In silico prediction of human genes as potential targets for rice miRNAs

Aizhan Rakhmetullina; Anna Pyrkova; Dana Aisina; Anatoliy Ivashchenko

doi:10.1016/j.compbiolchem.2020.107305

In silico prediction of human genes as potential targets for rice miRNAs

Comput Biol Chem. 2020 Jun 9:87:107305. doi: 10.1016/j.compbiolchem.2020.107305. Online ahead of print.

Authors

Aizhan Rakhmetullina¹, Anna Pyrkova¹, Dana Aisina¹, Anatoliy Ivashchenko²

Affiliations

¹ Department of Biotechnology, SRI of Biology and Biotechnology Problems, Al-Farabi Kazakh National University, Almaty, Al-Farabi 71, Almaty, 050040, Kazakhstan.
² Department of Biotechnology, SRI of Biology and Biotechnology Problems, Al-Farabi Kazakh National University, Almaty, Al-Farabi 71, Almaty, 050040, Kazakhstan. Electronic address: a.iavashchenko@gmail.com.

PMID: 32570176
DOI: 10.1016/j.compbiolchem.2020.107305

Abstract

Background: Exogenous microRNAs (miRNAs) enter the human body through food, and their effects on metabolic processes can be considerable. It is important to determine which miRNAs from plants affect the expression of human genes and the extent of their influence.

Method: The binding sites of 738Oryza sativa miRNAs (osa-miRNAs) that interact with 17 508 mRNAs of human genes were determined using the MirTarget program.

Result: The characteristics of the binding of 46 single osa-miRNAs to 86 mRNAs of human genes with a value of free energy (ΔG) interaction equal 94%-100% from maximum ΔG were established. The findings showed that osa-miR2102-5p, osa-miR5075-3p, osa-miR2097-5p, osa-miR2919 targeted the largest number of genes at 38, 36, 23, 19 sites, respectively. mRNAs of 86 human genes were identified as targets for 93 osa-miRNAs of all family osa-miRNAs with ΔG values equal 94%-98% from maximum ΔG. Each miRNA of the osa-miR156-5p, osa-miR164-5p, osa-miR168-5p, osa-miR395-3p, osa-miR396-3p, osa-miR396-5p, osa-miR444-3p, osa-miR529-3p, osa-miR1846-3p, osa-miR2907-3p families had binding sites in mRNAs of several human target genes. The binding sites of osa-miRNAs in mRNAs of the target genes for each family of osa-miRNAs were conserved when compared to flanking nucleotide sequences.

Conclusion: Target mRNA human genes of osa-miRNAs are also candidate genes of cancer, cardiovascular and neurodegenerative diseases.

Keywords: Binding site; Gene regulation; Human; Rice; mRNA; miRNA.