Chromatin association sites of KSHV and RRV PAN RNA. Chromatin association sites of KSHV and RRV PAN RNA

During lytic replication of Kaposi’s sarcoma-associated herpesvirus (KSHV), a nuclear viral long noncoding RNA known as PAN RNA becomes the most abundant polyadenylated transcript in the cell. Knockout or knockdown of KSHV PAN RNA results in loss of late lytic viral gene expression and, consequently, reduction of progeny virion release from the cell. We studied KSHV and RRV PAN RNA homologs using capture hybridization analysis of RNA targets (CHART) and observed their reproducible associations with host chromatin, but the loci differ between PAN RNA homologs. Overall design: Examination of the binding sites of viral PAN RNA in KSHV-infected BCBL-1 cells and RRV-infected BJAB-RRV cells. Latent samples, as well as three timepoints of lytic viral induction were analyzed for each cell type (BCBL-1: 16 hr, 24 hr and 48 hr; BJAB-RRV: 18 hr, 24 hr, 36 hr).