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Quantifying the strength of miRNA-target interactions

Breda, Jeremie and Rzepiela, Andrzej J. and Gumienny, Rafal and van Nimwegen, Erik and Zavolan, Mihaela. (2015) Quantifying the strength of miRNA-target interactions. Methods, Vol. 85. S. 90-9.

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Official URL: http://edoc.unibas.ch/dok/A6428724

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Abstract

We quantify the strength of miRNA-target interactions with MIRZA, a recently introduced biophysical model. We show that computationally predicted energies of interaction correlate strongly with the energies of interaction estimated from biochemical measurements of Michaelis-Menten constants. We further show that the accuracy of the MIRZA model can be improved taking into account recently emerged experimental data types. In particular, we use chimeric miRNA-mRNA sequences to infer a MIRZA-CHIMERA model and we provide a framework for inferring a similar model from measurements of rate constants of miRNA-mRNA interaction in the context of Argonaute proteins. Finally, based on a simple model of miRNA-based regulation, we discuss the importance of interaction energy and its variability between targets for the modulation of miRNA target expression in vivo.
Faculties and Departments:05 Faculty of Science > Departement Biozentrum > Computational & Systems Biology > Bioinformatics (van Nimwegen)
UniBasel Contributors:van Nimwegen, Erik and Breda, Jeremie and Rzepiela, Andrzej and Gumienny, Rafal Wojciech and Zavolan, Mihaela
Item Type:Article, refereed
Bibsysno:Link to catalogue
Publisher:Academic Press
ISSN:1046-2023
Note:Publication type according to Uni Basel Research Database: Journal article
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Last Modified:02 Oct 2015 10:01
Deposited On:02 Oct 2015 10:01

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