Journal
CELL
Volume 181, Issue 4, Pages 914-+Publisher
CELL PRESS
DOI: 10.1016/j.cell.2020.04.011
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Funding
- National Culture Collection for Pathogens, Korea National Institute of Health [NCCP43326]
- Institute for Basic Science from the Ministry of Science and ICT of Korea [IBS-R008-D1]
- BK21 Research Fellowship from the Ministry of Education of Korea
- New Faculty Startup Fund from Seoul National University
- Korea Centers for Disease Control and Prevention [4845-300[19-NG044]]
- National Research Foundation of Korea [IBS-R008-D1-2020-A00] Funding Source: Korea Institute of Science & Technology Information (KISTI), National Science & Technology Information Service (NTIS)
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SARS-CoV-2 is a betacoronavirus responsible for the COVID-19 pandemic. Although the SARS-CoV-2 genome was reported recently, its transcriptomic architecture is unknown. Utilizing two complementary sequencing techniques, we present a high-resolution map of the SARS-CoV-2 transcriptome and epitran-scriptome. DNA nanoball sequencing shows that the transcriptome is highly complex owing to numerous discontinuous transcription events. In addition to the canonical genomic and 9 subgenomic RNAs, SARS-CoV-2 produces transcripts encoding unknown ORFs with fusion, deletion, and/or frameshift. Using nano pore direct RNA sequencing, we further find at least 41 RNA modification sites on viral transcripts, with the most frequent motif, AAGAA. Modified RNAs have shorter poly(A) tails than unmodified RNAs, suggesting a link between the modification and the 3' tail. Functional investigation of the unknown transcripts and RNA modifications discovered in this study will open new directions to our understanding of the life cycle and pathogenicity of SARS-CoV-2.
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