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A structural view of microRNA–target recognition

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 th...

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Autores principales: Leoni, Guido, Tramontano, Anna
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2016
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4872079/
https://www.ncbi.nlm.nih.gov/pubmed/26825463
http://dx.doi.org/10.1093/nar/gkw043
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author Leoni, Guido
Tramontano, Anna
author_facet Leoni, Guido
Tramontano, Anna
author_sort Leoni, Guido
collection PubMed
description 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.
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spelling pubmed-48720792016-05-27 A structural view of microRNA–target recognition Leoni, Guido Tramontano, Anna Nucleic Acids Res Methods Online 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. Oxford University Press 2016-05-19 2016-01-28 /pmc/articles/PMC4872079/ /pubmed/26825463 http://dx.doi.org/10.1093/nar/gkw043 Text en © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research. http://creativecommons.org/licenses/by-nc/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
spellingShingle Methods Online
Leoni, Guido
Tramontano, Anna
A structural view of microRNA–target recognition
title A structural view of microRNA–target recognition
title_full A structural view of microRNA–target recognition
title_fullStr A structural view of microRNA–target recognition
title_full_unstemmed A structural view of microRNA–target recognition
title_short A structural view of microRNA–target recognition
title_sort structural view of microrna–target recognition
topic Methods Online
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4872079/
https://www.ncbi.nlm.nih.gov/pubmed/26825463
http://dx.doi.org/10.1093/nar/gkw043
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