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In vivo structure and dynamics of the RNA genome of SARS-Cov-2

ABSTRACT: The SARS-CoV-2 coronavirus, which causes the COVID-19 pandemic, is one of the largest positive strand RNA viruses. Here we developed a simplified SPLASH assay and comprehensively mapped the in vivo RNA-RNA interactome of SARS-CoV-2 RNA during the viral life cycle. We observed canonical and alternative structures including 3’-UTR and 5’-UTR, frameshifting element (FSE) pseudoknot and genome cyclization in cells and in virions. We provide the first evidence of comprehensive interactions between Transcription Regulating Sequences (TRS-L and TRS-Bs), which facilitate discontinuous transcription. In addition, we find alternative short and long distance arches around FSE, forming a “high-order pseudoknot” embedding FSE, which might help ribosome stalling at frameshift sites. We found that during packaging, SARS-CoV-2 genome RNA undergoes compaction while genome domains remain stable and genome cyclization is weakened. Our data provides a structural basis for the regulation of replication, discontinuous transcription and translational frameshifting describes dynamics on RNA structures during life cycle of SARS-CoV-2, and will help to develop antiviral strategies.

ORGANISM(S): Chlorocebus sabaeus Severe acute respiratory syndrome coronavirus 2

PROVIDER: GSE164565 | GEO | 2021/08/29

REPOSITORIES: GEO

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Structure of the full SARS-CoV-2 RNA genome in infected cells

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2020-09-01 | GSE153851 | GEO

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2020-10-21 | GSE154662 | GEO

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