Complexities of gammaherpesvirus transcription revealed by microarrays and RNAseq

•Genome-wide transcript studies define novel splicing events and transcript boundaries for annotated genes.•Recently identified expressed genomic regions (EGRs) are transcripts that are intergenic or antisense to annotated genes.•Antisense viral transcription is extensive and has regulatory and coding potential.•Viral RNAs are selectively packaged in the virions and exosomes to modulate target cell processes.•Regulation, biogenesis, and RNA function studies require systems biology integration of transcriptome.

Technological advances in genome-wide transcript analysis, referred to as the transcriptome, using microarrays and deep RNA sequencing methodologies are rapidly extending our understanding of the genetic content of the gammaherpesviruses (γHVs). These vast transcript analyses continue to uncover the complexity of coding transcripts due to alternative splicing, translation initiation and termination, as well as regulatory RNAs of the γHVs. A full assessment of the transcriptome requires that our analysis be extended to the virion and exosomes of infected cells since viral and host mRNAs, miRNAs, and other noncoding RNAs seem purposefully incorporated to exert function upon delivery to naïve cells. Understanding the regulation, biogenesis and function of the recently discovered transcripts will extend beyond pathogenesis and oncogenic events to offer key insights for basic RNA processes of the cell.

Graphical abstractNovel transcripts discovered by microarray and RNAseq include antisense RNAs, spliced isoforms, internal ORFs, miRNAs, and long noncoding RNAs.Figure optionsDownload full-size imageDownload as PowerPoint slide