Prediction of miRNAs interaction with gastrointestinal tract cancer candidate genes

Abstract

miRNAs play an important role in regulating the expression of prevailing number of genes in the human genome. The vast majority of miRNAs are involved in the development of several diseases. Of the more than six thousand human miRNAs, only miR-619-5p has more than 200 genes with which it interacts fully complementary. These genes include several genes involved in the development of cancer of the gastrointestinal tract, which is a rare property among other miRNAs. It is required to establish the features of miR-619-5p and other miRNAs binding with candidate genes of gastrointestinal tract cancer. The location of miRNA binding sites in mRNA, the free energy of miRNA-mRNA interaction, the miRNA-mRNA nucleotide interaction scheme, and other quantitative characteristics of the miRNA-mRNA interaction were determined using the MirTarget programme. The overwhelming number of miRNAs binding sites, including miR-619-5p, are located in the 3’UTR of CYP2W1, KIAA1456, SLC26A2, SPATA13 and UQCRB genes mRNA. In the mRNA of these genes, in addition to the miR-619-5p binding sites, the binding sites of seven, twenty, nine, five and four miRNAs were detected, respectively. In mRNA of these genes, clusters of miRNAs binding sites from two and three binding sites were identified. The identified miRNAs binding sites are conserved in mRNA of orthologous primates genes, which indicates the evolutionarily early emergence of a link between miRNAs and their target genes. Schemes of interaction between miRNA and mRNA nucleotides show high efficiency in determination the quantitative characteristics of this interaction. The important role of non-canonical nucleotide pairs, which increase the free energy of the interaction between miRNA and mRNA, is shown. The revealed associations of miRNA and CYP2W1, KIAA1456, SLC26A2, SPATA13 and UQCRB target genes allow us to recommend them as markers in the development of methods for the diagnosis of the gastrointestinal tract cancer.