小柯机器人

德国亥姆霍兹感染研究中心Redmond P. Smyth团队近期取得重要工作进展，他们研究开发了Nano-DMS-MaP工具，该工具能允许异构体特异性RNA结构的测定。相关研究成果2023年4月27日在线发表于《自然—方法学》杂志上。

据介绍，RNA结构的全基因组测量可以使用与不成对碱基反应的试剂来获得，从而产生加合物，这些加合物可以在下一代测序机上通过突变分析来鉴定。这些实验的一个缺点是，短测序读数很少能映射到特定的转录物异构体。因此，在转录本之间共享的区域中，信息是作为平均值获得的，从而模糊了潜在的结构信息。

研究人员提出了纳米孔二甲基硫酸酯突变谱（Nano-DMS MaP），这是一种利用长读测序提供高度相似RNA分子的异构体解析结构信息的方法。研究人员通过解析感染细胞中人类免疫缺陷病毒-1转录物的复杂结构图谱，证明了Nano-DMS-MaP的价值。研究人员发现未剪接和剪接的转录物在常见的5′内的包装位点具有不同的结构未翻译区域，这可能解释了为什么剪接的病毒RNA被排除在病毒颗粒之外。

因此，Nano-DMS-MaP是一种简单直接的方法，可以解决以前隐藏在短读集合分析中的生物重要转录特异性RNA结构。

附：英文原文

Title: Nano-DMS-MaP allows isoform-specific RNA structure determination

Author: Bohn, Patrick, Gribling-Burrer, Anne-Sophie, Ambi, Uddhav B., Smyth, Redmond P.

Issue&Volume: 2023-04-27

Abstract: Genome-wide measurements of RNA structure can be obtained using reagents that react with unpaired bases, leading to adducts that can be identified by mutational profiling on next-generation sequencing machines. One drawback of these experiments is that short sequencing reads can rarely be mapped to specific transcript isoforms. Consequently, information is acquired as a population average in regions that are shared between transcripts, thus blurring the underlying structural landscape. Here, we present nanopore dimethylsulfate mutational profiling (Nano-DMS-MaP)—a method that exploits long-read sequencing to provide isoform-resolved structural information of highly similar RNA molecules. We demonstrate the value of Nano-DMS-MaP by resolving the complex structural landscape of human immunodeficiency virus-1 transcripts in infected cells. We show that unspliced and spliced transcripts have distinct structures at the packaging site within the common 5′untranslated region, likely explaining why spliced viral RNAs are excluded from viral particles. Thus, Nano-DMS-MaP is a straightforward method to resolve biologically important transcript-specific RNA structures that were previously hidden in short-read ensemble analyses.

DOI: 10.1038/s41592-023-01862-7

Source: https://www.nature.com/articles/s41592-023-01862-7

Nature Methods：《自然—方法学》，创刊于2004年。隶属于施普林格·自然出版集团，最新IF：47.99
官方网址：https://www.nature.com/nmeth/
投稿链接：https://mts-nmeth.nature.com/cgi-bin/main.plex