Affinage

INTS11

Integrator complex subunit 11 · UniProt Q5TA45

Length
600 aa
Mass
67.7 kDa
Annotated
2026-04-28
12 papers in source corpus 10 papers cited in narrative 10 extracted findings

Mechanistic narrative

Synthesis pass · prose summary of the discoveries below

INTS11 is the catalytic endonuclease subunit of the Integrator complex, functioning broadly in RNA Polymerase II-dependent transcription termination, nascent RNA processing, and chromatin regulation during development and hematopoiesis. INTS11 belongs to the metallo-β-lactamase/β-CASP superfamily and obligately heterodimerizes with INTS9 via a continuous nine-stranded β-sheet formed by their C-terminal domains; its active site accommodates mixed metal ions (Fe, Zn, Mn) that support RNA cleavage (PMID:28396433, PMID:36822327). In the cytoplasm, INTS11 is stabilized by the chaperone BRAT1, whose conserved C-terminal cysteine inserts into the INTS11 active site to coordinate catalytic metals, and loss of BRAT1 phenocopies Integrator dysfunction in neural organoids (PMID:39032490). INTS11 enforces promoter directionality by terminating antisense transcription in opposition to CDK9, maintains long 3′UTR isoforms essential for neuronal gene expression, physically interacts with PRC2 to sustain H3K27me3 in hematopoietic progenitors, and possesses an endonuclease-independent role in RNA Pol II recruitment and pioneer factor engagement during zygotic genome activation (PMID:38976490, PMID:42035222, PMID:34516911, PMID:41955115).

Mechanistic history

Synthesis pass · year-by-year structured walk · 8 steps
  1. 2017 High

    Determining how INTS11 engages the Integrator complex resolved the structural basis for snRNA 3′-end processing: INTS11 heterodimerizes with INTS9 through a continuous nine-stranded β-sheet formed by their CTDs, and disruption of this interface abolishes snRNA cleavage.

    Evidence 2.1-Å crystal structure of INTS9–INTS11 CTDs, yeast two-hybrid, Co-IP, and snRNA processing assays with interface mutants

    PMID:28396433

    Open questions at the time
    • Full-length Integrator complex architecture not resolved
    • Substrate specificity determinants beyond snRNAs unknown
    • How other Integrator subunits modulate INTS11 catalysis not addressed
  2. 2021 Medium

    Whether INTS11 has functions beyond RNA processing was answered by showing it physically interacts with PRC2, stabilizes the complex, and maintains H3K27me3 in hematopoietic stem/progenitor cells — establishing a chromatin-regulatory role for INTS11.

    Evidence Conditional Ints11 knockout in murine HSPCs, Co-IP of INTS11–PRC2 interaction, H3K27me3 western blots, rescue by re-expression of INTS11 or PRC2 subunits

    PMID:34516911

    Open questions at the time
    • Whether INTS11 catalytic activity is required for PRC2 stabilization not tested
    • Mechanism by which INTS11 maintains PRC2 protein levels not defined
    • Single-lab observation awaiting independent replication
  3. 2023 High

    Biochemical characterization of the INTS11 active site revealed that mixed metal ions (Fe, Zn, Mn) occupy the catalytic center and that the enzyme tolerates metal heterogeneity without losing RNA cleavage activity, clarifying the metalloenzyme mechanism.

    Evidence ICP-MS, X-ray crystallography, and in vitro RNA cleavage assays on recombinant INTS11

    PMID:36822327

    Open questions at the time
    • Physiological metal ion identity in vivo not determined
    • How metal identity affects cleavage kinetics or specificity not characterized
  4. 2023 Medium

    Human genetic and in vivo complementation studies established that INTS11 loss-of-function variants cause a neurodevelopmental disorder: catalytic-site variants fail to rescue Drosophila null lethality, and patient-derived cells show impaired endonuclease activity, mitotic defects, and delayed neural progenitor differentiation.

    Evidence Drosophila null mutant complementation with human variant transgenes; patient iPSC knockin lines with RNA substrate accumulation, cell cycle, and NPC differentiation assays

    PMID:37054711 PMID:37980560

    Open questions at the time
    • Precise genotype–phenotype correlations across the variant spectrum not established
    • Whether mitotic defects are direct or secondary to transcriptional changes not resolved
  5. 2024 High

    The mechanism by which INTS11 enforces transcription directionality was resolved: INTS11 terminates antisense transcription at divergent promoters, while CDK9 protects sense transcription from INTS11-dependent attenuation — establishing an antagonistic CDK9–INTS11 axis governing promoter directionality.

    Evidence Auxin-degron depletion of INTS11, pharmacological CDK9 inhibition, nascent RNA-seq, and engineered CDK9 recruitment assays in human cells

    PMID:38976490

    Open questions at the time
    • Phosphorylation targets on INTS11 or Pol II CTD that mediate CDK9 protection not identified
    • Whether other Integrator subunits contribute to directional specificity not tested
  6. 2024 High

    How INTS11 is delivered to the nucleus was answered by the discovery that BRAT1 acts as a cytoplasmic chaperone: its C-terminal cysteine occupies the INTS11 active site, coordinating catalytic metals and stabilizing INTS11 prior to nuclear import.

    Evidence Crystal structures of human INTS9–INTS11–BRAT1 and Drosophila dIntS11–CG7044, biochemical fractionation, neural organoid BRAT1 knockdown with transcriptomics

    PMID:39032490

    Open questions at the time
    • Mechanism of BRAT1 release upon nuclear entry not characterized
    • Whether BRAT1 chaperoning is regulated by signaling not addressed
  7. 2026 Medium

    INTS11's role in neural development was mechanistically refined: it binds chromatin at loci with long 3′UTR isoforms, maintains their expression and stability, and its loss causes 3′UTR shortening and G1 arrest in neuroblasts — linking Integrator-dependent RNA processing to neuronal morphogenesis gene regulation.

    Evidence Drosophila MARCM clonal analysis, FUCCI cell cycle imaging, scRNA-seq, ChIP-qPCR

    PMID:42035222

    Open questions at the time
    • Whether 3′UTR maintenance requires INTS11 catalytic activity or a scaffolding role not dissected
    • Mammalian validation of 3′UTR-length regulation by INTS11 lacking
  8. 2026 Medium

    A catalysis-independent function of INTS11 was uncovered: maternal IntS11 drives de novo RNA Pol II loading and pioneer factor (Zelda/GAF) engagement at regulatory elements during zygotic genome activation, operating upstream of and independently from its endonuclease activity.

    Evidence Maternal IntS11 depletion in Drosophila embryos, genome-wide Pol II ChIP-seq, pioneer factor binding assays, catalytic mutant analysis

    PMID:41955115

    Open questions at the time
    • Structural basis for the endonuclease-independent Pol II recruitment function unknown
    • Whether this non-catalytic role operates in mammalian zygotic genome activation not tested
    • Protein partners mediating Pol II loading independently of catalysis not identified

Open questions

Synthesis pass · forward-looking unresolved questions
  • Key unresolved questions include the structural basis of full-length Integrator complex assembly around INTS11, the mechanism by which INTS11 stabilizes PRC2, whether the non-catalytic Pol II recruitment function is conserved in mammals, and how BRAT1 release is triggered upon nuclear import.
  • No full-length Integrator holocomplex structure with INTS11 resolved
  • Mechanism of INTS11-mediated PRC2 stabilization undefined
  • Mammalian validation of non-catalytic INTS11 functions in ZGA absent

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0140098 catalytic activity, acting on RNA 5 GO:0003723 RNA binding 3
Localization
GO:0005634 nucleus 4 GO:0005694 chromosome 2 GO:0005829 cytosol 1
Pathway
R-HSA-8953854 Metabolism of RNA 5 R-HSA-1266738 Developmental Biology 4 R-HSA-74160 Gene expression (Transcription) 2 R-HSA-4839726 Chromatin organization 1
Partners
BRAT1CDK9EZH2INTS9SUZ12
Complex memberships
INTS9–INTS11 heterodimerINTS9–INTS11–BRAT1 trimerIntegrator complex

Evidence

Reading pass · 10 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
2017 INTS11 is the endonuclease subunit of the Integrator complex, belonging to the metallo-β-lactamase superfamily and acting as a paralog of CPSF-73. INTS11 forms a stable complex with INTS9 through their C-terminal domains (CTDs), forming a continuous nine-stranded β-sheet (four strands from INTS9, five from INTS11). This interaction is required for INT-mediated snRNA 3'-end processing, as demonstrated by structure-based mutagenesis of conserved interface residues. Crystal structure at 2.1-Å resolution, yeast two-hybrid, coimmunoprecipitation, functional snRNA 3'-end processing assays with interface mutants Proceedings of the National Academy of Sciences of the United States of America High 28396433
2023 A mixture of metal ions (Fe, Zn, Mn) occupies the active site of INTS11, coordinated by conserved His and Asp residues in its metallo-β-lactamase domain. The identity and abundance of metal ions varies with expression host but the enzyme remains active for RNA cleavage regardless of which metal predominates. Inductively coupled plasma mass spectrometry (ICP-MS), X-ray diffraction, in vitro RNA cleavage assay The Journal of biological chemistry High 36822327
2024 BRAT1 (and its Drosophila ortholog CG7044) binds INTS11 in the cytoplasm, stabilizing it; the conserved C terminus of BRAT1 is captured in the active site of INTS11 with a cysteine residue directly coordinating the catalytic metal ions. BRAT1 acts as a cytoplasmic chaperone required for Integrator function in the nucleus. Loss of BRAT1 in neural organoids causes transcriptomic disruption and precocious expression of neurogenesis-driving transcription factors. Crystal structures of human INTS9-INTS11-BRAT1 and Drosophila dIntS11-CG7044 complexes, neural organoid knockdown with transcriptomic analysis, biochemical fractionation Molecular cell High 39032490
2024 INTS11 maintains promoter directionality by terminating antisense transcription, while sense transcription is protected from INTS11-dependent attenuation by CDK9 activity. Upon CDK9 inhibition, INTS11 attenuates transcription in both directions; engineered CDK9 recruitment desensitizes transcription to INTS11, establishing antagonistic roles for CDK9 and INTS11 in directional transcription. Genetic and pharmacological CDK9 inhibition, auxin-inducible degron depletion of INTS11, nascent RNA sequencing, engineered CDK9 recruitment assays eLife High 38976490
2021 INTS11 physically interacts with Polycomb repressive complex 2 (PRC2). Loss of INTS11 in hematopoietic stem and progenitor cells destabilizes the PRC2 complex, decreases H3K27me3 levels, and derepresses PRC2 target genes, causing cell cycle arrest. Re-expression of INTS11 or PRC2 subunits restores PRC2 levels, H3K27me3, and HSPC function. Conditional Ints11 knockout in mice, co-immunoprecipitation identifying INTS11-PRC2 interaction, western blotting for H3K27me3, rescue experiments with INTS11 or PRC2 re-expression Science advances Medium 34516911
2023 A homozygous INTS11 variant impairs its catalytic endonuclease activity (evidenced by accumulation of RNA substrates) and causes G2/M arrest in patient-derived cells with length-dependent dysregulation of mitosis and neural development genes, including CDKL5. Mutant knockin iPSCs show disrupted mitotic spindle organization, slow proliferation, increased apoptosis, and decreased ERK pathway activity linked to reduced CDKL5 levels. Neural progenitor cell generation from mutant iPSCs is delayed. Patient-derived cells, INTS11 variant knockin iPSCs, RNA substrate accumulation assay, mitotic spindle imaging, cell cycle analysis, NPC differentiation assay, ERK pathway biochemical analysis Cell reports Medium 37980560
2023 INTS11 and INTS9 form a trimeric complex with BRAT1 in human cells. BRAT1 is required for INTS11 recruitment to promoters of neuronal target genes (REST-regulated genes), and disease-causing BRAT1 mutations (E522K) diminish BRAT1 association with the INTS11/INTS9 heterodimer, linking disease phenotype to impaired transcriptional activation of neuronal genes. Co-immunoprecipitation in HEK293T and NT2 cells, chromatin immunoprecipitation (ChIP), BRAT1 depletion with neural differentiation assay, disease-mutant interaction assays bioRxivpreprint Medium 37609215
2023 Loss-of-function variants in INTS11 (including catalytic site residue p.His414Tyr and p.Arg17Leu) fail to rescue lethality in Drosophila null mutants, while partial loss-of-function variants cause shortened lifespan and locomotor defects, demonstrating that INTS11 endonuclease integrity is essential for neurological development. Drosophila null mutant complementation assays, bang sensitivity and locomotor activity assays with human variant transgenes American journal of human genetics Medium 37054711
2026 In Drosophila, IntS11 absence causes G1 arrest in neuroblasts (not apoptosis or NB loss) and impairs clonal expansion. IntS11 binds chromatin at loci with long 3'UTR isoforms to maintain their expression and mRNA stability; loss of IntS11 leads to 3'UTR shortening and downregulation of ~80% of neuronal morphogenesis genes with shortened 3'UTRs. Drosophila MARCM clonal analysis, live imaging, FUCCI cell cycle analysis, single-cell RNA-seq, ChIP-qPCR Cell & bioscience Medium 42035222
2026 In Drosophila early embryos, maternal IntS11 functions upstream of pioneer factors Zelda and GAF: IntS11 is required for RNA Pol II recruitment to regulatory elements, which in turn enables pioneer factor binding and zygotic genome activation. IntS11 has dual roles: its canonical endonuclease activity sustains major-wave ZGA, while an enzyme-independent function drives de novo Pol II loading and pioneer factor engagement. Maternal IntS11 depletion in Drosophila embryos, genome-wide Pol II ChIP-seq, pioneer factor (Zelda/GAF) binding assays, catalytic mutant analysis Proceedings of the National Academy of Sciences of the United States of America Medium 41955115

Source papers

Stage 0 corpus · 12 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
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 61 28396433
2023 Bi-allelic variants in INTS11 are associated with a complex neurological disorder. American journal of human genetics 30 37054711
2021 INTS11 regulates hematopoiesis by promoting PRC2 function. Science advances 14 34516911
2023 A homozygous variant in INTS11 links mitosis and neurogenesis defects to a severe neurodevelopmental disorder. Cell reports 11 37980560
2024 Cytoplasmic binding partners of the Integrator endonuclease INTS11 and its paralog CPSF73 are required for their nuclear function. Molecular cell 8 39032490
2023 An examination of the metal ion content in the active sites of human endonucleases CPSF73 and INTS11. The Journal of biological chemistry 8 36822327
2024 Human promoter directionality is determined by transcriptional initiation and the opposing activities of INTS11 and CDK9. eLife 7 38976490
2023 BRAT1 associates with INTS11/INTS9 heterodimer to regulate key neurodevelopmental genes. bioRxiv : the preprint server for biology 5 37609215
2024 INTS11-related neurodevelopmental disorder: a case report and literature review. Journal of human genetics 3 39030370
2026 Neurotrophic Modulation Restores Motor and Developmental Defects in Zebrafish Models of ints11 Deficiency. Journal of neurochemistry 0 41837557
2026 Maternal IntS11 primes embryonic totipotency by organizing early zygotic transcription initiation. Proceedings of the National Academy of Sciences of the United States of America 0 41955115
2026 Integrator subunit IntS11 orchestrates the temporal dynamics of neural lineage progression in Drosophila. Cell & bioscience 0 42035222