Londin et al. previously identified a large group of novel microRNAs, here referred to as LmiRNAs; however, their biological functions remain poorly understood. In this study, we investigated fully complementary interactions between LmiRNAs and the mRNAs of human genes using the MirTarget program. Analysis of 3,707 LmiRNAs revealed numerous target genes containing fully complementary LmiRNA binding sites characterized by high interaction free energy values. Binding sites for 75 LmiRNAs were identified in the 5′ untranslated regions (5′UTRs) of target gene mRNAs, whereas 81 target genes contained binding sites within coding sequences (CDSs). Only seven LmiRNAs formed fully complementary interactions within 3′ untranslated regions (3′UTRs). Notably, mRNAs of several genes, including KIFC3, PHF15, RPL15, and SNX11, were identified as capable of binding to LmiRNA-5p and LmiRNA-3p. Most target gene mRNAs interacted with only a single LmiRNA. In addition, the BMP8B, FGFRL1, and SDC3 genes contained binding sites for the LmiRNA pair ID00121.5p and ID02992.5p. These findings expand current understanding of the interaction properties of LmiRNAs and suggest their potential utility as diagnostic and therapeutic biomarkers for human diseases.

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.