CPSF73 activation and 3’ Pol II pausing are lost during read-through transcription after heat shock [ChIP-seq]

Multiple types of cellular stress induce RNA polymerase II (Pol II) to read through normal termination sites at mRNA genes, causing long downstream regions to be transcribed. We observed strong read-through transcription downstream of thousands of genes after heat shock. Additionally, the 3’ Pol II pause that normally occurs during termination was globally lost. Heat shock also increased phosphorylation of Tyr1 and Ser2 residues in the Pol II C-terminal domain (CTD) at the 3’ ends of genes, with smaller increases observed at genes with read-through transcription. We found that 3’ RNA cleavage, a key step of transcription termination, was defective at read-through genes after heat shock; however, the CPSF73 endonuclease responsible for cleavage remained at the 3’ ends of genes. Over-expressing an activator of CPSF73 activity, RBBP6, during heat shock rescued the loss of cleavage and attenuated read-through transcription. Our data suggest that heat shock alters Pol II speed, CTD phosphorylation, and CPSF73 activity via RBBP6, contributing to a multifaceted mechanism that enables transcription to continue far downstream of normal termination sites during cellular stress.