Journal
MOLECULAR CELL
Volume 80, Issue 5, Pages 903-+Publisher
CELL PRESS
DOI: 10.1016/j.molcel.2020.11.014
Keywords
-
Categories
Funding
- NIH [R01-HG004659, U41-HG009889, R01-HL137219, R01-HL137223, R01-HD085902, R01-HG004361, R35-CA209919]
- ALS Association Milton Safenowitz Post-doctoral Fellowship
Ask authors/readers for more resources
Discovering the interaction mechanismand location of RNA-binding proteins (RBPs) on RNA is critical for understanding gene expression regulation. Here, we apply selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) on in vivo transcripts compared to protein-absent transcripts in four human cell lines to identify transcriptome-wide footprints (fSHAPE) on RNA. Structural analyses indicate that fSHAPE precisely detects nucleobases that hydrogen bond with protein. We demonstrate that fSHAPE patterns predict binding sites of known RBPs, such as iron response elements in both known loci and previously unknown loci in CDC34, SLC2A4RG, COASY, and H19. Furthermore, by integrating SHAPE and fSHAPE with crosslinking and immunoprecipitation (eCLIP) of desired RBPs, we interrogate specific RNA-protein complexes, such as histone stem-loop elements and their nucleotides that hydrogen bond with stem-loop-binding proteins. Together, these technologies greatly expand our ability to study and understand specific cellular RNA interactions in RNA-protein complexes.
Authors
I am an author on this paper
Click your name to claim this paper and add it to your profile.
Reviews
Recommended
No Data Available