Characterization of viral RNA splicing using whole-transcriptome datasets from host species.
Characterization of viral RNA splicing using whole-transcriptome datasets from host species.
复制标题
DOI：
10.1038/s41598-018-21190-7
复制
发表时间：
2018-02-19
影响因子：
4.6
通讯作者：
Zhou X
中科院分区：
文献类型：
--
作者：
Zhou C;Liu S;Song W;Luo S;Meng G;Yang C;Yang H;Ma J;Wang L;Gao S;Wang J;Yang H;Zhao Y;Wang H;Zhou X
RNA选择性剪接（AS）是一种重要的转录后机制，使单个基因产生多个蛋白质。已经很好地证明，病毒部署宿主AS机器用于病毒蛋白质生产。然而，关于病毒AS的知识仅限于模型物种中的少数致病病毒。在这里，我们报告了一种新的方法来表征病毒AS使用整个转录组数据集从宿主物种。在1，000昆虫转录组进化（1KITE）项目中生成的两种昆虫转录组（Acheta aceticus和Planococcus citri）被用作使用新管道的概念验证。检测到两种密切相关的浓核病毒（Acheta aceticus浓核病毒，AdDNV和Planococcus citri浓核病毒，PcDNV，Ambidensovirus，浓核病毒亚科，细小病毒科），并分析了AS模式。结果表明，虽然这两种病毒共享的主要AS功能，戏剧性的AS分歧观察。对剪接接头的详细分析显示，AS事件簇发生在病毒基因组的两个区域，表明转录组分析可以获得对病毒剪接的有价值的见解。当应用于具有不同分类学采样的大规模转录组学项目时，我们的新方法有望迅速扩展我们对各种病毒的RNA剪接机制的知识。
RNA alternative splicing (AS) is an important post-transcriptional mechanism enabling single genes to produce multiple proteins. It has been well demonstrated that viruses deploy host AS machinery for viral protein productions. However, knowledge on viral AS is limited to a few disease-causing viruses in model species. Here we report a novel approach to characterizing viral AS using whole transcriptome dataset from host species. Two insect transcriptomes (Acheta domesticus and Planococcus citri) generated in the 1,000 Insect Transcriptome Evolution (1KITE) project were used as a proof of concept using the new pipeline. Two closely related densoviruses (Acheta domesticus densovirus, AdDNV, and Planococcus citri densovirus, PcDNV, Ambidensovirus, Densovirinae, Parvoviridae) were detected and analyzed for AS patterns. The results suggested that although the two viruses shared major AS features, dramatic AS divergences were observed. Detailed analysis of the splicing junctions showed clusters of AS events occurred in two regions of the virus genome, demonstrating that transcriptome analysis could gain valuable insights into viral splicing. When applied to large-scale transcriptomics projects with diverse taxonomic sampling, our new method is expected to rapidly expand our knowledge on RNA splicing mechanisms for a wide range of viruses.
登录
查看更多内容
影响因子：
46.9
作者：
Bray, Nicolas L.;Pimentel, Harold;Pachter, Lior
通讯作者：
Pachter, Lior
影响因子：
14.9
作者：
Burset, M;Seledtsov, IA;Solovyev, VV
通讯作者：
Solovyev, VV
影响因子：
16
作者：
Burge, CB;Padgett, RA;Sharp, PA
通讯作者：
Sharp, PA
影响因子：
6.4
作者：
Dubois J;Terrier O;Rosa-Calatrava M
通讯作者：
Rosa-Calatrava M
影响因子：
3.7
作者：
Wang Y;Wang H;Xu K;Ni P;Zhang H;Ma J;Yang H;Xu F
通讯作者：
Xu F