RT Journal Article
SR Electronic
T1 Native RNA sequencing on nanopore arrays redefines the transcriptional complexity of a viral pathogen
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 373522
DO 10.1101/373522
A1 Daniel P. Depledge
A1 Kalanghad Puthankalam Srinivas
A1 Tomohiko Sadaoka
A1 Devin Bready
A1 Yasuko Mori
A1 Dimitris G. Placantonakis
A1 Ian Mohr
A1 Angus C Wilson
YR 2018
UL http://biorxiv.org/content/early/2018/07/20/373522.abstract
AB Viral genomes exhibit a higher gene density and more diversified transcriptome than the host cell. Coding potential is maximized through the use of multiple reading frames, placement of genes on opposing strands, inefficient or modified use of termination signals, and the deployment of complex alternative splicing patterns. As a consequence, detailed characterization of viral transcriptomes by conventional methods can be challenging. Full length native RNA sequencing (nRNA-seq) using nanopore arrays offers an exciting alternative. Individual transcripts are sequenced directly, without the biases inherent to the recoding or amplification steps included in other sequencing methodologies. nRNA-seq simplifies the detection of variation brought about by RNA splicing, use of alternative transcription initiation and termination sites, and other RNA modifications. Here we use nRNA-seq to profile the herpes simplex virus type 1 transcriptome during early and late stages of productive infection of primary cells. We demonstrate the effectiveness of the approach and identify a novel class of intergenic transcripts, including an mRNA that accumulates late in infection that codes for a novel fusion of the viral E3 ubiquitin ligase ICP0 and viral membrane glycoprotein L.