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Open AccessArticle

The RNA Architecture of the SARS-CoV-2 3′-Untranslated Region

1
Department of Medicinal Chemistry, University of Kansas, Lawrence, KS 66047, USA
2
Department of Microbiology, Molecular Genetics & Immunology, University of Kansas Medical Center, Kansas, KS 66160, USA
3
Genome Sequencing Core, University of Kansas, Lawrence, KS 66045, USA
*
Author to whom correspondence should be addressed.
Academic Editor: John S. L. Parker
Viruses 2020, 12(12), 1473; https://doi.org/10.3390/v12121473
Received: 23 October 2020 / Revised: 11 December 2020 / Accepted: 15 December 2020 / Published: 21 December 2020
(This article belongs to the Section SARS-CoV-2 and COVID-19)
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is responsible for the current COVID-19 pandemic. The 3′ untranslated region (UTR) of this β-CoV contains essential cis-acting RNA elements for the viral genome transcription and replication. These elements include an equilibrium between an extended bulged stem-loop (BSL) and a pseudoknot. The existence of such an equilibrium is supported by reverse genetic studies and phylogenetic covariation analysis and is further proposed as a molecular switch essential for the control of the viral RNA polymerase binding. Here, we report the SARS-CoV-2 3′ UTR structures in cells that transcribe the viral UTRs harbored in a minigene plasmid and isolated infectious virions using a chemical probing technique, namely dimethyl sulfate (DMS)-mutational profiling with sequencing (MaPseq). Interestingly, the putative pseudoknotted conformation was not observed, indicating that its abundance in our systems is low in the absence of the viral nonstructural proteins (nsps). Similarly, our results also suggest that another functional cis-acting element, the three-helix junction, cannot stably form. The overall architectures of the viral 3′ UTRs in the infectious virions and the minigene-transfected cells are almost identical. View Full-Text
Keywords: SARS-CoV-2; COVID-19; DMS; DMS-MaPseq; ShapeKnots; DREEM; pseudoknot; three-helix junction; 3′ UTR; minigene SARS-CoV-2; COVID-19; DMS; DMS-MaPseq; ShapeKnots; DREEM; pseudoknot; three-helix junction; 3′ UTR; minigene
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MDPI and ACS Style

Zhao, J.; Qiu, J.; Aryal, S.; Hackett, J.L.; Wang, J. The RNA Architecture of the SARS-CoV-2 3′-Untranslated Region. Viruses 2020, 12, 1473. https://doi.org/10.3390/v12121473

AMA Style

Zhao J, Qiu J, Aryal S, Hackett JL, Wang J. The RNA Architecture of the SARS-CoV-2 3′-Untranslated Region. Viruses. 2020; 12(12):1473. https://doi.org/10.3390/v12121473

Chicago/Turabian Style

Zhao, Junxing; Qiu, Jianming; Aryal, Sadikshya; Hackett, Jennifer L.; Wang, Jingxin. 2020. "The RNA Architecture of the SARS-CoV-2 3′-Untranslated Region" Viruses 12, no. 12: 1473. https://doi.org/10.3390/v12121473

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