Herpes Simplex Virus 1 dramatically alters loading and positioning of RNA Polymerase II on host genes early in infection

We used precision nuclear run on (PRO-seq) to determine the location of Pol II at 3 hours post infection with HSV-1 in human epithelial cells. We found HSV-1 decreased Pol II on approxomately 2/3 of cellular genes, but increased Pol II on others. For more than 85% of genes for which transcriptional terminatin could be statistically assed, Pol II was displaced to positions downstream of the normal termination zone suggesting extensive termination defects. Pol II amounts at the promoter, prooter proximal apuse site, and gene bnody were also modulated in a gene-specific manner. PRO-seq data from two separate experiments looking at Pol II location at 3 hours post infection with HSV-1. Each experiment had 3 biological replicates of Mock and HSV-1 infected sequencing libraries prepared from Hep-2 cells. One experiment included a Drosophila nuclei spike-in as a control.