PAF1C restores transcription after DNA damage independently of promoting histone mark deposition

Abstract When RNA polymerase II (RNAPII) stalls at transcription-blocking lesions, the transcription-coupled DNA repair (TCR) pathway is activated to remove the damage. After repair, efficient transcription restart requires the PAF1 elongation complex (PAF1C). PAF1C promotes deposition of transcription-associated histone marks, which are enriched at active genes and proposed to support post-repair transcription recovery. Using conditional knockouts of writers of PAF1C-associated histone marks, we show that deposition of H3K79 me , H3K4 me3 , and H2BK120 Ub is dispensable for transcription restart. While H3K4 me3 levels remain mostly unchanged during DNA damage-induced transcription inhibition, H2BK120 Ub levels decrease after damage and are co-transcriptionally restored upon transcription restart. We further find that, unlike the core subunits PAF1 and CTR9, the dissociable PAF1C subunit RTF1 does not contribute to transcription restart. Finally, we show that the TCR core factor CSB is not required for the transient PAF1C interaction during normal transcription, but specifically stabilizes PAF1C on RNAPII in response to DNA damage-induced stalling. Together, these findings indicate that transcription restoration after DNA damage is driven by PAF1C independently of transcription-associated histone mark deposition.