PARIS: Psoralen Analysis of RNA Interactions and Structures with High Throughput and Resolution.
PARIS: Psoralen Analysis of RNA Interactions and Structures with High Throughput and Resolution.
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DOI：
10.1007/978-1-4939-7213-5_4
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发表时间：
2018
期刊：
影响因子：
--
通讯作者：
Zhang QC
中科院分区：
文献类型：
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作者：
Lu Z;Gong J;Zhang QC
RNA具有形成碱基对的内在倾向，导致复杂的分子内和分子间螺旋。活细胞中碱基配对相互作用的直接测量对于解决转录组结构和相互作用以及研究它们的功能至关重要（Lu和Chang，Curr Opin Struct Biol 36：142-148，2016）。为了这个目标，我们开发了一种实验方法巴黎（RNA相互作用和结构的Pesticen分析），以直接确定转录组范围的碱基配对相互作用（Lu等人，Cell 165（5）：1267-1279，2016）。巴黎结合了四个关键步骤，即体内交联、2D凝胶纯化、邻位连接和高通量测序，以实现活细胞中RNA结构组和相互作用组的高通量和近碱基对分辨率测定。在本章中，我们的目标是提供一个全面的讨论背后的实验和计算策略的原则，并逐步描述的实验和分析。
RNA has the intrinsic propensity to form base pairs, leading to complex intramolecular and intermolecular helices. Direct measurement of base pairing interactions in living cells is critical to solving transcriptome structure and interactions, and investigating their functions (Lu and Chang, Curr Opin Struct Biol 36:142–148, 2016). Toward this goal, we developed an experimental method, PARIS (Psoralen Analysis of RNA Interactions and Structures), to directly determine transcriptome-wide base pairing interactions (Lu et al., Cell 165(5):1267–1279, 2016). PARIS combines four critical steps, in vivo cross-linking, 2D gel purification, proximity ligation, and high-throughput sequencing to achieve high-throughput and near-base pair resolution determination of the RNA structurome and interactome in living cells. In this chapter, we aim to provide a comprehensive discussion on the principles behind the experimental and computational strategies, and a step-by-step description of the experiment and analysis.