{"gene":"INTS13","run_date":"2026-04-28T18:06:54","timeline":{"discoveries":[{"year":2018,"finding":"INTS13 functions as an independent sub-module of the Integrator complex that targets enhancers through Early Growth Response transcription factors (EGR1/2) and their co-factor NAB2, binding poised monocytic enhancers to elicit chromatin looping and activation, thereby driving monocytic/macrophagic differentiation.","method":"ChIP-seq, chromatin conformation capture, siRNA depletion of INTS13/EGR1/NAB2 with differentiation phenotype readout in cell lines and primary human progenitors","journal":"Molecular cell","confidence":"High","confidence_rationale":"Tier 2 — multiple orthogonal genomic and functional methods, replicated across cell lines and primary cells","pmids":["30008316"],"is_preprint":false},{"year":2020,"finding":"INTS10, INTS13, and INTS14 form a separable, functional Integrator module; the crystal structure of INTS13-INTS14 reveals a strongly entwined complex with a unique chain interlink and structural homology to Ku70-Ku80, conferring nucleic acid (DNA/RNA) binding affinity with preference for RNA hairpins; the C-terminal motif of INTS13 directly binds the Integrator cleavage module to facilitate snRNA processing and transcription termination after pausing.","method":"X-ray crystallography, in vitro RNA/DNA binding assays, crosslinking mass spectrometry, co-purification, mutagenesis of C-terminal motif, snRNA processing and termination assays","journal":"Nature communications","confidence":"High","confidence_rationale":"Tier 1 — crystal structure combined with in vitro binding assays and mutagenesis in a single study","pmids":["32647223"],"is_preprint":false},{"year":2022,"finding":"INTS13 utilizes its C-terminus to bind the Integrator cleavage module; germline variants p.S652L and p.K668Nfs*9 disrupt this interaction, impair Integrator complex assembly, and cause ciliopathy; depletion of INTS13 in human cells disrupts ciliogenesis and dysregulates ciliary gene expression, and knockdown in Xenopus embryos causes motile cilia anomalies.","method":"Exome sequencing, co-immunoprecipitation, INTS13 knockdown in human cultured cells (ciliogenesis assay), Xenopus morpholino knockdown with cilia phenotype readout","journal":"Nature communications","confidence":"High","confidence_rationale":"Tier 2 — reciprocal co-IP, loss-of-function in two model systems with defined cellular phenotypes and genetic variant validation","pmids":["36229431"],"is_preprint":false},{"year":2023,"finding":"INTS15 assembles primarily with the INTS13/14/10 module and interfaces with the Int-PP2A module within the Integrator complex, forming an expanded nucleic-acid-binding sub-module; INTS15 modulates RNA Pol II pausing at a subset of genes.","method":"Proteomics, AlphaFold2 structure prediction, functional genomics (ChIP-seq/PRO-seq), co-purification","journal":"Cell reports","confidence":"Medium","confidence_rationale":"Tier 2/3 — structural predictions supported by proteomics and functional genomics but lacking reconstitution or mutagenesis of the INTS13 interaction specifically","pmids":["36920904"],"is_preprint":false},{"year":2024,"finding":"Cryo-EM structures of the complete Integrator-PP2A complex reveal that INTS10-INTS13-INTS14-INTS15 form a scorpion-tail-shaped module; in the pre-termination complex, this module's 'sting' contacts the DSIF DNA clamp, suggesting it facilitates opening of the DSIF clamp to promote Pol II termination.","method":"Cryo-electron microscopy (three functional states of Integrator-PP2A), structural modeling","journal":"Nature","confidence":"High","confidence_rationale":"Tier 1 — high-resolution cryo-EM structures of multiple functional states in a single rigorous study","pmids":["38570683"],"is_preprint":false},{"year":2024,"finding":"Cryo-EM structures of INTS10/13/14/15 and INTS5/8/10/15 sub-complexes, together with an integrative model of fully assembled Integrator on paused RNAPII, reveal that INTS13 acts as a platform for recruitment of transcription factors; an in silico screen identified ZNF655 as a direct binding partner of INTS13 within the fully assembled complex.","method":"Cryo-EM structure determination, AlphaFold2-based in silico protein-protein interaction screen of >1,500 transcription factors, co-purification validation","journal":"Molecular cell","confidence":"High","confidence_rationale":"Tier 1/2 — cryo-EM structures combined with computational screen and experimental validation of TF interaction","pmids":["38823386"],"is_preprint":false},{"year":2005,"finding":"Mat89Bb (the Drosophila ortholog of INTS13/Asunder) is a substrate of PAN GU kinase; RNAi depletion of Mat89Bb produces a polyploid phenotype similar to pan gu mutants, and morpholino knockdown in Xenopus causes polyploid nuclei arrest, establishing a conserved role in cell cycle regulation (S-M cycles).","method":"Drosophila in vitro expression cloning (DIVEC) kinase substrate screen, RNAi in Drosophila and HeLa cells, Xenopus morpholino injection with polyploidy phenotype readout","journal":"Developmental cell","confidence":"Medium","confidence_rationale":"Tier 2 — biochemical substrate identification plus loss-of-function in multiple model systems, but mechanistic link to INTS13 function in Integrator not established","pmids":["15737938"],"is_preprint":false}],"current_model":"INTS13 (also known as Asunder/Mat89Bb) is a core subunit of the Integrator complex that, together with INTS10, INTS14, and INTS15, forms a nucleic acid-binding module with structural homology to Ku70-Ku80; its C-terminal motif directly contacts the Integrator cleavage module to coordinate snRNA processing and promoter-proximal RNA Pol II termination, while its exposed surface acts as a recruitment platform for lineage-specific transcription factors (EGR1/2 via NAB2, ZNF655) to target Integrator to specific enhancers or gene loci, and loss-of-function disrupts ciliogenesis, myeloid differentiation, and cell cycle fidelity."},"narrative":{"teleology":[{"year":2005,"claim":"Before a link to the Integrator complex was known, identification of Mat89Bb (Drosophila ortholog of INTS13) as a PAN GU kinase substrate revealed a conserved requirement in S-M cell cycle transitions, establishing that loss of this gene causes polyploidy across species.","evidence":"DIVEC kinase substrate screen in Drosophila, RNAi in Drosophila/HeLa, morpholino in Xenopus with polyploidy readout","pmids":["15737938"],"confidence":"Medium","gaps":["Mechanism connecting INTS13/Mat89Bb to cell cycle control is undefined","Whether PAN GU phosphorylation is conserved in vertebrates is untested","Relationship to Integrator complex function not established"]},{"year":2018,"claim":"The discovery that INTS13 operates as a separable sub-module targeting EGR1/2-bound monocytic enhancers via NAB2 established that INTS13 has a gene-specific transcription factor recruitment function beyond bulk snRNA processing, directly linking Integrator to enhancer activation and myeloid differentiation.","evidence":"ChIP-seq, chromatin conformation capture, siRNA depletion in cell lines and primary human progenitors with differentiation readout","pmids":["30008316"],"confidence":"High","gaps":["Direct binding interface between INTS13 and NAB2/EGR not structurally resolved","Whether enhancer-targeting function requires the full Integrator or only the INTS13-containing sub-module is unclear"]},{"year":2020,"claim":"Crystallography of the INTS13-INTS14 dimer revealed a Ku70-Ku80-like architecture with nucleic acid binding capacity, and mutagenesis showed that the INTS13 C-terminal motif directly contacts the cleavage module, answering how the INTS10/13/14 sub-module connects to snRNA processing and Pol II termination.","evidence":"X-ray crystallography, in vitro DNA/RNA binding assays, crosslinking mass spectrometry, C-terminal motif mutagenesis with snRNA processing and termination assays","pmids":["32647223"],"confidence":"High","gaps":["Structure of the full INTS10/13/14 trimer not resolved at this stage","How the module discriminates RNA hairpin substrates in vivo is unknown"]},{"year":2022,"claim":"Genetic and biochemical evidence that germline INTS13 variants (p.S652L, p.K668Nfs*9) disrupt cleavage-module binding and cause ciliopathy established INTS13 as a disease gene and revealed ciliogenesis as a key downstream cellular process controlled by Integrator integrity.","evidence":"Exome sequencing of affected families, co-immunoprecipitation of variants, INTS13 depletion in human cells (ciliogenesis assay), Xenopus morpholino with cilia phenotype","pmids":["36229431"],"confidence":"High","gaps":["Which ciliary gene targets are directly versus indirectly regulated by INTS13 is unresolved","Whether ciliopathy phenotypes reflect snRNA processing, Pol II termination, or enhancer defects is unclear"]},{"year":2023,"claim":"Discovery that INTS15 assembles primarily with the INTS13/14/10 module and bridges to the Int-PP2A module expanded the sub-module to a four-subunit nucleic acid-binding unit and connected it to Pol II pause regulation.","evidence":"Proteomics, AlphaFold2 prediction, ChIP-seq/PRO-seq functional genomics, co-purification","pmids":["36920904"],"confidence":"Medium","gaps":["Direct INTS13-INTS15 interface not validated by mutagenesis or reconstitution","Contribution of INTS15 to the nucleic acid binding properties of the module untested"]},{"year":2024,"claim":"Cryo-EM structures of the complete Integrator-PP2A complex in multiple functional states showed that the INTS10/13/14/15 module forms a scorpion-tail 'sting' that contacts the DSIF clamp, explaining how this module mechanically promotes Pol II termination, while an independent cryo-EM and computational study demonstrated that the INTS13 surface recruits ZNF655, generalizing the transcription-factor recruitment function beyond EGR/NAB2.","evidence":"Cryo-EM of Integrator-PP2A in three states; cryo-EM of sub-complexes plus AlphaFold2 screen of >1,500 TFs with co-purification validation","pmids":["38570683","38823386"],"confidence":"High","gaps":["Functional consequence of ZNF655-INTS13 interaction on gene regulation not characterized","Whether DSIF clamp opening requires catalytic activity or is purely mechanical is unresolved","Full catalog of transcription factors recruited via the INTS13 surface is incomplete"]},{"year":null,"claim":"It remains unknown how INTS13's transcription-factor recruitment, snRNA processing, and Pol II termination functions are coordinated in vivo, and whether the cell cycle role of the Drosophila ortholog reflects a distinct Integrator-independent function.","evidence":"","pmids":[],"confidence":"Low","gaps":["No separation-of-function alleles distinguishing enhancer recruitment from cleavage-module bridging","Mechanistic basis for cell cycle phenotype (polyploidy) remains unconnected to known Integrator functions","In vivo structural dynamics of the INTS13 module during transcription termination are unresolved"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0003723","term_label":"RNA binding","supporting_discovery_ids":[1]},{"term_id":"GO:0003677","term_label":"DNA binding","supporting_discovery_ids":[1]},{"term_id":"GO:0060090","term_label":"molecular adaptor activity","supporting_discovery_ids":[0,5]},{"term_id":"GO:0005198","term_label":"structural molecule activity","supporting_discovery_ids":[1,4]}],"localization":[{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[0,1,2]},{"term_id":"GO:0005694","term_label":"chromosome","supporting_discovery_ids":[0]}],"pathway":[{"term_id":"R-HSA-8953854","term_label":"Metabolism of RNA","supporting_discovery_ids":[1,4]},{"term_id":"R-HSA-74160","term_label":"Gene expression (Transcription)","supporting_discovery_ids":[0,4,5]},{"term_id":"R-HSA-1266738","term_label":"Developmental Biology","supporting_discovery_ids":[2]},{"term_id":"R-HSA-1640170","term_label":"Cell Cycle","supporting_discovery_ids":[6]}],"complexes":["Integrator complex","INTS10/INTS13/INTS14/INTS15 module"],"partners":["INTS14","INTS10","INTS15","INTS5","INTS8","NAB2","ZNF655"],"other_free_text":[]},"mechanistic_narrative":"INTS13 is a subunit of the Integrator complex that, together with INTS10, INTS14, and INTS15, forms a scorpion-tail-shaped nucleic acid-binding module with structural homology to Ku70-Ku80; this module contacts the DSIF DNA clamp in the pre-termination complex to facilitate RNA Pol II termination [PMID:32647223, PMID:38570683]. The C-terminal motif of INTS13 directly bridges the nucleic acid-binding module to the Integrator cleavage module, coordinating snRNA 3′-end processing, and germline variants disrupting this interaction cause ciliopathy by impairing Integrator assembly and ciliogenesis [PMID:32647223, PMID:36229431]. The exposed surface of INTS13 serves as a recruitment platform for lineage-specific transcription factors—including EGR1/2 (via NAB2) at monocytic enhancers to drive chromatin looping and myeloid differentiation, and ZNF655 within the fully assembled paused-Pol II complex—establishing INTS13 as a key determinant of Integrator targeting to specific genomic loci [PMID:30008316, PMID:38823386]. The Drosophila ortholog Mat89Bb/Asunder is a PAN GU kinase substrate whose depletion causes polyploidy, indicating an additional conserved role in cell cycle fidelity [PMID:15737938]."},"prefetch_data":{"uniprot":{"accession":"Q9NVM9","full_name":"Integrator complex subunit 13","aliases":["Cell cycle regulator Mat89Bb homolog","Germ cell tumor 1","Protein asunder homolog","Sarcoma antigen NY-SAR-95"],"length_aa":706,"mass_kda":80.2,"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:38570683, PubMed:38823386). 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: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:32647223). Within the integrator complex, INTS13 is part of the integrator tail module and acts as a platform for the recruitment of transcription factors at promoters (PubMed:38823386, PubMed:38906142). At prophase, mediates recruitment of cytoplasmic dynein to the nuclear envelope, a step important for proper centrosome-nucleus coupling (PubMed:23097494, PubMed:23904267). At G2/M phase, may be required for proper spindle formation and execution of cytokinesis (PubMed:23097494, PubMed:23904267)","subcellular_location":"Nucleus; Cytoplasm","url":"https://www.uniprot.org/uniprotkb/Q9NVM9/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/INTS13","classification":"Not Classified","n_dependent_lines":440,"n_total_lines":1208,"dependency_fraction":0.36423841059602646},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[{"gene":"PPP2CA","stoichiometry":4.0},{"gene":"SSRP1","stoichiometry":4.0},{"gene":"SUPT5H","stoichiometry":4.0},{"gene":"POLR2K","stoichiometry":0.2},{"gene":"SEM1","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/search/INTS13","total_profiled":1310},"omim":[{"mim_id":"621239","title":"INTEGRATOR COMPLEX SUBUNIT 15; INTS15","url":"https://www.omim.org/entry/621239"},{"mim_id":"620878","title":"INTEGRATOR COMPLEX SUBUNIT 14; INTS14","url":"https://www.omim.org/entry/620878"},{"mim_id":"615079","title":"INTEGRATOR COMPLEX SUBUNIT 13; INTS13","url":"https://www.omim.org/entry/615079"},{"mim_id":"611353","title":"INTEGRATOR COMPLEX SUBUNIT 10; INTS10","url":"https://www.omim.org/entry/611353"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Supported","locations":[{"location":"Nucleoplasm","reliability":"Supported"},{"location":"Nuclear bodies","reliability":"Additional"},{"location":"Vesicles","reliability":"Additional"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/INTS13"},"hgnc":{"alias_symbol":["FLJ10637","NET48","Mat89Bb","SPATA30"],"prev_symbol":["C12orf11","ASUN"]},"alphafold":{"accession":"Q9NVM9","domains":[{"cath_id":"3.40.50.410","chopping":"8-30_44-255","consensus_level":"high","plddt":94.5836,"start":8,"end":255},{"cath_id":"-","chopping":"258-300_311-388","consensus_level":"high","plddt":84.3079,"start":258,"end":388},{"cath_id":"-","chopping":"415-516_524-561","consensus_level":"medium","plddt":90.204,"start":415,"end":561}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9NVM9","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q9NVM9-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q9NVM9-F1-predicted_aligned_error_v6.png","plddt_mean":78.56},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=INTS13","jax_strain_url":"https://www.jax.org/strain/search?query=INTS13"},"sequence":{"accession":"Q9NVM9","fasta_url":"https://rest.uniprot.org/uniprotkb/Q9NVM9.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q9NVM9/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9NVM9"}},"corpus_meta":[{"pmid":"30008316","id":"PMC_30008316","title":"Targeted Enhancer Activation by a Subunit of the Integrator Complex.","date":"2018","source":"Molecular cell","url":"https://pubmed.ncbi.nlm.nih.gov/30008316","citation_count":58,"is_preprint":false},{"pmid":"32647223","id":"PMC_32647223","title":"INTS10-INTS13-INTS14 form a functional module of Integrator that binds nucleic acids and the cleavage module.","date":"2020","source":"Nature communications","url":"https://pubmed.ncbi.nlm.nih.gov/32647223","citation_count":52,"is_preprint":false},{"pmid":"38570683","id":"PMC_38570683","title":"Structural basis of Integrator-dependent RNA polymerase II termination.","date":"2024","source":"Nature","url":"https://pubmed.ncbi.nlm.nih.gov/38570683","citation_count":49,"is_preprint":false},{"pmid":"28468258","id":"PMC_28468258","title":"Pan-Cancer Mutational and Transcriptional Analysis of the Integrator Complex.","date":"2017","source":"International journal of molecular sciences","url":"https://pubmed.ncbi.nlm.nih.gov/28468258","citation_count":48,"is_preprint":false},{"pmid":"36920904","id":"PMC_36920904","title":"A combinatorial approach to uncover an additional Integrator subunit.","date":"2023","source":"Cell reports","url":"https://pubmed.ncbi.nlm.nih.gov/36920904","citation_count":29,"is_preprint":false},{"pmid":"36229431","id":"PMC_36229431","title":"INTS13 variants causing a recessive developmental ciliopathy disrupt assembly of the Integrator complex.","date":"2022","source":"Nature communications","url":"https://pubmed.ncbi.nlm.nih.gov/36229431","citation_count":27,"is_preprint":false},{"pmid":"38130634","id":"PMC_38130634","title":"A pan-cancer analysis of the oncogenic role of Golgi transport 1B in human tumors.","date":"2023","source":"Journal of translational internal medicine","url":"https://pubmed.ncbi.nlm.nih.gov/38130634","citation_count":26,"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":25,"is_preprint":false},{"pmid":"15737938","id":"PMC_15737938","title":"Drosophila genome-scale screen for PAN GU kinase substrates identifies Mat89Bb as a cell cycle regulator.","date":"2005","source":"Developmental cell","url":"https://pubmed.ncbi.nlm.nih.gov/15737938","citation_count":19,"is_preprint":false},{"pmid":"9799434","id":"PMC_9799434","title":"A testis-specifically expressed gene is embedded within a cluster of maternally expressed genes at 89B in Drosophila melanogaster.","date":"1998","source":"Development genes and evolution","url":"https://pubmed.ncbi.nlm.nih.gov/9799434","citation_count":7,"is_preprint":false},{"pmid":"37563198","id":"PMC_37563198","title":"A cryptic microdeletion del(12)(p11.21p11.23) within an unbalanced translocation t(7;12)(q21.13;q23.1) implicates new candidate loci for intellectual disability and Kallmann syndrome.","date":"2023","source":"Scientific reports","url":"https://pubmed.ncbi.nlm.nih.gov/37563198","citation_count":3,"is_preprint":false},{"pmid":"41429980","id":"PMC_41429980","title":"Unveiling the ZNF384-INTS13-hnRNPC axis as a therapeutic vulnerability in cervical cancer.","date":"2025","source":"Cell death & disease","url":"https://pubmed.ncbi.nlm.nih.gov/41429980","citation_count":0,"is_preprint":false},{"pmid":"37034680","id":"PMC_37034680","title":"A microdeletion del(12)(p11.21p11.23) with a cryptic unbalanced translocation t(7;12)(q21.13;q23.1) implicates new candidate loci for intellectual disability and Kallmann syndrome.","date":"2023","source":"Research square","url":"https://pubmed.ncbi.nlm.nih.gov/37034680","citation_count":0,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":7597,"output_tokens":1907,"usd":0.025698},"stage2":{"model":"claude-opus-4-6","input_tokens":5160,"output_tokens":2410,"usd":0.129075},"total_usd":0.154773,"stage1_batch_id":"msgbatch_01DzrsgVgYngY1hvM3DU1yF2","stage2_batch_id":"msgbatch_01KA9b7iRzKFdhoBUT7vCvSe","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2018,\n      \"finding\": \"INTS13 functions as an independent sub-module of the Integrator complex that targets enhancers through Early Growth Response transcription factors (EGR1/2) and their co-factor NAB2, binding poised monocytic enhancers to elicit chromatin looping and activation, thereby driving monocytic/macrophagic differentiation.\",\n      \"method\": \"ChIP-seq, chromatin conformation capture, siRNA depletion of INTS13/EGR1/NAB2 with differentiation phenotype readout in cell lines and primary human progenitors\",\n      \"journal\": \"Molecular cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — multiple orthogonal genomic and functional methods, replicated across cell lines and primary cells\",\n      \"pmids\": [\"30008316\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"INTS10, INTS13, and INTS14 form a separable, functional Integrator module; the crystal structure of INTS13-INTS14 reveals a strongly entwined complex with a unique chain interlink and structural homology to Ku70-Ku80, conferring nucleic acid (DNA/RNA) binding affinity with preference for RNA hairpins; the C-terminal motif of INTS13 directly binds the Integrator cleavage module to facilitate snRNA processing and transcription termination after pausing.\",\n      \"method\": \"X-ray crystallography, in vitro RNA/DNA binding assays, crosslinking mass spectrometry, co-purification, mutagenesis of C-terminal motif, snRNA processing and termination assays\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — crystal structure combined with in vitro binding assays and mutagenesis in a single study\",\n      \"pmids\": [\"32647223\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"INTS13 utilizes its C-terminus to bind the Integrator cleavage module; germline variants p.S652L and p.K668Nfs*9 disrupt this interaction, impair Integrator complex assembly, and cause ciliopathy; depletion of INTS13 in human cells disrupts ciliogenesis and dysregulates ciliary gene expression, and knockdown in Xenopus embryos causes motile cilia anomalies.\",\n      \"method\": \"Exome sequencing, co-immunoprecipitation, INTS13 knockdown in human cultured cells (ciliogenesis assay), Xenopus morpholino knockdown with cilia phenotype readout\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — reciprocal co-IP, loss-of-function in two model systems with defined cellular phenotypes and genetic variant validation\",\n      \"pmids\": [\"36229431\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"INTS15 assembles primarily with the INTS13/14/10 module and interfaces with the Int-PP2A module within the Integrator complex, forming an expanded nucleic-acid-binding sub-module; INTS15 modulates RNA Pol II pausing at a subset of genes.\",\n      \"method\": \"Proteomics, AlphaFold2 structure prediction, functional genomics (ChIP-seq/PRO-seq), co-purification\",\n      \"journal\": \"Cell reports\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2/3 — structural predictions supported by proteomics and functional genomics but lacking reconstitution or mutagenesis of the INTS13 interaction specifically\",\n      \"pmids\": [\"36920904\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"Cryo-EM structures of the complete Integrator-PP2A complex reveal that INTS10-INTS13-INTS14-INTS15 form a scorpion-tail-shaped module; in the pre-termination complex, this module's 'sting' contacts the DSIF DNA clamp, suggesting it facilitates opening of the DSIF clamp to promote Pol II termination.\",\n      \"method\": \"Cryo-electron microscopy (three functional states of Integrator-PP2A), structural modeling\",\n      \"journal\": \"Nature\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — high-resolution cryo-EM structures of multiple functional states in a single rigorous study\",\n      \"pmids\": [\"38570683\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"Cryo-EM structures of INTS10/13/14/15 and INTS5/8/10/15 sub-complexes, together with an integrative model of fully assembled Integrator on paused RNAPII, reveal that INTS13 acts as a platform for recruitment of transcription factors; an in silico screen identified ZNF655 as a direct binding partner of INTS13 within the fully assembled complex.\",\n      \"method\": \"Cryo-EM structure determination, AlphaFold2-based in silico protein-protein interaction screen of >1,500 transcription factors, co-purification validation\",\n      \"journal\": \"Molecular cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1/2 — cryo-EM structures combined with computational screen and experimental validation of TF interaction\",\n      \"pmids\": [\"38823386\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2005,\n      \"finding\": \"Mat89Bb (the Drosophila ortholog of INTS13/Asunder) is a substrate of PAN GU kinase; RNAi depletion of Mat89Bb produces a polyploid phenotype similar to pan gu mutants, and morpholino knockdown in Xenopus causes polyploid nuclei arrest, establishing a conserved role in cell cycle regulation (S-M cycles).\",\n      \"method\": \"Drosophila in vitro expression cloning (DIVEC) kinase substrate screen, RNAi in Drosophila and HeLa cells, Xenopus morpholino injection with polyploidy phenotype readout\",\n      \"journal\": \"Developmental cell\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — biochemical substrate identification plus loss-of-function in multiple model systems, but mechanistic link to INTS13 function in Integrator not established\",\n      \"pmids\": [\"15737938\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"INTS13 (also known as Asunder/Mat89Bb) is a core subunit of the Integrator complex that, together with INTS10, INTS14, and INTS15, forms a nucleic acid-binding module with structural homology to Ku70-Ku80; its C-terminal motif directly contacts the Integrator cleavage module to coordinate snRNA processing and promoter-proximal RNA Pol II termination, while its exposed surface acts as a recruitment platform for lineage-specific transcription factors (EGR1/2 via NAB2, ZNF655) to target Integrator to specific enhancers or gene loci, and loss-of-function disrupts ciliogenesis, myeloid differentiation, and cell cycle fidelity.\"\n}\n```","stage2_raw":"```json\n{\n  \"mechanistic_narrative\": \"INTS13 is a subunit of the Integrator complex that, together with INTS10, INTS14, and INTS15, forms a scorpion-tail-shaped nucleic acid-binding module with structural homology to Ku70-Ku80; this module contacts the DSIF DNA clamp in the pre-termination complex to facilitate RNA Pol II termination [PMID:32647223, PMID:38570683]. The C-terminal motif of INTS13 directly bridges the nucleic acid-binding module to the Integrator cleavage module, coordinating snRNA 3′-end processing, and germline variants disrupting this interaction cause ciliopathy by impairing Integrator assembly and ciliogenesis [PMID:32647223, PMID:36229431]. The exposed surface of INTS13 serves as a recruitment platform for lineage-specific transcription factors—including EGR1/2 (via NAB2) at monocytic enhancers to drive chromatin looping and myeloid differentiation, and ZNF655 within the fully assembled paused-Pol II complex—establishing INTS13 as a key determinant of Integrator targeting to specific genomic loci [PMID:30008316, PMID:38823386]. The Drosophila ortholog Mat89Bb/Asunder is a PAN GU kinase substrate whose depletion causes polyploidy, indicating an additional conserved role in cell cycle fidelity [PMID:15737938].\",\n  \"teleology\": [\n    {\n      \"year\": 2005,\n      \"claim\": \"Before a link to the Integrator complex was known, identification of Mat89Bb (Drosophila ortholog of INTS13) as a PAN GU kinase substrate revealed a conserved requirement in S-M cell cycle transitions, establishing that loss of this gene causes polyploidy across species.\",\n      \"evidence\": \"DIVEC kinase substrate screen in Drosophila, RNAi in Drosophila/HeLa, morpholino in Xenopus with polyploidy readout\",\n      \"pmids\": [\"15737938\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Mechanism connecting INTS13/Mat89Bb to cell cycle control is undefined\",\n        \"Whether PAN GU phosphorylation is conserved in vertebrates is untested\",\n        \"Relationship to Integrator complex function not established\"\n      ]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"The discovery that INTS13 operates as a separable sub-module targeting EGR1/2-bound monocytic enhancers via NAB2 established that INTS13 has a gene-specific transcription factor recruitment function beyond bulk snRNA processing, directly linking Integrator to enhancer activation and myeloid differentiation.\",\n      \"evidence\": \"ChIP-seq, chromatin conformation capture, siRNA depletion in cell lines and primary human progenitors with differentiation readout\",\n      \"pmids\": [\"30008316\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Direct binding interface between INTS13 and NAB2/EGR not structurally resolved\",\n        \"Whether enhancer-targeting function requires the full Integrator or only the INTS13-containing sub-module is unclear\"\n      ]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Crystallography of the INTS13-INTS14 dimer revealed a Ku70-Ku80-like architecture with nucleic acid binding capacity, and mutagenesis showed that the INTS13 C-terminal motif directly contacts the cleavage module, answering how the INTS10/13/14 sub-module connects to snRNA processing and Pol II termination.\",\n      \"evidence\": \"X-ray crystallography, in vitro DNA/RNA binding assays, crosslinking mass spectrometry, C-terminal motif mutagenesis with snRNA processing and termination assays\",\n      \"pmids\": [\"32647223\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Structure of the full INTS10/13/14 trimer not resolved at this stage\",\n        \"How the module discriminates RNA hairpin substrates in vivo is unknown\"\n      ]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Genetic and biochemical evidence that germline INTS13 variants (p.S652L, p.K668Nfs*9) disrupt cleavage-module binding and cause ciliopathy established INTS13 as a disease gene and revealed ciliogenesis as a key downstream cellular process controlled by Integrator integrity.\",\n      \"evidence\": \"Exome sequencing of affected families, co-immunoprecipitation of variants, INTS13 depletion in human cells (ciliogenesis assay), Xenopus morpholino with cilia phenotype\",\n      \"pmids\": [\"36229431\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Which ciliary gene targets are directly versus indirectly regulated by INTS13 is unresolved\",\n        \"Whether ciliopathy phenotypes reflect snRNA processing, Pol II termination, or enhancer defects is unclear\"\n      ]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Discovery that INTS15 assembles primarily with the INTS13/14/10 module and bridges to the Int-PP2A module expanded the sub-module to a four-subunit nucleic acid-binding unit and connected it to Pol II pause regulation.\",\n      \"evidence\": \"Proteomics, AlphaFold2 prediction, ChIP-seq/PRO-seq functional genomics, co-purification\",\n      \"pmids\": [\"36920904\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Direct INTS13-INTS15 interface not validated by mutagenesis or reconstitution\",\n        \"Contribution of INTS15 to the nucleic acid binding properties of the module untested\"\n      ]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Cryo-EM structures of the complete Integrator-PP2A complex in multiple functional states showed that the INTS10/13/14/15 module forms a scorpion-tail 'sting' that contacts the DSIF clamp, explaining how this module mechanically promotes Pol II termination, while an independent cryo-EM and computational study demonstrated that the INTS13 surface recruits ZNF655, generalizing the transcription-factor recruitment function beyond EGR/NAB2.\",\n      \"evidence\": \"Cryo-EM of Integrator-PP2A in three states; cryo-EM of sub-complexes plus AlphaFold2 screen of >1,500 TFs with co-purification validation\",\n      \"pmids\": [\"38570683\", \"38823386\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Functional consequence of ZNF655-INTS13 interaction on gene regulation not characterized\",\n        \"Whether DSIF clamp opening requires catalytic activity or is purely mechanical is unresolved\",\n        \"Full catalog of transcription factors recruited via the INTS13 surface is incomplete\"\n      ]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"It remains unknown how INTS13's transcription-factor recruitment, snRNA processing, and Pol II termination functions are coordinated in vivo, and whether the cell cycle role of the Drosophila ortholog reflects a distinct Integrator-independent function.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"No separation-of-function alleles distinguishing enhancer recruitment from cleavage-module bridging\",\n        \"Mechanistic basis for cell cycle phenotype (polyploidy) remains unconnected to known Integrator functions\",\n        \"In vivo structural dynamics of the INTS13 module during transcription termination are unresolved\"\n      ]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0003723\", \"supporting_discovery_ids\": [1]},\n      {\"term_id\": \"GO:0003677\", \"supporting_discovery_ids\": [1]},\n      {\"term_id\": \"GO:0060090\", \"supporting_discovery_ids\": [0, 5]},\n      {\"term_id\": \"GO:0005198\", \"supporting_discovery_ids\": [1, 4]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [0, 1, 2]},\n      {\"term_id\": \"GO:0005694\", \"supporting_discovery_ids\": [0]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-8953854\", \"supporting_discovery_ids\": [1, 4]},\n      {\"term_id\": \"R-HSA-74160\", \"supporting_discovery_ids\": [0, 4, 5]},\n      {\"term_id\": \"R-HSA-1266738\", \"supporting_discovery_ids\": [2]},\n      {\"term_id\": \"R-HSA-1640170\", \"supporting_discovery_ids\": [6]}\n    ],\n    \"complexes\": [\n      \"Integrator complex\",\n      \"INTS10/INTS13/INTS14/INTS15 module\"\n    ],\n    \"partners\": [\n      \"INTS14\",\n      \"INTS10\",\n      \"INTS15\",\n      \"INTS5\",\n      \"INTS8\",\n      \"NAB2\",\n      \"ZNF655\"\n    ],\n    \"other_free_text\": []\n  }\n}\n```"}