Direct RNA sequencing on nanopore arrays redefines the transcriptional complexity of a viral pathogen

Daniel P. Depledge (), Kalanghad Puthankalam Srinivas, Tomohiko Sadaoka, Devin Bready, Yasuko Mori, Dimitris G. Placantonakis, Ian Mohr and Angus C. Wilson ()
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Daniel P. Depledge: New York University School of Medicine
Kalanghad Puthankalam Srinivas: New York University School of Medicine
Tomohiko Sadaoka: Kobe University Graduate School of Medicine
Devin Bready: New York University School of Medicine
Yasuko Mori: Kobe University Graduate School of Medicine
Dimitris G. Placantonakis: New York University School of Medicine
Ian Mohr: New York University School of Medicine
Angus C. Wilson: New York University School of Medicine

Nature Communications, 2019, vol. 10, issue 1, 1-13

Abstract: Abstract Characterizing complex viral transcriptomes by conventional RNA sequencing approaches is complicated by high gene density, overlapping reading frames, and complex splicing patterns. Direct RNA sequencing (direct RNA-seq) using nanopore arrays offers an exciting alternative whereby individual polyadenylated RNAs are sequenced directly, without the recoding and amplification biases inherent to other sequencing methodologies. Here we use direct RNA-seq to profile the herpes simplex virus type 1 (HSV-1) transcriptome during productive infection of primary cells. We show how direct RNA-seq data can be used to define transcription initiation and RNA cleavage sites associated with all polyadenylated viral RNAs and demonstrate that low level read-through transcription produces a novel class of chimeric HSV-1 transcripts, including a functional mRNA encoding a fusion of the viral E3 ubiquitin ligase ICP0 and viral membrane glycoprotein L. Thus, direct RNA-seq offers a powerful method to characterize the changing transcriptional landscape of viruses with complex genomes.

Date: 2019
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DOI: 10.1038/s41467-019-08734-9

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