Friedel, Caroline C and Whisnant, Adam W and Djakovic, Lara and Rutkowski,Andrzej J and Friedl, Marie-Sophie and Kluge, Michael and Williamson, JamesC and Sai, Somesh and Vidal, Ramon Oliveira and Sauer, Sascha and Hennig,Thomas and Grothey, Arnhild an
Herpes simplex virus 1 (HSV-1) induces a profound host shut-off during lytic infection. The virion host shut-off () protein plays a key role in this process by efficiently cleaving host and viral mRNAs. Furthermore, the onset of viral DNA replication is accompanied by a rapid decline in host transcriptional activity. To dissect relative contributions of both mechanisms and elucidate gene-specific host transcriptional responses throughout the first 8h of lytic HSV-1 infection, we employed RNA-seq of total, newly transcribed (4sU-labelled) and chromatin-associated RNA in wild-type (WT) and Δ infection of primary human fibroblasts. Following virus entry, v activity rapidly plateaued at an elimination rate of around 30\% of cellular mRNAs per hour until 8h p.i. In parallel, host transcriptional activity dropped to 10-20\%. While the combined effects of both phenomena dominated infection-induced changes in total RNA, extensive gene-specific transcriptional regulation was observable in chromatin-associated RNA and was surprisingly concordant between WT and Δ infection. Both induced strong transcriptional up-regulation of a small subset of genes that were poorly expressed prior to infection but already primed by H3K4me3 histone marks at their promoters. Most interestingly, analysis of chromatin-associated RNA revealed -nuclease-activity-dependent transcriptional down-regulation of at least 150 cellular genes, in particular of many integrin adhesome and extracellular matrix components. This was accompanied by a -dependent reduction in protein levels by 8h p.i. for many of these genes. In summary, our study provides a comprehensive picture of the molecular mechanisms that govern cellular RNA metabolism during the first 8h of lytic HSV-1 infection. The HSV-1 virion host shut-off () protein efficiently cleaves both host and viral mRNAs in a translation-dependent manner. In this study, we model and quantify changes in activity as well as virus-induced global loss of host transcriptional activity during productive HSV-1 infection. In general, HSV-1-induced alterations in total RNA levels were dominated by these two global effects. In contrast, chromatin-associated RNA depicted gene-specific transcriptional changes. This revealed highly concordant transcriptional changes in WT and infection, confirmed DUX4 as a key transcriptional regulator in HSV-1 infection and depicted -dependent, transcriptional down-regulation of the integrin adhesome and extracellular matrix components. The latter explained seemingly gene-specific effects previously attributed to -mediated mRNA degradation and resulted in a concordant loss in protein levels by 8h p.i. for many of the respective genes.