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.
journal_name
Nat Communjournal_title
Nature communicationsauthors
Depledge DP,Srinivas KP,Sadaoka T,Bready D,Mori Y,Placantonakis DG,Mohr I,Wilson ACdoi
10.1038/s41467-019-08734-9subject
Has Abstractpub_date
2019-02-14 00:00:00pages
754issue
1issn
2041-1723pii
10.1038/s41467-019-08734-9journal_volume
10pub_type
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