The Human Integrator Complex Facilitates Transcriptional Elongation by Endonucleolytic Cleavage of Nascent Transcripts

Abstract

SUMMARY Transcription by RNA polymerase II (RNAPII) is pervasive in the human genome. However, the mechanisms controlling transcription at promoters and enhancers remain enigmatic. Here, we demonstrate that Integrator subunit 11 (INTS11), the catalytic subunit of the Integrator complex, regulates transcription at these loci through its endonuclease activity. Promoters of genes require INTS11 to cleave nascent transcripts associated with paused RNAPII and induce their premature termination in the proximity of the +1 nucleosome. The turnover of RNAPII permits the subsequent recruitment of an elongation-competent RNAPII complex, leading to productive elongation. In contrast, enhancers require INTS11 catalysis not to evict paused RNAPII but rather to terminate enhancer RNA transcription beyond the +1 nucleosome. These findings are supported by the differential occupancy of negative elongation factor (NELF), SPT5, and tyrosine-1-phosphorylated RNAPII. This study elucidates the role of Integrator in mediating transcriptional elongation at human promoters through the endonucleolytic cleavage of nascent transcripts and the dynamic turnover of RNAPII.

Integrator-Dependent and Allosteric/Intrinsic Mechanisms Ensure Efficient Termination of snRNA Transcription

“…In budding yeast, Cell Reports 33, 108319, October 27, 2020 5 Report ll OPEN ACCESS termination of snRNA transcription uses the Sen1 helicase, and mapping of its terminated transcripts reveals U-rich regions at the 3 0 ends that could aid this process (Schaughency et al, 2014). Finally, Integrator is broadly involved in early Pol II termination, including at promoter proximal and enhancer regions (Beckedorff et al, 2020;Lai et al, 2015;Nojima et al, 2018;Stadelmayer et al, 2014). In those cases, its depletion does not prevent termination to the extent that CPSF73 elimination does at protein-coding genes, which might be due to alternative pathways akin to those identified here.…”

“…Recent findings implicate Integrator in promoterproximal regulation of Pol II transcription (Beckedorff et al, 2020;Elrod et al, 2019;Stadelmayer et al, 2014;Tatomer et al, 2019). Integrator is also involved in the termination of other non-coding transcripts, including enhancer RNAs and promoter upstream transcripts (Beckedorff et al, 2020;Lai et al, 2015;Nojima et al, 2018). Lastly, Integrator mutations are associated with some neurological diseases (Oegema et al, 2017).…”

Structure of the catalytic core of the Integrator complex

“…Since its discovery, the Integrator has been shown to be involved in several other pathways, including biogenesis of enhancer RNAs ( Lai et al., 2015 ), telomerase RNA ( Rubtsova et al., 2019 ), long non-coding RNAs ( Nojima et al., 2018 ), viral microRNA (miRNA) biogenesis during Herpesvirus saimiri infection ( Cazalla et al., 2011 ; Xie et al., 2015 ), as well as regulation of the RNAPII transcription pause/release cycle ( Beckedorff et al., 2020 ; Gardini et al., 2014 ; Rienzo and Casamassimi, 2016 ; Skaar et al., 2015 ; Yamamoto et al., 2014 ). Most recent studies show that the Integrator can destabilize promoter-proximally paused RNAPII, leading to nascent RNA cleavage and transcription attenuation in a wide range of protein-coding genes ( Elrod et al., 2019 ; Lykke-Andersen et al., 2020 ; Tatomer et al., 2019 ).…”

ZC3H4 restricts non-coding transcription in human cells

“…The Integrator complex aids termination of many non-coding transcripts, with the archetypal example being snRNAs (Baillat et al, 2005;Davidson et al, 2020;O'Reilly et al, 2014). Integrator is also implicated in the termination of promoter upstream transcripts (PROMPTs) and enhancer RNAs (eRNAs) (Beckedorff et al, 2020;Lai et al, 2015;Nojima et al, 2018). The mechanism is analogous to that at protein-coding genes, driven by endonucleolytic cleavage by INTS11.…”