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

DaSilva, Luis; Blumenthal, Ezra; Beckedorff, Felipe; Cingaram, Pradeep Reddy; Santos, Helena; Edupuganti, Raghu Ram; Zhang, Anda; Dokaneheifard, Sadat; Aoi, Yuki; Yue, Jingyin; Kirstein, Nina; Tayari, Mina M.; Shilatifard, Ali; Shiekhattar, Ramin

doi:10.1126/sciadv.abe3393

Cited by 34 publications

(22 citation statements)

References 60 publications

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“…S1, A and C to F). Because of the modular nature of Integrator and multiple interactions among different subunits ( 32 , 41 ), it is difficult to fully assess the impact of depletion of any individual subunit on the complex composition (fig. S1B).…”

Section: Resultsmentioning

confidence: 99%

The Integrator complex regulates microRNA abundance through RISC loading

et al. 2023

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MicroRNA (miRNA) homeostasis is crucial for the posttranscriptional regulation of their target genes during development and in disease states. miRNAs are derived from primary transcripts and are processed from a hairpin precursor intermediary to a mature 22-nucleotide duplex RNA. Loading of the duplex into the Argonaute (AGO) protein family is pivotal to miRNA abundance and its posttranscriptional function. The Integrator complex plays a key role in protein coding and noncoding RNA maturation, RNA polymerase II pause-release, and premature transcriptional termination. Here, we report that loss of Integrator results in global destabilization of mature miRNAs. Enhanced ultraviolet cross-linking and immunoprecipitation of Integrator uncovered an association with duplex miRNAs before their loading onto AGOs. Tracing miRNA fate from biogenesis to stabilization by incorporating 4-thiouridine in nascent transcripts pinpointed a critical role for Integrator in miRNA assembly into AGOs.

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Section: Resultsmentioning

confidence: 99%

The Integrator complex regulates microRNA abundance through RISC loading

et al. 2023

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“…To experimentally evaluate the impact of APA usage on 5′ UPT biogenesis, we performed a series of knockdowns of the most prominent positive and negative APA regulators. Loss of either PCF11 or INTS11 (an APA termination factor and the endonuclease factor of integrator I, respectively) was recently shown to inhibit APA and promote 3′ UTR lengthening ( Dasilva et al., 2021 ; Wang et al., 2019 ). We therefore knocked down PCF11 and INTS11 using small interfering RNA (siRNA) in HeLa cells (Figure S5B) and performed HMM and Z score analyses for each condition in TEX control and treated samples ( Table S13: HMM analysis (HeLa cells, control for PCF11KD and INTS11KD) after TEX treatment, related to Figure 4 , Table S14: HMM analysis (HeLa cells, PCF11KD) after TEX treatment, related to Figure 4 , Table S15: HMM analysis (HeLa cells, INTS11KD) after TEX treatment, related to Figure 4 for control, PCF11 KD , and INTS11 KD , respectively, and Figure S5C–E).…”

Section: Resultsmentioning

confidence: 99%

Alternative cleavage and polyadenylation generates downstream uncapped RNA isoforms with translation potential

Malka

Alkan

et al. 2022

Molecular Cell

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“…A future question would be to determine whether Tyr1 hyperphosphorylation is involved in the recruitment of the nuclear RNA exosome to the chromatin. Interestingly, Integrator activity is required for transcription termination of some protein-coding genes (61). While Integrator recruitment is not enriched in the gene body of the siEX(3)+ genes, we found a specific Integrator signal peak at the 3’end of these RNA exosome sensitive genes.…”

Section: Discussionmentioning

confidence: 99%

Cytoplasmic mRNA levels are regulated by a combination of chromatin retention and RNA stability

Henfrey

Murphy

Tellier

2022

Preprint

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Transcription and co-transcriptional processes, including pre-mRNA splicing and mRNA cleavage and polyadenylation, regulate the production of a mature mRNA. The carboxyl terminal domain (CTD) of RNA polymerase (pol) II, which comprises 52 repeats of the Tyr1Ser2Pro3Thr4Ser5Pro6Ser7 peptide, is involved in the coordination of transcription with co-transcriptional processes. The pol II CTD is dynamically modified by protein phosphorylation, which regulates recruitment of transcription and co-transcriptional factors. We have investigated whether cytoplasmic levels of mature mRNA from intron-containing protein-coding genes can be inferred from RNA processing efficiency, CTD phosphorylation, and/or association of proteins complexes regulating RNA production. Surprisingly, we found that genes associated with efficient RNA processing have relatively low phosphorylation of the pol II CTD. In contrast, protein-coding genes that produce a low level of mature mRNA are associated with high pol II CTD phosphorylation, poor RNA processing, and increased chromatin retention. Unexpectedly, the transcripts from this subset of genes are not actively degraded by the RNA exosome. RNA exosome-regulated genes are instead characterised by Tyr1 hyperphosphorylation and Integrator recruitment around the poly(A) site. Our results indicate that in addition to the transcription level, CTD phosphorylation and RNA processing efficiency play important roles in the regulation of chromatin retention of transcripts.

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

Abstract: Integrator directly binds and terminates protein-coding transcripts enriched in alternative polyadenylation sequences.

Cited by 34 publications

References 60 publications

The Integrator complex regulates microRNA abundance through RISC loading

The Integrator complex regulates microRNA abundance through RISC loading

Alternative cleavage and polyadenylation generates downstream uncapped RNA isoforms with translation potential

Cytoplasmic mRNA levels are regulated by a combination of chromatin retention and RNA stability

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