A viral transcriptional regulator from a dsRNA virus antagonizes the innate immune response by manipulating the host co-transcription factor DHX9 [ChIP-Seq]

Viral transcriptional regulators (vTRs) have emerged as potent factors that shape the host anti-viral gene expression programs. Delineating the molecular mechanisms by which vTRs inhibit or promote transcription would provide fundamental insights for developing anti-viral strategies. Using Mammalian orthoreovirus (REOV) as a model system, we identified a new viral mechanism by which viruses antagonize the host innate immune response. We found that the REOV outer capsid protein sigma3 functions as a vTR that limits RNA polymerase II (Pol II) recruitment to the promoter regions of NF-?B-dependent genes via its direct interaction with the host helicase DHX9. sigma3 competes with DHX9 for its interaction with Pol II, which led to marked attenuation of Pol II loading onto chromatin. More interestingly, sigma3 also suppresses DHX9 helicase activity, leading to aberrant accumulation of R-loops at promoter-proximal regions and a decrease in NF-?B-dependent gene expression. Together, our findings uncover an unprecedented strategy of a viral protein that regulates anti-viral gene expression by directly manipulating host transcription factor DHX9. Overall design: RNA Pol II/R-Loop/H3K4me3 occupancy on chromatin upon TNFa treatment in sigma3 overexpressing cells were assessed by Cut&Tag assay.