期刊
NATURE COMMUNICATIONS
卷 10, 期 -, 页码 -出版社
NATURE PUBLISHING GROUP
DOI: 10.1038/s41467-019-08734-9
关键词
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资金
- National Institutes of Health (NIH) through a National Center for Advancing Translational Sciences [NCATS UL1 TR00038]
- Cancer Center Support Grant [P30CA016087]
- NIH [AI073898, GM056927, AI130618]
- Ministry of Education, Culture, Sports, Science, and Technology [MEXT KAKENHI JP17H05816, JP16H06429, JP16K21723]
- Japan Society for the Promotion of Science [JSPS KAKENHI JP17K008858]
- Takeda Science Foundation
- Daiichi Sankyo Foundation of Life Science
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.
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