Department of Microbiology and Immunology, University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia.
Department of Microbiology and Immunology, University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia; Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia.
Cell Rep. 2021 May 11;35(6):109108. doi: 10.1016/j.celrep.2021.109108. Epub 2021 Apr 23.
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) uses subgenomic RNA (sgRNA) to produce viral proteins for replication and immune evasion. We apply long-read RNA and cDNA sequencing to in vitro human and primate infection models to study transcriptional dynamics. Transcription-regulating sequence (TRS)-dependent sgRNA upregulates earlier in infection than TRS-independent sgRNA. An abundant class of TRS-independent sgRNA consisting of a portion of open reading frame 1ab (ORF1ab) containing nsp1 joins to ORF10, and the 3' untranslated region (UTR) upregulates at 48 h post-infection in human cell lines. We identify double-junction sgRNA containing both TRS-dependent and -independent junctions. We find multiple sites at which the SARS-CoV-2 genome is consistently more modified than sgRNA and that sgRNA modifications are stable across transcript clusters, host cells, and time since infection. Our work highlights the dynamic nature of the SARS-CoV-2 transcriptome during its replication cycle.
严重急性呼吸综合征冠状病毒 2（SARS-CoV-2）利用亚基因组 RNA（sgRNA）产生病毒蛋白以进行复制和免疫逃逸。我们应用长读长 RNA 和 cDNA 测序技术，对体外人类和灵长类动物感染模型进行研究，以探讨转录动力学。转录调节序列（TRS）依赖性 sgRNA 在感染中比 TRS 非依赖性 sgRNA 更早地上调。一类丰富的 TRS 非依赖性 sgRNA 由开放阅读框 1ab（ORF1ab）的一部分组成，其中包含 nsp1 与 ORF10 连接，并且在人细胞系中感染后 48 小时上调 3'非翻译区（UTR）。我们鉴定了包含 TRS 依赖性和非依赖性连接的双链 sgRNA。我们发现 SARS-CoV-2 基因组在多个位点比 sgRNA 更频繁地被修饰，并且 sgRNA 的修饰在转录簇、宿主细胞和感染后时间上是稳定的。我们的工作强调了 SARS-CoV-2 转录组在复制周期中的动态性质。
