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

Nature. 2020 Jun;582(7812):432-437. doi: 10.1038/s41586-020-2249-1. Epub 2020 May 6.

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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Cell Line
  • Chromatin / genetics
  • Chromatin / metabolism
  • Chromosomes, Human / genetics
  • Enhancer Elements, Genetic / genetics
  • Genes, myc / genetics
  • Genes, rRNA / genetics
  • Heterogeneous-Nuclear Ribonucleoprotein K / metabolism
  • Humans
  • Nucleic Acid Conformation*
  • Promoter Regions, Genetic / genetics
  • RNA / chemistry*
  • RNA / genetics*
  • RNA, Long Noncoding / chemistry
  • RNA, Long Noncoding / genetics
  • Reproducibility of Results
  • Sequence Analysis, RNA / methods*
  • Transcription, Genetic

Substances

  • CCAT1 long noncoding RNA, human
  • Chromatin
  • Heterogeneous-Nuclear Ribonucleoprotein K
  • RNA, Long Noncoding
  • HNRNPK protein, human
  • RNA