Abstract
It is well established that the correct identification of the messenger RNA targeted by a given microRNA (miRNA) is a difficult problem, and that available methods all suffer from low specificity. We hypothesize that the correct identification of the pairing should take into account the effect of the Argonaute protein (AGO), an essential catalyst of the recognition process. Therefore, we developed a strategy named MiREN for building and scoring three-dimensional models of the ternary complex formed by AGO, a miRNA and 22 nt of a target mRNA that putatively interacts with it. We show here that MiREN can be used to assess the likelihood that an RNA molecule is the target of a given miRNA and that this approach is more accurate than other existing methods, usually based on sequence or sequence-related features. Our results also suggest that AGO plays a relevant role in the selection of the miRNA targets. Our method can represent an additional step for refining predictions made by faster but less accurate classical methods for the identification of miRNA targets.
| Original language | English (US) |
|---|---|
| Pages (from-to) | e82-e82 |
| Number of pages | 1 |
| Journal | Nucleic Acids Research |
| Volume | 44 |
| Issue number | 9 |
| DOIs | |
| State | Published - Jan 28 2016 |
| Externally published | Yes |
Bibliographical note
KAUST Repository Item: Exported on 2020-10-01Acknowledged KAUST grant number(s): KUK-I1–012–43
Acknowledgements: Epigenomics Flagship Project—EPIGEN; KAUST [KUK-I1–012–43]; PRIN Project [20108XYHJS]. Funding for open access charge: Epigenomics Flagship Project—EPIGEN.
This publication acknowledges KAUST support, but has no KAUST affiliated authors.