Transcriptional and epi-transcriptional dynamics of SARS-CoV-2 during cellular infection

Jessie J-Y Chang; Daniel Rawlinson; Miranda E Pitt; George Taiaroa; Josie Gleeson; Chenxi Zhou; Francesca L Mordant; Ricardo De Paoli-Iseppi; Leon Caly; Damian FJ Purcell; Timothy P Stinear; Sarah L Londrigan; Michael B Clark; Deborah A Williamson; Kanta Subbarao; Lachlan JM Coin

Journal article

Transcriptional and epi-transcriptional dynamics of SARS-CoV-2 during cellular infection

Jessie J-Y Chang, Daniel Rawlinson, Miranda E Pitt, George Taiaroa, Josie Gleeson, Chenxi Zhou, Francesca L Mordant, Ricardo De Paoli-Iseppi, Leon Caly, Damian FJ Purcell, Timothy P Stinear, Sarah L Londrigan, Michael B Clark, Deborah A Williamson, Kanta Subbarao, Lachlan JM Coin

CELL REPORTS | CELL PRESS | Published : 2021

DOI: 10.1016/j.celrep.2021.109108

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Abstract

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) uses subgenomic RNA (sgRNA) to produce viral proteins for replication and immune evasion. We apply long-read RNA and cDNA sequencing to in vitro human and primate infection models to study transcriptional dynamics. Transcription-regulating sequence (TRS)-dependent sgRNA upregulates earlier in infection than TRS-independent sgRNA. An abundant class of TRS-independent sgRNA consisting of a portion of open reading frame 1ab (ORF1ab) containing nsp1 joins to ORF10, and the 3' untranslated region (UTR) upregulates at 48 h post-infection in human cell lines. We identify double-junction sgRNA containing both TRS-dependent and -independent..

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University of Melbourne Researchers

Lachlan Coin Author Microbiology and Immunology

Ric De Paoli-Iseppi Author Anatomy and Physiology

Francesca Mordant Author Microbiology and Immunology

George Taiaroa Author Microbiology and Immunology

Tim Stinear Author Microbiology and Immunology

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Funding Acknowledgements

We would like to acknowledge Josh Lee and Uli Feltzmann for assistance with the Shiny app. We would like to thank Georgia Deliyannis for assistance with culturing cell lines, and Dr. Eva Maria Novoa Pardo for her advice regarding the analysis of SARS-CoV-2 modifications. L.J.M.C. was supported by a Career Development Fellowship from NHMRC (GNT1130084). This research was supported by a University of Melbourne "Driving research momentum" award (to L.J.M.C.) and NHMRC EU project grant (GNT1195743 to L.J.M.C.). K.S. is supported by an NHMRC Investigator grant. The Melbourne WHO Collaborating Centre for Reference and Research on Influenza is supported by the Australian Government Department of Health. J.J.-Y.C was supported by the Miller Foundation and the Australian Government Research Training Programme (RTP) scholarship. Computational analysis of data was made possible with access to two server systems: Spartan at University of Melbourne (Lafayette et al., 2016) and Nectar from the Australia Research Data Commons.