PUBLICATION
RESA identifies mRNA-regulatory sequences at high resolution
- Authors
- Yartseva, V., Takacs, C.M., Vejnar, C.E., Lee, M.T., Giraldez, A.J.
- ID
- ZDB-PUB-161227-1
- Date
- 2017
- Source
- Nature Methods 14(2): 201-207 (Journal)
- Registered Authors
- Giraldez, Antonio, Lee, Miler, Takacs, Carter M., Vejnar, Charles
- Keywords
- none
- MeSH Terms
-
- 3' Untranslated Regions
- Animals
- Embryo, Nonmammalian
- Genetic Techniques*
- High-Throughput Nucleotide Sequencing/methods*
- Immunoprecipitation
- RNA Stability
- RNA, Messenger*/genetics
- Regulatory Sequences, Nucleic Acid*
- Sulfites
- Zebrafish/embryology
- PubMed
- 28024160 Full text @ Nat. Methods
Citation
Yartseva, V., Takacs, C.M., Vejnar, C.E., Lee, M.T., Giraldez, A.J. (2017) RESA identifies mRNA-regulatory sequences at high resolution. Nature Methods. 14(2):201-207.
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).
Genes / Markers
Expression
Phenotype
Mutations / Transgenics
Human Disease / Model
Sequence Targeting Reagents
Fish
Orthology
Engineered Foreign Genes
Mapping