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

机译：RIC-SEQ用于RNA-RNA空间相互作用的全球原位分析

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摘要

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.
机译：摘要高度结构的RNA分子通常彼此相互作用，并与各种RNA结合蛋白相关联，以调节关键的生物方法。然而，完整细胞中的RNA结构和相互作用仍然很大程度上是未知的。这里，通过耦合由RNA结合蛋白介导的具有深度测序的接近连接，我们在原位构象测序（RIC-SEQ）技术中报告了用于和分子间RNA-RNA相互作用的全球性分析的RNA。该技术不仅重新承载已知的RNA二次结构和三级相互作用，还促进了人细胞中RNA的三维（3D）相互作用图的产生。使用这些地图，我们识别全球的非分量RNA靶标，以及辨别RNA拓扑结构域和跨交互枢纽。我们揭示了增强剂和启动子的功能连接可以使用它们的成对相互作用的RNA来分配。此外，我们表明CCAT1-5L-A超强增强剂中心RNA与RNA结合蛋白HNRNPK相互作用，以及衍生自MyC启动子和增强子的RNA，通过调节染色质循环来促进MyC转录。我们的研究表明RIC-SEQ在发现RNA的3D结构，相互作用和调节作用方面的功率和适用性。

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  • 来源
    《Nature》 |2020年第7812期|432-437|共6页
  • 作者

    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; Yuanchao Xue;

  • 作者单位

    Chinese Academy of Sciences|University of Chinese Academy of Sciences;

    Chinese Academy of Sciences;

    Chinese Academy of Sciences;

    Chinese Academy of Sciences|University of Chinese Academy of Sciences;

    Chinese Academy of Sciences|University of Chinese Academy of Sciences;

    Henan Normal University;

    Chinese Academy of Sciences|University of Chinese Academy of Sciences;

    Chinese Academy of Sciences|University of Chinese Academy of Sciences;

    Chinese Academy of Sciences|University of Chinese Academy of Sciences;

    Chinese Academy of Sciences;

    Chinese Academy of Sciences;

    Chinese Academy of Sciences|Xinyang Normal University;

    Henan Normal University;

    Chinese Academy of Sciences;

    Chinese Academy of Sciences|University of Chinese Academy of Sciences;

  • 收录信息 美国《科学引文索引》(SCI);美国《工程索引》(EI);美国《生物学医学文摘》(MEDLINE);美国《化学文摘》(CA);
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  • 正文语种 eng
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