RIC-seq for global in situ profiling of RNA–RNA spatial interactions

Zhaokui Cai, Changchang Cao, Lei Ji, Rong Ye, Di Wang, Cong Xia, Sui Wang, Zongchang Du, Naijing Hu, Xiaohua Yu, Juan Chen, Lei Wang, Xianguang Yang, Shunmin He and Yuanchao Xue ()
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Zhaokui Cai: Chinese Academy of Sciences
Changchang Cao: Chinese Academy of Sciences
Lei Ji: Chinese Academy of Sciences
Rong Ye: Chinese Academy of Sciences
Di Wang: Chinese Academy of Sciences
Cong Xia: Henan Normal University
Sui Wang: Chinese Academy of Sciences
Zongchang Du: Chinese Academy of Sciences
Naijing Hu: Chinese Academy of Sciences
Xiaohua Yu: Chinese Academy of Sciences
Juan Chen: Chinese Academy of Sciences
Lei Wang: Chinese Academy of Sciences
Xianguang Yang: Henan Normal University
Shunmin He: Chinese Academy of Sciences
Yuanchao Xue: Chinese Academy of Sciences

Nature, 2020, vol. 582, issue 7812, 432-437

Abstract: Abstract 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 and trans-interacting hubs. We reveal that the functional connectivity of enhancers and promoters can be assigned using their pairwise-interacting RNAs. Furthermore, we show that CCAT1-5L—a super-enhancer hub RNA—interacts with the RNA-binding protein hnRNPK, as well as RNA derived from the MYC promoter and enhancer, to boost MYC transcription 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.

Date: 2020
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DOI: 10.1038/s41586-020-2249-1

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