title: RESA identifies mRNA-regulatory sequences at high resolution.
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).
authors.affiliation: Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA.
authors.forename: Valeria
authors.initials: V
authors.lastname: Yartseva
authors.affiliation: Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA.
authors.forename: Carter M
authors.initials: CM
authors.lastname: Takacs
authors.affiliation: Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA.
authors.forename: Charles E
authors.initials: CE
authors.lastname: Vejnar
authors.affiliation: Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA.|Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.
authors.forename: Miler T
authors.identifier: 0000-0003-0933-0551
authors.initials: MT
authors.lastname: Lee
authors.affiliation: Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA.|Yale Stem Cell Center, Yale University School of Medicine, New Haven, Connecticut, USA.|Yale Cancer Center, Yale University School of Medicine, New Haven, Connecticut, USA.
authors.forename: Antonio J
authors.initials: AJ
authors.lastname: Giraldez
mesh_terms: D020413:3' Untranslated Regions; D000818:Animals; D004625:Embryo, Nonmammalian; D005821:Genetic Techniques; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D047468:Immunoprecipitation; D020871:RNA Stability; D012333:RNA, Messenger / Q000235:genetics; D012045:Regulatory Sequences, Nucleic Acid; D013447:Sulfites; D015027:Zebrafish / Q000196:embryology
chemical_list: D020413:3' Untranslated Regions; D012333:RNA, Messenger; D013447:Sulfites; C042345:hydrogen sulfite