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Mol Cell. 2016 May 19;62(4):618-26. doi: 10.1016/j.molcel.2016.04.030. Epub 2016 May 12.

Global Mapping of Human RNA-RNA Interactions.

Author information

1
Donnelly Centre, University of Toronto, Toronto, ON M53 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M53 3E1, Canada.
2
Donnelly Centre, University of Toronto, Toronto, ON M53 3E1, Canada.
3
Donnelly Centre, University of Toronto, Toronto, ON M53 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M53 3E1, Canada. Electronic address: b.blencowe@utoronto.ca.

Abstract

The majority of the human genome is transcribed into non-coding (nc)RNAs that lack known biological functions or else are only partially characterized. Numerous characterized ncRNAs function via base pairing with target RNA sequences to direct their biological activities, which include critical roles in RNA processing, modification, turnover, and translation. To define roles for ncRNAs, we have developed a method enabling the global-scale mapping of RNA-RNA duplexes crosslinked in vivo, "LIGation of interacting RNA followed by high-throughput sequencing" (LIGR-seq). Applying this method in human cells reveals a remarkable landscape of RNA-RNA interactions involving all major classes of ncRNA and mRNA. LIGR-seq data reveal unexpected interactions between small nucleolar (sno)RNAs and mRNAs, including those involving the orphan C/D box snoRNA, SNORD83B, that control steady-state levels of its target mRNAs. LIGR-seq thus represents a powerful approach for illuminating the functions of the myriad of uncharacterized RNAs that act via base-pairing interactions.

PMID:
27184080
DOI:
10.1016/j.molcel.2016.04.030
[Indexed for MEDLINE]
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