Lu Zhipeng, Zhang Qiangfeng Cliff, Lee Byron, Flynn Ryan A, Smith Martin A, Robinson James T, Davidovich Chen, Gooding Anne R, Goodrich Karen J, Mattick John S, Mesirov Jill P, Cech Thomas R, Chang Howard Y
Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, USA.
Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, USA; MOE Key Laboratory of Bioinformatics, Beijing Advanced Innovation Center for Structural Biology, Center for Synthetic and Systems Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China.
Cell. 2016 May 19;165(5):1267-1279. doi: 10.1016/j.cell.2016.04.028. Epub 2016 May 12.
RNA has the intrinsic property to base pair, forming complex structures fundamental to its diverse functions. Here, we develop PARIS, a method based on reversible psoralen crosslinking for global mapping of RNA duplexes with near base-pair resolution in living cells. PARIS analysis in three human and mouse cell types reveals frequent long-range structures, higher-order architectures, and RNA-RNA interactions in trans across the transcriptome. PARIS determines base-pairing interactions on an individual-molecule level, revealing pervasive alternative conformations. We used PARIS-determined helices to guide phylogenetic analysis of RNA structures and discovered conserved long-range and alternative structures. XIST, a long noncoding RNA (lncRNA) essential for X chromosome inactivation, folds into evolutionarily conserved RNA structural domains that span many kilobases. XIST A-repeat forms complex inter-repeat duplexes that nucleate higher-order assembly of the key epigenetic silencing protein SPEN. PARIS is a generally applicable and versatile method that provides novel insights into the RNA structurome and interactome. VIDEO ABSTRACT.
RNA具有碱基配对的内在特性，能形成对其多种功能至关重要的复杂结构。在此，我们开发了PARIS，这是一种基于可逆补骨脂素交联的方法，用于在活细胞中以近碱基对分辨率全局绘制RNA双链体图谱。在三种人类和小鼠细胞类型中进行的PARIS分析揭示了转录组中频繁出现的长程结构、高阶结构以及反式RNA-RNA相互作用。PARIS在单分子水平上确定碱基配对相互作用，揭示了普遍存在的替代构象。我们利用PARIS确定的螺旋来指导RNA结构的系统发育分析，并发现了保守的长程和替代结构。XIST是X染色体失活所必需的长链非编码RNA（lncRNA），它折叠成跨越数千碱基的进化保守RNA结构域。XIST A重复序列形成复杂的重复间双链体，这些双链体是关键表观遗传沉默蛋白SPEN高阶组装的核心。PARIS是一种普遍适用且多功能的方法，为RNA结构组和相互作用组提供了新的见解。视频摘要。
