Precise regulation of RNA polymerase II (Pol II) is necessary for maintaining cellular homeostasis. The fate of a transcript can be determined by several processes after Pol II initiates transcription. The Integrator complex has a role in 3ʹ-end formation of small nuclear RNAs (snRNAs) and is known to interact with transcribing Pol II. A new study now shows that Integrator also fine-tunes mRNA production.

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In search of regulators of transcription elongation, Tatomer et al. performed an RNAi screen in fruit fly cells employing an eGFP gene under the control of the metallothionein A (MtnA) gene promoter, which is activated by high copper levels (the protein chelates metal ions). Because the reporter transcript is unspliced and non-polyadenylated, changes in eGFP expression preferentially uncover transcription (and translation) regulators.

Automated microscopy and image analysis identified 232 factors required for reporter expression in cells subjected to copper stress. Unexpectedly, nearly all Integrator subunits scored as potent negative regulators of both the reporter gene and the endogenous MtnA gene. This function required the RNA endonuclease activity of Integrator complex subunit 11 (IntS11).

Among positive transcription regulators identified in the screen were several subunits of the nuclear RNA exosome, such as Mtr4, which catalyses 3ʹ–5ʹ degradation of nuclear transcripts. Intriguingly, Mtr4 depletion not only reduced the levels of full-length MtnA mRNA, but also increased the production of shorter MtnA RNAs. These short RNAs were capped, shared the same transcription start site with full-length MtnA and were lost upon co-depletion of Mtr4 and Integrator.

Given that Integrator and the nuclear exosome interact directly, the authors suggest that Integrator cleaves nascent MtnA mRNAs, which are in turn degraded by the exosome, thereby inducing premature transcription termination. This role is mechanistically related to the cleavage of nascent snRNAs, suggesting that Integrator function at snRNAs has been repurposed to regulate protein-coding genes.

Next, the authors identified 409 genes upregulated in IntS9-depleted and copper-treated cells. Many of the genes are involved in cellular responses to stimuli, indicating that Integrator has a wide role in triggering mRNA transcription termination. Integrator was recruited to the 5ʹ-end of all tested loci and generated short RNAs, which were cleared by the exosome. The discrete size of Integrator-dependent short RNAs does not seem to depend on mRNA sequence, but possibly on nucleosome positioning or Pol II pausing or stalling.

Integrator attenuates productive transcription elongation, thereby providing an additional layer of Pol II regulation

In summary, Integrator fine-tunes mRNA levels in response to cellular stress. By cleaving nascent transcripts and transferring them to the nuclear exosome, Integrator attenuates productive transcription elongation, thereby providing an additional layer of Pol II regulation.