Department of Medical Biology, Albert Szent-Györgyi Medical School, University of Szeged, Szeged 6720, Hungary.
Complex Medical Center, Budapest 1012, Hungary.
Gigascience. 2022 Oct 17;11. doi: 10.1093/gigascience/giac094.
Recent studies have disclosed the genome, transcriptome, and epigenetic compositions of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and the effect of viral infection on gene expression of the host cells. It has been demonstrated that, besides the major canonical transcripts, the viral genome also codes for noncanonical RNA molecules. While the structural characterizations have revealed a detailed transcriptomic architecture of the virus, the kinetic studies provided poor and often misleading results on the dynamics of both the viral and host transcripts due to the low temporal resolution of the infection event and the low virus/cell ratio (multiplicity of infection [MOI] = 0.1) applied for the infection. It has never been tested whether the alteration in the host gene expressions is caused by aging of the cells or by the viral infection.
In this study, we used Oxford Nanopore's direct cDNA and direct RNA sequencing methods for the generation of a high-coverage, high temporal resolution transcriptomic dataset of SARS-CoV-2 and of the primate host cells, using a high infection titer (MOI = 5). Sixteen sampling time points ranging from 1 to 96 hours with a varying time resolution and 3 biological replicates were used in the experiment. In addition, for each infected sample, corresponding noninfected samples were employed. The raw reads were mapped to the viral and to the host reference genomes, resulting in 49,661,499 mapped reads (54,62 Gbs). The genome of the viral isolate was also sequenced and phylogenetically classified.
This dataset can serve as a valuable resource for profiling the SARS-CoV-2 transcriptome dynamics, the virus-host interactions, and the RNA base modifications. Comparison of expression profiles of the host gene in the virally infected and in noninfected cells at different time points allows making a distinction between the effect of the aging of cells in culture and the viral infection. These data can provide useful information for potential novel gene annotations and can also be used for studying the currently available bioinformatics pipelines.
最近的研究揭示了严重急性呼吸综合征冠状病毒 2（SARS-CoV-2）的基因组、转录组和表观遗传组成，以及病毒感染对宿主细胞基因表达的影响。已经证明，除了主要的规范转录本外，病毒基因组还编码非规范 RNA 分子。虽然结构特征揭示了病毒的详细转录组结构，但由于感染事件的时间分辨率低以及用于感染的低病毒/细胞比（感染倍数 [MOI]=0.1），动力学研究对病毒和宿主转录本的动态提供了较差且经常具有误导性的结果。从未测试过宿主基因表达的改变是由细胞老化还是由病毒感染引起的。
在这项研究中，我们使用牛津纳米孔公司的直接 cDNA 和直接 RNA 测序方法，使用高感染滴度（MOI=5）生成 SARS-CoV-2 和灵长类宿主细胞的高覆盖率、高时间分辨率转录组数据集。实验中使用了 16 个时间点，时间范围从 1 小时到 96 小时不等，时间分辨率不同，有 3 个生物学重复。此外，为每个感染样本，还使用了相应的未感染样本。将原始读数映射到病毒和宿主参考基因组上，得到 49661499 个映射读数（5462 Gbs）。还对病毒分离株的基因组进行了测序和系统发育分类。
该数据集可作为 SARS-CoV-2 转录组动力学、病毒-宿主相互作用和 RNA 碱基修饰分析的有价值资源。比较不同时间点病毒感染和未感染细胞中宿主基因的表达谱，可以区分细胞在培养中的老化和病毒感染的影响。这些数据可以为潜在的新基因注释提供有用信息，也可用于研究当前可用的生物信息学管道。
Zotero 插件
