Insights into the secondary structural ensembles of the full SARS-CoV-2 RNA genome in infected cells

• DOI: 10.1101/2020.06.29.178343
• Publication Date: 2020-07-01T09:15:12Z
• Authors: Tammy C. T. Lan; Matthew F. Allan; Lauren E. Malsick; Stuti Khandwala; Sherry S. Y. Nyeo; Yu Sun; Junjie U. Guo; Mark Bathe; Anthony Griffiths; Silvi Rouskin
• Keywords: Nucleic acid structure; Coronaviridae; Coronavirus

Summary SARS-CoV-2 is a betacoronavirus with single-stranded, positive-sense, 30-kilobase RNA genome responsible for the ongoing COVID-19 pandemic. Currently, there are no antiviral drugs proven efficacy, and development of these treatments hampered by our limited understanding molecular structural biology virus. Like many other viruses, structures in coronaviruses regulate gene expression crucial viral replication. Although transcriptome data were recently reported, to date little experimental on native most putative regulatory sequences functionally uncharacterized. Here we report secondary structure ensembles entire infected cells at single nucleotide resolution using dimethyl sulfate mutational profiling sequencing (DMS-MaPseq) algorithm ‘detection folding expectation–maximization’ clustering (DREEM). Our results reveal previously undescribed alternative conformations across genome, including frameshift stimulating element (FSE), major drug target, that drastically different from prevailing vitro population average models. Importantly, find this ensemble promotes frameshifting rates (~40%) similar vivo ribosome studies much higher than canonical minimal FSE (~20%). Overall, result highlight value studying its native, dynamic cellular context. The genomic detailed here lays groundwork coronavirus will guide design RNA-based therapeutics.