title: A structural view of microRNA-target recognition.
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.
authors.affiliation: Department of Physics, Sapienza University, Piazzale Aldo Moro, 5-00184 Rome, Italy.
authors.forename: Guido
authors.initials: G
authors.lastname: Leoni
authors.affiliation: Department of Physics, Sapienza University, Piazzale Aldo Moro, 5-00184 Rome, Italy Istituto Pasteur-Fondazione Cenci Bolognetti, Viale Regina Elena 291, 00161 Rome, Italy Anna.tramontano@uniroma1.it.
authors.forename: Anna
authors.initials: A
authors.lastname: Tramontano
mesh_terms: D060565:Argonaute Proteins / Q000235:genetics* / Q000648:ultrastructure; D001665:Binding Sites / Q000235:genetics; D019295:Computational Biology / Q000379:methods*; D006801:Humans; D035683:MicroRNAs / Q000235:genetics*; D008958:Models, Molecular; D012333:RNA, Messenger / Q000235:genetics*; D016601:RNA-Binding Proteins / Q000378:metabolism* / Q000648:ultrastructure
chemical_list: D060565:Argonaute Proteins; D035683:MicroRNAs; D012333:RNA, Messenger; D016601:RNA-Binding Proteins
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