Emerging insights into the function and structure of the Integrator complex

Pfleiderer, Moritz M.; Galej, Wojciech P.

doi:10.1080/21541264.2022.2047583

Cited by 13 publications

(11 citation statements)

References 99 publications

(219 reference statements)

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“…Integrator complex assembles from fifteen canonical subunits (INTS1-15), including recently uncovered INTS15 [26][27][28][29][30] and together with PP2A-C heterodimer forms a 1.5 MDa Integrator-PP2A complex that harbours endonuclease (INTS11) and phosphatase (PP2A-C) enzymatic activities [31][32][33][34] .…”

Section: Introductionmentioning

confidence: 99%

“…Integrator complex assembles from fifteen canonical subunits (INTS1-15), including recently uncovered INTS15 26–30 and together with PP2A-C heterodimer forms a 1.5 MDa Integrator-PP2A complex that harbours endonuclease (INTS11) and phosphatase (PP2A-C) enzymatic activities 31–34 . Numerous other factors have been reported to interact with the Integrator, most notably transcription regulators (e.g.…”

Section: Introductionmentioning

confidence: 99%

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Structural basis of the Integrator complex assembly and association with transcription factors

Razew,

Fraudeau,

Pfleiderer

et al. 2024

Preprint

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SummaryIntegrator is a multi-subunit protein complex responsible for premature transcription termination of coding and non-coding RNAs in Metazoans. This is achieved via Integrator’s two enzymatic activities, RNA endonuclease and protein phosphatase, acting on the promoter-proximally paused RNA Polymerase II (RNAPII). Yet, it remains unclear how Integrator assembly and recruitment are regulated and what are the functions of many of its core subunits. Here we report two cryo-EM reconstructions of large Integrator sub-complexes: INTS10/13/14/15 (Arm module) and INTS5/8/10/15, which allowed integrative modelling of the fully-assembled Integrator bound to the RNAPII paused elongating complex (PEC). INTS13/14 are positioned near the DNA upstream from the transcription pause site, suggesting a potential role in the chromatin context. Anin silicoprotein interaction screen of over 1500 transcription factors (TFs), identified Zinc Finger Protein 655 (ZNF655) as a direct interacting partner of INTS13 that associates with a fully assembled, 17-subunit Integrator complex. We propose a model wherein the Arm module acts as a platform for the recruitment of TFs that could modulate the stability of the Integrator’s association at specific loci and modulate transcription attenuation of the target genes.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Structural basis of the Integrator complex assembly and association with transcription factors

Razew,

Fraudeau,

Pfleiderer

et al. 2024

Preprint

Self Cite

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“…Various experiments showed that the Integrator complex assembles in a stepwise manner from separate stable modules including the shoulder module (INTS5/8), the backbone module (INTS1/2/7/12), the cleavage module (INTS4/9/11) and the ternary complex INTS10/13/14 which has been shown to bind RNA ( 47 , 48 ). Based on our finding that INTS10 levels decrease in patients’ cells, we first tested whether limited amounts of INTS10/13/14 are immunoprecipitated using anti-INTS13 antibodies.…”

Section: Resultsmentioning

confidence: 99%

Mutations in the non-codingRNU4ATACgene affect the homeostasis and function of the Integrator complex

Shidi

Cologne

Delous

et al. 2022

Nucleic Acids Research

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Various genetic diseases associated with microcephaly and developmental defects are due to pathogenic variants in the U4atac small nuclear RNA (snRNA), a component of the minor spliceosome essential for the removal of U12-type introns from eukaryotic mRNAs. While it has been shown that a few RNU4ATAC mutations result in impaired binding of essential protein components, the molecular defects of the vast majority of variants are still unknown. Here, we used lymphoblastoid cells derived from RNU4ATAC compound heterozygous (g.108_126del;g.111G>A) twin patients with MOPD1 phenotypes to analyze the molecular consequences of the mutations on small nuclear ribonucleoproteins (snRNPs) formation and on splicing. We found that the U4atac108_126del mutant is unstable and that the U4atac111G>A mutant as well as the minor di- and tri-snRNPs are present at reduced levels. Our results also reveal the existence of 3’-extended snRNA transcripts in patients’ cells. Moreover, we show that the mutant cells have alterations in splicing of INTS7 and INTS10 minor introns, contain lower levels of the INTS7 and INTS10 proteins and display changes in the assembly of Integrator subunits. Altogether, our results show that compound heterozygous g.108_126del;g.111G>A mutations induce splicing defects and affect the homeostasis and function of the Integrator complex.

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“…Integrator-dependent premature termination is emerging as an integral way to regulate Pol II transcription 20 , 21 , 50 , but our understanding of how Integrator terminates Pol II is limited. Here we present three cryo-EM structures of the complete Integrator: one bound to the PEC in the pre-termination state; one bound to Pol II in the post-termination state; and one of the complete, free complex in an inactive state.…”

Section: Discussionmentioning

confidence: 99%

“…Integrator not only targets paused Pol II during the transcription of protein-coding genes, but is also involved in terminating the synthesis of noncoding Pol II transcripts, including enhancer RNAs 16 , small nuclear RNAs 17 , telomerase RNA 18 and long noncoding RNAs 19 . Indeed, Integrator is a genome-wide regulator of Pol II transcription 20 , 21 .…”

Section: Mainmentioning

confidence: 99%

Structural basis of Integrator-dependent RNA polymerase II termination

Fianu,

Ochmann,

Walshe

et al. 2024

Nature

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The Integrator complex can terminate RNA polymerase II (Pol II) in the promoter-proximal region of genes. Previous work has shed light on how Integrator binds to the paused elongation complex consisting of Pol II, the DRB sensitivity-inducing factor (DSIF) and the negative elongation factor (NELF) and how it cleaves the nascent RNA transcript1, but has not explained how Integrator removes Pol II from the DNA template. Here we present three cryo-electron microscopy structures of the complete Integrator–PP2A complex in different functional states. The structure of the pre-termination complex reveals a previously unresolved, scorpion-tail-shaped INTS10–INTS13–INTS14–INTS15 module that may use its ‘sting’ to open the DSIF DNA clamp and facilitate termination. The structure of the post-termination complex shows that the previously unresolved subunit INTS3 and associated sensor of single-stranded DNA complex (SOSS) factors prevent Pol II rebinding to Integrator after termination. The structure of the free Integrator–PP2A complex in an inactive closed conformation2 reveals that INTS6 blocks the PP2A phosphatase active site. These results lead to a model for how Integrator terminates Pol II transcription in three steps that involve major rearrangements.

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Emerging insights into the function and structure of the Integrator complex

Cited by 13 publications

References 99 publications

Structural basis of the Integrator complex assembly and association with transcription factors

Structural basis of the Integrator complex assembly and association with transcription factors

Mutations in the non-codingRNU4ATACgene affect the homeostasis and function of the Integrator complex

Structural basis of Integrator-dependent RNA polymerase II termination

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