Post‐transcriptional polyadenylation site cleavage maintains 3′‐end processing upon DNA damage

Abstract

The recognition of polyadenylation signals (PAS) in eukaryotic pre‐mRNAs is usually coupled to transcription termination, occurring while pre‐mRNA is chromatin‐bound. However, for some pre‐mRNAs, this 3′‐end processing occurs post‐transcriptionally, i.e., through a co‐transcriptional cleavage (CoTC) event downstream of the PAS, leading to chromatin release and subsequent PAS cleavage in the nucleoplasm. While DNA‐damaging agents trigger the shutdown of co‐transcriptional chromatin‐associated 3′‐end processing, specific compensatory mechanisms exist to ensure efficient 3′‐end processing for certain pre‐mRNAs, including those that encode proteins involved in the DNA damage response, such as the tumor suppressor p53. We show that cleavage at the p53 polyadenylation site occurs in part post‐transcriptionally following a co‐transcriptional cleavage event. Cells with an engineered deletion of the p53 CoTC site exhibit impaired p53 3′‐end processing, decreased mRNA and protein levels of p53 and its transcriptional target p21, and altered cell cycle progression upon UV‐induced DNA damage. Using a transcriptome‐wide analysis of PAS cleavage, we identify additional pre‐mRNAs whose PAS cleavage is maintained in response to UV irradiation and occurring post‐transcriptionally. These findings indicate that CoTC‐type cleavage of pre‐mRNAs, followed by PAS cleavage in the nucleoplasm, allows certain pre‐mRNAs to escape 3′‐end processing inhibition in response to UV‐induced DNA damage.