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

Viruses. 2020 Dec 21;12(12):1473. doi: 10.3390/v12121473.


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.

Keywords: 3′ UTR; COVID-19; DMS; DMS-MaPseq; DREEM; SARS-CoV-2; ShapeKnots; minigene; pseudoknot; three-helix junction.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • 3' Untranslated Regions / genetics*
  • Animals
  • Base Sequence
  • COVID-19 / virology*
  • Cell Line
  • Conserved Sequence
  • Cricetinae
  • High-Throughput Nucleotide Sequencing
  • Humans
  • Mesocricetus
  • Models, Molecular
  • Nucleic Acid Conformation*
  • Pandemics*
  • Plasmids
  • Point Mutation
  • RNA, Viral / genetics*
  • Reverse Genetics / methods
  • SARS-CoV-2 / genetics*
  • SARS-CoV-2 / physiology
  • Sequence Alignment
  • Sequence Homology, Nucleic Acid
  • Sulfuric Acid Esters
  • Transcription, Genetic
  • Virion / genetics
  • Virion / physiology


  • 3' Untranslated Regions
  • RNA, Viral
  • Sulfuric Acid Esters
  • dimethyl sulfate