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 F J Purcell; Timothy P Stinear; Sarah L Londrigan; Michael B Clark; Deborah A Williamson; Kanta Subbarao; Lachlan J M Coin

doi:10.1016/j.celrep.2021.109108

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 F J Purcell, Timothy P Stinear, Sarah L Londrigan, Michael B Clark, Deborah A Williamson, Kanta Subbarao, Lachlan J M Coin

School of Medicine

Research output: Contribution to journal › Article › peer-review

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 junctions. We find 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.

Original language	English
Article number	109108
Journal	Cell Reports
Volume	35
Issue number	6
Early online date	23 Apr 2021
DOIs	https://doi.org/10.1016/j.celrep.2021.109108
Publication status	Published - 11 May 2021

Keywords

Animals
COVID-19/genetics
Caco-2 Cells
Cell Line
Chlorocebus aethiops
Epigenesis, Genetic
Genome, Viral/genetics
Humans
Immune Evasion
Open Reading Frames
RNA, Viral/genetics
SARS-CoV-2/genetics
Transcription, Genetic/genetics
Transcriptome
Vero Cells
Viral Proteins/genetics

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Chang, J. J.-Y., Rawlinson, D., Pitt, M. E., Taiaroa, G., Gleeson, J., Zhou, C., Mordant, F. L., De Paoli-Iseppi, R., Caly, L., Purcell, D. F. J., Stinear, T. P., Londrigan, S. L., Clark, M. B., Williamson, D. A., Subbarao, K., & Coin, L. J. M. (2021). Transcriptional and epi-transcriptional dynamics of SARS-CoV-2 during cellular infection. Cell Reports, 35(6), Article 109108. https://doi.org/10.1016/j.celrep.2021.109108

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title = "Transcriptional and epi-transcriptional dynamics of SARS-CoV-2 during cellular infection",

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 junctions. We find 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.",

keywords = "Animals, COVID-19/genetics, Caco-2 Cells, Cell Line, Chlorocebus aethiops, Epigenesis, Genetic, Genome, Viral/genetics, Humans, Immune Evasion, Open Reading Frames, RNA, Viral/genetics, SARS-CoV-2/genetics, Transcription, Genetic/genetics, Transcriptome, Vero Cells, Viral Proteins/genetics",

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

note = "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. ",

year = "2021",

month = may,

day = "11",

doi = "10.1016/j.celrep.2021.109108",

language = "English",

volume = "35",

journal = "Cell Reports",

issn = "2211-1247",

publisher = "Elsevier",

number = "6",

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Chang, JJ-Y, Rawlinson, D, Pitt, ME, Taiaroa, G, Gleeson, J, Zhou, C, Mordant, FL, De Paoli-Iseppi, R, Caly, L, Purcell, DFJ, Stinear, TP, Londrigan, SL, Clark, MB, Williamson, DA, Subbarao, K & Coin, LJM 2021, 'Transcriptional and epi-transcriptional dynamics of SARS-CoV-2 during cellular infection', Cell Reports, vol. 35, no. 6, 109108. https://doi.org/10.1016/j.celrep.2021.109108

TY - JOUR

T1 - Transcriptional and epi-transcriptional dynamics of SARS-CoV-2 during cellular infection

AU - Chang, Jessie J-Y

AU - Rawlinson, Daniel

AU - Pitt, Miranda E

AU - Taiaroa, George

AU - Gleeson, Josie

AU - Zhou, Chenxi

AU - Mordant, Francesca L

AU - De Paoli-Iseppi, Ricardo

AU - Caly, Leon

AU - Purcell, Damian F J

AU - Stinear, Timothy P

AU - Londrigan, Sarah L

AU - Clark, Michael B

AU - Williamson, Deborah A

AU - Subbarao, Kanta

AU - Coin, Lachlan J M

N1 - 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.

PY - 2021/5/11

Y1 - 2021/5/11

N2 - 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 junctions. We find 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.

AB - 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 junctions. We find 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.

KW - Animals

KW - COVID-19/genetics

KW - Caco-2 Cells

KW - Cell Line

KW - Chlorocebus aethiops

KW - Epigenesis, Genetic

KW - Genome, Viral/genetics

KW - Humans

KW - Immune Evasion

KW - Open Reading Frames

KW - RNA, Viral/genetics

KW - SARS-CoV-2/genetics

KW - Transcription, Genetic/genetics

KW - Transcriptome

KW - Vero Cells

KW - Viral Proteins/genetics

U2 - 10.1016/j.celrep.2021.109108

DO - 10.1016/j.celrep.2021.109108

M3 - Article

C2 - 33961822

SN - 2211-1247

VL - 35

JO - Cell Reports

JF - Cell Reports

IS - 6

M1 - 109108

ER -

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

Abstract

Keywords

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