RNA decay during gammaherpesvirus infection reduces RNA polymerase II occupancy of host promoters but spares viral promoters
(A) Diagram showing the experimental setup for the TMT-MS. (B) Graphs showing the nuclear distribution of poly(A) binding proteins from the TMT-MS data. Graphs display the mean with SEM of 3 biological replicates. (C) Molecular functions classification by Pantherdb of nuclear proteins differentially expressed by 1.15 fold or more in R443I compared to WT MHV68 infection of 3T3 cells in the TMT-MS data. Categories with fold enrichment greater than 5 are shown. (D) Graphs showing the relative nuclear abundance of 7 Pol II subunits and 2 general transcription factors from the TMT-MS data that are reduced in MHV68 infection compared to R443I. Graphs display the mean with SEM of 3 biological replicates. (E) A heatmap displaying normalized reporter ion abundance of all 12 Pol II subunits in the nucleus and cytoplasm, where light blue represents lower abundance and dark blue represents higher abundance. (F) Representative western blot showing the levels of Rpb1, Rpb2, TFIIB and TBP upon mock infection versus infection with WT MHV68 or R443I MHV68 in MC57G cells at the indicated times post infection in whole cell lysate. Gapdh serves as a loading control. Densitometry of band intensity was normalized first to Gapdh and then mock infection are indicated below blots.