Affinage

INTS9

Integrator complex subunit 9 · UniProt Q9NV88

Length
658 aa
Mass
73.8 kDa
Annotated
2026-06-10
19 papers in source corpus 14 papers cited in narrative 15 extracted findings
Cross-family judge vs UniProt: Affinage preferred faithfulness: 6/7 claims corpus-supported (86%)

Mechanistic narrative

Synthesis pass · prose summary of the discoveries below

INTS9 is a catalytically inactive subunit of the Integrator complex that pairs with the endonuclease INTS11 to enable RNA 3'-end processing and transcriptional regulation (PMID:15684398, PMID:22252320). Originally identified as the exclusively nuclear protein RC-74 that lacks the histidine motif required for catalysis but stably associates with the active nuclease RC-68 (INTS11), INTS9 forms a complex distinct from canonical CPSF machinery (PMID:15684398). The INTS9-INTS11 interaction is mediated by a discrete C-terminal domain of each protein that assembles into a continuous nine-stranded β-sheet interface, an architecture essential for snRNA 3'-end processing (PMID:22252320, PMID:28396433). INTS4 joins this heterodimer—binding only when both INTS9 and INTS11 are present—to form the heterotrimeric Integrator cleavage module (INTS4/9/11) that drives UsnRNA biogenesis, Cajal body integrity, and histone locus body formation, with INTS4 stabilizing the nuclease domains and all three subunits contributing to a composite electropositive RNA-binding groove (PMID:29471365, PMID:33548203). Inositol hexakisphosphate binds an electropositive pocket at the three-subunit interface and is required for cleavage module function in snRNA processing and mRNA transcription attenuation (PMID:36180473). Module biogenesis is chaperoned by BRAT1, which blocks the INTS11 active site via a C-terminal cysteine coordinating the catalytic metal ions, keeps the INTS9-INTS11 dimer inactive during maturation, facilitates its nuclear import, and is released upon IP6-dependent locking of the mature module (PMID:39032489, PMID:39032490). Beyond constitutive processing, the INTS9-INTS11-BRAT1 trimer activates REST-responsive neuronal genes during differentiation, and disease-causing BRAT1 mutations that weaken association with INTS9/INTS11 impair this activation (PMID:38805275).

Mechanistic history

Synthesis pass · year-by-year structured walk · 10 steps
  1. 2005 Medium

    Established that INTS9 (RC-74) is a nuclear, catalytically dead partner of the INTS11 (RC-68) endonuclease, defining a processing entity separate from canonical CPSF.

    Evidence Co-immunoprecipitation, subcellular fractionation, and sequence analysis in HeLa and mouse cells, with RNAi cell cycle readout

    PMID:15684398

    Open questions at the time
    • No in vitro reconstitution of the dimer
    • RNA substrate not yet identified
    • G1 arrest phenotype not mechanistically tied to a specific processing event
  2. 2012 Medium

    Mapped the INTS9-INTS11 interaction to discrete C-terminal domains and showed this contact is functionally required for snRNA 3'-end processing.

    Evidence Domain mapping, cell-based complementation, RNAi, and dominant-negative overexpression

    PMID:22252320

    Open questions at the time
    • No structural detail of the interface
    • Does not address how the dimer engages RNA
  3. 2017 High

    Resolved the atomic basis of the INTS9-INTS11 interaction as a continuous nine-stranded β-sheet, explaining the obligate nature of the heterodimer.

    Evidence 2.1-Å X-ray crystallography with yeast two-hybrid, Co-IP, and structure-based mutagenesis validated by snRNA processing assay

    PMID:28396433

    Open questions at the time
    • Structure limited to CTDs, not full-length proteins
    • No view of the assembled cleavage module or RNA
  4. 2018 High

    Defined INTS4 as the third obligate subunit completing the heterotrimeric cleavage module and linked the module to nuclear body integrity.

    Evidence Co-IP, domain mapping, UsnRNA processing, and Cajal/histone locus body imaging

    PMID:29471365

    Open questions at the time
    • No structure of the trimer
    • Mechanism of RNA recognition unresolved
  5. 2021 High

    Provided the near-atomic architecture of the INTS4/9/11 module, showing INTS4 stabilizes the nuclease domains and a shared electropositive groove suggests the RNA path.

    Evidence 3.5-Å cryo-EM with biochemical subcomplex characterization

    PMID:33548203

    Open questions at the time
    • RNA not captured in the structure
    • Cofactor requirements not yet identified
  6. 2022 High

    Identified IP6 as an essential structural cofactor bound at the tri-subunit interface required for cleavage module activity.

    Evidence 2.74-Å Drosophila cryo-EM, human ICM biochemistry, mutagenesis, snRNA processing and transcription attenuation assays

    PMID:36180473

    Open questions at the time
    • How IP6 (55 Å from active site) influences catalysis allosterically not fully defined
  7. 2022 Medium

    Showed that BRAT1 physically associates with INTS9/INTS11 and is required for multiple Integrator RNA processing functions, and that INTS11 SUMOylation regulates complex assembly.

    Evidence Co-IP with BRAT1 knockout cells and RNA processing assays; INTS11 SUMO-site mutagenesis with localization and Co-IP readouts

    PMID:36028512 PMID:36454007

    Open questions at the time
    • Mechanism of BRAT1 action not yet structural
    • Functional consequence of SUMOylation on catalysis not directly measured
  8. 2024 High

    Defined the assembly pathway in which BRAT1 (with WDR73) chaperones the cytoplasmic INTS9-11 dimer by occluding the INTS11 active site, mediates nuclear import, and is released upon IP6-dependent maturation.

    Evidence Biochemical reconstitution, cryo-EM of INTS9-INTS11-BRAT1 showing a BRAT1 cysteine coordinating active-site metals, nuclear import and complementation assays

    PMID:39032489 PMID:39032490

    Open questions at the time
    • Precise role of WDR73 relative to BRAT1 not fully separated
    • Timing of INTS4 incorporation in vivo not directly observed
  9. 2024 Medium

    Demonstrated a non-canonical role for the INTS9-INTS11-BRAT1 trimer in activating REST-responsive neuronal genes, linking the module to neuronal differentiation and BRAT1 disease mutations.

    Evidence Co-IP, ChIP, BRAT1 depletion/reconstitution with disease mutants in NT2 and mouse ESC differentiation; corroborated by prior preprint

    PMID:37609215 PMID:38805275

    Open questions at the time
    • Whether transcriptional activation requires INTS11 catalysis unresolved
    • Single lab; mechanism of promoter recruitment incompletely defined
  10. 2026 Medium

    Connected the INTS9/INTS11 module to downstream RNA surveillance by showing the exosome-linked factor ZC3H18 directly recognizes the endonuclease module.

    Evidence Cryo-EM and in vitro binding assays with structure-prediction-guided interface mapping

    PMID:41641703

    Open questions at the time
    • Functional consequence of ZC3H18 binding for termination not yet established in cells
    • Single study

Open questions

Synthesis pass · forward-looking unresolved questions
  • How INTS9 contributes to RNA substrate selection and how the module switches between constitutive 3'-end processing and gene-activating roles remains unresolved.
  • No structure of the module bound to RNA substrate
  • Determinants directing the trimer to attenuation versus neuronal gene activation unknown

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0140098 catalytic activity, acting on RNA 4 GO:0060090 molecular adaptor activity 3
Localization
GO:0005634 nucleus 2
Pathway
R-HSA-8953854 Metabolism of RNA 4 R-HSA-74160 Gene expression (Transcription) 3
Partners
BRAT1INTS11INTS4WDR73ZC3H18
Complex memberships
INTS9-INTS11 heterodimerINTS9-INTS11-BRAT1 trimerIntegrator cleavage module (INTS4-INTS9-INTS11)

Evidence

Reading pass · 15 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
2005 RC-74 (INTS9) is exclusively nuclear and forms a complex with RC-68 (INTS11) in HeLa and mouse cells. RC-74 lacks the histidine motif required for catalysis (unlike INTS11/RC-68 which retains it), and does not interact with CPSF-73 or CPSF-160, indicating that the RC-68/RC-74 complex is a separate entity from the canonical CPSF complex involved in a distinct pre-mRNA processing event. Co-immunoprecipitation, subcellular fractionation, sequence analysis, RNAi-mediated depletion with cell cycle phenotype readout Molecular and cellular biology Medium 15684398
2005 RNAi-mediated depletion of RC-68 (INTS11), the catalytic partner of RC-74 (INTS9), arrests HeLa cells early in G1 phase while cells continue to grow, indicating a role for the RC-68/RC-74 complex in cell cycle progression through G1 into S phase. RNA interference with cell cycle analysis by flow cytometry Molecular and cellular biology Medium 15684398
2012 INTS9 and INTS11 form a specific heterodimer mediated by a discrete C-terminal domain (CTD) of INTS9 and a corresponding region within the C-terminus of INTS11 adjacent to the predicted active site. This heterodimeric interaction is required for snRNA 3' end processing, as overexpression of the interaction domains alone causes dominant-negative snRNA misprocessing, and INTS11 lacking the INTS9-interaction domain cannot restore snRNA 3' end processing after RNAi depletion. Domain mapping, cell-based complementation assay, RNAi, dominant-negative overexpression Molecular and cellular biology Medium 22252320
2017 Crystal structure of the INTS9-INTS11 CTD complex at 2.1-Å resolution reveals that the complex is composed of a continuous nine-stranded β-sheet with four strands from INTS9 and five from INTS11, with highly conserved residues forming an extensive interface. Structure-based mutagenesis confirmed that this interaction is crucial for snRNA 3' end processing. X-ray crystallography, yeast two-hybrid, co-immunoprecipitation, structure-based mutagenesis, snRNA 3' end processing functional assay Proceedings of the National Academy of Sciences of the United States of America High 28396433
2018 INTS4 is a specific and conserved interaction partner of the INTS9/INTS11 heterodimer, forming a heterotrimeric cleavage module (INTS4/9/11). INTS4 does not interact with either INTS9 or INTS11 individually and requires both. INTS4 possesses N-terminal HEAT repeats and a β-sheet-rich C-terminal region both important for binding INTS9/INTS11. This trimeric complex is the most critical for UsnRNA biogenesis, Cajal body structural integrity, and histone locus body formation. Co-immunoprecipitation, domain mapping, UsnRNA 3' end processing assay, Cajal body/histone locus body imaging Nucleic acids research High 29471365
2021 Cryo-EM structure of the INTS4/9/11 ternary complex at 3.5-Å resolution reveals spatial organization of the catalytic nuclease INTS11 bound to its catalytically impaired homolog INTS9 via several interdependent interfaces, with INTS4 playing a key role in stabilizing the nuclease domains. All three proteins form a composite electropositive groove suggesting a putative RNA-binding path within the complex. Cryo-electron microscopy at 3.5-Å resolution, biochemical characterization of subcomplexes Molecular cell High 33548203
2021 WDR73 interacts with INTS9 and INTS11 components of the Integrator complex and is implicated in two Integrator-regulated cellular pathways: UsnRNA 3' end processing and mediating the transcriptional response to EGF stimulation. Co-immunoprecipitation, UsnRNA processing assay, transcriptional response assay Scientific reports Medium 33686175
2022 Inositol hexakisphosphate (IP6) stably associates with the Integrator cleavage module (INTS4-INTS9-INTS11) at a highly electropositive pocket at the interface among all three subunits, 55 Å from the INTS11 active site. IP6 binding is conserved in human ICM and is required for Integrator function in snRNA 3' end processing and mRNA transcription attenuation; mutations in the IP6 binding site or disruption of IP6 biosynthesis significantly reduce Integrator function. Cryo-EM structure at 2.74 Å (Drosophila ICM), biochemical IP6-binding confirmation in human ICM, site-directed mutagenesis, snRNA processing assay, mRNA transcription attenuation assay Nature communications High 36180473
2022 BRAT1 tightly interacts with INTS9/INTS11 subunits of the Integrator complex, and BRAT1 deletion disrupts Integrator functions including UsnRNA and snoRNA 3' end processing, replication-dependent histone pre-mRNA processing, and coding gene expression. Co-immunoprecipitation, BRAT1 knockout cells, RNA processing assays, transcriptomic analysis Nature communications Medium 36028512
2022 SUMOylation of INTS11 (at Lys381, Lys462, Lys475) is regulated by SUMO isopeptidases USPL1 and SENP6 and modulates INTS11 subcellular localization and Integrator activity. An INTS11 SUMOylation-deficient mutant retains interaction with INTS4 and INTS9 but loses interactions with other Integrator subunits, suggesting SUMO conjugation on INTS11 regulates complex assembly. SUMO site mutagenesis, subcellular localization imaging, Co-immunoprecipitation, snRNA 3' end processing assay, USPL1/SENP6 overexpression Nucleic acids research Medium 36454007
2024 BRAT1 and WDR73 are critical biogenesis factors for the Integrator cleavage module (INTS4-9-11). BRAT1 and WDR73 maintain INTS9-11 inactive during maturation by physically blocking the INTS11 endonuclease active site and prevent premature INTS4 association. BRAT1 facilitates nuclear import of the INTS9-11 heterodimer, and final BRAT1 release requires locking of the mature cleavage module conformation by IP6. Biochemical reconstitution, structural analysis, nuclear import assays, functional complementation assays Molecular cell High 39032489
2024 Cryo-EM structure of the human INTS9-INTS11-BRAT1 complex reveals that the conserved C-terminus of BRAT1 is captured in the active site of INTS11, with a cysteine residue directly coordinating the metal ions, explaining how BRAT1 acts as a cytoplasmic chaperone that stabilizes INTS11 and is required for Integrator function in the nucleus. Cryo-EM structure determination, co-immunoprecipitation, neural organoid transcriptomic analysis, active-site mutagenesis inference from structure Molecular cell High 39032490
2024 INTS11 and INTS9 form a distinct trimeric complex with BRAT1, and this complex is required for activation of REST-responsive neuronal genes during differentiation. BRAT1 recruits INTS11 to promoters of neuronal genes, and disease-causing mutations in BRAT1 (e.g., E522K) diminish association with INTS11/INTS9, preventing transcriptional activation and neuronal differentiation. Co-immunoprecipitation, ChIP, BRAT1 depletion/reconstitution with differentiation assay (NT2 cells), mouse ESC neuronal differentiation Proceedings of the National Academy of Sciences of the United States of America Medium 38805275
2023 INTS9 and INTS11 subunits of the Integrator complex interact with BRAT1 to form a trimeric complex in HEK293T and NT2 cells. Disease-causing mutations in BRAT1 (E522K) diminish its association with the INTS11/INTS9 heterodimer, and BRAT1 depletion disrupts INTS11 recruitment to neuronal gene promoters and impairs neural differentiation. Co-immunoprecipitation, ChIP, RNAi-mediated depletion, differentiation assay bioRxivpreprint Medium 37609215
2026 ZC3H18, a component linking nuclear exosome adaptors to transcription termination, directly recognizes the INTS9/INTS11 endonuclease module of the Integrator complex via a dedicated domain, as shown by in vitro biochemical approaches and cryo-EM. Cryo-EM, in vitro biochemical binding assays, in silico structure prediction-guided interface identification Nucleic acids research Medium 41641703

Source papers

Stage 0 corpus · 19 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
2005 A CPSF-73 homologue is required for cell cycle progression but not cell growth and interacts with a protein having features of CPSF-100. Molecular and cellular biology 85 15684398
2018 Integrator subunit 4 is a 'Symplekin-like' scaffold that associates with INTS9/11 to form the Integrator cleavage module. Nucleic acids research 67 29471365
2017 Molecular basis for the interaction between Integrator subunits IntS9 and IntS11 and its functional importance. Proceedings of the National Academy of Sciences of the United States of America 62 28396433
2012 snRNA 3' end formation requires heterodimeric association of integrator subunits. Molecular and cellular biology 58 22252320
2021 Structure of the catalytic core of the Integrator complex. Molecular cell 55 33548203
2021 Disruption of pathways regulated by Integrator complex in Galloway-Mowat syndrome due to WDR73 mutations. Scientific reports 23 33686175
2022 BRAT1 links Integrator and defective RNA processing with neurodegeneration. Nature communications 20 36028512
2022 Inositol hexakisphosphate is required for Integrator function. Nature communications 17 36180473
2024 Neuronal differentiation requires BRAT1 complex to remove REST from chromatin. Proceedings of the National Academy of Sciences of the United States of America 12 38805275
2022 SUMO conjugation regulates the activity of the Integrator complex. Nucleic acids research 10 36454007
2024 Assembly mechanism of Integrator's RNA cleavage module. Molecular cell 9 39032489
2024 Cytoplasmic binding partners of the Integrator endonuclease INTS11 and its paralog CPSF73 are required for their nuclear function. Molecular cell 8 39032490
2020 Vitamin D Sufficiency Has a Limited Effect on Placental Structure and Pathology: Placental Phenotypes in the VDAART Trial. Endocrinology 8 32270179
2007 The 73 kDa subunit of the CPSF complex binds to the HIV-1 LTR promoter and functions as a negative regulatory factor that is inhibited by the HIV-1 Tat protein. Journal of molecular biology 6 17669424
2023 BRAT1 associates with INTS11/INTS9 heterodimer to regulate key neurodevelopmental genes. bioRxiv : the preprint server for biology 5 37609215
2023 Coevolution combined with molecular dynamics simulations provides structural and mechanistic insights into the interactions between the integrator complex subunits. Computational and structural biotechnology journal 3 38074468
2020 The integrator complex subunit 11 is involved in the post-diapaused embryonic development and stress response of Artemia sinica. Gene 3 32165292
2024 DNA Methylation Patterns Associated with Tinnitus in Young Adults-A Pilot Study. Journal of the Association for Research in Otolaryngology : JARO 2 39147981
2026 Direct coupling of the human nuclear exosome adaptors NEXT and PAXT with transcription termination and processing machineries. Nucleic acids research 0 41641703

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