RNA conformation capture by proximity ligation

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RNA proximity ligation is a set of molecular biology techniques used to analyze the conformations and spatial proximity of RNA molecules within cells. A typical experiment starts with cross-linking of a biological sample using UV light or psoralen, followed by partial fragmentation of RNA, RNA–RNA ligation, library preparation, and high-throughput sequencing. In the past decade, proximity ligation has been used to study structures of individual RNAs, networks of interactions between small RNAs and their targets, and whole RNA–RNA interactomes, in models ranging from bacteria to animal tissues and whole animals. Here, we provide an overview of the field, highlight the main findings, review the recent experimental and computational developments, and provide troubleshooting advice for new users. In the final section, we draw parallels between DNA and RNA proximity ligation and speculate on possible future research directions.
Original languageEnglish
JournalAnnual review of genomics and human genetics
Issue number1
Early online date22 Apr 2020
Publication statusPublished - 31 Aug 2020


  • hiCLIP
  • LIGR-Seq
  • HiC
  • RNA-RNA interactome
  • miRNA
  • sRNA
  • piRNA
  • RNA structure
  • RNA viruses
  • Zika


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