INTS13

INTS13 is a subunit of the Integrator complex that, together with INTS10, INTS14, and INTS15, forms a scorpion-tail-shaped nucleic acid-binding module with structural homology to Ku70-Ku80; this module contacts the DSIF DNA clamp in the pre-termination complex to facilitate RNA Pol II termination (PMID:32647223, PMID:38570683). The C-terminal motif of INTS13 directly bridges the nucleic acid-binding module to the Integrator cleavage module, coordinating snRNA 3′-end processing, and germline variants disrupting this interaction cause ciliopathy by impairing Integrator assembly and ciliogenesis (PMID:32647223, PMID:36229431). The exposed surface of INTS13 serves as a recruitment platform for lineage-specific transcription factors—including EGR1/2 (via NAB2) at monocytic enhancers to drive chromatin looping and myeloid differentiation, and ZNF655 within the fully assembled paused-Pol II complex—establishing INTS13 as a key determinant of Integrator targeting to specific genomic loci (PMID:30008316, PMID:38823386). The Drosophila ortholog Mat89Bb/Asunder is a PAN GU kinase substrate whose depletion causes polyploidy, indicating an additional conserved role in cell cycle fidelity (PMID:15737938).

1. 2005 Medium

   Before a link to the Integrator complex was known, identification of Mat89Bb (Drosophila ortholog of INTS13) as a PAN GU kinase substrate revealed a conserved requirement in S-M cell cycle transitions, establishing that loss of this gene causes polyploidy across species.

   Evidence DIVEC kinase substrate screen in Drosophila, RNAi in Drosophila/HeLa, morpholino in Xenopus with polyploidy readout

   PMID:15737938

   Open questions at the time

   • Mechanism connecting INTS13/Mat89Bb to cell cycle control is undefined
   • Whether PAN GU phosphorylation is conserved in vertebrates is untested
   • Relationship to Integrator complex function not established
2. 2018 High

   The discovery that INTS13 operates as a separable sub-module targeting EGR1/2-bound monocytic enhancers via NAB2 established that INTS13 has a gene-specific transcription factor recruitment function beyond bulk snRNA processing, directly linking Integrator to enhancer activation and myeloid differentiation.

   Evidence ChIP-seq, chromatin conformation capture, siRNA depletion in cell lines and primary human progenitors with differentiation readout

   PMID:30008316

   Open questions at the time

   • Direct binding interface between INTS13 and NAB2/EGR not structurally resolved
   • Whether enhancer-targeting function requires the full Integrator or only the INTS13-containing sub-module is unclear
3. 2020 High

   Crystallography of the INTS13-INTS14 dimer revealed a Ku70-Ku80-like architecture with nucleic acid binding capacity, and mutagenesis showed that the INTS13 C-terminal motif directly contacts the cleavage module, answering how the INTS10/13/14 sub-module connects to snRNA processing and Pol II termination.

   Evidence X-ray crystallography, in vitro DNA/RNA binding assays, crosslinking mass spectrometry, C-terminal motif mutagenesis with snRNA processing and termination assays

   PMID:32647223

   Open questions at the time

   • Structure of the full INTS10/13/14 trimer not resolved at this stage
   • How the module discriminates RNA hairpin substrates in vivo is unknown
4. 2022 High

   Genetic and biochemical evidence that germline INTS13 variants (p.S652L, p.K668Nfs*9) disrupt cleavage-module binding and cause ciliopathy established INTS13 as a disease gene and revealed ciliogenesis as a key downstream cellular process controlled by Integrator integrity.

   Evidence Exome sequencing of affected families, co-immunoprecipitation of variants, INTS13 depletion in human cells (ciliogenesis assay), Xenopus morpholino with cilia phenotype

   PMID:36229431

   Open questions at the time

   • Which ciliary gene targets are directly versus indirectly regulated by INTS13 is unresolved
   • Whether ciliopathy phenotypes reflect snRNA processing, Pol II termination, or enhancer defects is unclear
5. 2023 Medium

   Discovery that INTS15 assembles primarily with the INTS13/14/10 module and bridges to the Int-PP2A module expanded the sub-module to a four-subunit nucleic acid-binding unit and connected it to Pol II pause regulation.

   Evidence Proteomics, AlphaFold2 prediction, ChIP-seq/PRO-seq functional genomics, co-purification

   PMID:36920904

   Open questions at the time

   • Direct INTS13-INTS15 interface not validated by mutagenesis or reconstitution
   • Contribution of INTS15 to the nucleic acid binding properties of the module untested
6. 2024 High

   Cryo-EM structures of the complete Integrator-PP2A complex in multiple functional states showed that the INTS10/13/14/15 module forms a scorpion-tail 'sting' that contacts the DSIF clamp, explaining how this module mechanically promotes Pol II termination, while an independent cryo-EM and computational study demonstrated that the INTS13 surface recruits ZNF655, generalizing the transcription-factor recruitment function beyond EGR/NAB2.

   Evidence Cryo-EM of Integrator-PP2A in three states; cryo-EM of sub-complexes plus AlphaFold2 screen of >1,500 TFs with co-purification validation

   PMID:38570683 PMID:38823386

   Open questions at the time

   • Functional consequence of ZNF655-INTS13 interaction on gene regulation not characterized
   • Whether DSIF clamp opening requires catalytic activity or is purely mechanical is unresolved
   • Full catalog of transcription factors recruited via the INTS13 surface is incomplete

• It remains unknown how INTS13's transcription-factor recruitment, snRNA processing, and Pol II termination functions are coordinated in vivo, and whether the cell cycle role of the Drosophila ortholog reflects a distinct Integrator-independent function.
• No separation-of-function alleles distinguishing enhancer recruitment from cleavage-module bridging
• Mechanistic basis for cell cycle phenotype (polyploidy) remains unconnected to known Integrator functions
• In vivo structural dynamics of the INTS13 module during transcription termination are unresolved