RNA Conformation Capture by Proximity Ligation

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 l...

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Bibliographic Details
Published in:Annual review of genomics and human genetics 2020-08, Vol.21 (1), p.81-100
Main Authors: Kudla, Grzegorz, Wan, Yue, Helwak, Aleksandra
Format: Article
Language:English
Subjects:
bioinformatics
CLASH
Computer applications
Conformation
Hi-C
miRNA
Next-generation sequencing
PARIS
Psoralen
Ribonucleic acid
RNA
RNA structure
RNA viruses
RNA-RNA interactome
SPLASH
Ultraviolet radiation
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Summary: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.
ISSN:1527-8204
1545-293X
DOI:10.1146/annurev-genom-120219-073756