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bioRxiv · 10.1101/2021.01.15.426526

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

Zhang, Y.·Huang, K.·Xie, D.·Lau, J. Y.·Shen, W.·Li, P.·Wang, D.·Zou, Z.·Shi, S.·Ren, H.·Jin, M.·Kudla, G.·Zhao, Z.
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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 direct evidence of interactions between Transcription Regulating Sequences (TRS-L and TRS-Bs), which facilitate discontinuous transcription. In addition, we reveal alternative short and long distance arches around FSE, forming a "high-order pseudoknot" embedding FSE, which might help ribosome stalling at frameshift sites. More importantly, we found that within virions, while SARS-CoV-2 genome RNA undergoes intensive compaction, genome cyclization is weakened and genome domains remain stable. Our data provides a structural basis for the regulation of replication, discontinuous transcription and translational frameshifting, describes dynamics of RNA structures during life cycle of SARS-CoV-2, and will help to develop antiviral strategies.

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Zhang, Y., Huang, K., Xie, D., Lau, J. Y., Shen, W., Li, P., Wang, D., Zou, Z., Shi, S., Ren, H., Jin, M., Kudla, G., Zhao, Z.. 2021-01-15. In vivo structure and dynamics of the RNA genome of SARS-Cov-2. https://doi.org/10.1101/2021.01.15.426526

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