Fully Complementary Interactions of Human mRNA Genes with miRNAs from NCBI Database

Ivashchenko At, Anna Pyrkova, Raigul Niyazova, Saltanat Orazova

2026

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DOI 10.3390/cimb48100976
Data confidence 70 medium
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Abstract

miRNA has been studied for over 30 years, but the interaction of miRNA with mRNA has not been sufficiently studied to date. Problems in this area of research include the lack of adequate methods for predicting the characteristics of miRNA-mRNA interactions, and wet lab experiments are many times more labor-intensive and time-consuming. The aim of this study was to determine the characteristics of fully complementary interactions of miRNAs from the 2568 miRNAs of the NCBI database with mRNAs of 17,508 protein-coding genes using the MirTarget program. It was found that mRNAs from 384 genes have binding sites (BSs) with 89 miRNAs. miR-619-5p has 220 BSs in mRNA from 201 genes. mRNA from 17 genes has two BSs for miR-619-5p and the mRNA of the CACNG8 gene has three BSs. Three mRNAs contained miR-619-5p BSs in the 5′UTR, only one gene had a CDS, and the remaining BSs were in the 3′UTR. miR-5096 binds to the mRNAs of 45 genes, 12 of which also bound miR-619-5p. IL18 mRNA bound two miR-5096s. MiR-1273f targeted 12 genes, miR-1273g-3p targeted nine genes, and miR-1273h-5p targeted four genes. MiR-1548ap-3p, miR-1285ap-5p, and miR-4478 each had four target genes. Several pairs of miRNA-5p and miRNA-3p were bound to mRNAs of the RTL, CCDC42B, FOXF2, GLYCTK, KAA2026, and LPPR3 genes. The highest free energy of interaction was found for miR-4665-3p (−159 kJ/mol), miR-1-356-5p (−146 kJ/mol), and miR-1-155-3p (−138 kJ/mol). miRNAs from the NCBI database can significantly suppress the translation of many mRNAs. The obtained data show reliable links between miRNAs and target genes that can be used to diagnose diseases caused by disturbances in these interactions.