RIC-seq for global in situ profiling of RNA-RNA spatial interactions
RIC-seq for global in situ profiling of RNA-RNA spatial interactions
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RIC-seq 用于 RNA–RNA 空间相互作用的全局原位分析
DOI：
10.1038/s41586-020-2249-1
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发表时间：
2020-06-18
期刊：
影响因子：
64.8
通讯作者：
Xue, Yuanchao
中科院分区：
文献类型：
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作者：
Cai, Zhaokui;Cao, Changchang;Xue, Yuanchao
高度结构化的RNA分子通常会相互作用，并与各种RNA结合蛋白相结合，以调控关键的生物学过程。然而，完整细胞内的RNA结构与相互作用在很大程度上仍不为人知。在此，通过将RNA结合蛋白介导的邻近连接与深度测序相结合，我们报告了一种RNA原位构象测序（RIC-seq）技术，用于对RNA分子内和分子间相互作用进行全局分析。该技术不仅重现了已知的RNA二级结构和三级相互作用，还助力生成了人类细胞中RNA的三维（3D）相互作用图谱。利用这些图谱，我们在全基因组范围内鉴定出非编码RNA的靶标，并识别出RNA拓扑结构域和反式相互作用枢纽。我们揭示出，增强子和启动子的功能连接性可通过它们之间相互作用的RNA对来确定。此外，我们表明CCAT1 - 5L（一种超级增强子枢纽RNA）与RNA结合蛋白hnRNPK以及源自MYC启动子和增强子的RNA相互作用，通过调节染色质环化来促进MYC转录。我们的研究展示了RIC - seq在揭示RNA的三维结构、相互作用及调控作用方面的强大能力和适用性。
Highly structured RNA molecules usually interact with each other, and associate with various RNA-binding proteins, to regulate critical biological processes. However, RNA structures and interactions in intact cells remain largely unknown. Here, by coupling proximity ligation mediated by RNA-binding proteins with deep sequencing, we report an RNA in situ conformation sequencing (RIC-seq) technology for the global profiling of intra- and intermolecular RNA–RNA interactions. This technique not only recapitulates known RNA secondary structures and tertiary interactions, but also facilitates the generation of three-dimensional (3D) interaction maps of RNA in human cells. Using these maps, we identify noncoding RNA targets globally, and discern RNA topological domains andtrans-interacting hubs. We reveal that the functional connectivity of enhancers and promoters can be assigned using their pairwise-interacting RNAs. Furthermore, we show thatCCAT1-5L—a super-enhancer hub RNA—interacts with the RNA-binding protein hnRNPK, as well as RNA derived from theMYCpromoter and enhancer, to boostMYCtranscription by modulating chromatin looping. Our study demonstrates the power and applicability of RIC-seq in discovering the 3D structures, interactions and regulatory roles of RNA.