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Molecular Biology

, Volume 53, Issue 4, pp 612–623 | Cite as

The Interaction of miRNA-5p and miRNA-3p with the mRNAs of Orthologous Genes

  • O. Yu. Yurikova
  • D. E. Aisina
  • R. E. Niyazova
  • Sh. A. Atambayeva
  • S. Labeit
  • A. T. IvashchenkoEmail author
BIOINFORMATICS

Abstract

miRNAs regulate the expression of many genes and are involved in the development of diseases. We studied miRNAs that interact partly or fully complementarily with the 5'UTR, CDS and 3'UTR of mRNAs of target genes. The MirTarget program used in this study allows for the discovery of miRNA binding sites (BS) in the entire nucleotide sequence of the mRNA and for determining the characteristics of the interactions of miRNAs with mRNAs. We identified five pairs of fully complementary BS for miR-127-5p and miR-127-3p, miR-136-5p and miR-136-3p, miR-431-5p and miR-431-3p, miR-432-5p and miR-432-3p, and miR-433-5p and miR-433-3p in the CDS of the human and animal mRNA of RTL1 gene. The fully complementary BS for miR-6720-5p, miR-6720-3p were identified in the CDS of the FOXF2 gene; BS for miR-3187-5p, miR-3187-3p were found in the CDS of the PLPPR3 gene; BS for miR-4665-5p, miR-4665-3p were found in the 5′UTR of the KIAA2026 gene; BS for miR-135a-5p, miR-135a-3p were found in the 3′UTR of the GLYCTK gene; BS for miR-7106-5p, miR-7106-3p were found in the 3′UTR of the CCDC42B gene. The miRNA-5p and miRNA-3p associated with the RTL1 gene have BS in the mRNAs of 32 target human genes. The miRNA-5p and miRNA-3p associated with the FOXF2, PLPPR3, KIAA2026, GLYCTK and CCDC42B genes have BS in the mRNAs of 27 target genes, involved in development of several diseases. Nucleotide sequences of miRNA-5p and miRNA-3p and BS are conserved over tens of millions of years of divergence of the studied animal species. Binding characteristics of miR-3120-3p and miR-3120-5p, miR-196b-3p and miR-196b-5p, miR-125a-3p and miR-125a-3p, let-7e-3p and let-7e-5p, miR-99b-3p in fully complementary BS of non-coding DMN3OS, HOXA10-AS, SPACA6P-AS genes have been established.

Keywords:

miRNA mRNA binding site nucleotides interaction bioinformatics orthologous gene 

Notes

ACKNOWLEDGMENTS

We are grateful to the students A. Akimniyazova and D. Bayzhigitova for their help in the collection of data.

FUNDING

This study was supported by a grant no. AP05132460 from the Ministry of Education and Science, Kazakhstan Republic, SRI of Biology and Biotechnology Problems, al-Farabi Kazakh National University.

COMPLIANCE WITH ETHICAL STANDARDS

Conflict of interest. The authors declare that they have no conflict of interest.

Statement of the welfare of animals. This article does not contain any studies involving animals or human participants performed by any of the authors.

AUTHORS’ CONTRIBUTIONS

Ivashchenko Anatoly and Siegfried Labeit conceived of the study, drafted the manuscript and gave final approval of the version to be published.

Raigul Niyazova and Shara Atambayeva conceived of the study and drafted the manuscript.

Oxana Yurikova obtained the data according to the RTL1 gene for analysis, editing of the manuscript.

Dana Aisina obtained the data according to the FOXF2, PLPPR3, KIAA2026, GLYCTK and CCDC42B genes for analysis, editing of the manuscript.

A. Ivashchenko, R. Niyazova, S. Atambayeva, O. Yurikova, D. Aisina made substantial contributions to acquisition of data, to interpretation and modification of the data.

All authors were involved in subsequent rounds of revisions, and read and approved the final manuscript.

Supplementary material

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Copyright information

© Pleiades Publishing, Inc. 2019

Authors and Affiliations

  • O. Yu. Yurikova
    • 1
  • D. E. Aisina
    • 1
  • R. E. Niyazova
    • 1
  • Sh. A. Atambayeva
    • 1
  • S. Labeit
    • 2
  • A. T. Ivashchenko
    • 1
    Email author
  1. 1.Scientific Research Institute of Biology and Biotechnology Problems, al-Farabi Kazakh National UniversityAlmatyKazakhstan
  2. 2.Institute for Anaesthesiology and Intensive Operative Care Medical Faculty MannheimMannheimGermany

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