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Computational Prediction of Functional MicroRNA–mRNA Interactions

  • Müşerref Duygu Saçar Demirci
  • Malik Yousef
  • Jens AllmerEmail author
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1912)

Abstract

Proteins have a strong influence on the phenotype and their aberrant expression leads to diseases. MicroRNAs (miRNAs) are short RNA sequences which posttranscriptionally regulate protein expression. This regulation is driven by miRNAs acting as recognition sequences for their target mRNAs within a larger regulatory machinery. A miRNA can have many target mRNAs and an mRNA can be targeted by many miRNAs which makes it difficult to experimentally discover all miRNA–mRNA interactions. Therefore, computational methods have been developed for miRNA detection and miRNA target prediction. An abundance of available computational tools makes selection difficult. Additionally, interactions are not currently the focus of investigation although they more accurately define the regulation than pre-miRNA detection or target prediction could perform alone. We define an interaction including the miRNA source and the mRNA target. We present computational methods allowing the investigation of these interactions as well as how they can be used to extend regulatory pathways. Finally, we present a list of points that should be taken into account when investigating miRNA–mRNA interactions. In the future, this may lead to better understanding of functional interactions which may pave the way for disease marker discovery and design of miRNA-based drugs.

Key words

MicroRNA Target Regulation Posttranscriptional regulation Pathway extension MiRNA–mRNA interaction 

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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  • Müşerref Duygu Saçar Demirci
    • 1
  • Malik Yousef
    • 2
  • Jens Allmer
    • 3
    Email author
  1. 1.Faculty of Life and Natural Sciences, Department of BioinformaticsAbdullah Gul UniversityKayseriTurkey
  2. 2.Department of Community Information SystemsZefat Academic CollegeZefatIsrael
  3. 3.Applied Bioinformatics, BioscienceWageningen University & ResearchWageningenThe Netherlands

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