The PNUTS-protein phosphatase 1 complex acts as an intrinsic barrier to KSHV replication [ChIP-seq]

Control of RNA Polymerase II (pol II) elongation is a critical component of gene expression in mammalian cells. The PNUTS-protein phosphatase 1 (PP1) complex controls elongation rates, slowing pol II after polyadenylation sites to promote termination. The Kaposi's sarcoma-associated herpesvirus (KSHV) co-opts pol II to express its genes, but little is known about its regulation of pol II elongation. We identified PNUTS as a suppressor of a KSHV reporter gene in a genome-wide CRISPR screen. PNUTS depletion also enhances global KSHV gene expression and overall viral replication. Reflecting its host gene activities, PNUTS binds viral RNAs downstream of polyadenylation sites, restricts transcription readthrough of viral genes, and requires PP1 interaction. Surprisingly, PNUTS represses the KSHV reporter by decreasing productive elongation at the 5´-end of the gene. From these data, we conclude that PNUTS' activity forms an intrinsic barrier to KSHV replication likely by suppressing pol II elongation at promoter-proximal regions. A viral gene reporter was integrated into the AAVS1 locus on chr19 of HCT116 cells. Pol II ChIP-seq using antibodies against RPB3 was performed on samples treated with either a nontargeting siRNA (siNT) or one of two siRNAs targeting PNUTS (siP1 or siP2). Pellets and inputs were analyzed for each sample; two biological replicates were perforemd (Rep_A and Rep_B).