PT  - JOURNAL ARTICLE
AU  - Tammy C. T. Lan
AU  - Matthew F. Allan
AU  - Lauren E. Malsick
AU  - Stuti Khandwala
AU  - Sherry S. Y. Nyeo
AU  - Yu Sun
AU  - Junjie U. Guo
AU  - Mark Bathe
AU  - Anthony Griffiths
AU  - Silvi Rouskin
TI  - Insights into the secondary structural ensembles of the full SARS-CoV-2 RNA genome in infected cells
AID  - 10.1101/2020.06.29.178343
DP  - 2021 Jan 01
TA  - bioRxiv
PG  - 2020.06.29.178343
4099  - http://biorxiv.org/content/early/2021/02/19/2020.06.29.178343.short
4100  - http://biorxiv.org/content/early/2021/02/19/2020.06.29.178343.full
AB  - SARS-CoV-2 is a betacoronavirus with a single-stranded, positive-sense, 30-kilobase RNA genome responsible for the ongoing COVID-19 pandemic. Currently, there are no antiviral drugs with proven efficacy, and development of these treatments are hampered by our limited understanding of the molecular and structural biology of the virus. Like many other RNA viruses, RNA structures in coronaviruses regulate gene expression and are crucial for viral replication. Although genome and transcriptome data were recently reported, there is to date little experimental data on native RNA structures in SARS-CoV-2 and most putative regulatory sequences are functionally uncharacterized. Here we report secondary structure ensembles of the entire SARS-CoV-2 genome in infected cells at single nucleotide resolution using dimethyl sulfate mutational profiling with sequencing (DMS-MaPseq) and the algorithm ‘detection of RNA folding ensembles using expectation–maximization’ clustering (DREEM). Our results reveal previously undescribed alternative RNA conformations across the genome, including structures of the frameshift stimulating element (FSE), a major drug target, that are drastically different from prevailing in vitro population average models. Importantly, we find that this structural ensemble promotes frameshifting rates (~40%) similar to in vivo ribosome profiling studies and much higher than the canonical minimal FSE (~20%). Overall, our result highlight the value of studying RNA folding in its native, dynamic and cellular context. The genomic structures detailed here lays the groundwork for coronavirus RNA biology and will guide the design of SARS-CoV-2 RNA-based therapeutics.Competing Interest StatementThe authors have declared no competing interest.