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A Practical Guide to miRNA Target Prediction

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MicroRNA Target Identification

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1970))

Abstract

MicroRNAs (miRNAs) are small endogenous noncoding RNA molecules that posttranscriptionally regulate gene expression. Since their discovery, a huge number of miRNAs have been identified in a wide range of species. Through binding to the 3′ UTR of mRNA, miRNA can block translation or stimulate degradation of the targeted mRNA, thus affecting nearly all biological processes. Prediction and identification of miRNA target genes is crucial toward understanding the biology of miRNAs. Currently, a number of sophisticated bioinformatics approaches are available to perform effective prediction of miRNA target sites. In this chapter, we present the major features that most algorithms take into account to efficiently predict miRNA target: seed match, free energy, conservation, target site accessibility, and contribution of multiple binding sites. We also give an overview of the frequently used bioinformatics tools for miRNA target prediction. Understanding the basis of these prediction methodologies may help users to better select the appropriate tools and analyze their output.

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Authors and Affiliations

  1. Laboratory of Experimental Pathology, Department of Clinical and Molecular Sciences, Università Politecnica delle Marche, Ancona, Italy

    Luigina Micolucci, Fabiola Olivieri & Antonio Domenico Procopio

  2. Computational Pathology Unit, Department of Clinical and Molecular Sciences, Università Politecnica delle Marche, Ancona, Italy

    Luigina Micolucci

  3. Department of Gynecology and Obstetrics, Johns Hopkins University, School of Medicine, Baltimore, USA

    Md Soriful Islam

  4. Center of Clinical Pathology and Innovative Therapies, Italian National Research Center on Aging (INRCA-IRCCS), Ancona, Italy

    Fabiola Olivieri & Antonio Domenico Procopio

  5. Bioinformatics, Asian University for Women, Chattogram, Bangladesh

    Most Mauluda Akhtar

Authors
  1. Most Mauluda Akhtar
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  2. Luigina Micolucci
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  3. Md Soriful Islam
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  4. Fabiola Olivieri
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  5. Antonio Domenico Procopio
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Editors and Affiliations

  1. Department of Genetics and Genomic Sciences, Mount Sinai School of Medicine, New York, NY, USA

    Alessandro Laganà

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Akhtar, M.M., Micolucci, L., Islam, M.S., Olivieri, F., Procopio, A.D. (2019). A Practical Guide to miRNA Target Prediction. In: Laganà, A. (eds) MicroRNA Target Identification. Methods in Molecular Biology, vol 1970. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-9207-2_1

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  • DOI: https://doi.org/10.1007/978-1-4939-9207-2_1

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-9206-5

  • Online ISBN: 978-1-4939-9207-2

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