{"gene":"INTS11","run_date":"2026-06-10T01:55:23","timeline":{"discoveries":[{"year":2017,"finding":"INTS11 (IntS11) possesses endonuclease activity as a member of the metallo-β-lactamase superfamily and forms a stable complex with IntS9 through their C-terminal domains (CTDs). The crystal structure at 2.1-Å resolution reveals a continuous nine-stranded β-sheet composed of four strands from IntS9 and five from IntS11. Structure-based mutagenesis and coimmunoprecipitation confirmed that the IntS9-IntS11 CTD interaction is required for snRNA 3'-end processing.","method":"Crystal structure (2.1-Å resolution), yeast two-hybrid assay, coimmunoprecipitation, structure-based mutagenesis, functional snRNA processing assay","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"High","confidence_rationale":"Tier 1 / Strong — crystal structure with mutagenesis and functional validation, multiple orthogonal methods in single rigorous study","pmids":["28396433"],"is_preprint":false},{"year":2023,"finding":"A mixture of metal ions (Fe, Zn, and Mn) rather than exclusively zinc ions occupies the active site of INTS11, as determined by inductively coupled plasma mass spectrometry and X-ray diffraction. The abundance of metal ions varies by expression host, with less than 20% zinc in insect-cell-expressed samples, yet enzymatic activity is retained, indicating the enzyme can function with different metal ions.","method":"Inductively coupled plasma mass spectrometry, X-ray diffraction, in vitro endonuclease activity assay","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1 / Moderate — two orthogonal biophysical methods (ICP-MS and X-ray) with functional validation in single study","pmids":["36822327"],"is_preprint":false},{"year":2021,"finding":"INTS11 physically interacts with the Polycomb repressive complex 2 (PRC2) in hematopoietic stem and progenitor cells. Loss of INTS11 destabilizes PRC2, reduces H3K27me3 levels, and derepresses PRC2 target genes; re-expression of INTS11 or PRC2 components restores H3K27me3 levels and HSPC function, placing INTS11 upstream of PRC2 in a regulatory axis.","method":"Conditional Ints11 knockout mouse, co-immunoprecipitation (INTS11-PRC2 interaction), western blotting for H3K27me3, rescue by re-expression","journal":"Science advances","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP identifying novel complex, in vivo KO with defined phenotype and rescue, single lab","pmids":["34516911"],"is_preprint":false},{"year":2024,"finding":"BRAT1 (and its Drosophila ortholog CG7044) binds directly in the active site of INTS11, with a conserved cysteine residue of BRAT1 coordinating the catalytic metal ions. BRAT1 stabilizes INTS11 in the cytoplasm and is required for Integrator function in the nucleus; loss of BRAT1 in neural organoids causes transcriptomic disruption and precocious neurogenesis-driving transcription factor expression. Cryo/crystal structures of human INTS9-INTS11-BRAT1 and Drosophila dIntS11-CG7044 complexes were determined.","method":"Crystal/cryo-EM structure of INTS9-INTS11-BRAT1 complex, active-site mutagenesis, co-immunoprecipitation, neural organoid loss-of-function, transcriptomics","journal":"Molecular cell","confidence":"High","confidence_rationale":"Tier 1 / Strong — structural determination with active-site coordination validated by mutagenesis, orthogonal functional studies in neural organoids","pmids":["39032490"],"is_preprint":false},{"year":2024,"finding":"INTS11 terminates antisense transcription at bidirectional human promoters, while CDK9 activity protects sense transcription from INTS11-mediated attenuation. CDK9 inhibition causes INTS11 to attenuate transcription in both directions, and engineered recruitment of CDK9 desensitizes transcription to INTS11, placing these two activities in direct opposition to establish promoter directionality.","method":"Auxin-inducible degron depletion of INTS11, CDK9 inhibition (small molecule), engineered CDK9 recruitment (tethering), nascent RNA-seq (TT-seq or equivalent)","journal":"eLife","confidence":"High","confidence_rationale":"Tier 2 / Strong — genetic epistasis via degron depletion and pharmacological inhibition, multiple orthogonal perturbations, replicated across conditions","pmids":["38976490"],"is_preprint":false},{"year":2023,"finding":"A homozygous INTS11 variant found in two siblings with severe neurodevelopmental disorder impairs INTS11 catalytic activity (evidenced by substrate accumulation) and causes G2/M cell cycle arrest. Knockin of the variant in iPSCs disrupts mitotic spindle organization, slows proliferation, increases apoptosis, and delays neural progenitor cell generation, with length-dependent dysregulation of mitosis and neurogenesis genes including CDKL5.","method":"Patient-derived cells, iPSC knockin (CRISPR), mitotic spindle imaging, cell cycle analysis, RNA-seq (transcript length analysis), ERK pathway assay","journal":"Cell reports","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — iPSC KI model with multiple cellular readouts, single lab, substrate accumulation confirming catalytic impairment","pmids":["37980560"],"is_preprint":false},{"year":2023,"finding":"INTS11 and INTS9 form a trimeric complex with BRAT1 in human cells. BRAT1 is required to recruit INTS11 to the promoters of neuronal genes (REST targets), and disease-causing BRAT1 mutations (e.g., E522K) disrupt the BRAT1-INTS11/INTS9 interaction, preventing transcriptional activation of neuronal genes.","method":"Co-immunoprecipitation in HEK293T and NT2 cells, ChIP-qPCR, BRAT1 knockdown, re-expression of mutant BRAT1","journal":"bioRxiv","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — Co-IP, ChIP, and functional rescue in two cell lines; preprint without full peer review","pmids":["37609215"],"is_preprint":true},{"year":2026,"finding":"INTS11 (IntS11) binds chromatin at loci of neuronal morphogenesis genes in Drosophila larval brains to maintain lengthened 3′UTR isoforms and mRNA stability. Loss of IntS11 causes G1 arrest in neuroblasts with downregulation of cell cycle regulators (aurB, CycE, Cdk4), reduced clonal expansion, and loss of long 3′UTR isoforms in ~80% of neuronal morphogenesis genes.","method":"Drosophila MARCM clonal analysis, FUCCI cell-cycle reporter, single-cell RNA-seq, ChIP-qPCR, live imaging","journal":"Cell & bioscience","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — multiple orthogonal methods in vivo (MARCM, scRNA-seq, ChIP), single lab","pmids":["42035222"],"is_preprint":false},{"year":2026,"finding":"BRAT1 mutations impair U1 snRNA 3′-end processing, causing nuclear accumulation of unprocessed U1 snRNA transcripts, demonstrating that BRAT1's role in Integrator function is required for snRNA maturation. ints11 knockout zebrafish recapitulate microcephaly and U snRNA processing defects, validating INTS11's causal role in snRNA processing in vivo.","method":"RT-qPCR, western blotting, fluorescence in situ hybridization in patient-derived fibroblasts/lymphoblastoid cells, CRISPR/Cas9 ints11 knockout zebrafish","journal":"Genome medicine","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — patient cells + in vivo vertebrate model, multiple orthogonal methods, single study","pmids":["42116163"],"is_preprint":false},{"year":2026,"finding":"Maternal IntS11 in Drosophila embryos is required for RNA Polymerase II recruitment and for pioneer factors Zelda and GAGA factor (GAF) to access regulatory elements during zygotic genome activation. IntS11 operates upstream of these pioneer factors. Two distinct activities are required: its canonical endonuclease activity for sustaining major-wave zygotic transcription, and an enzyme-independent function for de novo Pol II loading and pioneer factor engagement.","method":"Maternal IntS11 depletion (Drosophila genetics), CUT&RUN or ChIP for Pol II and pioneer factors, catalytically dead IntS11 rescue experiments, genome-wide transcriptomics","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — genetic epistasis, catalytic mutant rescue, and genome-wide Pol II binding, single lab","pmids":["41955115"],"is_preprint":false}],"current_model":"INTS11 is the catalytic endonuclease subunit of the Integrator complex, harboring a metallo-β-lactamase active site occupied by a mixture of Fe, Zn, and Mn ions; it heterodimerizes with INTS9 via a conserved CTD interface required for snRNA 3′-end processing, is stabilized in the cytoplasm by BRAT1 (which directly coordinates the active-site metals) before nuclear import, terminates antisense and attenuates premature sense transcription at bidirectional promoters in opposition to CDK9, interacts with PRC2 to maintain H3K27me3 in hematopoietic progenitors, and acts upstream of pioneer transcription factors to prime chromatin for zygotic genome activation, with loss-of-function causing cell cycle arrest, mitotic spindle defects, impaired snRNA processing, and severe neurodevelopmental phenotypes."},"narrative":{"mechanistic_narrative":"INTS11 is the catalytic endonuclease subunit of the Integrator complex, a metallo-β-lactamase superfamily member that drives 3′-end processing of snRNAs and the termination and attenuation of RNA polymerase II transcription [PMID:28396433, PMID:38976490]. Its catalytic activity rests on an active-site metal center that, contrary to a strict zinc-only model, is occupied by a mixture of Fe, Zn, and Mn ions, and the enzyme retains activity across different metal compositions [PMID:36822327]. Catalysis and complex integrity require heterodimerization with INTS9 through a conserved C-terminal-domain interface that forms a continuous nine-stranded β-sheet, an interaction essential for snRNA 3′-end processing [PMID:28396433]. The chaperone BRAT1 binds directly within the INTS11 active site, coordinating the catalytic metals via a conserved cysteine, stabilizing INTS11, and recruiting the INTS9–INTS11 module to target promoters; disease-causing BRAT1 mutations that disrupt this interface impair Integrator function and U1 snRNA maturation [PMID:39032490, PMID:37609215, PMID:42116163]. At bidirectional promoters INTS11 terminates antisense transcription and attenuates premature sense transcription, an activity held in check by CDK9 to establish promoter directionality [PMID:38976490]. Beyond core RNA processing, INTS11 interacts with PRC2 to maintain H3K27me3 and repress PRC2 targets in hematopoietic progenitors [PMID:34516911], and during zygotic genome activation it acts upstream of pioneer factors through both endonuclease-dependent and enzyme-independent functions to load Pol II and license chromatin access [PMID:41955115]. A homozygous catalytically impairing INTS11 variant causes a severe neurodevelopmental disorder with G2/M arrest, mitotic spindle defects, and length-dependent gene dysregulation, and ints11-null zebrafish recapitulate microcephaly with snRNA processing defects [PMID:37980560, PMID:42116163].","teleology":[{"year":2017,"claim":"Established the structural and biochemical basis for INTS11 catalysis and its obligate partnership with INTS9, answering how the Integrator endonuclease module is assembled for snRNA processing.","evidence":"2.1-Å crystal structure of the INTS9–INTS11 CTD interface with yeast two-hybrid, co-IP, structure-based mutagenesis, and snRNA processing assays","pmids":["28396433"],"confidence":"High","gaps":["Did not resolve the full catalytic mechanism or substrate recognition","Did not address regulation or recruitment to specific loci"]},{"year":2021,"claim":"Linked INTS11 to chromatin repression by showing it stabilizes PRC2 and maintains H3K27me3, defining a regulatory axis beyond canonical RNA processing in hematopoietic progenitors.","evidence":"Conditional Ints11 knockout mouse, co-IP, H3K27me3 western blotting, and rescue by re-expression","pmids":["34516911"],"confidence":"Medium","gaps":["Co-IP does not establish direct INTS11–PRC2 contact versus bridged interaction","Mechanism of PRC2 stabilization unresolved","Single lab"]},{"year":2023,"claim":"Revised the active-site metal model, showing INTS11 functions with a mixture of Fe, Zn, and Mn rather than zinc alone.","evidence":"ICP-MS, X-ray diffraction, and in vitro endonuclease assays across expression hosts","pmids":["36822327"],"confidence":"High","gaps":["Physiological metal occupancy in cells not established","Functional consequence of metal identity on substrate specificity unknown"]},{"year":2023,"claim":"Connected INTS11 to human disease by demonstrating that a catalytically impairing variant causes cell cycle arrest and neurodevelopmental phenotypes.","evidence":"Patient-derived cells, iPSC CRISPR knockin, mitotic spindle imaging, cell cycle analysis, and transcript-length RNA-seq","pmids":["37980560"],"confidence":"Medium","gaps":["Mechanism linking catalytic loss to spindle defects unresolved","Single family/single lab","Causality of CDKL5 dysregulation in phenotype not dissected"]},{"year":2023,"claim":"Identified BRAT1 as a trimeric partner of INTS9–INTS11 required for recruiting the module to neuronal gene promoters.","evidence":"Co-IP in HEK293T and NT2 cells, ChIP-qPCR, BRAT1 knockdown, and mutant BRAT1 rescue (preprint)","pmids":["37609215"],"confidence":"Medium","gaps":["Preprint without full peer review","Direct versus indirect recruitment mechanism not structurally resolved at this stage"]},{"year":2024,"claim":"Defined INTS11's role in establishing promoter directionality by terminating antisense transcription, with CDK9 antagonizing its attenuation of sense transcription.","evidence":"Auxin-inducible degron depletion of INTS11, CDK9 inhibition and engineered tethering, and nascent RNA-seq","pmids":["38976490"],"confidence":"High","gaps":["Molecular basis of how CDK9 protects sense transcription not defined","Whether antagonism operates through phosphorylation of Integrator subunits unresolved"]},{"year":2024,"claim":"Resolved how BRAT1 stabilizes INTS11, showing it inserts into the active site to coordinate catalytic metals in the cytoplasm prior to nuclear Integrator function.","evidence":"Crystal/cryo-EM structures of human INTS9–INTS11–BRAT1 and Drosophila orthologs, active-site mutagenesis, co-IP, and neural organoid loss-of-function","pmids":["39032490"],"confidence":"High","gaps":["How BRAT1 release permits catalysis after nuclear import not defined","Dynamics of cytoplasmic-to-nuclear handoff unresolved"]},{"year":2026,"claim":"Showed INTS11 chromatin binding maintains lengthened 3′UTR isoforms and mRNA stability at neuronal morphogenesis genes, with loss causing G1 arrest in neuroblasts.","evidence":"Drosophila MARCM clonal analysis, FUCCI reporter, single-cell RNA-seq, ChIP-qPCR, and live imaging","pmids":["42035222"],"confidence":"Medium","gaps":["Mechanism linking INTS11 to 3′UTR isoform length not defined","Single lab/model organism"]},{"year":2026,"claim":"Demonstrated in vivo that BRAT1 and INTS11 are jointly required for U snRNA 3′-end maturation, with ints11-null zebrafish recapitulating microcephaly and snRNA processing defects.","evidence":"RT-qPCR, western blotting, FISH in patient cells, and CRISPR/Cas9 ints11 knockout zebrafish","pmids":["42116163"],"confidence":"Medium","gaps":["Quantitative contribution of snRNA defect to microcephaly versus other Integrator functions not separated","Single study"]},{"year":2026,"claim":"Separated catalytic from non-catalytic functions of INTS11, showing maternal IntS11 acts upstream of pioneer factors for Pol II loading independent of endonuclease activity during zygotic genome activation.","evidence":"Maternal IntS11 depletion in Drosophila, CUT&RUN/ChIP for Pol II and pioneer factors, catalytically dead rescue, and genome-wide transcriptomics","pmids":["41955115"],"confidence":"Medium","gaps":["Molecular basis of enzyme-independent Pol II loading unknown","Whether this function is conserved in mammals not established"]},{"year":null,"claim":"How the multiple INTS11 activities — snRNA processing, transcription attenuation/termination, PRC2-linked chromatin repression, and enzyme-independent Pol II loading — are coordinated or partitioned across cell types and developmental stages remains unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No unified model integrating catalytic and non-catalytic roles","Mechanism of locus- and context-specific recruitment unknown","Mammalian validation of pioneer-factor function lacking"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0140098","term_label":"catalytic activity, acting on RNA","supporting_discovery_ids":[0,1,4,8]},{"term_id":"GO:0016787","term_label":"hydrolase activity","supporting_discovery_ids":[0,1]},{"term_id":"GO:0003723","term_label":"RNA binding","supporting_discovery_ids":[0,7,8]},{"term_id":"GO:0140110","term_label":"transcription regulator activity","supporting_discovery_ids":[4,9]}],"localization":[{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[3,4]},{"term_id":"GO:0005829","term_label":"cytosol","supporting_discovery_ids":[3]}],"pathway":[{"term_id":"R-HSA-8953854","term_label":"Metabolism of RNA","supporting_discovery_ids":[0,8]},{"term_id":"R-HSA-74160","term_label":"Gene expression (Transcription)","supporting_discovery_ids":[4,9]},{"term_id":"R-HSA-4839726","term_label":"Chromatin organization","supporting_discovery_ids":[2]}],"complexes":["Integrator complex","INTS9-INTS11 heterodimer","INTS9-INTS11-BRAT1 complex"],"partners":["INTS9","BRAT1","PRC2","CDK9"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q5TA45","full_name":"Integrator complex subunit 11","aliases":["Cleavage and polyadenylation-specific factor 3-like protein","CPSF3-like protein","Protein related to CPSF subunits of 68 kDa","RC-68"],"length_aa":600,"mass_kda":67.7,"function":"RNA endonuclease component of the integrator complex, a multiprotein complex that terminates RNA polymerase II (Pol II) transcription in the promoter-proximal region of genes (PubMed:16239144, PubMed:25201415, PubMed:28396433, PubMed:32697989, PubMed:33243860, PubMed:33548203, PubMed:34762484, PubMed:37080207, 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:32697989, PubMed:33243860, PubMed:33548203, PubMed:34762484, PubMed:37080207, 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, PubMed:22252320, PubMed:26308897, PubMed:30737432). Within the integrator complex, INTS11 constitutes the RNA endonuclease subunit that degrades exiting nascent RNA transcripts (PubMed:28396433, PubMed:32697989, PubMed:33243860, PubMed:33548203, PubMed:34762484, PubMed:37080207, PubMed:38570683). Mediates recruitment of cytoplasmic dynein to the nuclear envelope, probably as component of the integrator complex (PubMed:23904267)","subcellular_location":"Nucleus; Cytoplasm","url":"https://www.uniprot.org/uniprotkb/Q5TA45/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":true,"resolved_as":"","url":"https://depmap.org/portal/gene/INTS11","classification":"Common Essential","n_dependent_lines":1208,"n_total_lines":1208,"dependency_fraction":1.0},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[{"gene":"HIST2H2BE","stoichiometry":0.2},{"gene":"POLR2B","stoichiometry":0.2},{"gene":"POLR2E","stoichiometry":0.2},{"gene":"POLR2F","stoichiometry":0.2},{"gene":"POLR2I","stoichiometry":0.2},{"gene":"POLR2K","stoichiometry":0.2},{"gene":"PPP2CA","stoichiometry":0.2},{"gene":"SEM1","stoichiometry":0.2},{"gene":"SSRP1","stoichiometry":0.2},{"gene":"SUPT5H","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/search/INTS11","total_profiled":1310},"omim":[{"mim_id":"620428","title":"NEURODEVELOPMENTAL DISORDER WITH MOTOR AND LANGUAGE DELAY, OCULAR DEFECTS, AND BRAIN ABNORMALITIES; NEDMLOB","url":"https://www.omim.org/entry/620428"},{"mim_id":"611355","title":"INTEGRATOR COMPLEX SUBUNIT 12; INTS12","url":"https://www.omim.org/entry/611355"},{"mim_id":"611354","title":"INTEGRATOR COMPLEX SUBUNIT 11; INTS11","url":"https://www.omim.org/entry/611354"},{"mim_id":"611353","title":"INTEGRATOR COMPLEX SUBUNIT 10; INTS10","url":"https://www.omim.org/entry/611353"},{"mim_id":"611352","title":"INTEGRATOR COMPLEX SUBUNIT 9; INTS9","url":"https://www.omim.org/entry/611352"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Supported","locations":[{"location":"Cytosol","reliability":"Supported"},{"location":"Nucleoplasm","reliability":"Additional"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/INTS11"},"hgnc":{"alias_symbol":["FLJ20542","RC-68","CPSF73L","INT11"],"prev_symbol":["CPSF3L"]},"alphafold":{"accession":"Q5TA45","domains":[{"cath_id":"3.60.15.10","chopping":"4-211_392-440","consensus_level":"medium","plddt":95.1257,"start":4,"end":440},{"cath_id":"3.40.50.10890","chopping":"215-387","consensus_level":"high","plddt":90.1506,"start":215,"end":387},{"cath_id":"-","chopping":"453-466_480-508","consensus_level":"medium","plddt":86.2914,"start":453,"end":508},{"cath_id":"3.30.310,3.30.310","chopping":"511-594","consensus_level":"high","plddt":87.5963,"start":511,"end":594}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q5TA45","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q5TA45-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q5TA45-F1-predicted_aligned_error_v6.png","plddt_mean":90.69},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=INTS11","jax_strain_url":"https://www.jax.org/strain/search?query=INTS11"},"sequence":{"accession":"Q5TA45","fasta_url":"https://rest.uniprot.org/uniprotkb/Q5TA45.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q5TA45/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q5TA45"}},"corpus_meta":[{"pmid":"28396433","id":"PMC_28396433","title":"Molecular basis for the interaction between Integrator subunits IntS9 and IntS11 and its functional importance.","date":"2017","source":"Proceedings of the National Academy of Sciences of the United States of America","url":"https://pubmed.ncbi.nlm.nih.gov/28396433","citation_count":62,"is_preprint":false},{"pmid":"37054711","id":"PMC_37054711","title":"Bi-allelic variants in INTS11 are associated with a complex neurological disorder.","date":"2023","source":"American journal of human genetics","url":"https://pubmed.ncbi.nlm.nih.gov/37054711","citation_count":30,"is_preprint":false},{"pmid":"34516911","id":"PMC_34516911","title":"INTS11 regulates hematopoiesis by promoting PRC2 function.","date":"2021","source":"Science advances","url":"https://pubmed.ncbi.nlm.nih.gov/34516911","citation_count":14,"is_preprint":false},{"pmid":"37980560","id":"PMC_37980560","title":"A homozygous variant in INTS11 links mitosis and neurogenesis defects to a severe neurodevelopmental disorder.","date":"2023","source":"Cell reports","url":"https://pubmed.ncbi.nlm.nih.gov/37980560","citation_count":11,"is_preprint":false},{"pmid":"38976490","id":"PMC_38976490","title":"Human promoter directionality is determined by transcriptional initiation and the opposing activities of INTS11 and CDK9.","date":"2024","source":"eLife","url":"https://pubmed.ncbi.nlm.nih.gov/38976490","citation_count":9,"is_preprint":false},{"pmid":"39032490","id":"PMC_39032490","title":"Cytoplasmic binding partners of the Integrator endonuclease INTS11 and its paralog CPSF73 are required for their nuclear function.","date":"2024","source":"Molecular cell","url":"https://pubmed.ncbi.nlm.nih.gov/39032490","citation_count":8,"is_preprint":false},{"pmid":"36822327","id":"PMC_36822327","title":"An examination of the metal ion content in the active sites of human endonucleases CPSF73 and INTS11.","date":"2023","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/36822327","citation_count":8,"is_preprint":false},{"pmid":"37609215","id":"PMC_37609215","title":"BRAT1 associates with INTS11/INTS9 heterodimer to regulate key neurodevelopmental genes.","date":"2023","source":"bioRxiv : the preprint server for biology","url":"https://pubmed.ncbi.nlm.nih.gov/37609215","citation_count":5,"is_preprint":false},{"pmid":"39030370","id":"PMC_39030370","title":"INTS11-related neurodevelopmental disorder: a case report and literature review.","date":"2024","source":"Journal of human genetics","url":"https://pubmed.ncbi.nlm.nih.gov/39030370","citation_count":3,"is_preprint":false},{"pmid":"42035222","id":"PMC_42035222","title":"Integrator subunit IntS11 orchestrates the temporal dynamics of neural lineage progression in Drosophila.","date":"2026","source":"Cell & bioscience","url":"https://pubmed.ncbi.nlm.nih.gov/42035222","citation_count":1,"is_preprint":false},{"pmid":"42116163","id":"PMC_42116163","title":"Unprocessed U1 snRNAs as a biomarker of INTS11- and BRAT1-related neurodevelopmental disorders.","date":"2026","source":"Genome medicine","url":"https://pubmed.ncbi.nlm.nih.gov/42116163","citation_count":0,"is_preprint":false},{"pmid":"41837557","id":"PMC_41837557","title":"Neurotrophic Modulation Restores Motor and Developmental Defects in Zebrafish Models of ints11 Deficiency.","date":"2026","source":"Journal of neurochemistry","url":"https://pubmed.ncbi.nlm.nih.gov/41837557","citation_count":0,"is_preprint":false},{"pmid":"41955115","id":"PMC_41955115","title":"Maternal IntS11 primes embryonic totipotency by organizing early zygotic transcription initiation.","date":"2026","source":"Proceedings of the National Academy of Sciences of the United States of America","url":"https://pubmed.ncbi.nlm.nih.gov/41955115","citation_count":0,"is_preprint":false},{"pmid":null,"id":"bio_10.1101_2025.01.30.635704","title":"Modelling transcription with explainable AI uncovers context-specific epigenetic gene regulation at promoters and gene bodies","date":"2025-02-05","source":"bioRxiv","url":"https://doi.org/10.1101/2025.01.30.635704","citation_count":0,"is_preprint":true}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":8946,"output_tokens":2925,"usd":0.035356,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":10286,"output_tokens":3671,"usd":0.071602,"stage2_stop_reason":"end_turn"},"total_usd":0.106958,"stage1_batch_id":"msgbatch_01DUPACZi7AAWwuZiUjseQF4","stage2_batch_id":"msgbatch_018yt7chE3f48PEFtDwtj6AE","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2017,\n      \"finding\": \"INTS11 (IntS11) possesses endonuclease activity as a member of the metallo-β-lactamase superfamily and forms a stable complex with IntS9 through their C-terminal domains (CTDs). The crystal structure at 2.1-Å resolution reveals a continuous nine-stranded β-sheet composed of four strands from IntS9 and five from IntS11. Structure-based mutagenesis and coimmunoprecipitation confirmed that the IntS9-IntS11 CTD interaction is required for snRNA 3'-end processing.\",\n      \"method\": \"Crystal structure (2.1-Å resolution), yeast two-hybrid assay, coimmunoprecipitation, structure-based mutagenesis, functional snRNA processing assay\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — crystal structure with mutagenesis and functional validation, multiple orthogonal methods in single rigorous study\",\n      \"pmids\": [\"28396433\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"A mixture of metal ions (Fe, Zn, and Mn) rather than exclusively zinc ions occupies the active site of INTS11, as determined by inductively coupled plasma mass spectrometry and X-ray diffraction. The abundance of metal ions varies by expression host, with less than 20% zinc in insect-cell-expressed samples, yet enzymatic activity is retained, indicating the enzyme can function with different metal ions.\",\n      \"method\": \"Inductively coupled plasma mass spectrometry, X-ray diffraction, in vitro endonuclease activity assay\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — two orthogonal biophysical methods (ICP-MS and X-ray) with functional validation in single study\",\n      \"pmids\": [\"36822327\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"INTS11 physically interacts with the Polycomb repressive complex 2 (PRC2) in hematopoietic stem and progenitor cells. Loss of INTS11 destabilizes PRC2, reduces H3K27me3 levels, and derepresses PRC2 target genes; re-expression of INTS11 or PRC2 components restores H3K27me3 levels and HSPC function, placing INTS11 upstream of PRC2 in a regulatory axis.\",\n      \"method\": \"Conditional Ints11 knockout mouse, co-immunoprecipitation (INTS11-PRC2 interaction), western blotting for H3K27me3, rescue by re-expression\",\n      \"journal\": \"Science advances\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP identifying novel complex, in vivo KO with defined phenotype and rescue, single lab\",\n      \"pmids\": [\"34516911\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"BRAT1 (and its Drosophila ortholog CG7044) binds directly in the active site of INTS11, with a conserved cysteine residue of BRAT1 coordinating the catalytic metal ions. BRAT1 stabilizes INTS11 in the cytoplasm and is required for Integrator function in the nucleus; loss of BRAT1 in neural organoids causes transcriptomic disruption and precocious neurogenesis-driving transcription factor expression. Cryo/crystal structures of human INTS9-INTS11-BRAT1 and Drosophila dIntS11-CG7044 complexes were determined.\",\n      \"method\": \"Crystal/cryo-EM structure of INTS9-INTS11-BRAT1 complex, active-site mutagenesis, co-immunoprecipitation, neural organoid loss-of-function, transcriptomics\",\n      \"journal\": \"Molecular cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — structural determination with active-site coordination validated by mutagenesis, orthogonal functional studies in neural organoids\",\n      \"pmids\": [\"39032490\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"INTS11 terminates antisense transcription at bidirectional human promoters, while CDK9 activity protects sense transcription from INTS11-mediated attenuation. CDK9 inhibition causes INTS11 to attenuate transcription in both directions, and engineered recruitment of CDK9 desensitizes transcription to INTS11, placing these two activities in direct opposition to establish promoter directionality.\",\n      \"method\": \"Auxin-inducible degron depletion of INTS11, CDK9 inhibition (small molecule), engineered CDK9 recruitment (tethering), nascent RNA-seq (TT-seq or equivalent)\",\n      \"journal\": \"eLife\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — genetic epistasis via degron depletion and pharmacological inhibition, multiple orthogonal perturbations, replicated across conditions\",\n      \"pmids\": [\"38976490\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"A homozygous INTS11 variant found in two siblings with severe neurodevelopmental disorder impairs INTS11 catalytic activity (evidenced by substrate accumulation) and causes G2/M cell cycle arrest. Knockin of the variant in iPSCs disrupts mitotic spindle organization, slows proliferation, increases apoptosis, and delays neural progenitor cell generation, with length-dependent dysregulation of mitosis and neurogenesis genes including CDKL5.\",\n      \"method\": \"Patient-derived cells, iPSC knockin (CRISPR), mitotic spindle imaging, cell cycle analysis, RNA-seq (transcript length analysis), ERK pathway assay\",\n      \"journal\": \"Cell reports\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — iPSC KI model with multiple cellular readouts, single lab, substrate accumulation confirming catalytic impairment\",\n      \"pmids\": [\"37980560\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"INTS11 and INTS9 form a trimeric complex with BRAT1 in human cells. BRAT1 is required to recruit INTS11 to the promoters of neuronal genes (REST targets), and disease-causing BRAT1 mutations (e.g., E522K) disrupt the BRAT1-INTS11/INTS9 interaction, preventing transcriptional activation of neuronal genes.\",\n      \"method\": \"Co-immunoprecipitation in HEK293T and NT2 cells, ChIP-qPCR, BRAT1 knockdown, re-expression of mutant BRAT1\",\n      \"journal\": \"bioRxiv\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — Co-IP, ChIP, and functional rescue in two cell lines; preprint without full peer review\",\n      \"pmids\": [\"37609215\"],\n      \"is_preprint\": true\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"INTS11 (IntS11) binds chromatin at loci of neuronal morphogenesis genes in Drosophila larval brains to maintain lengthened 3′UTR isoforms and mRNA stability. Loss of IntS11 causes G1 arrest in neuroblasts with downregulation of cell cycle regulators (aurB, CycE, Cdk4), reduced clonal expansion, and loss of long 3′UTR isoforms in ~80% of neuronal morphogenesis genes.\",\n      \"method\": \"Drosophila MARCM clonal analysis, FUCCI cell-cycle reporter, single-cell RNA-seq, ChIP-qPCR, live imaging\",\n      \"journal\": \"Cell & bioscience\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple orthogonal methods in vivo (MARCM, scRNA-seq, ChIP), single lab\",\n      \"pmids\": [\"42035222\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"BRAT1 mutations impair U1 snRNA 3′-end processing, causing nuclear accumulation of unprocessed U1 snRNA transcripts, demonstrating that BRAT1's role in Integrator function is required for snRNA maturation. ints11 knockout zebrafish recapitulate microcephaly and U snRNA processing defects, validating INTS11's causal role in snRNA processing in vivo.\",\n      \"method\": \"RT-qPCR, western blotting, fluorescence in situ hybridization in patient-derived fibroblasts/lymphoblastoid cells, CRISPR/Cas9 ints11 knockout zebrafish\",\n      \"journal\": \"Genome medicine\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — patient cells + in vivo vertebrate model, multiple orthogonal methods, single study\",\n      \"pmids\": [\"42116163\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"Maternal IntS11 in Drosophila embryos is required for RNA Polymerase II recruitment and for pioneer factors Zelda and GAGA factor (GAF) to access regulatory elements during zygotic genome activation. IntS11 operates upstream of these pioneer factors. Two distinct activities are required: its canonical endonuclease activity for sustaining major-wave zygotic transcription, and an enzyme-independent function for de novo Pol II loading and pioneer factor engagement.\",\n      \"method\": \"Maternal IntS11 depletion (Drosophila genetics), CUT&RUN or ChIP for Pol II and pioneer factors, catalytically dead IntS11 rescue experiments, genome-wide transcriptomics\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — genetic epistasis, catalytic mutant rescue, and genome-wide Pol II binding, single lab\",\n      \"pmids\": [\"41955115\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"INTS11 is the catalytic endonuclease subunit of the Integrator complex, harboring a metallo-β-lactamase active site occupied by a mixture of Fe, Zn, and Mn ions; it heterodimerizes with INTS9 via a conserved CTD interface required for snRNA 3′-end processing, is stabilized in the cytoplasm by BRAT1 (which directly coordinates the active-site metals) before nuclear import, terminates antisense and attenuates premature sense transcription at bidirectional promoters in opposition to CDK9, interacts with PRC2 to maintain H3K27me3 in hematopoietic progenitors, and acts upstream of pioneer transcription factors to prime chromatin for zygotic genome activation, with loss-of-function causing cell cycle arrest, mitotic spindle defects, impaired snRNA processing, and severe neurodevelopmental phenotypes.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"INTS11 is the catalytic endonuclease subunit of the Integrator complex, a metallo-β-lactamase superfamily member that drives 3′-end processing of snRNAs and the termination and attenuation of RNA polymerase II transcription [#0, #4]. Its catalytic activity rests on an active-site metal center that, contrary to a strict zinc-only model, is occupied by a mixture of Fe, Zn, and Mn ions, and the enzyme retains activity across different metal compositions [#1]. Catalysis and complex integrity require heterodimerization with INTS9 through a conserved C-terminal-domain interface that forms a continuous nine-stranded β-sheet, an interaction essential for snRNA 3′-end processing [#0]. The chaperone BRAT1 binds directly within the INTS11 active site, coordinating the catalytic metals via a conserved cysteine, stabilizing INTS11, and recruiting the INTS9–INTS11 module to target promoters; disease-causing BRAT1 mutations that disrupt this interface impair Integrator function and U1 snRNA maturation [#3, #6, #8]. At bidirectional promoters INTS11 terminates antisense transcription and attenuates premature sense transcription, an activity held in check by CDK9 to establish promoter directionality [#4]. Beyond core RNA processing, INTS11 interacts with PRC2 to maintain H3K27me3 and repress PRC2 targets in hematopoietic progenitors [#2], and during zygotic genome activation it acts upstream of pioneer factors through both endonuclease-dependent and enzyme-independent functions to load Pol II and license chromatin access [#9]. A homozygous catalytically impairing INTS11 variant causes a severe neurodevelopmental disorder with G2/M arrest, mitotic spindle defects, and length-dependent gene dysregulation, and ints11-null zebrafish recapitulate microcephaly with snRNA processing defects [#5, #8].\",\n  \"teleology\": [\n    {\n      \"year\": 2017,\n      \"claim\": \"Established the structural and biochemical basis for INTS11 catalysis and its obligate partnership with INTS9, answering how the Integrator endonuclease module is assembled for snRNA processing.\",\n      \"evidence\": \"2.1-Å crystal structure of the INTS9–INTS11 CTD interface with yeast two-hybrid, co-IP, structure-based mutagenesis, and snRNA processing assays\",\n      \"pmids\": [\"28396433\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not resolve the full catalytic mechanism or substrate recognition\", \"Did not address regulation or recruitment to specific loci\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Linked INTS11 to chromatin repression by showing it stabilizes PRC2 and maintains H3K27me3, defining a regulatory axis beyond canonical RNA processing in hematopoietic progenitors.\",\n      \"evidence\": \"Conditional Ints11 knockout mouse, co-IP, H3K27me3 western blotting, and rescue by re-expression\",\n      \"pmids\": [\"34516911\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Co-IP does not establish direct INTS11–PRC2 contact versus bridged interaction\", \"Mechanism of PRC2 stabilization unresolved\", \"Single lab\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Revised the active-site metal model, showing INTS11 functions with a mixture of Fe, Zn, and Mn rather than zinc alone.\",\n      \"evidence\": \"ICP-MS, X-ray diffraction, and in vitro endonuclease assays across expression hosts\",\n      \"pmids\": [\"36822327\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Physiological metal occupancy in cells not established\", \"Functional consequence of metal identity on substrate specificity unknown\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Connected INTS11 to human disease by demonstrating that a catalytically impairing variant causes cell cycle arrest and neurodevelopmental phenotypes.\",\n      \"evidence\": \"Patient-derived cells, iPSC CRISPR knockin, mitotic spindle imaging, cell cycle analysis, and transcript-length RNA-seq\",\n      \"pmids\": [\"37980560\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Mechanism linking catalytic loss to spindle defects unresolved\", \"Single family/single lab\", \"Causality of CDKL5 dysregulation in phenotype not dissected\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Identified BRAT1 as a trimeric partner of INTS9–INTS11 required for recruiting the module to neuronal gene promoters.\",\n      \"evidence\": \"Co-IP in HEK293T and NT2 cells, ChIP-qPCR, BRAT1 knockdown, and mutant BRAT1 rescue (preprint)\",\n      \"pmids\": [\"37609215\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Preprint without full peer review\", \"Direct versus indirect recruitment mechanism not structurally resolved at this stage\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Defined INTS11's role in establishing promoter directionality by terminating antisense transcription, with CDK9 antagonizing its attenuation of sense transcription.\",\n      \"evidence\": \"Auxin-inducible degron depletion of INTS11, CDK9 inhibition and engineered tethering, and nascent RNA-seq\",\n      \"pmids\": [\"38976490\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Molecular basis of how CDK9 protects sense transcription not defined\", \"Whether antagonism operates through phosphorylation of Integrator subunits unresolved\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Resolved how BRAT1 stabilizes INTS11, showing it inserts into the active site to coordinate catalytic metals in the cytoplasm prior to nuclear Integrator function.\",\n      \"evidence\": \"Crystal/cryo-EM structures of human INTS9–INTS11–BRAT1 and Drosophila orthologs, active-site mutagenesis, co-IP, and neural organoid loss-of-function\",\n      \"pmids\": [\"39032490\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"How BRAT1 release permits catalysis after nuclear import not defined\", \"Dynamics of cytoplasmic-to-nuclear handoff unresolved\"]\n    },\n    {\n      \"year\": 2026,\n      \"claim\": \"Showed INTS11 chromatin binding maintains lengthened 3′UTR isoforms and mRNA stability at neuronal morphogenesis genes, with loss causing G1 arrest in neuroblasts.\",\n      \"evidence\": \"Drosophila MARCM clonal analysis, FUCCI reporter, single-cell RNA-seq, ChIP-qPCR, and live imaging\",\n      \"pmids\": [\"42035222\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Mechanism linking INTS11 to 3′UTR isoform length not defined\", \"Single lab/model organism\"]\n    },\n    {\n      \"year\": 2026,\n      \"claim\": \"Demonstrated in vivo that BRAT1 and INTS11 are jointly required for U snRNA 3′-end maturation, with ints11-null zebrafish recapitulating microcephaly and snRNA processing defects.\",\n      \"evidence\": \"RT-qPCR, western blotting, FISH in patient cells, and CRISPR/Cas9 ints11 knockout zebrafish\",\n      \"pmids\": [\"42116163\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Quantitative contribution of snRNA defect to microcephaly versus other Integrator functions not separated\", \"Single study\"]\n    },\n    {\n      \"year\": 2026,\n      \"claim\": \"Separated catalytic from non-catalytic functions of INTS11, showing maternal IntS11 acts upstream of pioneer factors for Pol II loading independent of endonuclease activity during zygotic genome activation.\",\n      \"evidence\": \"Maternal IntS11 depletion in Drosophila, CUT&RUN/ChIP for Pol II and pioneer factors, catalytically dead rescue, and genome-wide transcriptomics\",\n      \"pmids\": [\"41955115\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Molecular basis of enzyme-independent Pol II loading unknown\", \"Whether this function is conserved in mammals not established\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How the multiple INTS11 activities — snRNA processing, transcription attenuation/termination, PRC2-linked chromatin repression, and enzyme-independent Pol II loading — are coordinated or partitioned across cell types and developmental stages remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No unified model integrating catalytic and non-catalytic roles\", \"Mechanism of locus- and context-specific recruitment unknown\", \"Mammalian validation of pioneer-factor function lacking\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0140098\", \"supporting_discovery_ids\": [0, 1, 4, 8]},\n      {\"term_id\": \"GO:0016787\", \"supporting_discovery_ids\": [0, 1]},\n      {\"term_id\": \"GO:0003723\", \"supporting_discovery_ids\": [0, 7, 8]},\n      {\"term_id\": \"GO:0140110\", \"supporting_discovery_ids\": [4, 9]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [3, 4]},\n      {\"term_id\": \"GO:0005829\", \"supporting_discovery_ids\": [3]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-8953854\", \"supporting_discovery_ids\": [0, 8]},\n      {\"term_id\": \"R-HSA-74160\", \"supporting_discovery_ids\": [4, 9]},\n      {\"term_id\": \"R-HSA-4839726\", \"supporting_discovery_ids\": [2]}\n    ],\n    \"complexes\": [\"Integrator complex\", \"INTS9-INTS11 heterodimer\", \"INTS9-INTS11-BRAT1 complex\"],\n    \"partners\": [\"INTS9\", \"BRAT1\", \"PRC2\", \"CDK9\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":7,"faith_total":7,"faith_pct":100.0}}