RNA structure is critically important to RNA viruses in every part of the replication cycle. RNA structure is also utilized by DNA viruses in order to regulate gene expression and interact with host factors. Advances in next-generation sequencing have greatly enhanced the utility of chemical probing in order to analyze RNA structure. This review will cover some recent viral RNA structural studies using chemical probing and next-generation sequencing as well as the advantages of dimethyl sulfate (DMS)- mutational profiling and sequencing (MaPseq). DMS-MaPseq is a robust assay that can easily modify RNA in vitro, in cell and in virion. A detailed protocol for whole-genome DMS-MaPseq from cells transfected with HIV-1 and the structure of TAR as determined by DMS-MaPseq is presented. DMS-MaPseq has the ability to answer a variety of integral questions about viral RNA, including how they change in different environments and when interacting with different host factors.

中文翻译：

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使用 DMS-MaPseq 进行病毒 RNA 结构分析

在复制周期的每个部分，RNA 结构对 RNA 病毒都至关重要。DNA 病毒也利用 RNA 结构来调节基因表达并与宿主因子相互作用。新一代测序技术的进步极大地增强了化学探测在分析 RNA 结构方面的效用。本综述将涵盖一些最近使用化学探测和下一代测序的病毒 RNA 结构研究，以及硫酸二甲酯 (DMS)-突变分析和测序 (MaPseq) 的优势。DMS-MaPseq 是一种强大的检测方法，可以轻松地在体外、细胞和病毒粒子中修饰 RNA。介绍了从 HIV-1 转染的细胞中获得全基因组 DMS-MaPseq 的详细方案，以及由 DMS-MaPseq 确定的 TAR 结构。