RT Journal Article
SR Electronic
T1 Novel splicing and open reading frames revealed by long-read direct RNA sequencing of adenovirus transcripts
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2019.12.13.876037
DO 10.1101/2019.12.13.876037
A1 Alexander M. Price
A1 Katharina E. Hayer
A1 Daniel P. Depledge
A1 Angus C. Wilson
A1 Matthew D. Weitzman
YR 2019
UL http://biorxiv.org/content/early/2019/12/13/2019.12.13.876037.abstract
AB Adenovirus is a common human pathogen that relies on host cell processes for production and processing of viral RNA. Although adenoviral promoters, splice junctions, and cleavage and polyadenylation sites have been characterized using low-throughput biochemical techniques or short read cDNA-based sequencing, these technologies do not fully capture the complexity of the adenoviral transcriptome. By combining Illumina short-read and nanopore long-read direct RNA sequencing approaches, we mapped transcription start sites and cleavage and polyadenylation sites across the adenovirus genome. The canonical viral early and late RNA cassettes were confirmed, but analysis of splice junctions within long RNA reads revealed an additional 20 novel viral transcripts. These RNAs include seven new splice junctions which lead to expression of canonical open reading frames (ORF), as well as 13 transcripts encoding for messages that potentially alter protein functions through truncations or the fusion of canonical ORFs. In addition, we also detect RNAs that bypass canonical cleavage sites and generate potential chimeric proteins by linking separate gene transcription units. Our work highlights how long-read sequencing technologies can reveal further complexity within viral transcriptomes.