Continuous transcription initiation guarantees robust repair of all transcribed genes and regulatory regions

Anastasios Liakos,Matthieu D Lavigne,Dimitris Konstantopoulos,Maria Fousteri

doi:10.1038/s41467-020-14566-9

Abstract

Inhibition of transcription caused by DNA damage-impaired RNA polymerase II (Pol II) elongation conceals a local increase in de novo transcription, slowly progressing from Transcription Start Sites (TSSs) to gene ends. Although associated with accelerated repair of Pol II-encountered lesions and limited mutagenesis, it is still unclear how this mechanism is maintained during genotoxic stress-recovery. Here we uncover a widespread gain in chromatin accessibility and preservation of the active H3K27ac mark after UV-irradiation. The concomitant increase in Pol II escape from promoter-proximal pause (PPP) sites of most active genes, PROMPTs and enhancer RNAs favors unrestrained initiation, as evidenced by the synthesis of nascent RNAs including start RNAs. Accordingly, drug-inhibition of PPP-release replenishes levels of pre-initiating Pol II at TSSs after UV. Our data show that such continuous engagement of Pol II molecules ensures maximal transcription-driven repair throughout expressed genes and regulatory loci. Importantly, revealing this unanticipated regulatory layer of UV-response provides physiological relevant traction to the emerging concept that Pol II initiation rate is determined by pause-release dynamics.

Highlights

Inhibition of transcription caused by DNA damage-impaired RNA polymerase II (Pol II) elongation conceals a local increase in de novo transcription, slowly progressing from Transcription Start Sites (TSSs) to gene ends
To characterize the impact that UV irradiation might have on the chromatin landscape of transcriptional regulatory regions during the early recovery times, and how this could be linked to the widespread promoter-proximal pause (PPP) release of elongating Pol II and the local increase in nRNA production downstream of TSS25,26,34, we first determined the genome-wide changes in chromatin accessibility
The establishment of precise maps of chromatin state helped us to query in detail the impact of transcription on DNA repair activities at important functional regions, including PROMPT and enhancer RNAs (eRNAs) loci

Summary

Introduction

Inhibition of transcription caused by DNA damage-impaired RNA polymerase II (Pol II) elongation conceals a local increase in de novo transcription, slowly progressing from Transcription Start Sites (TSSs) to gene ends. The concomitant increase in Pol II escape from promoter-proximal pause (PPP) sites of most active genes, PROMPTs and enhancer RNAs favors unrestrained initiation, as evidenced by the synthesis of nascent RNAs including start RNAs. drug-inhibition of PPPrelease replenishes levels of pre-initiating Pol II at TSSs after UV. Our data show that such continuous engagement of Pol II molecules ensures maximal transcription-driven repair throughout expressed genes and regulatory loci Revealing this unanticipated regulatory layer of UV-response provides physiological relevant traction to the emerging concept that Pol II initiation rate is determined by pause-release dynamics. If this step does not occur rapidly, start-RNAs are terminated[12,14], implying that Pol II turnover at PPP sites is high at steady state, and that replenishment of Pol II engaged in early transcription (initiation to PPP) is achieved through the continuous re-entry of pre-initiating Pol II into PICs14,15

Methods

Results

Conclusion