Murid herpesvirus 68 Transcriptome or Gene expression

Pervasive transcription is observed in a wide range of organisms, including humans, mice and viruses, but the functional significance of these transcripts remains uncertain. Current genetic approaches are often limited by their emphasis on protein coding open reading frames (ORFs). We previously identified extensive pervasive transcription from the murine gammaherpesvirus (MHV68) genome outside of known ORFs and antisense to known genes (termed expressed genomic regions, EGRs). Similar antisense transcripts have been identified in many other herpesviruses, including Kaposi's sarcoma-associated herpesvirus and human and murine cytomegalovirus. Despite their prevalence, whether these RNAs have any functional importance in the viral life cycle is not known and one interpretation is that these are merely "noise" generated by functionally unimportant transcriptional events. We first used RNAseq to verify, and more finely map, pervasive transcription from the MHV68 genome detected earlier using tiled arrays. To determine whether pervasive transcription of a herpesvirus genome generates RNA molecules that are functionally important, we used a strand-specific functional approach to target transcripts from thirteen EGRs in MHV68. We found that targeting transcripts from six EGRs reduced viral protein expression, proving that pervasive transcription can generate functionally important RNAs. We characterized transcripts emanating from EGRs 26 and 27 in detail using several methods, including RNA sequencing, to map several novel polyadenylated transcripts that were enriched in the nucleus of infected cells. These data provide the first evidence of the functional importance of regions of pervasive transcription emanating from MHV68 EGRs, and demonstrate that transcripts from genome regions outside of known ORFs in herpesviruses can play critical roles in the viral life cycle.