Herpesvirus infection reduces Pol II occupancy of host promoters but spares viral promoters

Ella N Hartenian; Britt A Glaunsinger

To confirm that viral promoters integrated into the host genome were also repressed in 186 the context of infection, we infected MC57G cells containing an integrated MHV68 M4 187 promoter-driven puromycin cassette with MHV68. Indeed, the M4 promoter was repressed to a 188 similar degree as host Fus and Rplp0 promoters during infection with WT MHV68 but not the 189 mRNA decay-deficient MHV68 R443I (Fig 4C) . In summary, these data argue against the promoter is strongly repressed during muSOX-induced mRNA decay. This is seen by 4SU 202 incorporation measuring nascent RNA production -similar to the control ActB gene -and by Pol 203 II recruitment, similar to the control Fus and Rplp0 promoters (Fig 5A and B) . However, in the 204 context of the replicating MHV68 genome, the CMV-GFP promoter had a Pol II ChIP-seq signal 205 during both MHV68 WT and R443I infection that was not markedly different from several other 206 viral genes (ORFs 4, 25, 48, 52, 72, M11) ( Fig 5C) . 207 . CC-BY-NC-ND 4.0 International license is made available under a The copyright holder for this preprint (which was not peer-reviewed) is the author/funder. It . https://doi.org/10.1101/585984 doi: bioRxiv preprint Finally, we evaluated whether the lytic stage of infection was necessary to confer escape 208 from transcriptional repression, or whether some other feature of the non-replicating viral 209 genome was important. To this end, we examined Pol II occupancy at promoters of several genes 210 expressed from the KSHV genome during latent infection in 293T cells, when the viral DNA is 211 maintained as an episome but not amplified in replication compartments. Latent infection does 212 not promote mRNA turnover, and thus we transfected muSOX into these cells to stimulate 213 mRNA turnover in the absence of lytic replication. Similar to the host genes Gapdh and Rplp0, 214