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Predicting effective microRNA target sites in mammalian mRNAs

Title
Predicting effective microRNA target sites in mammalian mRNAs
Author
남진우
Keywords
GENOME BROWSER DATABASE; BINDING-SITES; ALTERNATIVE POLYADENYLATION; TRANSLATIONAL REPRESSION; WIDE IDENTIFICATION; ANIMAL DEVELOPMENT; PROTEIN-SYNTHESIS; GENE-EXPRESSION; OFF-TARGETS; PAR-CLIP
Issue Date
2015-08
Publisher
ELIFE SCIENCES PUBLICATIONS LTD
Citation
ELIFE, v. 4, NO e05005, Page. 1-38
Abstract
MicroRNA targets are often recognized through pairing between the miRNA seed region and complementary sites within target mRNAs, but not all of these canonical sites are equally effective, and both computational and in vivo UV-crosslinking approaches suggest that many mRNAs are targeted through non-canonical interactions. Here, we show that recently reported non-canonical sites do not mediate repression despite binding the miRNA, which indicates that the vast majority of functional sites are canonical. Accordingly, we developed an improved quantitative model of canonical targeting, using a compendium of experimental datasets that we pre-processed to minimize confounding biases. This model, which considers site type and another 14 features to predict the most effectively targeted mRNAs, performed significantly better than existing models and was as informative as the best high-throughput in vivo crosslinking approaches. It drives the latest version of TargetScan (v7.0; targetscan.org), thereby providing a valuable resource for placing miRNAs into gene-regulatory networks.
URI
https://elifesciences.org/content/4/e05005http://hdl.handle.net/20.500.11754/26925
ISSN
2050-084X
DOI
10.7554/eLife.05005
Appears in Collections:
COLLEGE OF NATURAL SCIENCES[S](자연과학대학) > LIFE SCIENCE(생명과학과) > Articles
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