A CSB-PAF1C axis restores processive transcription elongation after DNA damage repair

Diana Van Den Heuvel,Di Zhou,Michiel Vermeulen,Kevin Yang,Michelle T Paulsen,Yana Van Der Weegen,Madelon Dijk,Lucia Daxinger,Haoyu Wu,Katja Apelt,Martijn S Luijsterburg,Mats Ljungman,Cornelia G Spruijt,Jurgen A Marteijn,Angela Kragten,Alfred C O Vertegaal,Román González-Prieto

doi:10.1038/s41467-021-21520-w

Abstract

Bulky DNA lesions in transcribed strands block RNA polymerase II (RNAPII) elongation and induce a genome-wide transcriptional arrest. The transcription-coupled repair (TCR) pathway efficiently removes transcription-blocking DNA lesions, but how transcription is restored in the genome following DNA repair remains unresolved. Here, we find that the TCR-specific CSB protein loads the PAF1 complex (PAF1C) onto RNAPII in promoter-proximal regions in response to DNA damage. Although dispensable for TCR-mediated repair, PAF1C is essential for transcription recovery after UV irradiation. We find that PAF1C promotes RNAPII pause release in promoter-proximal regions and subsequently acts as a processivity factor that stimulates transcription elongation throughout genes. Our findings expose the molecular basis for a non-canonical PAF1C-dependent pathway that restores transcription throughout the human genome after genotoxic stress.

Highlights

Bulky DNA lesions in transcribed strands block RNA polymerase II (RNAPII) elongation and induce a genome-wide transcriptional arrest
Co-IP experiments confirmed that CSB associated with RNAPII as well as with PAF1 complex (PAF1C) subunits PAF1, LEO1, and CTR9 after UV irradiation (Fig. 1c, d) and treatment with Illudin S (Supplementary Fig. 1c)
PAF1C is known to interact with RNAPII in a p-TEFb-dependent manner to regulate transcription elongation[3,5,33]

Summary

Introduction

Bulky DNA lesions in transcribed strands block RNA polymerase II (RNAPII) elongation and induce a genome-wide transcriptional arrest. We find that PAF1C promotes RNAPII pause release in promoter-proximal regions and subsequently acts as a processivity factor that stimulates transcription elongation throughout genes. The regulation of RNAPII pause release in response to environmental cues involves positive elongation factors, such as p-TEFb and the PAF1 complex (PAF1C)[1,2,3]. Both PAF1C and DSIF act beyond pause release by stimulating the acceleration of RNAPII in promoter-proximal regions to ensure processive transcription elongation throughout genes[4,5,6,7]. It is essential that cells overcome this arrest and restore transcription after repair to maintain gene expression

Methods

Results

Conclusion