RNA結構多樣性的確定及其在HIV1 RNA剪接中的作用
作者：
小柯機器人發布時間：2020/5/7 14:43:23
RNA結構多樣性的確定及其在人類免疫缺陷病毒1（HIV-1）RNA剪接中的作用，這一成果由美國Whitehead生物醫學研究所Silvi Rouskin研究組經過不懈努力而取得。這一研究成果在線發表在2020年5月6日出版的《自然》上。
研究人員使用硫酸二甲酯突變譜結合測序（DMS-MaPseq）的方法來研究細胞中HIV-1 RNA的結構；同時研究人員還開發了一種算法，並將其命名為「使用期望最大化檢測RNA摺疊體」（DREEM），該算法揭示了相同RNA序列假定的其他構象。
與先前分析種群平均值的模型相反，該結果揭示整個HIV-1基因組中RNA結構的異質區域。除了揭示HIV-1 Rev響應元件的體外表徵，其替代結構還存在於細胞之外；研究人員還在關鍵剪接位點發現了影響轉錄亞型比率的替代構象。通過對剪接和細胞內RNA結構的同時測量，該研究為長期存在的假說提供了證據，即RNA構象的異質性調節了剪接位點的使用和病毒基因的表達。
據了解，HIV-1是一種逆轉錄病毒，其基因組由十個鹼基單鏈RNA組成。HIV-1必須通過單一的初級轉錄本來表達其所有基因產物，該轉錄產物需要經過選擇性剪接才能產生出包括結構蛋白和調節因子在內的多種蛋白產物。儘管選擇性剪接起著至關重要的作用，但對剪接位點選擇機制的了解甚少。造成剪接和病毒複製嚴重缺陷的同義RNA突變表明存在未知的順式調控元件。
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