1. Transcriptional and epi-transcriptional dynamics of SARS-CoV-2 during cellular infection
- Author
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Lachlan J. M. Coin, Kanta Subbarao, Chenxi Zhou, Michael B. Clark, Daniel Rawlinson, Miranda E. Pitt, Leon Caly, George Taiaroa, Damian F. J. Purcell, Francesca L Mordant, Sarah L. Londrigan, Ricardo De Paoli-Iseppi, Jessie J.-Y. Chang, Timothy P. Stinear, Josie Gleeson, and Deborah A Williamson
- Subjects
0301 basic medicine ,Untranslated region ,Transcription, Genetic ,Polyadenylation ,coronavirus ,poly(A) tail ,Genome, Viral ,Biology ,medicine.disease_cause ,Genome ,General Biochemistry, Genetics and Molecular Biology ,Article ,differential expression ,Cell Line ,Epigenesis, Genetic ,Transcriptome ,Open Reading Frames ,Viral Proteins ,03 medical and health sciences ,discontinuous transcription ,Immune system ,0302 clinical medicine ,Downregulation and upregulation ,Transcription (biology) ,Chlorocebus aethiops ,medicine ,Animals ,Humans ,nanopore ,Vero Cells ,Immune Evasion ,Subgenomic mRNA ,Coronavirus ,Genetics ,NSP1 ,direct RNA sequencing ,SARS-CoV-2 ,RNA ,COVID-19 ,RNA modification ,In vitro ,Cell biology ,030104 developmental biology ,direct cDNA sequencing ,RNA, Viral ,Caco-2 Cells ,030217 neurology & neurosurgery - Abstract
SARS-CoV-2 uses subgenomic (sg)RNA to produce viral proteins for replication and immune evasion. We applied long-read RNA and cDNA sequencing to in vitro human and primate infection models to study transcriptional dynamics. Transcription-regulating sequence (TRS)-dependent sgRNA was upregulated earlier in infection than TRS-independent sgRNA. An abundant class of TRS-independent sgRNA consisting of a portion of ORF1ab containing nsp1 joined to ORF10 and 3’UTR was upregulated at 48 hours post infection in human cell lines. We identified double-junction sgRNA containing both TRS-dependent and independent junctions. We found multiple sites at which the SARS-CoV-2 genome is consistently more modified than sgRNA, and that sgRNA modifications are stable across transcript clusters, host cells and time since infection. Our work highlights the dynamic nature of the SARS-CoV-2 transcriptome during its replication cycle. Our results are available via an interactive web-app at http://coinlab.mdhs.unimelb.edu.au/., Graphical Abstract, SARS-CoV-2 is the pathogen which is responsible for the global COVID-19 pandemic. Chang et al. demonstrate that the transcriptome of SARS-CoV-2 is dynamic and complex, with expression and relative proportions of viral mRNA changing to reflect the stage of infection in vitro. In contrast, the epi-transcriptome is stable throughout infection.
- Published
- 2021