Manipulation of RNA Polymerase III by Herpes Simplex Virus-1

Abstract

RNA Polymerase III (Pol III) transcribes noncoding RNA, including transfer RNA (tRNA), and acts as a pathogen sensor during the innate immune response. To promote enhanced proliferation, the Pol III machinery is commonly targeted during cancer and viral infection. Herein we employ DM-RNA-Seq, 4SU-Seq, ChIP-Seq, and ATAC-Seq to characterize how Herpes Simplex Virus-1 (HSV-1) perturbs the Pol III landscape. We find that HSV-1 stimulates tRNA expression 10-fold, with mature tRNAs exhibiting a 2-fold increase within 12 hours of infection. Perturbation of host tRNA synthesis requires nuclear viral entry, but not synthesis of specific viral transcripts, nascent viral genomes, or viral progeny. Host tRNA with a specific codon bias were not targeted, rather increased transcription was observed from euchromatic, actively transcribed loci. tRNA upregulation is linked to unique crosstalk between the Pol II and III transcriptional machinery. While viral infection is known to mediate host transcriptional shut off and lead to a depletion of Pol II on host mRNA promoters, we find that Pol II binding to tRNA loci increases. Finally, we report Pol III and associated factors bind the HSV genome, which suggests a previously unrecognized role in HSV-1 gene expression. These data provide insight into novel mechanisms by which HSV-1 alters the host nuclear environment, shifting key processes in favor of the pathogen.

Murine gammaherpesvirus 68 ORF45 stimulates B2 retrotransposon and pre-tRNA activation in a manner dependent on mitogen-activated protein kinase (MAPK) signaling

“…RNAPIII transcription is modulated during infection with several DNA viruses, leading to the upregulation of specific RNAPIII transcripts alteration of viral gene expression (39-43, 45, 46, 54, 74). Together with our prior work (53), we have now screened 90% of the known MHV68 ORFs (75) and identified two, ORF36 and ORF45, as having independent RNAPIII activation functions.…”

“…Many DNA viruses encode their own RNAPIII transcribed genes whose expression is stimulated by enhanced RNAPIII activity during infection (40,43,44). Infection with DNA viruses can also enhance transcription and abundance of host premature tRNAs (pre-tRNAs); recent genome wide studies have identified a global increase in pre-tRNA levels during MHV68 and HSV-1 infection (45,46). SINE ncRNAs induced during cellular stress have a variety of documented functions.…”

Shiftless, A Critical Piece of the Innate Immune Response to Viral Infection

“…While transcription and translation are considered the cornerstones of gene expression, RNA fate is undoubtedly the linchpin that inexorably ties these two processes together. Studies across years of RNA biology have uncovered hundreds of positive and negative feedback loops that allow the cell to finely tune gene expression in response to environmental challenges, especially that of viral infection [34][35][36][37][38]. This interconnectedness presents a significant challenge when investigating the mechanisms of RNA-binding proteins such as SHFL.…”