Interactions of intergenic microRNAs with mRNAs of genes involved in carcinogenesis

Assel Issabekova 1 Olga Berillo 1 Mireille Regnier 2, 3 Anatoly Ivashchenko 1, *
* Corresponding author
2 AMIB - Algorithms and Models for Integrative Biology
LIX - Laboratoire d'informatique de l'École polytechnique [Palaiseau], LRI - Laboratoire de Recherche en Informatique, UP11 - Université Paris-Sud - Paris 11, Inria Saclay - Ile de France
Abstract : miRNAs regulate gene expression by binding with mRNAs of many genes. Studying their effects on genes involved in oncogenesis is important in cancer diagnostics and therapeutics. The RNAHybrid 2.1 program was used to predict the strong miRNA binding sites (p < 0.0005) in target mRNAs. The program Finder 2.2 was created to verify 784 intergenic miRNAs (ig-miRNA) origin. Among 54 considered oncogenes and tumor suppressor genes, 47 genes are the best targets for ig-miRNAs. Accordingly, these genes are strongly regulated by 111 ig-miRNAs. Some miRNAs bind several mRNAs, and some mRNAs have several binding sites for miRNAs. Of the 54 mRNAs, 21.8%, 43.0%, and 35.2% of the miRNA binding sites are present in the 5'UTRs, CDSes, and 3'UTRs, respectively. The average density of the binding sites for miRNAs in the 5'UTR was 4.4 times and 4.1 times greater than in the CDS and the 3'UTR, respectively. Three types of interactions between miRNAs and mRNAs were identified, which differ according to the region of the miRNA bound to the mRNA: 1) binding occurs predominantly via the 3'-region of the miRNA; 2) binding occurs predominantly through the central region of the miRNA; and 3) binding occurs predominantly via the 5'-region of the miRNA. Several miRNAs effectively regulate only one gene, and this information could be useful in molecular medicine to modulate translation of the target mRNA. We recommend described new sites for validation by experimental investigation.
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Submitted on : Friday, September 28, 2012 - 5:35:25 PM
Last modification on : Wednesday, March 27, 2019 - 4:41:29 PM

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Assel Issabekova, Olga Berillo, Mireille Regnier, Anatoly Ivashchenko. Interactions of intergenic microRNAs with mRNAs of genes involved in carcinogenesis. Bioinformation, Biomedical Informatics Publishing Group, 2012, 8 (11), pp.513-518. ⟨10.6026/97320630008513⟩. ⟨hal-00736694⟩



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