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. 2019 Nov 13:7:e8049.
doi: 10.7717/peerj.8049. eCollection 2019.

Prediction of clusters of miRNA binding sites in mRNA candidate genes of breast cancer subtypes

Dana Aisina #  1 , Raigul Niyazova  1 , Shara Atambayeva  1 , Anatoliy Ivashchenko #  1
Affiliations

Prediction of clusters of miRNA binding sites in mRNA candidate genes of breast cancer subtypes

Dana Aisina et al. PeerJ. .

Abstract

The development of breast cancer (BC) subtypes is controlled by distinct sets of candidate genes, and the expression of these genes is regulated by the binding of their mRNAs with miRNAs. Predicting miRNA associations and target genes is thus essential when studying breast cancer. The MirTarget program identifies the initiation of miRNA binding to mRNA, the localization of miRNA binding sites in mRNA regions, and the free energy from the binding of all miRNA nucleotides with mRNA. Candidate gene mRNAs have clusters (miRNA binding sites with overlapping nucleotide sequences). mRNAs of EPOR, MAZ and NISCH candidate genes of the HER2 subtype have clusters, and there are four clusters in mRNAs of MAZ, BRCA2 and CDK6 genes. Candidate genes of the triple-negative subtype are targets for multiple miRNAs. There are 11 sites in CBL mRNA, five sites in MMP2 mRNA, and RAB5A mRNA contains two clusters in each of the three sites. In SFN mRNA, there are two clusters in three sites, and one cluster in 21 sites. Candidate genes of luminal A and B subtypes are targets for miRNAs: there are 21 sites in FOXA1 mRNA and 15 sites in HMGA2 mRNA. There are clusters of five sites in mRNAs of ITGB1 and SOX4 genes. Clusters of eight sites and 10 sites are identified in mRNAs of SMAD3 and TGFB1 genes, respectively. Organizing miRNA binding sites into clusters reduces the proportion of nucleotide binding sites in mRNAs. This overlapping of miRNA binding sites creates a competition among miRNAs for a binding site. From 6,272 miRNAs studied, only 29 miRNAs from miRBase and 88 novel miRNAs had binding sites in clusters of target gene mRNA in breast cancer. We propose using associations of miRNAs and their target genes as markers in breast cancer subtype diagnosis.

Keywords: Binding site; Breast cancer; Cluster; Gene; miRNA.

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Conflict of interest statement

There are no competing interests.

Figures

Figure 1
Figure 1. Location of nucleotide sequences of miRNA binding sites cluster in mRNA CBL gene.
Figure 2
Figure 2. Schemes of interactions of miRNAs with mRNA of CBL gene in cluster of binding sites.
miRNA; the miRNA region; start of binding site (nt); the free energy, ΔG (kJ/mole); the ΔG/ΔGm (%); length of miRNA (nt). The upper and lower nucleotide sequences of mRNA and miRNA, respectively. The nucleotides of non-canonical pairs G–U and A–C highlighted in bold type.
Figure 3
Figure 3. Logo plots of variation of amino acids in the region of orthologous MAZ proteins.
Orthologous MAZ proteins containing: APAPPPTPQA oligopeptide (A), AAAAAAAAAAAAAVAAAPPAPAAA oligopeptide (B), APPASAAT oligopeptide (C), and GAGGGGGEAG oligopeptide (D) of Hsa, Pab, Ptr, Csa. Conservative oligopeptides are highlighted in blue.
See this image and copyright information in PMC

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