1. In vivo structure and dynamics of the SARS-CoV-2 RNA genome
- Author
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Youzhi Mao, Yan Zhang, Meilin Jin, Ping Li, Zhong Zou, Shu Shi, Youliang Wang, Hongguang Ren, De-Jian Xie, Dong Wang, Grzegorz Kudla, Zhihu Zhao, Jian You Lau, Kun Huang, and Wenlong Shen
- Subjects
Transcription, Genetic ,viruses ,Science ,General Physics and Astronomy ,Computational biology ,Genome, Viral ,Biology ,Virus Replication ,Genome ,General Biochemistry, Genetics and Molecular Biology ,Article ,Nucleic acid secondary structure ,Transcription (biology) ,Chlorocebus aethiops ,Animals ,Humans ,RNA-Seq ,Nucleic acid structure ,Vero Cells ,Translational frameshift ,Multidisciplinary ,SARS-CoV-2 ,RNA ,COVID-19 ,Frameshifting, Ribosomal ,General Chemistry ,Viral replication ,RNA, Viral ,Pseudoknot - Abstract
The dynamics of SARS-CoV-2 RNA structure and their functional relevance are largely unknown. Here we develop a simplified SPLASH assay and comprehensively map the in vivo RNA-RNA interactome of SARS-CoV-2 genome across viral life cycle. We report canonical and alternative structures including 5′-UTR and 3′-UTR, frameshifting element (FSE) pseudoknot and genome cyclization in both cells and virions. We provide direct evidence of interactions between Transcription Regulating Sequences, which facilitate discontinuous transcription. In addition, we reveal alternative short and long distance arches around FSE. More importantly, we find that within virions, while SARS-CoV-2 genome RNA undergoes intensive compaction, genome domains remain stable but with strengthened demarcation of local domains and weakened global cyclization. Taken together, our analysis reveals the structural basis for the regulation of replication, discontinuous transcription and translational frameshifting, the alternative conformations and the maintenance of global genome organization during the whole life cycle of SARS-CoV-2, which we anticipate will help develop better antiviral strategies., RNA secondary structure is important for viral replication, transcription and translation. Here the authors employ SPLASH method and map in vivo RNA interactions and dynamics of SARS-CoV-2 RNA genome in different viral life cycles.
- Published
- 2021