The global and local distribution of RNA structure throughout the SARS-CoV-2 genome.

Journal of Virology
Rafael de Cesaris Araujo TavaresAnna Marie Pyle

Abstract

SARS-CoV-2 is the causative viral agent of COVID-19, the disease at the center of the current global pandemic. While knowledge of highly structured regions is integral for mechanistic insights into the viral infection cycle, very little is known about the location and folding stability of functional elements within the massive, ∼30kb SARS-CoV-2 RNA genome. In this study, we analyze the folding stability of this RNA genome relative to the structural landscape of other well-known viral RNAs. We present an in-silico pipeline to predict regions of high base pair content across long genomes and to pinpoint hotspots of well-defined RNA structures, a method that allows for direct comparisons of RNA structural complexity within the several domains in SARS-CoV-2 genome. We report that the SARS-CoV-2 genomic propensity for stable RNA folding is exceptional among RNA viruses, superseding even that of HCV, one of the most structured viral RNAs in nature. Furthermore, our analysis suggests varying levels of RNA structure across genomic functional regions, with accessory and structural ORFs containing the highest structural density in the viral genome. Finally, we take a step further to examine how individual RNA structures formed by these O...Continue Reading

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Citations

Dec 18, 2020·The Journal of General Virology·Peter SimmondsHeli Harvala
Dec 29, 2020·Biochemical Society Transactions·Ilaria Manfredonia, Danny Incarnato
Jun 26, 2021·Nature Communications·Changchang CaoYuanchao Xue

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