FIG 2.

HSV-1 infection causes a global loss of Pol II occupancy across repressed mRNA genes. (A) The occupancy of promoter-proximally paused Pol II is sharply reduced after HSV-1 infection. Normalized sequence tag counts were histogrammed in 10-bp bins for 2 kb around the TSS. Shown are data from control cells (green), HSV-1-infected cells (red), and input chromatin (gray). (B) Pol II binding profiles around transcription start sites of repressed mRNA genes in mock-infected and HSV-1-infected cells. Each row of the heat map represents Pol II occupancy for one gene from −500 to +500 in 10-bp bins centered on the TSS (indicated by the arrows). The genes are ranked by the Pol II promoter-proximal signal in the mock-infected data. (C) Pol II ChIP-seq data across the Egr1 gene, viewed using the UCSC Genome Browser. The y axis for the HSV-1 data in the bottom plot has a different scale. (D) Occupancy of Pol II around the 3′ ends of repressed mRNA genes is sharply reduced after HSV-1 infection. Normalized sequence tag counts were histogrammed in 100-bp bins for 4 kb, centered on the 3′ end. Shown are data from control cells (green), HSV-1-infected cells (red), and input chromatin (gray).