An integrative approach identifies direct targets of the late viral transcription complex and an expanded promoter recognition motif in Kaposi’s sarcoma-associated herpesvirus
Fig 2
Differential expression analysis of ORF24-Pol II interaction mutant and mutant rescue.
iSLK cells harboring ORF24RAAAG and ORF24RAAAG -MR were reactivated with doxycycline and sodium butyrate for 24 and 48 h, whereupon total RNA was extracted and subjected to library preparation and RNA sequencing. (A) Bar plot showing log2 fold change of the viral genes in the ORF24RAAAG -MR at 48 h relative to 24 h. Genes were color coded by kinetic class as defined in (30). (B) Bar plot showing log2 fold change of the viral genes in the mutant relative to the MR. Genes were color coded by kinetic class as defined in (30). (C) Heatmap of the scaled log2 fold change of the genes induced in the MR between 24 to 48 h and genes repressed in the mutant compared to MR at 48 h. Gene clusters with different kinetics and dependence on ORF24-Pol II interaction are indicated. (D) Consensus motif identified by MEME analysis of promoters from 14 genes that showed greater than one standard deviation repression in the mutant relative to the MR.