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Published on: June 12, 2018
Prediction of miRNA interaction with mRNA of stroke candidate genes
Аida Kondybayeva1, Aigul Akimniyazova2, Saltanat Kamenova1
1Join-Stock Company "National Medical University", Almaty, Kazakhstan, 050012.
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.
Insights
MicroRNAs (miRNAs) and their target genes are crucial in stroke development. This study identified specific miRNA-mRNA interactions and binding site clusters, offering potential biomarkers for stroke diagnosis.
Area of Science:
- Molecular biology
- Genomics
- Biochemistry
Background:
- The role of microRNAs (miRNAs) in stroke pathogenesis is under investigation.
- Identifying specific miRNAs and their target genes in stroke development is crucial but remains unclear.
Purpose of the Study:
- To investigate the interactions between miRNAs and messenger RNAs (mRNAs) of stroke candidate genes.
- To identify potential miRNA biomarkers for stroke diagnosis.
Main Methods:
- Utilized the MirTarget program to define miRNA-mRNA binding features, including binding site location and free energy.
- Analyzed interactions between 6565 miRNAs and mRNAs of stroke candidate genes.
Main Results:
- Determined miRNA-mRNA interactions for 6565 miRNAs and stroke candidate genes.
- Identified specific miRNAs (e.g., miR-619-5p, miR-5095) targeting highly expressed genes through clustered binding sites.
- Observed that miRNA-mRNA associations depend on gene expression levels, with some miRNAs binding to multiple genes.
Conclusions:
- miRNA binding site organization into clusters influences mRNA binding and creates competition among miRNAs.
- The identified miRNA-target gene characteristics can serve as potential diagnostic markers for stroke.
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