小柯机器人

RNA结构多样性的确定及其在人类免疫缺陷病毒1（HIV-1）RNA剪接中的作用，这一成果由美国Whitehead生物医学研究所Silvi Rouskin研究组经过不懈努力而取得。这一研究成果在线发表在2020年5月6日出版的《自然》上。

研究人员使用硫酸二甲酯突变谱结合测序（DMS-MaPseq）的方法来研究细胞中HIV-1 RNA的结构；同时研究人员还开发了一种算法，并将其命名为“使用期望最大化检测RNA折叠体”（DREEM），该算法揭示了相同RNA序列假定的其他构象。

与先前分析种群平均值的模型相反，该结果揭示整个HIV-1基因组中RNA结构的异质区域。除了揭示HIV-1 Rev响应元件的体外表征，其替代结构还存在于细胞之外；研究人员还在关键剪接位点发现了影响转录亚型比率的替代构象。通过对剪接和细胞内RNA结构的同时测量，该研究为长期存在的假说提供了证据，即RNA构象的异质性调节了剪接位点的使用和病毒基因的表达。

据了解，HIV-1是一种逆转录病毒，其基因组由十个碱基单链RNA组成。HIV-1必须通过单一的初级转录本来表达其所有基因产物，该转录产物需要经过选择性剪接才能产生出包括结构蛋白和调节因子在内的多种蛋白产物。尽管选择性剪接起着至关重要的作用，但对剪接位点选择机制的了解甚少。造成剪接和病毒复制严重缺陷的同义RNA突变表明存在未知的顺式调控元件。

附：英文原文

Title: Determination of RNA structural diversity and its role in HIV-1 RNA splicing

Author: Phillip J. Tomezsko, Vincent D. A. Corbin, Paromita Gupta, Harish Swaminathan, Margalit Glasgow, Sitara Persad, Matthew D. Edwards, Lachlan Mcintosh, Anthony T. Papenfuss, Ann Emery, Ronald Swanstrom, Trinity Zang, Tammy C. T. Lan, Paul Bieniasz, Daniel R. Kuritzkes, Athe Tsibris, Silvi Rouskin

Issue&Volume: 2020-05-06

Abstract: Human immunodeficiency virus 1 (HIV-1) is a retrovirus with a ten-kilobase single-stranded RNA genome. HIV-1 must express all of its gene products from a single primary transcript, which undergoes alternative splicing to produce diverse protein products that include structural proteins and regulatory factors1,2. Despite the critical role of alternative splicing, the mechanisms that drive the choice of splice site are poorly understood. Synonymous RNA mutations that lead to severe defects in splicing and viral replication indicate the presence of unknown cis-regulatory elements3. Here we use dimethyl sulfate mutational profiling with sequencing (DMS-MaPseq) to investigate the structure of HIV-1 RNA in cells, and develop an algorithm that we name ‘detection of RNA folding ensembles using expectation–maximization’ (DREEM), which reveals the alternative conformations that are assumed by the same RNA sequence. Contrary to previous models that have analysed population averages4, our results reveal heterogeneous regions of RNA structure across the entire HIV-1 genome. In addition to confirming that in vitro characterized5 alternative structures for the HIV-1 Rev responsive element also exist in cells, we discover alternative conformations at critical splice sites that influence the ratio of transcript isoforms. Our simultaneous measurement of splicing and intracellular RNA structure provides evidence for the long-standing hypothesis6,7,8 that heterogeneity in RNA conformation regulates splice-site use and viral gene expression.

DOI: 10.1038/s41586-020-2253-5

Source: https://www.nature.com/articles/s41586-020-2253-5

Nature：《自然》，创刊于1869年。隶属于施普林格·自然出版集团，最新IF：69.504
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