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).
journal_name
Nat Methodsjournal_title
Nature methodsauthors
Yartseva V,Takacs CM,Vejnar CE,Lee MT,Giraldez AJdoi
10.1038/nmeth.4121subject
Has Abstractpub_date
2017-02-01 00:00:00pages
201-207issue
2eissn
1548-7091issn
1548-7105pii
nmeth.4121journal_volume
14pub_type
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