Examining lncRNAs in highly transcribed, gene-dense genomes

Recent studies using high-throughput methods have revealed an extraordinarily complex transcriptional landscape across the genomes of multiple herpesviruses, with noncoding RNA transcripts overlapping and antisense to protein-coding genes as well as arising from presumed intergenic regions. This pervasive transcription across dense viral genomes presents challenges in correctly delineating individual transcripts and their functions. We have used Pacific Biosciences SMRT sequencing and Illumina RNA-seq to generate detailed transcriptome annotation for the ubiquitous human gammaherpesvirus Epstein-Barr virus (EBV) during lytic reactivation. We report the structures of over 100 novel polyadenylated transcripts, more than doubling the number of known EBV lytic genes. More detailed investigations into several specific transcripts reveal viral “late” gene kinetics, suggesting roles in processes such as viral genome packaging or virion assembly, though functional assays indicate that some of these transcripts influence viral and cellular mRNA levels. These multifold novel transcripts likely possess as diverse an array of functions as their protein-coding counterparts and could represent the key to elucidating some of the enduring mysteries of the herpesvirus lytic cycle, such as control of late gene expression and virion envelopment and egress.