known.","evidence":"Antisense morpholino knockdown in zebrafish with RT-PCR of snRNA processing and smad splicing and blood smear analysis","pmids":["19605500"],"confidence":"Medium","gaps":["Morpholino knockdown not confirmed with a genetic null or rescue","Direct biochemical role of INTS5 in the processing reaction not defined","Mechanism linking snRNA processing defects to smad mis-splicing not resolved"]},{"year":2019,"claim":"Extended INTS5 function to chromatin-associated transcriptional control by showing it binds specific loci and is required to maintain a transcription factor program that suppresses progenitor dedifferentiation.","evidence":"Drosophila loss-of-function and INP-specific RNAi, cell-type-specific DamID, and genetic interaction analysis","pmids":["31018143"],"confidence":"Medium","gaps":["Whether INTS5 acts at earmuff through snRNA processing or direct transcriptional regulation is unresolved","Single Drosophila ortholog system; human relevance not directly tested","Direct versus indirect nature of the 1413 binding sites not dissected"]},{"year":2021,"claim":"Defined INTS5 as a discrete structural module of Integrator, showing it pairs with INTS8 as a subcomplex separate from the catalytic core and other peripheral modules.","evidence":"Biochemical fractionation and subcomplex reconstitution with cryo-EM of the catalytic core","pmids":["33548203"],"confidence":"High","gaps":["Functional contribution of the INTS5/8 module to catalysis not assigned","How the module contacts the catalytic core within intact Integrator not yet shown"]},{"year":2024,"claim":"Resolved the architectural role of INTS5 by placing the INTS5/8/10/15 subcomplex within fully assembled Integrator bound to paused RNA Pol II.","evidence":"Cryo-EM of the INTS5/8/10/15 subcomplex and integrative modeling of the full Integrator-paused elongation complex","pmids":["38823386"],"confidence":"High","gaps":["Functional consequence of INTS5 positioning for cleavage or termination not directly tested","Dynamics of module engagement with the paused polymerase not captured"]},{"year":null,"claim":"How INTS5's structural position within Integrator mechanistically enables snRNA 3' end processing and locus-specific transcriptional control across species remains unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No direct enzymatic or biochemical activity assigned to INTS5 itself","Link between the structural module and the developmental phenotypes not mechanistically bridged"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0005198","term_label":"structural molecule activity","supporting_discovery_ids":[0,1]}],"localization":[{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[1,3]}],"pathway":[{"term_id":"R-HSA-8953854","term_label":"Metabolism of RNA","supporting_discovery_ids":[0,2]},{"term_id":"R-HSA-74160","term_label":"Gene expression (Transcription)","supporting_discovery_ids":[1,3]}],"complexes":["Integrator complex","INTS5/INTS8 subcomplex","INTS5/8/10/15 subcomplex"],"partners":["INTS8","INTS10","INTS15"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q6P9B9","full_name":"Integrator complex subunit 5","aliases":[],"length_aa":1019,"mass_kda":108.0,"function":"Component of the integrator complex, a multiprotein complex that terminates RNA polymerase II (Pol II) transcription in the promoter-proximal region of genes (PubMed:33243860, PubMed:38570683). The integrator complex provides a quality checkpoint during transcription elongation by driving premature transcription termination of transcripts that are unfavorably configured for transcriptional elongation: the complex terminates transcription by (1) catalyzing dephosphorylation of the C-terminal domain (CTD) of Pol II subunit POLR2A/RPB1 and SUPT5H/SPT5, (2) degrading the exiting nascent RNA transcript via endonuclease activity and (3) promoting the release of Pol II from bound DNA (PubMed:33243860, PubMed:38570683). The integrator complex is also involved in terminating the synthesis of non-coding Pol II transcripts, such as enhancer RNAs (eRNAs), small nuclear RNAs (snRNAs), telomerase RNAs and long non-coding RNAs (lncRNAs) (PubMed:16239144). Mediates recruitment of cytoplasmic dynein to the nuclear envelope, probably as component of the integrator complex (PubMed:23904267)","subcellular_location":"Nucleus; Cytoplasm; Nucleus membrane","url":"https://www.uniprot.org/uniprotkb/Q6P9B9/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":true,"resolved_as":"","url":"https://depmap.org/portal/gene/INTS5","classification":"Common Essential","n_dependent_lines":1191,"n_total_lines":1208,"dependency_fraction":0.9859271523178808},"opencell":{"profiled":true,"resolved_as":"","ensg_id":"ENSG00000185085","cell_line_id":"CID001871","localizations":[{"compartment":"nuclear_punctae","grade":3},{"compartment":"chromatin","grade":2}],"interactors":[{"gene":"INTS1","stoichiometry":0.2},{"gene":"POLR2K","stoichiometry":0.2},{"gene":"INTS9","stoichiometry":0.2},{"gene":"NELFE","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/target/CID001871","total_profiled":1310},"omim":[{"mim_id":"611349","title":"INTEGRATOR COMPLEX SUBUNIT 5; INTS5","url":"https://www.omim.org/entry/611349"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Supported","locations":[{"location":"Nucleoplasm","reliability":"Supported"},{"location":"Cytosol","reliability":"Additional"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/INTS5"},"hgnc":{"alias_symbol":["INT5"],"prev_symbol":["KIAA1698"]},"alphafold":{"accession":"Q6P9B9","domains":[{"cath_id":"-","chopping":"827-1010","consensus_level":"high","plddt":84.3755,"start":827,"end":1010},{"cath_id":"1.20.190","chopping":"29-92_119-234","consensus_level":"high","plddt":86.1566,"start":29,"end":234}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q6P9B9","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q6P9B9-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q6P9B9-F1-predicted_aligned_error_v6.png","plddt_mean":77.12},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=INTS5","jax_strain_url":"https://www.jax.org/strain/search?query=INTS5"},"sequence":{"accession":"Q6P9B9","fasta_url":"https://rest.uniprot.org/uniprotkb/Q6P9B9.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q6P9B9/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q6P9B9"}},"corpus_meta":[{"pmid":"8764102","id":"PMC_8764102","title":"Overexpression of int-5/aromatase in mammary glands of transgenic mice results in the induction of hyperplasia and nuclear abnormalities.","date":"1996","source":"Cancer research","url":"https://pubmed.ncbi.nlm.nih.gov/8764102","citation_count":91,"is_preprint":false},{"pmid":"7478601","id":"PMC_7478601","title":"The physical map of the human RET proto-oncogene.","date":"1995","source":"Oncogene","url":"https://pubmed.ncbi.nlm.nih.gov/7478601","citation_count":79,"is_preprint":false},{"pmid":"33548203","id":"PMC_33548203","title":"Structure of the catalytic core of the Integrator complex.","date":"2021","source":"Molecular cell","url":"https://pubmed.ncbi.nlm.nih.gov/33548203","citation_count":55,"is_preprint":false},{"pmid":"3475186","id":"PMC_3475186","title":"A fission yeast chromosome can replicate autonomously in mouse cells.","date":"1987","source":"Cell","url":"https://pubmed.ncbi.nlm.nih.gov/3475186","citation_count":53,"is_preprint":false},{"pmid":"12620253","id":"PMC_12620253","title":"IGS sequence variation, group-I introns and the complete nuclear ribosomal DNA of the entomopathogenic fungus Metarhizium: excellent tools for isolate detection and phylogenetic analysis.","date":"2003","source":"Fungal genetics and biology : FG & B","url":"https://pubmed.ncbi.nlm.nih.gov/12620253","citation_count":42,"is_preprint":false},{"pmid":"19605500","id":"PMC_19605500","title":"The Integrator subunits function in hematopoiesis by modulating Smad/BMP signaling.","date":"2009","source":"Development (Cambridge, England)","url":"https://pubmed.ncbi.nlm.nih.gov/19605500","citation_count":38,"is_preprint":false},{"pmid":"38823386","id":"PMC_38823386","title":"Structural basis of the Integrator complex assembly and association with transcription factors.","date":"2024","source":"Molecular cell","url":"https://pubmed.ncbi.nlm.nih.gov/38823386","citation_count":27,"is_preprint":false},{"pmid":"31018143","id":"PMC_31018143","title":"The Integrator Complex Prevents Dedifferentiation of Intermediate Neural Progenitors back into Neural Stem Cells.","date":"2019","source":"Cell reports","url":"https://pubmed.ncbi.nlm.nih.gov/31018143","citation_count":25,"is_preprint":false},{"pmid":"1705320","id":"PMC_1705320","title":"Characterization of Int-5, a locus associated with early events in mammary carcinogenesis.","date":"1991","source":"Oncogene research","url":"https://pubmed.ncbi.nlm.nih.gov/1705320","citation_count":24,"is_preprint":false},{"pmid":"20522624","id":"PMC_20522624","title":"Molecular characterization of Mycobacterium intracellulare-related strains based on the sequence analysis of hsp65, internal transcribed spacer and 16S rRNA genes.","date":"2010","source":"Journal of medical microbiology","url":"https://pubmed.ncbi.nlm.nih.gov/20522624","citation_count":21,"is_preprint":false},{"pmid":"7812938","id":"PMC_7812938","title":"The nature and expression of int-5, a novel MMTV integration locus gene in carcinogen-induced mammary tumors.","date":"1994","source":"Cancer letters","url":"https://pubmed.ncbi.nlm.nih.gov/7812938","citation_count":20,"is_preprint":false},{"pmid":"33405298","id":"PMC_33405298","title":"iTRAQ-based proteomic analysis of the molecular mechanisms and downstream effects of fatty acid synthase in osteosarcoma cells.","date":"2021","source":"Journal of clinical laboratory analysis","url":"https://pubmed.ncbi.nlm.nih.gov/33405298","citation_count":14,"is_preprint":false},{"pmid":"26865931","id":"PMC_26865931","title":"A Large Cohort Study of Genotype and Phenotype Correlations of Beta- Thalassemia in Iranian Population.","date":"2015","source":"International journal of hematology-oncology and stem cell research","url":"https://pubmed.ncbi.nlm.nih.gov/26865931","citation_count":13,"is_preprint":false},{"pmid":"7874687","id":"PMC_7874687","title":"The overexpression of int-5/Aromatase, a novel MMTV integration locus gene, is responsible for D2 mammary tumor cell proliferation.","date":"1995","source":"Cancer letters","url":"https://pubmed.ncbi.nlm.nih.gov/7874687","citation_count":12,"is_preprint":false},{"pmid":"34094537","id":"PMC_34094537","title":"PA-Int5: An isatin-thiosemicarbazone derivative that exhibits anti-nociceptive and anti-inflammatory effects in Swiss mice.","date":"2021","source":"Biomedical reports","url":"https://pubmed.ncbi.nlm.nih.gov/34094537","citation_count":11,"is_preprint":false},{"pmid":"29949961","id":"PMC_29949961","title":"DisruPPI: structure-based computational redesign algorithm for protein binding disruption.","date":"2018","source":"Bioinformatics (Oxford, England)","url":"https://pubmed.ncbi.nlm.nih.gov/29949961","citation_count":10,"is_preprint":false},{"pmid":"12027830","id":"PMC_12027830","title":"Western blotting analysis of the beta-hexosaminidase alpha- and beta-subunits in cultured fibroblasts from cases of various forms of GM2 gangliosidosis.","date":"2002","source":"Acta neurologica Scandinavica","url":"https://pubmed.ncbi.nlm.nih.gov/12027830","citation_count":10,"is_preprint":false},{"pmid":"23122059","id":"PMC_23122059","title":"Detection of genetic association and functional polymorphisms of UGDH affecting milk production trait in Chinese Holstein cattle.","date":"2012","source":"BMC genomics","url":"https://pubmed.ncbi.nlm.nih.gov/23122059","citation_count":8,"is_preprint":false},{"pmid":"23065270","id":"PMC_23065270","title":"Novel single nucleotide polymorphisms of bovine SREBP1 gene is association with fatty acid composition and marbling score in commercial Korean cattle (Hanwoo).","date":"2012","source":"Molecular biology reports","url":"https://pubmed.ncbi.nlm.nih.gov/23065270","citation_count":6,"is_preprint":false},{"pmid":"27031100","id":"PMC_27031100","title":"Molecular Taxonomic Evidence for Two Distinct Genotypes of Mycobacterium yongonense via Genome-Based Phylogenetic Analysis.","date":"2016","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/27031100","citation_count":6,"is_preprint":false},{"pmid":"7632740","id":"PMC_7632740","title":"Structure of the int-5, a novel MMTV integration genomic locus containing mouse early transposon LTR homology region.","date":"1995","source":"Biochimica et biophysica acta","url":"https://pubmed.ncbi.nlm.nih.gov/7632740","citation_count":5,"is_preprint":false},{"pmid":"19493003","id":"PMC_19493003","title":"Bacteriophage content of M49 strains of Streptococcus pyogenes.","date":"2009","source":"FEMS microbiology letters","url":"https://pubmed.ncbi.nlm.nih.gov/19493003","citation_count":5,"is_preprint":false},{"pmid":"16158289","id":"PMC_16158289","title":"Coordinates, DNA content and heterogeneity of cell nuclei and segments of the Caenorhabditis elegans intestine.","date":"2005","source":"Histochemistry and cell biology","url":"https://pubmed.ncbi.nlm.nih.gov/16158289","citation_count":4,"is_preprint":false},{"pmid":"25536767","id":"PMC_25536767","title":"[Frequency of diseases caused by group A streptococci among invasive infections of soft tissues and characteristics of the causative agent].","date":"2014","source":"Zhurnal mikrobiologii, epidemiologii i immunobiologii","url":"https://pubmed.ncbi.nlm.nih.gov/25536767","citation_count":1,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":13289,"output_tokens":1621,"usd":0.032091,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":7755,"output_tokens":2037,"usd":0.04485,"stage2_stop_reason":"end_turn"},"total_usd":0.076941,"stage1_batch_id":"msgbatch_01DUPACZi7AAWwuZiUjseQF4","stage2_batch_id":"msgbatch_018yt7chE3f48PEFtDwtj6AE","note":"batch pricing = 50% of standard"},"stage1_raw":"Looking at the 24 papers, I need to identify which ones are about the human/mammalian INTS5 gene (Integrator Complex Subunit 5, also known as INT5/KIAA1698 in the context of the Integrator complex).\n\n**Classification:**\n- Papers [1], [9], [11], [14], [21]: About \"int-5\" as an MMTV integration locus (= aromatase/CYP19 gene) — NOT INTS5\n- Papers [2]: About RET intron 5 — NOT INTS5\n- Papers [3], [7]: About Integrator complex structure — INCLUDE (INTS5 directly studied)\n- Papers [4]: S. pombe Int5 chromosome — NOT INTS5\n- Papers [5]: Fungal intron — NOT INTS5\n- Papers [6]: Integrator subunit 5 in zebrafish hematopoiesis — INCLUDE (ortholog)\n- Papers [8]: Drosophila Integrator complex, intS5 — INCLUDE (ortholog)\n- Papers [10], [20]: Mycobacterium genotypes — NOT INTS5\n- Papers [12]: INTS5 mentioned as upregulated protein in proteomics screen — pan-catalog, no mechanism\n- Papers [13], [17], [18], [19]: Various \"int5\" in unrelated contexts — NOT INTS5\n- Papers [15]: Chemical compound PA-Int5 — NOT INTS5\n- Papers [16]: INT5 as a computational scoring method — NOT INTS5\n- Papers [22], [23], [24]: Streptococcal phage integrase / C. elegans intestinal segments — NOT INTS5\n\n```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2021,\n      \"finding\": \"INTS5 forms a stable subcomplex with INTS8 (INTS5/8 subcomplex) within the Integrator complex, biochemically characterized as a distinct module separate from the INTS10/13/14 subcomplex and the INTS4/9/11 catalytic core.\",\n      \"method\": \"Biochemical fractionation and subcomplex reconstitution; cryo-EM structural determination of the catalytic core\",\n      \"journal\": \"Molecular cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — biochemical reconstitution of subcomplexes with cryo-EM structural validation, single lab but multiple orthogonal methods\",\n      \"pmids\": [\"33548203\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"INTS5 forms a structural subcomplex with INTS8, INTS10, and INTS15 (INTS5/8/10/15), as determined by cryo-EM; this subcomplex is positioned within the fully assembled Integrator bound to the paused RNA Polymerase II elongation complex (PEC), defining the architectural role of INTS5 in Integrator assembly.\",\n      \"method\": \"Cryo-EM structure determination of INTS5/8/10/15 subcomplex and integrative modeling of the full Integrator-PEC\",\n      \"journal\": \"Molecular cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — cryo-EM structure with integrative modeling, single lab, multiple orthogonal structural and biochemical methods\",\n      \"pmids\": [\"38823386\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2009,\n      \"finding\": \"Antisense morpholino knockdown of zebrafish Ints5 disrupts U1 and U2 snRNA 3' end processing, leading to aberrant splicing of smad1 and smad5 mRNAs, reduced expression of hematopoietic genes scl and gata1, and arrested red blood cell differentiation, placing INTS5 function upstream of BMP/Smad signaling in hematopoiesis.\",\n      \"method\": \"Antisense morpholino knockdown in zebrafish embryos; RT-PCR analysis of snRNA processing and smad splicing; blood smear analysis\",\n      \"journal\": \"Development (Cambridge, England)\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — clean morpholino KD with defined cellular and molecular phenotypes (snRNA processing, splicing, hematopoiesis) and genetic epistasis placement, single lab\",\n      \"pmids\": [\"19605500\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"Loss of Drosophila intS5 (ortholog of INTS5) in neuroblast lineages causes dedifferentiation of intermediate neural progenitors (INPs) into ectopic type II neuroblasts; cell-type-specific DamID identified 1413 IntS5-binding sites in INPs including the earmuff (erm) transcription factor locus, and erm expression is lost in intS5 mutants, placing Integrator/INTS5 upstream of Erm in suppressing INP dedifferentiation.\",\n      \"method\": \"Drosophila genetics (loss-of-function mutants and INP-specific RNAi knockdown); cell-type-specific DamID chromatin binding analysis; genetic interaction (intS8 × erm double mutants)\",\n      \"journal\": \"Cell reports\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — genetic loss-of-function with defined cellular phenotype, DamID binding data, and epistasis analysis; single lab, Drosophila ortholog\",\n      \"pmids\": [\"31018143\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"INTS5 is a structural subunit of the Integrator complex that forms a dedicated INTS5/INTS8 subcomplex (and a larger INTS5/8/10/15 module) positioned within the fully assembled Integrator bound to paused RNA Polymerase II; it is required for proper 3' end processing of snRNAs, and loss of INTS5 function disrupts snRNA processing, causes aberrant splicing of downstream signaling transcripts (e.g., smad1/5), and leads to failure of transcriptional regulation at specific genomic loci, resulting in hematopoietic defects in zebrafish and neural progenitor dedifferentiation in Drosophila.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"INTS5 is a structural subunit of the Integrator complex that contributes to the 3' end processing of small nuclear RNAs and to Integrator-dependent transcriptional regulation at RNA Polymerase II [#0, #2]. Within Integrator it nucleates a dedicated module, forming a stable subcomplex with INTS8 that is biochemically distinct from the INTS10/13/14 subcomplex and the INTS4/9/11 catalytic core [#0]; this module expands into an INTS5/8/10/15 assembly that cryo-EM and integrative modeling place within the fully assembled Integrator bound to the paused RNA Polymerase II elongation complex, defining INTS5's architectural role in Integrator organization [#1]. Functionally, loss of INTS5 disrupts U1 and U2 snRNA 3' end processing, which in zebrafish causes aberrant splicing of smad1 and smad5, reduced expression of the hematopoietic genes scl and gata1, and arrested erythroid differentiation, placing INTS5 upstream of BMP/Smad signaling in hematopoiesis [#2]. In Drosophila neuroblast lineages, intS5 binds thousands of genomic sites including the earmuff transcription factor locus and is required for earmuff expression, so that its loss leads to dedifferentiation of intermediate neural progenitors into ectopic neuroblasts [#3].\",\n  \"teleology\": [\n    {\n      \"year\": 2009,\n      \"claim\": \"Established that INTS5 is functionally required for snRNA 3' end processing and links this activity to a developmental signaling and differentiation program, defining its biological role before its structural place in Integrator was known.\",\n      \"evidence\": \"Antisense morpholino knockdown in zebrafish with RT-PCR of snRNA processing and smad splicing and blood smear analysis\",\n      \"pmids\": [\"19605500\"],\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"\",\n      \"gaps\": [\n        \"Morpholino knockdown not confirmed with a genetic null or rescue\",\n        \"Direct biochemical role of INTS5 in the processing reaction not defined\",\n        \"Mechanism linking snRNA processing defects to smad mis-splicing not resolved\"\n      ]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Extended INTS5 function to chromatin-associated transcriptional control by showing it binds specific loci and is required to maintain a transcription factor program that suppresses progenitor dedifferentiation.\",\n      \"evidence\": \"Drosophila loss-of-function and INP-specific RNAi, cell-type-specific DamID, and genetic interaction analysis\",\n      \"pmids\": [\"31018143\"],\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"\",\n      \"gaps\": [\n        \"Whether INTS5 acts at earmuff through snRNA processing or direct transcriptional regulation is unresolved\",\n        \"Single Drosophila ortholog system; human relevance not directly tested\",\n        \"Direct versus indirect nature of the 1413 binding sites not dissected\"\n      ]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Defined INTS5 as a discrete structural module of Integrator, showing it pairs with INTS8 as a subcomplex separate from the catalytic core and other peripheral modules.\",\n      \"evidence\": \"Biochemical fractionation and subcomplex reconstitution with cryo-EM of the catalytic core\",\n      \"pmids\": [\"33548203\"],\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"\",\n      \"gaps\": [\n        \"Functional contribution of the INTS5/8 module to catalysis not assigned\",\n        \"How the module contacts the catalytic core within intact Integrator not yet shown\"\n      ]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Resolved the architectural role of INTS5 by placing the INTS5/8/10/15 subcomplex within fully assembled Integrator bound to paused RNA Pol II.\",\n      \"evidence\": \"Cryo-EM of the INTS5/8/10/15 subcomplex and integrative modeling of the full Integrator-paused elongation complex\",\n      \"pmids\": [\"38823386\"],\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"\",\n      \"gaps\": [\n        \"Functional consequence of INTS5 positioning for cleavage or termination not directly tested\",\n        \"Dynamics of module engagement with the paused polymerase not captured\"\n      ]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How INTS5's structural position within Integrator mechanistically enables snRNA 3' end processing and locus-specific transcriptional control across species remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"\",\n      \"gaps\": [\n        \"No direct enzymatic or biochemical activity assigned to INTS5 itself\",\n        \"Link between the structural module and the developmental phenotypes not mechanistically bridged\"\n      ]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0005198\", \"supporting_discovery_ids\": [0, 1]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [1, 3]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-8953854\", \"supporting_discovery_ids\": [0, 2]},\n      {\"term_id\": \"R-HSA-74160\", \"supporting_discovery_ids\": [1, 3]}\n    ],\n    \"complexes\": [\n      \"Integrator complex\",\n      \"INTS5/INTS8 subcomplex\",\n      \"INTS5/8/10/15 subcomplex\"\n    ],\n    \"partners\": [\n      \"INTS8\",\n      \"INTS10\",\n      \"INTS15\"\n    ],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":4,"faith_total":4,"faith_pct":100.0}}