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Nat Methods. 2017 Feb;14(2):201-207. doi: 10.1038/nmeth.4121. Epub 2016 Dec 26.

RESA identifies mRNA-regulatory sequences at high resolution.

Author information

1
Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA.
2
Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.
3
Yale Stem Cell Center, Yale University School of Medicine, New Haven, Connecticut, USA.
4
Yale Cancer Center, Yale University School of Medicine, New Haven, Connecticut, USA.

Abstract

Gene expression is extensively regulated at the levels of mRNA stability, localization and translation. However, decoding functional RNA-regulatory features remains a limitation to understanding post-transcriptional regulation in vivo. Here, we developed RNA-element selection assay (RESA), a method that selects RNA elements on the basis of their activity in vivo and uses high-throughput sequencing to provide a quantitative measurement of their regulatory functions at near-nucleotide resolution. We implemented RESA to identify sequence elements modulating mRNA stability during zebrafish embryogenesis. RESA provides a sensitive and quantitative measure of microRNA activity in vivo and also identifies novel regulatory sequences. To uncover specific sequence requirements within regulatory elements, we developed a bisulfite-mediated nucleotide-conversion strategy for large-scale mutational analysis (RESA-bisulfite). Finally, we used the versatile RESA platform to map candidate protein-RNA interactions in vivo (RESA-CLIP).

PMID:
28024160
PMCID:
PMC5423094
DOI:
10.1038/nmeth.4121
[Indexed for MEDLINE]
Free PMC Article
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