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 provided direct evidence of interactions between Transcription Regulating Sequences (TRS-L and TRS-Bs), which facilitate discontinuous transcription. In addition, we revealed 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, during SARS-CoV-2 genome RNA undergoing 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.

中文翻译：

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SARS-Cov-2 RNA基因组的体内结构和动力学

引起COVID-19大流行的SARS-CoV-2冠状病毒是最大的正链RNA病毒之一。在这里，我们开发了一种简化的SPLASH分析方法，并在病毒生命周期中全面绘制了SARS-CoV-2 RNA的体内RNA-RNA相互作用组。我们观察到规范和替代结构，包括3'-UTR和5'-UTR，移码元件（FSE）假结和细胞和病毒粒子中的基因组环化。我们提供了转录调控序列（TRS-L和TRS-Bs）之间相互作用的直接证据，该序列可促进不连续转录。此外，我们揭示了FSE周围的短距离和长距离拱门，形成了嵌入FSE的“高阶假结”，这可能有助于核糖体停滞在移码位点。更重要的是，我们发现在病毒粒子中，在SARS-CoV-2基因组RNA进行密集压缩期间，基因组环化作用减弱，基因组结构域保持稳定。我们的数据为调控复制，不连续转录和翻译移码提供了结构基础，描述了SARS-CoV-2生命周期中RNA结构的动态变化，并将有助于制定抗病毒策略。