Mechanism and consequences of herpes simplex virus 1-mediated regulation of host mRNA alternative polyadenylation

Eukaryotic gene expression is extensively regulated by cellular stress and pathogen infections. We have previously shown that herpes simplex virus 1 (HSV-1) and several cellular stresses cause widespread disruption of transcription termination (DoTT) of RNA polymerase II (RNAPII) in host genes and that the viral immediate early factor ICP27 plays an important role in HSV-1-induced DoTT. Here, we show that HSV-1 infection also leads to widespread changes in alternative polyadenylation (APA) of host mRNAs. In the majority of cases, polyadenylation shifts to upstream poly(A) sites (PAS), including many intronic PAS. Mechanistically, ICP27 contributes to HSV-1-mediated APA regulation. HSV-1- and ICP27-induced activation of intronic PAS is sequence-dependent and does not involve general inhibition of U1 snRNP. HSV1-induced intronic polyadenylation is accompanied by early termination of RNAPII. HSV-1-induced mRNAs polyadenylated at intronic PAS (IPA) are exported into the cytoplasm while APA isoforms with extended 3’ UTRs are sequestered in the nuclei, both preventing the expression of the full-length gene products. Finally we provide evidence that HSV-induced IPA isoforms are translated. Together with other recent studies, our results suggest that viral infection and cellular stresses induce a multi-faceted host response that includes DoTT and changes in APA profiles.
Author summary Viral infections profoundly alter host cell gene expression. It is important to understand both how viruses hijack the host cell machineries to express their own genes and how host cells respond to viral infection for defense. We have previously shown that herpes simplex virus-1 (HSV-1) blocks host cell transcription termination, at least in part, through the viral immediate early protein ICP27. Here we show that HSV-1 infection also alters mRNA 3’ end formation and promotes the formation of truncated mRNAs. Some of these aberrant mRNAs are exported into the cytoplasm and translated. This viral activity requires ICP27 and other viral factors. Our study, together with other recent reports, suggests that viral infections and cellular stress elicit similar responses in mammalian cells.