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Prediction of miRNA interaction with mRNA of stroke candidate genes

  • Аida Kondybayeva
  • Aigul Akimniyazova
  • Saltanat Kamenova
  • Gulsum Duchshanova
  • Dana Aisina
  • Alla Goncharova
  • Аnatoliy IvashchenkoEmail author
Original Article
  • 14 Downloads

Abstract

Background

The role of miRNA in tissue affected by stroke is actively studied, but it remains unclear which miRNAs and target genes are involved in the development of stroke.

Methods

The MirTarget program defines the following features of a miRNA binding to a mRNA: the binding start site, the location of the binding site in mRNA, the free energy of a miRNA binding with a mRNA, and the interaction schemes of miRNA and mRNA.

Results

The interaction of 6565 miRNAs with mRNAs of stroke candidate genes was determined. The association of the mRNAs of stroke candidate genes with miRNAs depends on the level of gene expression. Some highly expressed candidate genes are targets of miR-619-5p and miR-5095, which have binding sites located on overlapping mRNA nucleotide sequences (clusters). miR-619-5p and miR-5095 bind to mRNA of 15 genes. Clusters for the binding of miR-1273f,d,e are in mRNAs of highly expressed genes. The start sites of miR-1273d and miR-1273e binding in all clusters are in sequences with one and ten nucleotides, respectively. The clusters of multiple miR-574-5p and ID00470.5p-miR binding sites and the clusters of the miR-466, ID01030.3p-miR, and ID00436.3p-miR binding sites are in mRNAs of some genes expressed at low levels.

Conclusion

The organization of miRNA binding sites into clusters reduces the length of mRNA and creates competition between miRNAs for binding to mRNA of a target gene. The characteristics of miRNA associations with target genes can be used to recommend markers for a diagnosis of stroke.

Keywords

Stroke miRNA mRNA Gene Expression 

Notes

Acknowledgments

We thank Pyrkova A.Yu, Niyazova R., Atambayeva Sh. for the help in the data analysis and interpretation and professor Natan M. Bornstein for advices in the writing of this article.

Funding information

This study was supported by a grant (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

Ethical Approval

Research involving Human Participants and/or Animals was not conducted.

Supplementary material

10072_2019_4158_MOESM1_ESM.pdf (273 kb)
ESM 1 (PDF 272 kb)
10072_2019_4158_MOESM2_ESM.pdf (414 kb)
ESM 2 (PDF 414 kb)

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Copyright information

© Fondazione Società Italiana di Neurologia 2019

Authors and Affiliations

  1. 1.Join-Stock Company “National Medical University”AlmatyKazakhstan
  2. 2.SRI of Biology and Biotechnology Problemsal-Farabi Kazakh National UniversityAlmatyKazakhstan
  3. 3.Join-Stock Company “South Kazakhstan Medical Academy”ShymkentKazakhstan

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