Lim Chun Shen, Brown Chris M
Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand.
Front Microbiol. 2018 Jan 4;8:2582. doi: 10.3389/fmicb.2017.02582. eCollection 2017.
Structured RNA elements may control virus replication, transcription and translation, and their distinct features are being exploited by novel antiviral strategies. Viral RNA elements continue to be discovered using combinations of experimental and computational analyses. However, the wealth of sequence data, notably from deep viral RNA sequencing, viromes, and metagenomes, necessitates computational approaches being used as an essential discovery tool. In this review, we describe practical approaches being used to discover functional RNA elements in viral genomes. In addition to success stories in new and emerging viruses, these approaches have revealed some surprising new features of well-studied viruses e.g., human immunodeficiency virus, hepatitis C virus, influenza, and dengue viruses. Some notable discoveries were facilitated by new comparative analyses of diverse viral genome alignments. Importantly, comparative approaches for finding RNA elements embedded in coding and non-coding regions differ. With the exponential growth of computer power we have progressed from stem-loop prediction on single sequences to cutting edge 3D prediction, and from command line to user friendly web interfaces. Despite these advances, many powerful, user friendly prediction tools and resources are underutilized by the virology community.
结构化RNA元件可能控制病毒的复制、转录和翻译，新型抗病毒策略正在利用它们的独特特性。通过实验分析和计算分析相结合的方法，不断发现新的病毒RNA元件。然而，大量的序列数据，特别是来自深度病毒RNA测序、病毒宏基因组和宏基因组的数据，使得计算方法成为必不可少的发现工具。在这篇综述中，我们描述了用于发现病毒基因组中功能性RNA元件的实用方法。除了在新出现的病毒方面取得的成功案例外，这些方法还揭示了一些经过充分研究的病毒（如人类免疫缺陷病毒、丙型肝炎病毒、流感病毒和登革热病毒）的一些惊人新特性。一些显著的发现得益于对不同病毒基因组比对的新的比较分析。重要的是，用于寻找嵌入编码区和非编码区的RNA元件的比较方法有所不同。随着计算机能力的指数级增长，我们已经从对单序列的茎环预测发展到前沿的三维预测，从命令行操作发展到用户友好的网络界面。尽管取得了这些进展，但病毒学界对许多强大、用户友好的预测工具和资源的利用仍然不足。
