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^*

^*Corresponding author for this work

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

26 Citations (Scopus)

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
DOIs	https://doi.org/10.1016/j.celrep.2021.109108
Publication status	Published - 11 May 2021
Externally published	Yes

Bibliographical note

Publisher Copyright:
© 2021 The Authors

Keywords

COVID-19
Nanopore sequencing
RNA modification
SARS-CoV-2
coronavirus
differential expression
direct RNA sequencing
direct cDNA sequencing
discontinuous transcription
poly(A) tail

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10.1016/j.celrep.2021.109108

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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.",

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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 = "Publisher Copyright: {\textcopyright} 2021 The Authors",

year = "2021",

month = may,

day = "11",

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

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Chang, JJY, 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

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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.

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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 - COVID-19

KW - Nanopore sequencing

KW - RNA modification

KW - SARS-CoV-2

KW - coronavirus

KW - differential expression

KW - direct RNA sequencing

KW - direct cDNA sequencing

KW - discontinuous transcription

KW - poly(A) tail

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U2 - 10.1016/j.celrep.2021.109108

DO - 10.1016/j.celrep.2021.109108

M3 - Article

C2 - 33961822

AN - SCOPUS:85105263135

SN - 2639-1856

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

Bibliographical note

Keywords

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