Pervasive generation of non-canonical subgenomic RNAs by SARS-CoV-2.
Pervasive generation of non-canonical subgenomic RNAs by SARS-CoV-2.
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DOI：
10.1186/s13073-020-00802-w
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发表时间：
2020-12-01
期刊：
影响因子：
12.3
通讯作者：
DeCaprio JA
中科院分区：
文献类型：
--
作者：
Nomburg J;Meyerson M;DeCaprio JA
SARS-CoV-2是冠状病毒科的一种正义RNA病毒，引起了2019年冠状病毒病（COVID-19）的全球大流行。冠状病毒通过位于5 ‘ UTR先导序列（TRS- l）之后的转录调控序列（TRS）与位于基因组3 ’末端编码结构蛋白和辅助蛋白的orf开始附近的TRS （TRS- b）之间的同源性过程产生一系列分层的亚基因组rna （sgRNAs）。除了SARS-CoV-2产生的规范sgrna外，还报道了非规范sgrna （nc- sgrna）。然而，这些nc- sgrna在病毒分离株和感染条件下的一致性尚不清楚。全面界定SARS-CoV-2 RNA产物是了解SARS-CoV-2发病机制的关键一步。在这里，我们报告了对使用三种测序策略、五种宿主系统和七种病毒分离物生成的八个独立SARS-CoV-2转录组的综合分析。使用SARS-CoV-2基因组的读图来确定这些样本中鉴定的病毒rna中所有连接的5 ‘和3 ’坐标。通过连接丰度，我们发现nc- sgrna占感染细胞培养模型中总sgrna的33%，在独立转录组中的丰度基本一致，并且在感染期间随着时间的推移而增加。通过评估5 ‘和3 ’连接点两侧序列之间的同源性，我们发现nc- sgrna与trs样同源性无关。通过整合读取覆盖信息，我们发现了亚基因组rna只包含ORF1a的5 '区域的有力证据。最后，我们表明非规范连接改变了病毒开放阅读框架的景观。我们鉴定了SARS-CoV-2 sgRNAs中的规范和非规范连接，并表明这些RNA产物一致地由许多独立的病毒分离株和测序方法产生。这些分析突出了SARS-CoV-2的多种转录活性，并为SARS-CoV-2生物学提供了重要见解。在线版本包含补充材料，可在10.1186/s13073-020-00802-w获得。
SARS-CoV-2, a positive-sense RNA virus in the family Coronaviridae, has caused a worldwide pandemic of coronavirus disease 2019 or COVID-19. Coronaviruses generate a tiered series of subgenomic RNAs (sgRNAs) through a process involving homology between transcriptional regulatory sequences (TRS) located after the leader sequence in the 5′ UTR (the TRS-L) and TRS located near the start of ORFs encoding structural and accessory proteins (TRS-B) near the 3′ end of the genome. In addition to the canonical sgRNAs generated by SARS-CoV-2, non-canonical sgRNAs (nc-sgRNAs) have been reported. However, the consistency of these nc-sgRNAs across viral isolates and infection conditions is unknown. The comprehensive definition of SARS-CoV-2 RNA products is a key step in understanding SARS-CoV-2 pathogenesis. Here, we report an integrative analysis of eight independent SARS-CoV-2 transcriptomes generated using three sequencing strategies, five host systems, and seven viral isolates. Read-mapping to the SARS-CoV-2 genome was used to determine the 5′ and 3′ coordinates of all junctions in viral RNAs identified in these samples. Using junctional abundances, we show nc-sgRNAs make up as much as 33% of total sgRNAs in cell culture models of infection, are largely consistent in abundance across independent transcriptomes, and increase in abundance over time during infection. By assessing the homology between sequences flanking the 5′ and 3′ junction points, we show that nc-sgRNAs are not associated with TRS-like homology. By incorporating read coverage information, we find strong evidence for subgenomic RNAs that contain only 5′ regions of ORF1a. Finally, we show that non-canonical junctions change the landscape of viral open reading frames. We identify canonical and non-canonical junctions in SARS-CoV-2 sgRNAs and show that these RNA products are consistently generated by many independent viral isolates and sequencing approaches. These analyses highlight the diverse transcriptional activity of SARS-CoV-2 and offer important insights into SARS-CoV-2 biology. The online version contains supplementary material available at 10.1186/s13073-020-00802-w.
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影响因子：
12.3
作者：
Rang FJ;Kloosterman WP;de Ridder J
通讯作者：
de Ridder J
影响因子：
3.1
作者：
Brooke CB
通讯作者：
Brooke CB
影响因子：
5.8
作者：
Li, Heng
通讯作者：
Li, Heng
DOI：
10.1073/pnas.0400576101
发表时间：
2004-06-01
影响因子：
11.1
作者：
Bosch, BJ;Martina, BEE;Rottier, PJM
通讯作者：
Rottier, PJM
影响因子：
3
作者：
Camacho C;Coulouris G;Avagyan V;Ma N;Papadopoulos J;Bealer K;Madden TL
通讯作者：
Madden TL