Integrator is a genome-wide attenuator of non-productive transcription

Lykke‐Andersen, Søren; Žumer, Kristina; Molska, Ewa; Rouvière, Jérôme O.; Wu, Guifen; Demel, Carina; Schwalb, Björn; Schmid, Manfred; Cramer, Patrick; Jensen, Torben Heick

doi:10.1016/j.molcel.2020.12.014

Cited by 114 publications

(147 citation statements)

References 69 publications

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“…Notably, we observed increased genomic occupancy of CPA components at the 3′ end of IRT genes, suggesting that, in the absence of INTS11, recruitment of the CPA machinery may compensate for the lack of 3′ end processing and sustains the recruitment of subsequent termination factors. A recent study suggests that Integrator and CPA machinery can occupy similar regions of DNA and cooperate to terminate human lncRNA transcription ( 30 ). Our results point to cooperative roles for the Integrator complex and CPA machinery in the processing of IRT genes, thereby extending this model to protein-coding genes ( Fig.…”

Section: Discussionmentioning

confidence: 99%

“…Previous work demonstrates that Integrator mediates the activation of immediate early genes, thereby controlling the transcriptional output of growth factor signaling (22,26,27). Notably, recent studies have shown that the catalytic activity of Integrator regulates elongation at coding genes by premature termination of transcripts associated with paused RNAPII (28)(29)(30)(31).…”

Section: Introductionmentioning

confidence: 99%

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Integrator enforces the fidelity of transcriptional termination at protein-coding genes

et al. 2021

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Integrator enforces the fidelity of transcriptional termination at protein-coding genes

et al. 2021

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“…NEXT- and PAXT-sensitive RNAs have been thoroughly characterized ( 19 , 22 , 25–28 ). Generally, the NEXT complex targets RNAs with unprotected and nonadenylated (pA − ) 3′ ends, exemplified by transcripts produced by the aforementioned PROMPT and eRNA loci as well as the large amount of TSS-proximal transcription termination at RNAPII transcription units (TUs) ( 29 ). Furthermore, the biogenesis of snoRNAs generates a sizable number of pA − and NEXT-sensitive processing intermediates ( 24 ).…”

Section: Introductionmentioning

confidence: 99%

“…While information about 5′–3′ trimming mechanisms is limited ( 30 , 32 , 33 ), some lines of evidence have implicated the RNA exosome and NEXT in the 3′–5′ exonucleolysis of snoRNA-hosting introns, and possibly also regular introns ( 24 , 34 , 35 ). In contrast to this vast production of pA − ends, polyadenylated (pA + ) RNA 3′ ends mostly originate from cleavage and polyadenylation-dependent processing ( 29 , 36 ). If the resulting transcript is not rapidly exported to the cytoplasm, such pA + 3′ ends can be subject to PAXT-mediated degradation, which targets many lncRNAs, PROMPTs, eRNAs, ptRNAs and a subset of mRNAs ( 19 , 22 , 25–27 , 37 ).…”

Section: Introductionmentioning

confidence: 99%

Rapid factor depletion highlights intricacies of nucleoplasmic RNA degradation

Gockert

Schmid

Jakobsen

et al. 2022

Nucleic Acids Research

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Turnover of nucleoplasmic transcripts by the mammalian multi-subunit RNA exosome is mediated by two adaptors: the Nuclear EXosome Targeting (NEXT) complex and the Poly(A) tail eXosome Targeting (PAXT) connection. Functional analyses of NEXT and PAXT have largely utilized long-term factor depletion strategies, facilitating the appearance of indirect phenotypes. Here, we rapidly deplete NEXT, PAXT and core exosome components, uncovering the direct consequences of their acute losses. Generally, proteome changes are sparse and largely dominated by co-depletion of other exosome and adaptor subunits, reflecting possible subcomplex compositions. While parallel high-resolution 3′ end sequencing of newly synthesized RNA confirms previously established factor specificities, it concomitantly demonstrates an inflation of long-term depletion datasets by secondary effects. Most strikingly, a general intron degradation phenotype, observed in long-term NEXT depletion samples, is undetectable upon short-term depletion, which instead emphasizes NEXT targeting of snoRNA-hosting introns. Further analysis of these introns uncovers an unusual mode of core exosome-independent RNA decay. Our study highlights the accumulation of RNAs as an indirect result of long-term decay factor depletion, which we speculate is, at least partly, due to the exhaustion of alternative RNA decay pathways.

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“…Integrator complex 13,14 functions as an RNA endonuclease to cleave different classes of RNAs [15][16][17][18][19] . More recent studies discovered that Integrator is enriched in the proximity of RNA promoters 20 and can associate with paused Pol II bound by DSIF and NELF 21,22 to trigger PTT and repress gene activity 18,[23][24][25][26][27][28] . We have recently found that Integrator associates with protein phosphatase 2A core enzyme (PP2A-AC) and dephosphorylates the C-terminal domain (CTD) of Pol II and determined the structure of Integrator-containing PP2A-AC (termed INTAC), showing how the RNA nuclease and protein phosphatase are organized in the INTAC complex 7 .…”

Section: Introductionmentioning

confidence: 99%

Structural basis of INTAC-regulated transcription

Zheng

Jin

et al. 2021

Preprint

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For the majority of expressed eukaryotic genes, RNA polymerase II (Pol II) forms a paused elongation complex (PEC) and undergoes promoter-proximal pausing downstream of the transcription start site 1–3. The polymerase either proceeds into productive elongation or undergoes promoter-proximal premature transcription termination 4–6. It remains incompletely understood how transcription is regulated at this stage. Here, we determined the structure of PEC bound to INTAC, an Integrator-containing PP2A complex 7, at near-atomic resolution. The structure shows that INTAC partially wraps around PEC through multiple contacts, permitting the memetic nascent RNA to run into substrate-entry tunnel of the endonuclease subunit INTS11 of INTAC for cleavage. Pol II C-terminal domain (CTD) winds over INTAC backbone module through multiple anchors and is suspended above the phosphatase of INTAC for dephosphorylation. Biochemical analysis shows that INTAC-PEC association requires unphosphorylated CTD and could tolerate CTD phosphorylation, suggesting an INTAC-mediated persistent CTD dephosphorylation followed by reinforcement of the INTAC-PEC complex. Our study reveals how INTAC binds PEC and orchestrates RNA cleavage and CTD dephosphorylation, two critical events in generating premature transcription termination.

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Integrator is a genome-wide attenuator of non-productive transcription

Cited by 114 publications

References 69 publications

Integrator enforces the fidelity of transcriptional termination at protein-coding genes

Integrator enforces the fidelity of transcriptional termination at protein-coding genes

Rapid factor depletion highlights intricacies of nucleoplasmic RNA degradation

Structural basis of INTAC-regulated transcription

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