Affinage

INTS5

Integrator complex subunit 5 · UniProt Q6P9B9

Round 2 corrected
Length
1019 aa
Mass
108.0 kDa
Annotated
2026-04-28
54 papers in source corpus 8 papers cited in narrative 9 extracted findings

Mechanistic narrative

Synthesis pass · prose summary of the discoveries below

INTS5 is a core structural subunit of the metazoan Integrator complex, a multi-subunit assembly that associates with the C-terminal domain of RNA polymerase II to mediate 3′ end processing of snRNAs and regulate transcription elongation. Within the Integrator architecture, INTS5 and INTS8 form a discrete biochemical module that bridges to INTS10 and INTS15, connecting the catalytic endonuclease core (INTS4/9/11) to the broader scaffold of the Integrator–PP2A (INTAC) complex, which couples nascent RNA cleavage by INTS11 with PP2A-mediated dephosphorylation of RNAPII-CTD Ser-2, -5, and -7 to attenuate transcription (PMID:16239144, PMID:33548203, PMID:33243860, PMID:34762484, PMID:38823386). Loss of INTS5 orthologs disrupts snRNA processing, leading to aberrant splicing of BMP/Smad pathway transcripts and blocked hematopoiesis in zebrafish, and causes dedifferentiation of neural progenitors in Drosophila through failure to sustain expression of key differentiation genes (PMID:19605500, PMID:31018143).

Mechanistic history

Synthesis pass · year-by-year structured walk · 6 steps
  1. 2005 High

    The identification of INTS5 as a subunit of the newly discovered Integrator complex established for the first time that a dedicated RNAPII-CTD-associated machinery mediates metazoan snRNA 3′ end processing.

    Evidence Affinity purification, co-IP, mass spectrometry, ChIP, and in vitro processing assays in human cells

    PMID:16239144

    Open questions at the time
    • Role of individual subunits including INTS5 within the complex was not resolved
    • No structural information on subunit organization
    • Functional scope beyond snRNA processing unknown
  2. 2009 High

    Demonstrating that loss of Ints5 disrupts snRNA processing and downstream splicing of Smad1/5 mRNAs established that the Integrator complex—through INTS5—feeds into BMP/Smad signaling and vertebrate hematopoiesis, extending its functional reach beyond snRNA biogenesis.

    Evidence Morpholino knockdown in zebrafish with snRNA processing assays, RT-PCR splicing analysis, and hematopoietic phenotyping

    PMID:19605500

    Open questions at the time
    • Whether INTS5 has a specific molecular role in this pathway beyond Integrator complex integrity is unknown
    • Mammalian validation not performed
  3. 2019 High

    Cell-type-specific binding and genetic analysis of IntS5 in Drosophila neural progenitors revealed that the Integrator complex directly occupies and activates differentiation gene loci such as earmuff, establishing INTS5 as required for neural progenitor identity maintenance.

    Evidence Loss-of-function genetics, cell-type-specific DamID, and genetic epistasis in Drosophila type II neuroblast lineage

    PMID:31018143

    Open questions at the time
    • Whether INTS5 has locus-specific recruitment determinants or acts genome-wide remains unclear
    • Mechanism by which Integrator loss triggers dedifferentiation not fully resolved
  4. 2020 High

    Structural and biochemical dissection revealed that INTS5/8 constitutes a separable module within the Integrator, and that INTS5 is part of the INTAC (Integrator–PP2A) assembly possessing dual endonuclease and protein phosphatase activities that dephosphorylate RNAPII-CTD, thereby defining the complex's transcriptional attenuation mechanism.

    Evidence Cryo-EM at 3.5 Å resolution, biochemical subcomplex reconstitution, phosphatase activity assays, and mass spectrometry

    PMID:33243860 PMID:33548203

    Open questions at the time
    • Specific contacts INTS5 makes within the INTAC scaffold not fully mapped
    • Whether INTS5 contributes allosterically to endonuclease or phosphatase activity is untested
  5. 2021 High

    Determination of the Integrator–PP2A pretermination complex bound to paused RNAPII showed how INTS5 participates in a scaffold that excludes elongation factors and positions both the INTS11 endonuclease and PP2A phosphatase for coordinated transcription termination.

    Evidence Cryo-EM structure of the pretermination complex with functional interpretation

    PMID:34762484

    Open questions at the time
    • Conformational dynamics of INTS5 during the transition from pausing to termination unresolved
    • In vivo contribution of INTS5 to the pretermination versus elongation decision not directly tested
  6. 2024 High

    Structures of the INTS5/8/10/15 sub-complex and an integrative model of the full Integrator on paused RNAPII clarified that INTS5/8 serves as a connector between the INTS10/15 periphery and the central scaffold, completing the modular assembly picture.

    Evidence Cryo-EM of INTS5/8/10/15 and INTS10/13/14/15 sub-complexes with integrative structural modeling

    PMID:38823386

    Open questions at the time
    • INTS5 mutational analysis within the context of the full complex has not been performed
    • Whether distinct INTS5/8-containing sub-assemblies exist in vivo with different functions is unknown

Open questions

Synthesis pass · forward-looking unresolved questions
  • The specific molecular contribution of INTS5 beyond serving as a scaffold—whether it allosterically regulates INTS11 endonuclease or PP2A phosphatase activity, or has locus-specific targeting roles—remains to be determined.
  • No INTS5-specific point mutations disrupting individual functions have been reported
  • No direct enzymatic activity attributed to INTS5 itself
  • No disease-causing mutations in INTS5 described

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0005198 structural molecule activity 5
Localization
GO:0005634 nucleus 2 GO:0005654 nucleoplasm 2
Pathway
R-HSA-74160 Gene expression (Transcription) 4 R-HSA-8953854 Metabolism of RNA 2
Partners
INTS10INTS11INTS15INTS4INTS8INTS9PP2A
Complex memberships
INTAC (Integrator-PP2A)INTS5/8 moduleIntegrator complex

Evidence

Reading pass · 9 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
2005 INTS5 is a subunit of the Integrator complex, a novel multi-subunit complex (at least 12 subunits) that associates with the C-terminal domain (CTD) of RNA polymerase II and mediates 3' end processing of U1 and U2 snRNAs. Integrator is recruited to snRNA genes and is evolutionarily conserved in metazoans. Affinity purification, co-immunoprecipitation, mass spectrometry, ChIP, in vitro processing assays Cell High 16239144
2009 Knockdown of zebrafish Ints5 (an ortholog of human INTS5) disrupts U1 and U2 snRNA 3' end processing, leading to aberrant splicing of smad1 and smad5 mRNAs, reduced expression of hematopoietic genes scl and gata1, and arrested red blood cell differentiation, establishing that Ints5 functions as part of the Integrator complex to regulate BMP/Smad signaling during hematopoiesis. Antisense morpholino knockdown in zebrafish, snRNA processing assays, RT-PCR splicing analysis, blood smear analysis Development High 19605500
2019 In Drosophila, loss of intS5 (ortholog of human INTS5) in intermediate neural progenitors (INPs) causes their dedifferentiation back into type II neuroblasts. Cell-type-specific DamID revealed 1413 IntS5-binding sites in INPs, including the transcription factor earmuff (erm), whose expression is lost in intS5 mutants. IntS5 thus regulates neural progenitor identity by driving transcription of key differentiation factors. Genetic loss-of-function (mutant analysis), cell-type-specific DamID (DNA adenine methyltransferase identification), genetic interaction analysis Cell reports High 31018143
2020 INTS5 and INTS8 form a distinct biochemical subcomplex within the larger Integrator complex, as demonstrated by biochemical characterization. The INTS4/9/11 ternary complex constitutes the catalytic core, while INTS5/8 is a separate module. Biochemical subcomplex purification, cryo-EM structural analysis Molecular cell High 33548203
2021 The INTS5/8 subcomplex is part of the modular Integrator architecture. INTS5/8 forms a separable module distinct from the catalytic INTS4/9/11 core and from the INTS10/13/14 module, supporting a modular assembly model for the full Integrator complex. Cryo-EM, biochemical subcomplex reconstitution Molecular cell High 33548203
2024 Structures of two human Integrator sub-complexes, INTS10/13/14/15 and INTS5/8/10/15, were determined, and INTS5/8 was shown to participate in a broader assembly that includes INTS10 and INTS15. An integrative model of fully assembled Integrator bound to RNAPII paused elongating complex was generated. INTS5/8 thus connects modules within the complete Integrator assembly. Cryo-EM structure determination, integrative structural modeling, in silico protein-protein interaction screening Molecular cell High 38823386
2020 INTS5 is a component of the INTAC complex (Integrator-PP2A), a cruciform-shaped assembly in which nine Integrator subunits and the PP2A core enzyme form a central scaffold. The complex has dual enzymatic activities: RNA endonuclease (INTS11) and protein phosphatase (PP2A-AC) that dephosphorylates RNAPII-CTD at Ser-2, -5, and -7 to regulate transcription. Cryo-EM at 3.5 Å, biochemical reconstitution, phosphatase activity assays, mass spectrometry Science High 33243860
2010 INTS5 was identified as a component of the endogenous human Integrator complex by immunoprecipitation/mass spectrometry, confirming its membership in this transcriptional co-regulator complex in human cells. Immunoprecipitation followed by mass spectrometry (IP/MS) of endogenous complexes Proceedings of the National Academy of Sciences of the United States of America Medium 20133760
2021 The structure of the human Integrator-PP2A pretermination complex bound to paused RNAPII was determined, revealing that INTS5 (as part of the Integrator scaffold) participates in a complex that excludes elongation factors SPT6 and PAF1C, positions PP2A to dephosphorylate RNAPII-CTD, and positions the INTS11 endonuclease at the RNA exit site to cleave nascent RNA ~20 nucleotides from the active site. Cryo-EM structural analysis of pretermination complex, functional validation Science High 34762484

Source papers

Stage 0 corpus · 54 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
2002 Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Proceedings of the National Academy of Sciences of the United States of America 1479 12477932
2004 Large-scale characterization of HeLa cell nuclear phosphoproteins. Proceedings of the National Academy of Sciences of the United States of America 1159 15302935
2015 The BioPlex Network: A Systematic Exploration of the Human Interactome. Cell 1118 26186194
2017 Architecture of the human interactome defines protein communities and disease networks. Nature 1085 28514442
2015 A human interactome in three quantitative dimensions organized by stoichiometries and abundances. Cell 1015 26496610
2020 A reference map of the human binary protein interactome. Nature 849 32296183
2003 Complete sequencing and characterization of 21,243 full-length human cDNAs. Nature genetics 754 14702039
2021 Dual proteome-scale networks reveal cell-specific remodeling of the human interactome. Cell 705 33961781
2011 Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Briefings in bioinformatics 656 21873635
2021 Multilevel proteomics reveals host perturbations by SARS-CoV-2 and SARS-CoV. Nature 532 33845483
2005 Integrator, a multiprotein mediator of small nuclear RNA processing, associates with the C-terminal repeat of RNA polymerase II. Cell 443 16239144
2004 The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). Genome research 438 15489334
2022 OpenCell: Endogenous tagging for the cartography of human cellular organization. Science (New York, N.Y.) 432 35271311
2015 Panorama of ancient metazoan macromolecular complexes. Nature 407 26344197
2016 The cell proliferation antigen Ki-67 organises heterochromatin. eLife 265 26949251
2018 Mapping the Genetic Landscape of Human Cells. Cell 225 30033366
2021 N6-Methyladenosine on mRNA facilitates a phase-separated nuclear body that suppresses myeloid leukemic differentiation. Cancer cell 207 34048709
2019 H4K20me0 recognition by BRCA1-BARD1 directs homologous recombination to sister chromatids. Nature cell biology 162 30804502
2021 The PP2A-Integrator-CDK9 axis fine-tunes transcription and can be targeted therapeutically in cancer. Cell 152 34004147
2020 Identification of Integrator-PP2A complex (INTAC), an RNA polymerase II phosphatase. Science (New York, N.Y.) 151 33243860
2021 Structural basis of Integrator-mediated transcription regulation. Science (New York, N.Y.) 112 34762484
2010 Streamlined analysis schema for high-throughput identification of endogenous protein complexes. Proceedings of the National Academy of Sciences of the United States of America 102 20133760
2020 The Human Integrator Complex Facilitates Transcriptional Elongation by Endonucleolytic Cleavage of Nascent Transcripts. Cell reports 94 32697989
1996 Overexpression of int-5/aromatase in mammary glands of transgenic mice results in the induction of hyperplasia and nuclear abnormalities. Cancer research 91 8764102
2017 The STUbL RNF4 regulates protein group SUMOylation by targeting the SUMO conjugation machinery. Nature communications 86 29180619
2000 Prediction of the coding sequences of unidentified human genes. XIX. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro. DNA research : an international journal for rapid publication of reports on genes and genomes 81 11214970
1995 The physical map of the human RET proto-oncogene. Oncogene 79 7478601
2019 The midbody interactome reveals unexpected roles for PP1 phosphatases in cytokinesis. Nature communications 74 31586073
2017 Systematic Analysis of Human Protein Phosphatase Interactions and Dynamics. Cell systems 65 28330616
2015 Temporal proteomics of NGF-TrkA signaling identifies an inhibitory role for the E3 ligase Cbl-b in neuroblastoma cell differentiation. Science signaling 61 25921289
2018 The Tumor Suppressor CIC Directly Regulates MAPK Pathway Genes via Histone Deacetylation. Cancer research 60 29844126
2021 Structure of the catalytic core of the Integrator complex. Molecular cell 54 33548203
1987 A fission yeast chromosome can replicate autonomously in mouse cells. Cell 53 3475186
2020 INTS10-INTS13-INTS14 form a functional module of Integrator that binds nucleic acids and the cleavage module. Nature communications 52 32647223
2003 IGS sequence variation, group-I introns and the complete nuclear ribosomal DNA of the entomopathogenic fungus Metarhizium: excellent tools for isolate detection and phylogenetic analysis. Fungal genetics and biology : FG & B 41 12620253
2009 The Integrator subunits function in hematopoiesis by modulating Smad/BMP signaling. Development (Cambridge, England) 38 19605500
2024 Structural basis of the Integrator complex assembly and association with transcription factors. Molecular cell 25 38823386
2019 The Integrator Complex Prevents Dedifferentiation of Intermediate Neural Progenitors back into Neural Stem Cells. Cell reports 24 31018143
1991 Characterization of Int-5, a locus associated with early events in mammary carcinogenesis. Oncogene research 24 1705320
2010 Molecular characterization of Mycobacterium intracellulare-related strains based on the sequence analysis of hsp65, internal transcribed spacer and 16S rRNA genes. Journal of medical microbiology 21 20522624
1994 The nature and expression of int-5, a novel MMTV integration locus gene in carcinogen-induced mammary tumors. Cancer letters 20 7812938
2021 iTRAQ-based proteomic analysis of the molecular mechanisms and downstream effects of fatty acid synthase in osteosarcoma cells. Journal of clinical laboratory analysis 14 33405298
2015 A Large Cohort Study of Genotype and Phenotype Correlations of Beta- Thalassemia in Iranian Population. International journal of hematology-oncology and stem cell research 13 26865931
1995 The overexpression of int-5/Aromatase, a novel MMTV integration locus gene, is responsible for D2 mammary tumor cell proliferation. Cancer letters 12 7874687
2021 PA-Int5: An isatin-thiosemicarbazone derivative that exhibits anti-nociceptive and anti-inflammatory effects in Swiss mice. Biomedical reports 11 34094537
2018 DisruPPI: structure-based computational redesign algorithm for protein binding disruption. Bioinformatics (Oxford, England) 10 29949961
2002 Western blotting analysis of the beta-hexosaminidase alpha- and beta-subunits in cultured fibroblasts from cases of various forms of GM2 gangliosidosis. Acta neurologica Scandinavica 9 12027830
2012 Detection of genetic association and functional polymorphisms of UGDH affecting milk production trait in Chinese Holstein cattle. BMC genomics 8 23122059
2016 Molecular Taxonomic Evidence for Two Distinct Genotypes of Mycobacterium yongonense via Genome-Based Phylogenetic Analysis. PloS one 6 27031100
2012 Novel single nucleotide polymorphisms of bovine SREBP1 gene is association with fatty acid composition and marbling score in commercial Korean cattle (Hanwoo). Molecular biology reports 6 23065270
2009 Bacteriophage content of M49 strains of Streptococcus pyogenes. FEMS microbiology letters 5 19493003
1995 Structure of the int-5, a novel MMTV integration genomic locus containing mouse early transposon LTR homology region. Biochimica et biophysica acta 5 7632740
2005 Coordinates, DNA content and heterogeneity of cell nuclei and segments of the Caenorhabditis elegans intestine. Histochemistry and cell biology 4 16158289
2014 [Frequency of diseases caused by group A streptococci among invasive infections of soft tissues and characteristics of the causative agent]. Zhurnal mikrobiologii, epidemiologii i immunobiologii 1 25536767