Global unleashing of transcription elongation waves in response to genotoxic stress restricts somatic mutation rate

Abstract

Complex molecular responses preserve gene expression accuracy and genome integrity in the face of environmental perturbations. Here we report that, in response to UV irradiation, RNA polymerase II (RNAPII) molecules are dynamically and synchronously released from promoter-proximal regions into elongation to promote uniform and accelerated surveillance of the whole transcribed genome. The maximised influx of de novo released RNAPII correlates with increased damage-sensing, as confirmed by RNAPII progressive accumulation at dipyrimidine sites and by the average slow-down of elongation rates in gene bodies. In turn, this transcription elongation ‘safe’ mode guarantees efficient DNA repair regardless of damage location, gene size and transcription level. Accordingly, we detect low and homogenous rates of mutational signatures associated with UV exposure or cigarette smoke across all active genes. Our study reveals a novel advantage for transcription regulation at the promoter-proximal level and provides unanticipated insights into how active transcription shapes the mutagenic landscape of cancer genomes.

Continuous transcription initiation guarantees robust repair of transcribed genes and regulatory regions in response to DNA damage

“…To characterise the impact that UV might have on the chromatin landscape of transcriptional regulatory regions and how this could be linked to the widespread PPP-release of elongating Pol II and the local increase in nRNA production downstream of TSS 28,29,38 , we first determined the genome-wide changes in chromatin accessibility. The omni-ATAC-seq protocol 43 was implemented in our system involving the irradiation with mild doses of UV-C of human skin fibroblasts synchronized in early G1 (see Methods and also 28 ). We reproducibly measured chromatin accessibility before (NO UV) and after (+UV) irradiation during the early phase of recovery ( Supplementary Fig.…”

“…Although TC-NER depends on lesion-sensing potential by elongating Pol II molecules, transcription elongation has been shown to be transiently inhibited after UV irradiation [28][29][30] due to a proportion of Pol II molecules stalling at encountered DNA damages 28,31 . Moreover, depletion of the pre-initiating hypo-phosphorylated Pol II(-hypo) isoform from chromatin shortly after UV irradiation 28,32,33 has led to the assumption that new transcription initiation events are transiently and globally repressed [32][33][34][35][36][37] . On the other hand, recent reports 28,29,38 have revealed a functionally essential stress-dependent global increase in 5' nascent RNA (nRNA) activity that depends on the UV-induced raise in active P-TEFb levels 39,40 and on the rapid dissociation of the NELF complex 41 .…”

“…Moreover, depletion of the pre-initiating hypo-phosphorylated Pol II(-hypo) isoform from chromatin shortly after UV irradiation 28,32,33 has led to the assumption that new transcription initiation events are transiently and globally repressed [32][33][34][35][36][37] . On the other hand, recent reports 28,29,38 have revealed a functionally essential stress-dependent global increase in 5' nascent RNA (nRNA) activity that depends on the UV-induced raise in active P-TEFb levels 39,40 and on the rapid dissociation of the NELF complex 41 . The ensuing fast and global release of de novo Pol II elongation waves from PPP sites into gene bodies boosts lesion-sensing activity and accelerates removal of DNA adducts by TC-NER in virtually all active mRNA genes 28 .…”

“…On the other hand, recent reports 28,29,38 have revealed a functionally essential stress-dependent global increase in 5' nascent RNA (nRNA) activity that depends on the UV-induced raise in active P-TEFb levels 39,40 and on the rapid dissociation of the NELF complex 41 . The ensuing fast and global release of de novo Pol II elongation waves from PPP sites into gene bodies boosts lesion-sensing activity and accelerates removal of DNA adducts by TC-NER in virtually all active mRNA genes 28 . Together these findings substantiate the possibility that UV might not as severely affect initiation of transcription, in contrary to previous beliefs.…”

“…Taking also into consideration recent evidence that supports the model of disengagement of a given Pol II molecule from DNA template after damage recognition 34,35,42 , it is tempting to assume that ensuring continuity in transcription initiation may bring advantages in the repair process. We thus hypothesized that the apparent loss of pre-initiating RNAPII may not be due to the absence of RNAPII recruitment at TSSs, but rather due to a decrease in the dwell-time of Pol II-hypo isoform at TSS, as justified by the concomitant increase in S5P-and S2P-pol II downstream of TSS 28 . In this way, cells would be able to uninterruptedly feed the global release of lesion-scanning enzymes into transcribable sequences and guarantee the detection of more lesions along DNA template strands.…”