Efficiency of the miRNA–mRNA Interaction Prediction Programs

Abstract

miRNAs play a key role in regulation of gene expression. Nowadays it is known more than 2500 human miRNAs, while a majority of miRNA–mRNA interactions remains unidentified. The recent development of a high-throughput CLASH (crosslinking, ligation and sequencing of hybrids) technique for discerning miRNA–mRNA interactions allowed an experimental analysis of the human miRNA–mRNA interactome. Therefore, it allowed us, for the first time, make an experimental analysis of the human miRNA–mRNA interactome as a whole and an evaluation of the quality of most commonly used miRNA prediction tools (TargetScan, PicTar, PITA, RNA22 and miRanda). To estimate efficiency of the miRNA–mRNA prediction tools, we used next parameters: sensitivity, positive predicted value, predictions in different mRNA regions (3' UTR, CDS, 5' UTR), predictions for different types of interactions (5 classes), predictions of “canonical” and “nocanonical” interactions, similarity with the random generated data. The analysis revealed low efficiency of all prediction programs in comparison with the CLASH data in terms of the all examined parameters.

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Abbreviations

AGO:

argonaute

CDS:

coding DNA sequence

CLASH:

crosslinking, ligation and sequencing of hybrids

CLIP:

UV crosslinking and immunoprecipitation

iCLIP:

individual-nucleotide resolution cross-linking and immunoprecipitation

HEK293:

Human Embryonic Kidney 293 cells

hg19:

human genome version 19

HITS-CLIP:

high-throughput sequencing of RNA isolated by crosslinking immunoprecipitation

miRNA:

microRNA

PAR-CLIP:

photoactivatableribonucleoside-enhanced-immunoprecipitation

PPV:

positive predictive value

RISC:

RNA-induced silencing complex

UTR:

untranslated region

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Correspondence to O. M. Plotnikova.

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Original Russian Text © O.M. Plotnikova, M.Y. Skoblov, 2018, published in Molekulyarnaya Biologiya, 2018, Vol. 52, No. 3, pp. 543–554.

The article was translated by the authors

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Plotnikova, O.M., Skoblov, M.Y. Efficiency of the miRNA–mRNA Interaction Prediction Programs. Mol Biol 52, 467–477 (2018). https://doi.org/10.1134/S0026893318020103

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Keywords

  • miRNA–mRNA interaction
  • miRNA binding sites
  • CLASH
  • prediction program
  • TargetScan
  • PicTar
  • PITA
  • RNA22
  • miRanda