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

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 s3 functions as a vTR to suppress NF-?B gene expression via its direct interaction with the host helicase DHX9. Mechanistically, s3 impairs the initial recruitment of Pol II by disrupting the interaction between DHX9 and Pol II. More interestingly, s3 suppresses DHX9 helicase activity, resulting in the aberrant accumulation of R-loops at promoter-proximal regions, thereby affecting Pol II pause-release and ultimately suppressing NF-?B gene expression. Together, our findings reveal an unprecedented strategy employed by a viral protein that regulates anti-viral gene expression by directly modulating the host transcription factor DHX9. Overall design: R-Loop occupancy on chromatin upon TNFa, IFNß or REOV treatment in 293T cells were assessed by Cut&Tag assay.