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Mapping RNA-RNA Interactions Globally Using Biotinylated Psoralen
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Global Mapping of Human RNA-RNA Interactions
Eesha Sharma1, Tim Sterne-Weiler2, Dave O'Hanlon2
1Donnelly Centre, University of Toronto, Toronto, ON M53 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M53 3E1, Canada.
Molecular Cell
|May 18, 2016
Summary
Researchers developed LIGR-seq to map RNA-RNA interactions in vivo. This method revealed novel functions for non-coding RNAs (ncRNAs), including small nucleolar RNAs (snoRNAs), in regulating messenger RNA (mRNA) levels.
Area of Science:
- Molecular Biology
- Genomics
- RNA Biology
Background:
- The human genome transcribes numerous non-coding RNAs (ncRNAs) with poorly understood functions.
- Many characterized ncRNAs regulate biological activities through base pairing with target RNAs, impacting RNA processing, modification, turnover, and translation.
Purpose of the Study:
- To develop a method for global-scale mapping of RNA-RNA duplexes crosslinked in vivo.
- To investigate the roles of ncRNAs in cellular processes by identifying their interaction partners.
Main Methods:
- Development of "LIGation of interacting RNA followed by high-throughput sequencing" (LIGR-seq).
- Application of LIGR-seq in human cells to capture and sequence crosslinked RNA-RNA interactions.
Main Results:
- LIGR-seq revealed a comprehensive map of RNA-RNA interactions involving various ncRNAs and messenger RNAs (mRNAs).
- Unexpected interactions between small nucleolar RNAs (snoRNAs) and mRNAs were identified.
- Specific interactions, such as those involving the SNORD83B snoRNA, were shown to control target mRNA levels.
Conclusions:
- LIGR-seq is a powerful tool for elucidating the functions of uncharacterized ncRNAs.
- The study highlights the significant role of ncRNAs, including snoRNAs, in regulating gene expression at the mRNA level.
- RNA-RNA interactions are crucial for diverse cellular functions, and LIGR-seq provides a means to uncover these.
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