{"gene":"INTS3","run_date":"2026-06-10T01:55:23","timeline":{"discoveries":[{"year":2009,"finding":"INTS3 (SOSS-A) serves as a central adaptor/scaffold protein required for assembly and stability of the heterotrimeric SOSS complex (consisting of hSSB1/2, INTS3, and C9orf80/SOSS-C), and is required for facilitating the accumulation of the SOSS complex to DNA ends. SOSS-depleted cells display increased ionizing radiation sensitivity, defective G2/M checkpoint, and impaired homologous recombination repair.","method":"Co-immunoprecipitation, tandem affinity purification, siRNA depletion with functional readouts (IR sensitivity, checkpoint assays, HR assays)","journal":"Molecular cell","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal Co-IP and functional cellular assays, independently replicated across multiple labs in the same year","pmids":["19683501"],"is_preprint":false},{"year":2009,"finding":"INTS3 forms separate but structurally similar complexes with hSSB1 and hSSB2, each also containing hSSBIP1 (C9ORF80). Depletion of INTS3 decreases the stability of hSSB1 and hSSBIP1, indicating INTS3 provides a scaffold for proper assembly. Cells depleted of INTS3 exhibit hypersensitivity to DNA-damaging reagents, chromosomal instability, and reduced ATM-dependent phosphorylation.","method":"Co-immunoprecipitation, siRNA depletion, cellular assays (survival, chromosomal instability, ATM signaling)","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal Co-IP with functional siRNA depletion studies, replicated independently from PMID:19683501","pmids":["19605351"],"is_preprint":false},{"year":2009,"finding":"INTS3 copurifies with a subset of Integrator complex subunits and C9orf80/MISE when pulled down with hSSB1. The INTS3-MISE-hSSB1 complex plays a key role in ATM activation and RAD51 recruitment to DNA damage foci. INTS3 controls hSSB1 transcription, demonstrating a regulatory network for hSSB1 function.","method":"Tandem affinity purification of hSSB1 mutants (phosphomimetic and non-phosphorylatable), mass spectrometry, functional assays (ATM activation, RAD51 foci)","journal":"The Journal of cell biology","confidence":"High","confidence_rationale":"Tier 2 / Moderate — tandem affinity purification with mass spectrometry plus functional validation, single lab with multiple orthogonal methods","pmids":["19786574"],"is_preprint":false},{"year":2013,"finding":"INTS6 is a major subunit of the core hSSB1 complex, forming a stable complex with INTS3 and hSSB1 both in vitro and in vivo. INTS6 directly interacts with INTS3. In response to DNA damage, INTS6 relocates along with INTS3 and hSSB1 to DNA damage sites. The hSSB1-INTS complex regulates the accumulation of RAD51 and BRCA1 at DNA damage sites and the corresponding homologous recombination.","method":"Protein affinity purification, co-immunoprecipitation, in vitro binding assay, immunofluorescence (foci formation), HR assay","journal":"Journal of cell science","confidence":"High","confidence_rationale":"Tier 2 / Moderate — reciprocal Co-IP, in vitro binding confirmation, and functional HR assay in single lab with multiple orthogonal methods","pmids":["23986477"],"is_preprint":false},{"year":2013,"finding":"mSSB1's interaction with INTS3 is required for its localization to damaged DNA, established in a mouse conditional knockout model. mSSB1 and mSSB2 localize to telomeres and are required to protect newly replicated telomeric G-overhangs.","method":"Conditional knockout mice, immunofluorescence, telomere dysfunction assays, co-immunoprecipitation","journal":"Cell research","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — genetic KO model with defined phenotype and Co-IP for localization dependency, but INTS3 mechanistic role is secondary finding","pmids":["23459151"],"is_preprint":false},{"year":2015,"finding":"Complexes containing INTS3 and either NABP1 or NABP2 are part of the Integrator complex, which binds RNA Polymerase II and regulates specific target genes. Integrator (including INTS3-containing complexes) binds to 3' ends of replication-dependent histones and promoter-proximal regions of polyadenylated-transcript genes; depletion of Integrator subunits causes transcription termination failure, disruption of histone mRNA processing, and polyadenylation of snRNAs and histone mRNAs. Integrator recruitment to all three gene classes is DSIF-dependent.","method":"Affinity purification, HIV Integration targeting-sequencing (HIT-Seq), subunit depletion with RNA processing readouts","journal":"Cell research","confidence":"High","confidence_rationale":"Tier 2 / Strong — affinity purification combined with genome-wide sequencing and functional depletion assays in single rigorous study","pmids":["25675981"],"is_preprint":false},{"year":2015,"finding":"INTS3 interacts with RUNX2 and BAZ1B as part of subnuclear, nuclear-matrix-associated complexes in cancer cells. RUNX2, INTS3, and BAZ1B form UV-responsive complexes with γH2AX (phospho-H2AX Ser139) following DNA damage. Subnuclear foci containing INTS3 change in intensity or number following UV irradiation.","method":"Proteomic analysis (nuclear matrix pulldown), co-immunoprecipitation, immunofluorescence","journal":"Journal of cell science","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — proteomic pulldown and Co-IP with immunofluorescence, but mechanistic role of INTS3 in this complex not deeply characterized","pmids":["25609707"],"is_preprint":false},{"year":2015,"finding":"In the absence of RPA, hSSB1 and INTS3 form subnuclear foci, associate with the ATR-ATRIP complex, and recruit it to sites of genomic stress. ATRIP foci formed after RPA depletion are abrogated upon INTS3 depletion, establishing that the hSSB-INTS3 complex recruits the ATR-ATRIP checkpoint complex. Depletion of hSSB1/2 and INTS3 in RPA-deficient cells attenuates Chk1 phosphorylation.","method":"siRNA depletion, co-immunoprecipitation, immunofluorescence (foci), Chk1 phosphorylation assay","journal":"Nucleic acids research","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — functional siRNA epistasis with biochemical readouts, single lab with multiple methods","pmids":["25916848"],"is_preprint":false},{"year":2017,"finding":"hSSB1 can interact with INTS3 even when hSSB1 forms tetramers under oxidizing conditions, establishing that hSSB1 oligomerization does not preclude its interaction with INTS3 in the SOSS1 complex.","method":"Solution NMR, biophysical assays, co-immunoprecipitation","journal":"Nucleic acids research","confidence":"Medium","confidence_rationale":"Tier 1-2 / Weak — NMR structural model combined with functional Co-IP, single lab","pmids":["28609781"],"is_preprint":false},{"year":2018,"finding":"INTS3 displays higher affinity toward ssRNA than ssDNA, requires a minimum of 30 nucleotides for binding, and does not bind dsDNA, dsRNA, or RNA:DNA hybrids. The N-terminus of INTS3 mediates protein-protein interactions, while the C-terminus is required for nucleic acid binding. In the reconstituted heterotrimeric complex, INTS3 (but not C9ORF80) affects the nucleic acid-binding ability of hNABP1 and hNABP2, suggesting INTS3 regulates their biological function.","method":"EMSA, GST pulldown, recombinant protein purification, gel filtration","journal":"The Biochemical journal","confidence":"High","confidence_rationale":"Tier 1 / Moderate — in vitro reconstitution with recombinant proteins, EMSA with domain mapping, single lab with multiple orthogonal methods","pmids":["29150435"],"is_preprint":false},{"year":2020,"finding":"The crystal structure of the Ints3 C-terminal domain reveals a HEAT-repeat superhelical fold that forms a stable dimer. The C-terminal dimer has a basic groove that binds ssRNA/ssDNA and a separate surface of conserved residues that binds INTS6. Dimerization is required for nucleic acid binding but not for INTS6 binding. In vitro experiments showed that INTS6 interaction is critical for maintaining SSB1 protein level.","method":"X-ray crystallography, mutagenesis, EMSA, co-immunoprecipitation, in vitro protein stability assay in HEK293T cells","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1 / Strong — crystal structure combined with mutagenesis and functional validation, multiple orthogonal methods in single rigorous study","pmids":["33434574"],"is_preprint":false},{"year":2021,"finding":"The crystal structure of the INTS3 C-terminus (INTS3c) in complex with the INTS6 C-terminus (INTS6c) at 2.4 Å resolution reveals that two INTS3c subunits dimerize and interact with INTS6c via conserved residues. INTS3c dimerization is important for recognizing longer ssDNA. Perturbation of INTS3c dimerization and disruption of the INTS3c/INTS6c interaction impair DSB repair.","method":"X-ray crystallography, biochemical binding assays, mutagenesis, DSB repair functional assay","journal":"Cell discovery","confidence":"High","confidence_rationale":"Tier 1 / Strong — crystal structure at 2.4 Å combined with mutagenesis and functional DSB repair assay, orthogonal to and consistent with PMID:33434574","pmids":["34400606"],"is_preprint":false},{"year":2022,"finding":"PARP1 binds directly to INTS3 (IntS3) via PARP1's C-terminal domain interacting with INTS3's C-terminal domain. The chromatin occupancy of INTS3 along PARP1 target genes mimics PARP1 occupancy. Knockdown of PARP1 results in differential chromatin association and gene occupancy of INTS3, and this effect is due to the physical presence of PARP1 rather than its PARylation activity.","method":"Co-immunoprecipitation (in vivo and in vitro), ChIP-seq, siRNA knockdown","journal":"Cells","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct binding confirmed in vitro and in vivo, ChIP-seq occupancy analysis, single lab","pmids":["36291070"],"is_preprint":false},{"year":2023,"finding":"The damage-activated tyrosine kinase c-Abl phosphorylates hSSB1, enabling its interaction with tyrosine-1-phosphorylated RNA Pol II (Y1P RNAPII) at DSBs. The trimeric SOSS1 complex (hSSB1, INTS3, c9orf80) binds to Y1P RNAPII in response to DNA damage in an R-loop-dependent manner, and the complex exhibits strong affinity for R-loops. The SOSS1 complex and RNAPII form dynamic liquid-like (liquid-liquid phase separation) repair compartments at DSBs, and depletion of the SOSS1 complex impairs DNA repair.","method":"Co-immunoprecipitation, in vitro binding assay, immunofluorescence, live-cell imaging (liquid droplet/phase separation assays), siRNA depletion with DNA repair readouts","journal":"Cell reports","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — multiple biochemical and cell biological methods in single lab, phase separation validated in vitro and in vivo","pmids":["38039132"],"is_preprint":false},{"year":2023,"finding":"INTS3 interacts with Nbs1 (of the MRN complex) via a phosphorylation-dependent mechanism: the forkhead-associated (FHA) domain of Nbs1 binds INTS3 at phospho-Threonine 592, with contributions from Serine 590. This interaction provides a mechanism for MRN complex recruitment to DSBs via INTS3.","method":"In silico modeling, biochemical binding assays (pulldown), phosphopeptide binding assays, functional cellular assays","journal":"Protein science","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — phosphorylation-dependent binding established biochemically with site-specific mutants, single lab","pmids":["37705456"],"is_preprint":false},{"year":2024,"finding":"Cryo-EM structures of the complete Integrator-PP2A complex reveal that the previously unresolved INTS3 subunit and associated SOSS factors, in the post-termination complex state, occupy a position that prevents Pol II rebinding to Integrator after transcription termination.","method":"Cryo-electron microscopy (three structures in different functional states)","journal":"Nature","confidence":"High","confidence_rationale":"Tier 1 / Strong — cryo-EM structures of complete complex in multiple functional states provide direct structural evidence for INTS3 role in post-termination","pmids":["38570683"],"is_preprint":false},{"year":2024,"finding":"INTS6 associates with the heterotrimeric SOSS1 complex (INTS3, INIP/c9orf80, hSSB1) to form a tetrameric SOSS1 complex. INTS6 binds to DNA:RNA hybrids, promotes PP2A recruitment to DSBs to facilitate dephosphorylation of RNAPII, prevents accumulation of damage-associated RNA transcripts (DARTs), and promotes senataxin (SETX) recruitment to DSBs for R-loop resolution.","method":"Co-immunoprecipitation, in vitro binding assays, immunofluorescence, functional assays (RNAPII phosphorylation, R-loop accumulation, SETX recruitment)","journal":"Nucleic acids research","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — multiple biochemical methods, single lab; INTS3 role as scaffold of tetrameric complex confirmed","pmids":["39445827"],"is_preprint":false},{"year":2024,"finding":"INTS3 deletion triggers apoptosis in colorectal cancer cells. INTS3 destabilizes pro-apoptotic gene transcripts, contributing to cancer cell survival. INTS3 loss delays CRC cell growth in vivo, identifying INTS3 as an RNA-binding protein with an anti-apoptotic role in CRC.","method":"CRISPR-Cas9 screen, siRNA knockdown, RNA sequencing, in vivo tumor growth assay, nanoparticle-mediated knockdown","journal":"iScience","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — CRISPR screen followed by validation with RNA-seq and in vivo assay, single lab","pmids":["38665208"],"is_preprint":false},{"year":2022,"finding":"Knockdown of SPT6 causes loss of INTS3 from U2 snRNA genes, indicating SPT6 is required for INTS3 recruitment/retention at snRNA gene loci.","method":"ChIP-seq, ChIP-qPCR, siRNA knockdown","journal":"Biomolecules","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single ChIP-based observation, secondary finding in a study focused on U2 snRNA gene factors","pmids":["35625631"],"is_preprint":false}],"current_model":"INTS3 functions as a scaffold subunit of the heterotrimeric SOSS1 complex (with hSSB1/2 and C9ORF80/INIP), where its N-terminus mediates protein-protein interactions and its HEAT-repeat C-terminal domain dimerizes to bind ssDNA/ssRNA and interact with INTS6, enabling assembly, stabilization, and ssDNA-end accumulation of the complex at DNA double-strand breaks to promote ATM/ATR signaling, RAD51/BRCA1 recruitment, and homologous recombination repair; INTS3 is also an integral subunit of the Integrator complex where cryo-EM structures reveal it occupies a post-termination position that prevents Pol II rebinding after transcription termination, and where it regulates snRNA processing, histone mRNA processing, and promoter-proximal pausing at DSIF-dependent Pol II pause sites."},"narrative":{"mechanistic_narrative":"INTS3 is a dual-function scaffold protein that links single-stranded nucleic acid recognition to genome stability and RNA Polymerase II transcription regulation [PMID:19683501, PMID:25675981]. As the central adaptor of the heterotrimeric SOSS1 complex (with hSSB1/2 and C9ORF80/INIP), INTS3 is required for assembly and stability of its partners and for accumulation of the complex at DNA ends, such that its loss confers ionizing-radiation sensitivity, defective G2/M checkpoint, chromosomal instability, and impaired homologous recombination [PMID:19683501, PMID:19605351]. Domain dissection shows a bipartite architecture: the N-terminus mediates protein-protein interactions while the HEAT-repeat C-terminal domain forms a stable dimer that binds ssRNA/ssDNA (with higher affinity for ssRNA and a ~30-nt minimum, excluding duplexes and hybrids) and simultaneously docks INTS6 on a separate conserved surface; dimerization and the INTS3c/INTS6c interface are both required for efficient ssDNA recognition and double-strand break repair [PMID:29150435, PMID:33434574, PMID:34400606]. Through these activities INTS3 promotes ATM/ATR-ATRIP checkpoint signaling, Chk1 phosphorylation, and the recruitment of RAD51 and BRCA1 to damage sites [PMID:19786574, PMID:23986477, PMID:25916848]. At breaks, the SOSS1 complex engages transcription-associated structures, binding R-loops and tyrosine-1-phosphorylated RNAPII to nucleate liquid-like repair compartments, and recruits the MRN complex via a phospho-dependent Nbs1-FHA interaction [PMID:38039132, PMID:37705456]. INTS3 is also an integral subunit of the Integrator complex, where it regulates snRNA processing, replication-dependent histone mRNA 3'-end processing, and promoter-proximal Pol II pausing in a DSIF-dependent manner [PMID:25675981]; cryo-EM of the Integrator-PP2A complex places INTS3 in a post-termination position that blocks Pol II rebinding after termination [PMID:38570683]. Consistent with an RNA-regulatory role, INTS3 destabilizes pro-apoptotic transcripts to support colorectal cancer cell survival [PMID:38665208].","teleology":[{"year":2009,"claim":"Established INTS3 as the organizing scaffold of a DNA-damage-response complex, answering how single-stranded DNA-binding factors are stabilized and delivered to DNA ends.","evidence":"Reciprocal Co-IP, tandem affinity purification, and siRNA depletion with IR-sensitivity, checkpoint, and HR readouts in human cells","pmids":["19683501","19605351","19786574"],"confidence":"High","gaps":["Did not define the structural basis of scaffolding","Direct nucleic-acid binding by INTS3 itself not yet shown","Relationship to Integrator transcription functions unaddressed"]},{"year":2013,"claim":"Identified INTS6 as a direct INTS3 partner that co-relocates to damage sites, extending the complex and linking it to RAD51/BRCA1 accumulation and HR.","evidence":"Affinity purification, in vitro binding, immunofluorescence foci, and HR assays; mouse conditional KO confirming SSB1 localization depends on INTS3","pmids":["23986477","23459151"],"confidence":"High","gaps":["INTS6-INTS3 binding interface not structurally defined","Mechanism of RAD51/BRCA1 recruitment downstream unresolved"]},{"year":2015,"claim":"Placed INTS3 within the Integrator complex on RNA Pol II and showed it functions in checkpoint signaling when RPA is limiting, connecting transcription machinery to DNA-damage response.","evidence":"Affinity purification with HIT-Seq and RNA-processing depletion assays; siRNA epistasis with ATR-ATRIP foci and Chk1 phosphorylation readouts; nuclear-matrix proteomics","pmids":["25675981","25916848","25609707"],"confidence":"High","gaps":["How INTS3 partitions between SOSS1 and Integrator roles unclear","Direct vs indirect role in snRNA/histone processing not separated for INTS3 specifically"]},{"year":2018,"claim":"Mapped INTS3 nucleic-acid binding to its C-terminus and protein interactions to its N-terminus, and showed it tunes hNABP1/2 binding, defining a bipartite functional architecture.","evidence":"EMSA, GST pulldown, and reconstitution with recombinant proteins; NMR showing hSSB1 tetramers retain INTS3 binding","pmids":["29150435","28609781"],"confidence":"High","gaps":["Atomic structure of binding domains not yet determined","Physiological significance of ssRNA preference unresolved"]},{"year":2021,"claim":"Crystal structures defined the HEAT-repeat C-terminal domain as a dimer that binds ssDNA/ssRNA and INTS6 via distinct surfaces, with both dimerization and the INTS6 interface required for DSB repair.","evidence":"X-ray crystallography of INTS3c and INTS3c-INTS6c, mutagenesis, EMSA, protein-stability assays, and DSB repair functional assays","pmids":["33434574","34400606"],"confidence":"High","gaps":["Structure of full-length INTS3 with hSSB1/C9ORF80 not solved","How dimerization couples to in vivo end resection unclear"]},{"year":2023,"claim":"Connected SOSS1 to transcription-coupled repair, showing it binds R-loops and Y1P RNAPII to form phase-separated repair compartments and recruits MRN via a phospho-Nbs1 interaction.","evidence":"Co-IP, in vitro binding, live-cell phase-separation imaging, siRNA repair assays; phosphopeptide binding with site-specific INTS3 mutants","pmids":["38039132","37705456"],"confidence":"Medium","gaps":["In vivo requirement of phase separation for repair not genetically isolated","Kinase responsible for INTS3 T592 phosphorylation not identified"]},{"year":2024,"claim":"Cryo-EM resolved INTS3 within the Integrator-PP2A complex in a post-termination position that prevents Pol II rebinding, and INTS6 was shown to extend SOSS1 to a tetramer coupling PP2A/SETX to R-loop resolution.","evidence":"Cryo-EM of Integrator-PP2A in multiple functional states; Co-IP and functional assays of tetrameric SOSS1 with RNAPII dephosphorylation and SETX recruitment readouts","pmids":["38570683","39445827"],"confidence":"High","gaps":["Structural state of INTS3 during active termination vs post-termination transition partly inferred","How the same INTS3 surface is shared between Integrator and SOSS1 roles in vivo unresolved"]},{"year":2024,"claim":"Defined an RNA-regulatory, anti-apoptotic role for INTS3 in cancer, destabilizing pro-apoptotic transcripts to sustain colorectal tumor cell survival.","evidence":"CRISPR-Cas9 screen, siRNA/RNA-seq, and in vivo tumor-growth assays with nanoparticle knockdown","pmids":["38665208"],"confidence":"Medium","gaps":["Direct transcript targets and binding sites not mapped","Whether this depends on Integrator or SOSS1 context unknown"]},{"year":2022,"claim":"Linked INTS3 chromatin occupancy to PARP1 and SPT6, indicating its genomic recruitment is directed by transcription-associated factors.","evidence":"Co-IP, ChIP-seq, and siRNA knockdown for PARP1; ChIP-based loss-of-recruitment for SPT6 at U2 snRNA genes","pmids":["36291070","35625631"],"confidence":"Medium","gaps":["SPT6 dependency rests on a single ChIP observation","Functional consequence of PARP1-directed INTS3 occupancy not established"]},{"year":null,"claim":"How INTS3 is partitioned between its SOSS1 DNA-repair role and its Integrator transcription-termination role, and whether the two functions are competitive or coordinated, remains unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No structure of full-length INTS3 simultaneously engaging both complexes","Regulatory switch governing complex choice unknown","Quantitative cellular distribution between the two roles unmeasured"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0003723","term_label":"RNA binding","supporting_discovery_ids":[9,17]},{"term_id":"GO:0003677","term_label":"DNA binding","supporting_discovery_ids":[9,10,11]},{"term_id":"GO:0060090","term_label":"molecular adaptor activity","supporting_discovery_ids":[0,1,9]},{"term_id":"GO:0005198","term_label":"structural molecule activity","supporting_discovery_ids":[0,1,15]}],"localization":[{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[6,7]},{"term_id":"GO:0000228","term_label":"nuclear chromosome","supporting_discovery_ids":[3,13]}],"pathway":[{"term_id":"R-HSA-73894","term_label":"DNA Repair","supporting_discovery_ids":[0,3,11]},{"term_id":"R-HSA-74160","term_label":"Gene expression (Transcription)","supporting_discovery_ids":[5,15]},{"term_id":"R-HSA-8953854","term_label":"Metabolism of RNA","supporting_discovery_ids":[5,16]},{"term_id":"R-HSA-1640170","term_label":"Cell Cycle","supporting_discovery_ids":[0]}],"complexes":["SOSS1 complex","Integrator complex","Integrator-PP2A complex"],"partners":["SSB1","C9ORF80","INTS6","NBN","PARP1","RNAPII","RUNX2","BAZ1B"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q68E01","full_name":"Integrator complex subunit 3","aliases":["SOSS complex subunit A","Sensor of single-strand DNA complex subunit A","SOSS-A","Sensor of ssDNA subunit A"],"length_aa":1043,"mass_kda":118.1,"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). 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:16239144). Within the integrator complex, INTS3 is involved in the post-termination step: INTS3 binds INTS7 in the open conformation of integrator complex and prevents the rebinding of Pol II to the integrator after termination cycle (PubMed:38570683). Mediates recruitment of cytoplasmic dynein to the nuclear envelope, probably as component of the integrator complex (PubMed:23904267) Component of the SOSS complex, a multiprotein complex that functions downstream of the MRN complex to promote DNA repair and G2/M checkpoint. The SOSS complex associates with single-stranded DNA at DNA lesions and influences diverse endpoints in the cellular DNA damage response including cell-cycle checkpoint activation, recombinational repair and maintenance of genomic stability. The SOSS complex is required for efficient homologous recombination-dependent repair of double-strand breaks (DSBs) and ATM-dependent signaling pathways. In the SOSS complex, it is required for the assembly of the complex and for stabilization of the complex at DNA damage sites","subcellular_location":"Nucleus; Cytoplasm","url":"https://www.uniprot.org/uniprotkb/Q68E01/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":true,"resolved_as":"","url":"https://depmap.org/portal/gene/INTS3","classification":"Common Essential","n_dependent_lines":1205,"n_total_lines":1208,"dependency_fraction":0.9975165562913907},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[{"gene":"INTS9","stoichiometry":10.0},{"gene":"INTS14","stoichiometry":4.0},{"gene":"CDS2","stoichiometry":0.2},{"gene":"HIST2H2BE","stoichiometry":0.2},{"gene":"HMGA1","stoichiometry":0.2},{"gene":"HMGN5","stoichiometry":0.2},{"gene":"NUCKS1","stoichiometry":0.2},{"gene":"NUMA1","stoichiometry":0.2},{"gene":"POLR2B","stoichiometry":0.2},{"gene":"POLR2E","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/search/INTS3","total_profiled":1310},"omim":[{"mim_id":"613273","title":"INST3- AND NABP-INTERACTING PROTEIN; INIP","url":"https://www.omim.org/entry/613273"},{"mim_id":"611479","title":"GPN-LOOP GTPase 1; GPN1","url":"https://www.omim.org/entry/611479"},{"mim_id":"611477","title":"RNA POLYMERASE II-ASSOCIATED PROTEIN 3; RPAP3","url":"https://www.omim.org/entry/611477"},{"mim_id":"611476","title":"RNA POLYMERASE II-ASSOCIATED PROTEIN 2; RPAP2","url":"https://www.omim.org/entry/611476"},{"mim_id":"611475","title":"RNA POLYMERASE II-ASSOCIATED PROTEIN 1; RPAP1","url":"https://www.omim.org/entry/611475"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Approved","locations":[{"location":"Nucleoli","reliability":"Approved"},{"location":"Nucleoplasm","reliability":"Additional"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/INTS3"},"hgnc":{"alias_symbol":["FLJ21919","INT3","SOSS-A"],"prev_symbol":["C1orf60"]},"alphafold":{"accession":"Q68E01","domains":[{"cath_id":"-","chopping":"44-132","consensus_level":"medium","plddt":95.597,"start":44,"end":132},{"cath_id":"-","chopping":"204-306","consensus_level":"medium","plddt":96.1454,"start":204,"end":306},{"cath_id":"-","chopping":"562-720","consensus_level":"medium","plddt":90.6922,"start":562,"end":720},{"cath_id":"1.25.40","chopping":"307-498","consensus_level":"high","plddt":94.5725,"start":307,"end":498},{"cath_id":"1.25.40","chopping":"853-901_920-976","consensus_level":"high","plddt":89.4217,"start":853,"end":976}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q68E01","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q68E01-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q68E01-F1-predicted_aligned_error_v6.png","plddt_mean":83.06},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=INTS3","jax_strain_url":"https://www.jax.org/strain/search?query=INTS3"},"sequence":{"accession":"Q68E01","fasta_url":"https://rest.uniprot.org/uniprotkb/Q68E01.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q68E01/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q68E01"}},"corpus_meta":[{"pmid":"31578525","id":"PMC_31578525","title":"Coordinated 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SOSS-depleted cells display increased ionizing radiation sensitivity, defective G2/M checkpoint, and impaired homologous recombination repair.\",\n      \"method\": \"Co-immunoprecipitation, tandem affinity purification, siRNA depletion with functional readouts (IR sensitivity, checkpoint assays, HR assays)\",\n      \"journal\": \"Molecular cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal Co-IP and functional cellular assays, independently replicated across multiple labs in the same year\",\n      \"pmids\": [\"19683501\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2009,\n      \"finding\": \"INTS3 forms separate but structurally similar complexes with hSSB1 and hSSB2, each also containing hSSBIP1 (C9ORF80). Depletion of INTS3 decreases the stability of hSSB1 and hSSBIP1, indicating INTS3 provides a scaffold for proper assembly. Cells depleted of INTS3 exhibit hypersensitivity to DNA-damaging reagents, chromosomal instability, and reduced ATM-dependent phosphorylation.\",\n      \"method\": \"Co-immunoprecipitation, siRNA depletion, cellular assays (survival, chromosomal instability, ATM signaling)\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal Co-IP with functional siRNA depletion studies, replicated independently from PMID:19683501\",\n      \"pmids\": [\"19605351\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2009,\n      \"finding\": \"INTS3 copurifies with a subset of Integrator complex subunits and C9orf80/MISE when pulled down with hSSB1. The INTS3-MISE-hSSB1 complex plays a key role in ATM activation and RAD51 recruitment to DNA damage foci. INTS3 controls hSSB1 transcription, demonstrating a regulatory network for hSSB1 function.\",\n      \"method\": \"Tandem affinity purification of hSSB1 mutants (phosphomimetic and non-phosphorylatable), mass spectrometry, functional assays (ATM activation, RAD51 foci)\",\n      \"journal\": \"The Journal of cell biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — tandem affinity purification with mass spectrometry plus functional validation, single lab with multiple orthogonal methods\",\n      \"pmids\": [\"19786574\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"INTS6 is a major subunit of the core hSSB1 complex, forming a stable complex with INTS3 and hSSB1 both in vitro and in vivo. INTS6 directly interacts with INTS3. In response to DNA damage, INTS6 relocates along with INTS3 and hSSB1 to DNA damage sites. The hSSB1-INTS complex regulates the accumulation of RAD51 and BRCA1 at DNA damage sites and the corresponding homologous recombination.\",\n      \"method\": \"Protein affinity purification, co-immunoprecipitation, in vitro binding assay, immunofluorescence (foci formation), HR assay\",\n      \"journal\": \"Journal of cell science\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal Co-IP, in vitro binding confirmation, and functional HR assay in single lab with multiple orthogonal methods\",\n      \"pmids\": [\"23986477\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"mSSB1's interaction with INTS3 is required for its localization to damaged DNA, established in a mouse conditional knockout model. mSSB1 and mSSB2 localize to telomeres and are required to protect newly replicated telomeric G-overhangs.\",\n      \"method\": \"Conditional knockout mice, immunofluorescence, telomere dysfunction assays, co-immunoprecipitation\",\n      \"journal\": \"Cell research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — genetic KO model with defined phenotype and Co-IP for localization dependency, but INTS3 mechanistic role is secondary finding\",\n      \"pmids\": [\"23459151\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"Complexes containing INTS3 and either NABP1 or NABP2 are part of the Integrator complex, which binds RNA Polymerase II and regulates specific target genes. Integrator (including INTS3-containing complexes) binds to 3' ends of replication-dependent histones and promoter-proximal regions of polyadenylated-transcript genes; depletion of Integrator subunits causes transcription termination failure, disruption of histone mRNA processing, and polyadenylation of snRNAs and histone mRNAs. Integrator recruitment to all three gene classes is DSIF-dependent.\",\n      \"method\": \"Affinity purification, HIV Integration targeting-sequencing (HIT-Seq), subunit depletion with RNA processing readouts\",\n      \"journal\": \"Cell research\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — affinity purification combined with genome-wide sequencing and functional depletion assays in single rigorous study\",\n      \"pmids\": [\"25675981\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"INTS3 interacts with RUNX2 and BAZ1B as part of subnuclear, nuclear-matrix-associated complexes in cancer cells. RUNX2, INTS3, and BAZ1B form UV-responsive complexes with γH2AX (phospho-H2AX Ser139) following DNA damage. Subnuclear foci containing INTS3 change in intensity or number following UV irradiation.\",\n      \"method\": \"Proteomic analysis (nuclear matrix pulldown), co-immunoprecipitation, immunofluorescence\",\n      \"journal\": \"Journal of cell science\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — proteomic pulldown and Co-IP with immunofluorescence, but mechanistic role of INTS3 in this complex not deeply characterized\",\n      \"pmids\": [\"25609707\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"In the absence of RPA, hSSB1 and INTS3 form subnuclear foci, associate with the ATR-ATRIP complex, and recruit it to sites of genomic stress. ATRIP foci formed after RPA depletion are abrogated upon INTS3 depletion, establishing that the hSSB-INTS3 complex recruits the ATR-ATRIP checkpoint complex. Depletion of hSSB1/2 and INTS3 in RPA-deficient cells attenuates Chk1 phosphorylation.\",\n      \"method\": \"siRNA depletion, co-immunoprecipitation, immunofluorescence (foci), Chk1 phosphorylation assay\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — functional siRNA epistasis with biochemical readouts, single lab with multiple methods\",\n      \"pmids\": [\"25916848\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"hSSB1 can interact with INTS3 even when hSSB1 forms tetramers under oxidizing conditions, establishing that hSSB1 oligomerization does not preclude its interaction with INTS3 in the SOSS1 complex.\",\n      \"method\": \"Solution NMR, biophysical assays, co-immunoprecipitation\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1-2 / Weak — NMR structural model combined with functional Co-IP, single lab\",\n      \"pmids\": [\"28609781\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"INTS3 displays higher affinity toward ssRNA than ssDNA, requires a minimum of 30 nucleotides for binding, and does not bind dsDNA, dsRNA, or RNA:DNA hybrids. The N-terminus of INTS3 mediates protein-protein interactions, while the C-terminus is required for nucleic acid binding. In the reconstituted heterotrimeric complex, INTS3 (but not C9ORF80) affects the nucleic acid-binding ability of hNABP1 and hNABP2, suggesting INTS3 regulates their biological function.\",\n      \"method\": \"EMSA, GST pulldown, recombinant protein purification, gel filtration\",\n      \"journal\": \"The Biochemical journal\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — in vitro reconstitution with recombinant proteins, EMSA with domain mapping, single lab with multiple orthogonal methods\",\n      \"pmids\": [\"29150435\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"The crystal structure of the Ints3 C-terminal domain reveals a HEAT-repeat superhelical fold that forms a stable dimer. The C-terminal dimer has a basic groove that binds ssRNA/ssDNA and a separate surface of conserved residues that binds INTS6. Dimerization is required for nucleic acid binding but not for INTS6 binding. In vitro experiments showed that INTS6 interaction is critical for maintaining SSB1 protein level.\",\n      \"method\": \"X-ray crystallography, mutagenesis, EMSA, co-immunoprecipitation, in vitro protein stability assay in HEK293T cells\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — crystal structure combined with mutagenesis and functional validation, multiple orthogonal methods in single rigorous study\",\n      \"pmids\": [\"33434574\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"The crystal structure of the INTS3 C-terminus (INTS3c) in complex with the INTS6 C-terminus (INTS6c) at 2.4 Å resolution reveals that two INTS3c subunits dimerize and interact with INTS6c via conserved residues. INTS3c dimerization is important for recognizing longer ssDNA. Perturbation of INTS3c dimerization and disruption of the INTS3c/INTS6c interaction impair DSB repair.\",\n      \"method\": \"X-ray crystallography, biochemical binding assays, mutagenesis, DSB repair functional assay\",\n      \"journal\": \"Cell discovery\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — crystal structure at 2.4 Å combined with mutagenesis and functional DSB repair assay, orthogonal to and consistent with PMID:33434574\",\n      \"pmids\": [\"34400606\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"PARP1 binds directly to INTS3 (IntS3) via PARP1's C-terminal domain interacting with INTS3's C-terminal domain. The chromatin occupancy of INTS3 along PARP1 target genes mimics PARP1 occupancy. Knockdown of PARP1 results in differential chromatin association and gene occupancy of INTS3, and this effect is due to the physical presence of PARP1 rather than its PARylation activity.\",\n      \"method\": \"Co-immunoprecipitation (in vivo and in vitro), ChIP-seq, siRNA knockdown\",\n      \"journal\": \"Cells\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct binding confirmed in vitro and in vivo, ChIP-seq occupancy analysis, single lab\",\n      \"pmids\": [\"36291070\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"The damage-activated tyrosine kinase c-Abl phosphorylates hSSB1, enabling its interaction with tyrosine-1-phosphorylated RNA Pol II (Y1P RNAPII) at DSBs. The trimeric SOSS1 complex (hSSB1, INTS3, c9orf80) binds to Y1P RNAPII in response to DNA damage in an R-loop-dependent manner, and the complex exhibits strong affinity for R-loops. The SOSS1 complex and RNAPII form dynamic liquid-like (liquid-liquid phase separation) repair compartments at DSBs, and depletion of the SOSS1 complex impairs DNA repair.\",\n      \"method\": \"Co-immunoprecipitation, in vitro binding assay, immunofluorescence, live-cell imaging (liquid droplet/phase separation assays), siRNA depletion with DNA repair readouts\",\n      \"journal\": \"Cell reports\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple biochemical and cell biological methods in single lab, phase separation validated in vitro and in vivo\",\n      \"pmids\": [\"38039132\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"INTS3 interacts with Nbs1 (of the MRN complex) via a phosphorylation-dependent mechanism: the forkhead-associated (FHA) domain of Nbs1 binds INTS3 at phospho-Threonine 592, with contributions from Serine 590. This interaction provides a mechanism for MRN complex recruitment to DSBs via INTS3.\",\n      \"method\": \"In silico modeling, biochemical binding assays (pulldown), phosphopeptide binding assays, functional cellular assays\",\n      \"journal\": \"Protein science\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — phosphorylation-dependent binding established biochemically with site-specific mutants, single lab\",\n      \"pmids\": [\"37705456\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"Cryo-EM structures of the complete Integrator-PP2A complex reveal that the previously unresolved INTS3 subunit and associated SOSS factors, in the post-termination complex state, occupy a position that prevents Pol II rebinding to Integrator after transcription termination.\",\n      \"method\": \"Cryo-electron microscopy (three structures in different functional states)\",\n      \"journal\": \"Nature\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — cryo-EM structures of complete complex in multiple functional states provide direct structural evidence for INTS3 role in post-termination\",\n      \"pmids\": [\"38570683\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"INTS6 associates with the heterotrimeric SOSS1 complex (INTS3, INIP/c9orf80, hSSB1) to form a tetrameric SOSS1 complex. INTS6 binds to DNA:RNA hybrids, promotes PP2A recruitment to DSBs to facilitate dephosphorylation of RNAPII, prevents accumulation of damage-associated RNA transcripts (DARTs), and promotes senataxin (SETX) recruitment to DSBs for R-loop resolution.\",\n      \"method\": \"Co-immunoprecipitation, in vitro binding assays, immunofluorescence, functional assays (RNAPII phosphorylation, R-loop accumulation, SETX recruitment)\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple biochemical methods, single lab; INTS3 role as scaffold of tetrameric complex confirmed\",\n      \"pmids\": [\"39445827\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"INTS3 deletion triggers apoptosis in colorectal cancer cells. INTS3 destabilizes pro-apoptotic gene transcripts, contributing to cancer cell survival. INTS3 loss delays CRC cell growth in vivo, identifying INTS3 as an RNA-binding protein with an anti-apoptotic role in CRC.\",\n      \"method\": \"CRISPR-Cas9 screen, siRNA knockdown, RNA sequencing, in vivo tumor growth assay, nanoparticle-mediated knockdown\",\n      \"journal\": \"iScience\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — CRISPR screen followed by validation with RNA-seq and in vivo assay, single lab\",\n      \"pmids\": [\"38665208\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"Knockdown of SPT6 causes loss of INTS3 from U2 snRNA genes, indicating SPT6 is required for INTS3 recruitment/retention at snRNA gene loci.\",\n      \"method\": \"ChIP-seq, ChIP-qPCR, siRNA knockdown\",\n      \"journal\": \"Biomolecules\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single ChIP-based observation, secondary finding in a study focused on U2 snRNA gene factors\",\n      \"pmids\": [\"35625631\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"INTS3 functions as a scaffold subunit of the heterotrimeric SOSS1 complex (with hSSB1/2 and C9ORF80/INIP), where its N-terminus mediates protein-protein interactions and its HEAT-repeat C-terminal domain dimerizes to bind ssDNA/ssRNA and interact with INTS6, enabling assembly, stabilization, and ssDNA-end accumulation of the complex at DNA double-strand breaks to promote ATM/ATR signaling, RAD51/BRCA1 recruitment, and homologous recombination repair; INTS3 is also an integral subunit of the Integrator complex where cryo-EM structures reveal it occupies a post-termination position that prevents Pol II rebinding after transcription termination, and where it regulates snRNA processing, histone mRNA processing, and promoter-proximal pausing at DSIF-dependent Pol II pause sites.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"INTS3 is a dual-function scaffold protein that links single-stranded nucleic acid recognition to genome stability and RNA Polymerase II transcription regulation [#0, #5]. As the central adaptor of the heterotrimeric SOSS1 complex (with hSSB1/2 and C9ORF80/INIP), INTS3 is required for assembly and stability of its partners and for accumulation of the complex at DNA ends, such that its loss confers ionizing-radiation sensitivity, defective G2/M checkpoint, chromosomal instability, and impaired homologous recombination [#0, #1]. Domain dissection shows a bipartite architecture: the N-terminus mediates protein-protein interactions while the HEAT-repeat C-terminal domain forms a stable dimer that binds ssRNA/ssDNA (with higher affinity for ssRNA and a ~30-nt minimum, excluding duplexes and hybrids) and simultaneously docks INTS6 on a separate conserved surface; dimerization and the INTS3c/INTS6c interface are both required for efficient ssDNA recognition and double-strand break repair [#9, #10, #11]. Through these activities INTS3 promotes ATM/ATR-ATRIP checkpoint signaling, Chk1 phosphorylation, and the recruitment of RAD51 and BRCA1 to damage sites [#2, #3, #7]. At breaks, the SOSS1 complex engages transcription-associated structures, binding R-loops and tyrosine-1-phosphorylated RNAPII to nucleate liquid-like repair compartments, and recruits the MRN complex via a phospho-dependent Nbs1-FHA interaction [#13, #14]. INTS3 is also an integral subunit of the Integrator complex, where it regulates snRNA processing, replication-dependent histone mRNA 3'-end processing, and promoter-proximal Pol II pausing in a DSIF-dependent manner [#5]; cryo-EM of the Integrator-PP2A complex places INTS3 in a post-termination position that blocks Pol II rebinding after termination [#15]. Consistent with an RNA-regulatory role, INTS3 destabilizes pro-apoptotic transcripts to support colorectal cancer cell survival [#17].\",\n  \"teleology\": [\n    {\n      \"year\": 2009,\n      \"claim\": \"Established INTS3 as the organizing scaffold of a DNA-damage-response complex, answering how single-stranded DNA-binding factors are stabilized and delivered to DNA ends.\",\n      \"evidence\": \"Reciprocal Co-IP, tandem affinity purification, and siRNA depletion with IR-sensitivity, checkpoint, and HR readouts in human cells\",\n      \"pmids\": [\"19683501\", \"19605351\", \"19786574\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not define the structural basis of scaffolding\", \"Direct nucleic-acid binding by INTS3 itself not yet shown\", \"Relationship to Integrator transcription functions unaddressed\"]\n    },\n    {\n      \"year\": 2013,\n      \"claim\": \"Identified INTS6 as a direct INTS3 partner that co-relocates to damage sites, extending the complex and linking it to RAD51/BRCA1 accumulation and HR.\",\n      \"evidence\": \"Affinity purification, in vitro binding, immunofluorescence foci, and HR assays; mouse conditional KO confirming SSB1 localization depends on INTS3\",\n      \"pmids\": [\"23986477\", \"23459151\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"INTS6-INTS3 binding interface not structurally defined\", \"Mechanism of RAD51/BRCA1 recruitment downstream unresolved\"]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"Placed INTS3 within the Integrator complex on RNA Pol II and showed it functions in checkpoint signaling when RPA is limiting, connecting transcription machinery to DNA-damage response.\",\n      \"evidence\": \"Affinity purification with HIT-Seq and RNA-processing depletion assays; siRNA epistasis with ATR-ATRIP foci and Chk1 phosphorylation readouts; nuclear-matrix proteomics\",\n      \"pmids\": [\"25675981\", \"25916848\", \"25609707\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"How INTS3 partitions between SOSS1 and Integrator roles unclear\", \"Direct vs indirect role in snRNA/histone processing not separated for INTS3 specifically\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Mapped INTS3 nucleic-acid binding to its C-terminus and protein interactions to its N-terminus, and showed it tunes hNABP1/2 binding, defining a bipartite functional architecture.\",\n      \"evidence\": \"EMSA, GST pulldown, and reconstitution with recombinant proteins; NMR showing hSSB1 tetramers retain INTS3 binding\",\n      \"pmids\": [\"29150435\", \"28609781\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Atomic structure of binding domains not yet determined\", \"Physiological significance of ssRNA preference unresolved\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Crystal structures defined the HEAT-repeat C-terminal domain as a dimer that binds ssDNA/ssRNA and INTS6 via distinct surfaces, with both dimerization and the INTS6 interface required for DSB repair.\",\n      \"evidence\": \"X-ray crystallography of INTS3c and INTS3c-INTS6c, mutagenesis, EMSA, protein-stability assays, and DSB repair functional assays\",\n      \"pmids\": [\"33434574\", \"34400606\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Structure of full-length INTS3 with hSSB1/C9ORF80 not solved\", \"How dimerization couples to in vivo end resection unclear\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Connected SOSS1 to transcription-coupled repair, showing it binds R-loops and Y1P RNAPII to form phase-separated repair compartments and recruits MRN via a phospho-Nbs1 interaction.\",\n      \"evidence\": \"Co-IP, in vitro binding, live-cell phase-separation imaging, siRNA repair assays; phosphopeptide binding with site-specific INTS3 mutants\",\n      \"pmids\": [\"38039132\", \"37705456\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"In vivo requirement of phase separation for repair not genetically isolated\", \"Kinase responsible for INTS3 T592 phosphorylation not identified\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Cryo-EM resolved INTS3 within the Integrator-PP2A complex in a post-termination position that prevents Pol II rebinding, and INTS6 was shown to extend SOSS1 to a tetramer coupling PP2A/SETX to R-loop resolution.\",\n      \"evidence\": \"Cryo-EM of Integrator-PP2A in multiple functional states; Co-IP and functional assays of tetrameric SOSS1 with RNAPII dephosphorylation and SETX recruitment readouts\",\n      \"pmids\": [\"38570683\", \"39445827\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Structural state of INTS3 during active termination vs post-termination transition partly inferred\", \"How the same INTS3 surface is shared between Integrator and SOSS1 roles in vivo unresolved\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Defined an RNA-regulatory, anti-apoptotic role for INTS3 in cancer, destabilizing pro-apoptotic transcripts to sustain colorectal tumor cell survival.\",\n      \"evidence\": \"CRISPR-Cas9 screen, siRNA/RNA-seq, and in vivo tumor-growth assays with nanoparticle knockdown\",\n      \"pmids\": [\"38665208\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct transcript targets and binding sites not mapped\", \"Whether this depends on Integrator or SOSS1 context unknown\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Linked INTS3 chromatin occupancy to PARP1 and SPT6, indicating its genomic recruitment is directed by transcription-associated factors.\",\n      \"evidence\": \"Co-IP, ChIP-seq, and siRNA knockdown for PARP1; ChIP-based loss-of-recruitment for SPT6 at U2 snRNA genes\",\n      \"pmids\": [\"36291070\", \"35625631\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"SPT6 dependency rests on a single ChIP observation\", \"Functional consequence of PARP1-directed INTS3 occupancy not established\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How INTS3 is partitioned between its SOSS1 DNA-repair role and its Integrator transcription-termination role, and whether the two functions are competitive or coordinated, remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No structure of full-length INTS3 simultaneously engaging both complexes\", \"Regulatory switch governing complex choice unknown\", \"Quantitative cellular distribution between the two roles unmeasured\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0003723\", \"supporting_discovery_ids\": [9, 17]},\n      {\"term_id\": \"GO:0003677\", \"supporting_discovery_ids\": [9, 10, 11]},\n      {\"term_id\": \"GO:0060090\", \"supporting_discovery_ids\": [0, 1, 9]},\n      {\"term_id\": \"GO:0005198\", \"supporting_discovery_ids\": [0, 1, 15]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [6, 7]},\n      {\"term_id\": \"GO:0000228\", \"supporting_discovery_ids\": [3, 13]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-73894\", \"supporting_discovery_ids\": [0, 3, 11]},\n      {\"term_id\": \"R-HSA-74160\", \"supporting_discovery_ids\": [5, 15]},\n      {\"term_id\": \"R-HSA-8953854\", \"supporting_discovery_ids\": [5, 16]},\n      {\"term_id\": \"R-HSA-1640170\", \"supporting_discovery_ids\": [0]}\n    ],\n    \"complexes\": [\"SOSS1 complex\", \"Integrator complex\", \"Integrator-PP2A complex\"],\n    \"partners\": [\"SSB1\", \"C9ORF80\", \"INTS6\", \"NBN\", \"PARP1\", \"RNAPII\", \"RUNX2\", \"BAZ1B\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":6,"faith_total":7,"faith_pct":85.71428571428571}}