Widespread disruption of host transcription termination in HSV-1 infection

Abstract

Herpes simplex virus 1 (HSV-1) is an important human pathogen and a paradigm for virus-induced host shut-off. Here we show that global changes in transcription and RNA processing and their impact on translation can be analysed in a single experimental setting by applying 4sU-tagging of newly transcribed RNA and ribosome profiling to lytic HSV-1 infection. Unexpectedly, we find that HSV-1 triggers the disruption of transcription termination of cellular, but not viral, genes. This results in extensive transcription for tens of thousands of nucleotides beyond poly(A) sites and into downstream genes, leading to novel intergenic splicing between exons of neighbouring cellular genes. As a consequence, hundreds of cellular genes seem to be transcriptionally induced but are not translated. In contrast to previous reports, we show that HSV-1 does not inhibit co-transcriptional splicing. Our approach thus substantially advances our understanding of HSV-1 biology and establishes HSV-1 as a model system for studying transcription termination.

Infection by Herpes Simplex Virus 1 Causes Near-Complete Loss of RNA Polymerase II Occupancy on the Host Cell Genome

“…Similar to what we observed by Pol II ChIP-seq, the transcriptional changes were dominated by repression; the vast majority of mRNA genes exhibited decreased transcription, and little activation was observed. Interestingly, at later time points of infection, 4sU-seq reads mapped well beyond the 3= ends of thousands of genes, indicating a transcriptional termination defect that was most pronounced 7 to 8 h postinfection (40). At time points correlating with our work, only a subtle increase in the fraction of 4sU-seq reads mapping to intergenic regions was observed.…”

“…It is also possible that Pol II is recruited to promoters but does not stably associate in a manner that allows the polymerase to be cross-linked to the DNA or to be captured by ChIP. Recently, 4-thiouridine labeling and deep sequencing (4sU-seq) was used to evaluate ongoing transcription in 1-h windows during HSV-1 infection of human cells (40). Similar to what we observed by Pol II ChIP-seq, the transcriptional changes were dominated by repression; the vast majority of mRNA genes exhibited decreased transcription, and little activation was observed.…”

Herpes simplex virus ICP27 regulates alternative pre-mRNA polyadenylation and splicing in a sequence-dependent manner

“…S7 and S8). Our findings, including identification of prematurely cleaved and polyadenylated transcripts by Northern hybridization in wild type, but not in ICP27 deletion mutant virus-infected cells, would not have been predicted by a recent report (14), which posited that ICP27 had no role in regulating cellular cotranscriptional pre-mRNA splicing or termination of cellular transcripts.…”

“…Early studies indicated that, in an in vitro pre-mRNA splicing system, ICP27 may nonspecifically inhibit host pre-mRNA splicing, impairing spliceosome assembly as a result of interaction with SR protein kinase 1 (SRPK1) through ICP27's N-terminal RGG RNA-binding motif and/or interaction with spliceosome-association protein 145 (SAP145 or SF3B2) through ICP27's C-terminal domain (8,11). A recent communication reported that HSV-1 does not inhibit cotranscriptional splicing and proposed that previous reports of ICP27-induced splicing inhibition were artifacts, due to misinterpretation of run-on transcription (14). Indeed, splicing of only a few viral and cellular pre-mRNAs have been reported to be inhibited by ICP27 in infected cell culture.…”

Le profilage ribosomique

“…Ainsi, la capacité à recruter les ribosomes sur les ARN viraux est capitale pour le succès de l'infection [19]. [23]. Une étude de profilage ribosomique récemment réalisée chez un coronavirus murin a, au contraire, montré un mécanisme alternatif pour augmenter la production de protéines virales lors du cycle de réplication [24].…”