RNA decay during gammaherpesvirus infection reduces RNA polymerase II occupancy of host promoters but spares viral promoters
(A) Pol II ChIP-seq signal profiles of host genes in mock-infected, MHV68 WT-infected and R443I-infected MC57G cells. Each row of the heat map displays Pol II occupancy of one gene from -1000 to +1000 in 25 bp bins. Genes are ranked by the Pol II-transcription start site (TSS) proximal signal in mock infected cells. (B) Sequence tags were plotted as a histogram with 25 bp bins for -2000 to +4000 around the TSS. Mock (red), MHV68 (blue) and MHV68 R443I (green) traces are shown. (C) Pol II ChIP-seq coverage across the Srsf2 gene for ChIP-seq replicate 1 and 2 with mock, WT MHV68 and R443I shown. Alignment files were converted to the tiled data file (tdf) format and visualized in the Integrative Genome Viewer. (D) ChIP-qPCR validation of Pol II occupancy at the Rplp0 and Fus promoters plotted with standard deviation. Pol II ChIP was performed on mock, MHV68 WT or MHV68 R443I infected MC57G cells and Pol II levels were assayed near the TSS of two repressed host genes during MHV68 infection from the ChIP-seq data. IgG is from the MHV68 infection condition. (* p < 0.05, students paired t-test on raw % input values) (E) Scatterplot of Pol II occupancy of promoters, averaging the sum of ChIP-seq tags from -50 to +200 across two replicate experiments with inputs subtracted out. Mock is compared to WT MHV68 infection on the left and to MHV68 R443I infection on the right. Linear regression lines are plotted in blue and equations are provided. A y = x line is plotted for reference in red. (F) Scatterplot of Pol II occupancy of gene bodies, averaging the sum of ChIP-seq tags from -50 to +200 across two replicate experiments with inputs subtracted out. Data as described for (E). (G) Pol II transcription termination is not dependent on RNA decay. Sequence tags were plotted as a histogram in 25 bp bins for transcription termination sequence (TTS) proximal Pol II for -1000 to +1000 around the TTS with the same color scheme as (B).