The interaction of miRNA WITH mRNA genes having nucleotide repeats

Eukaryotic genomes contain several types of repetitive sequences like long repeats, satellite DNA and many other sequences of diverse sizes and repetitive levels not yet classified [1].All diseases caused by dynamic mutations, the severity of the clinical manifestations directly proportional to the correlation with the magnitude of the expansion of nucleotide repeats, that is, with the severity of the genetic defect.All triplet repeat disorders show anticipation and a significant correlation between age at onset of the disease and length of the expanded repeat is observed. A large number of human diseases are caused by expansion of repeat sequences typically trinucleotide repeats within the respective disease genes [2]. Despite last decade efforts of researchers in the development of treatments for unstable repeat expansions, triplet repeat diseases are still not curable [3].

The human genome is known to contain thousands of miRNAs. MiRNAs regulate gene expression by binding with mRNAs of many genes. Normally, one miRNA interacts with the mRNA of one gene. However, there are miRNAs that can bind to many mRNAs, and one mRNA can be the target of many miRNAs. This significantly complicates the study of the properties of miRNAs and their diagnostic and medical applications [4]. Unfortunately, at present there is no complete database of genes and miRNAs associated with human having nucleotide repeat diseases. Therefore, the aim of the study was to establish miRNAs associations with candidate genes that can be biomarkers for the diagnosis of these diseases and play a key role in their emergence and development. When calculating the interaction of miRNA with mRNA genes, we proceeded from the assumption that these molecules are present in the cell in equal concentrations, but the real change in the level of gene expression under the influence of miRNA depends not only on the binding energy of miRNA to mRNA, but also on the ratio of their concentrations, which is necessary take into account in experimental verification of the results.

The interaction of miRNAs with mRNAs of genes having nucleotide repeats was studied. Nucleotide sequences of mRNAs of 35 human genes were obtained from Genbank and 2567 miRNAs taken from miRBase. The search for target genes for miRNAs was carried out according to the MirTarget program. The MirTarget program defines the following features of binding: start of the initiation of microRNA binding to mRNA, localization of miRNA binding sites 3’UTR, 5’UTR and CDS, free energy of binding, schemes of nucleotide interactions between miRNA and mRNA [5].

The search of 2567 human miRNAs binding sites in 35 mRNAs of human genes having nucleotide repeats in 3’UTR, 5’UTR and CDS using the MirTarget program has been completed. Based on the results, 356 miRNAs interacted with 35 mRNAs genes having nucleotide repeats. Of these, 110 miRNAs were attached in the 3’UTR, 103 miRNAs in the 5’UTR and 143 miRNAs in the CDS. miRNAs bind with mRNA of genes with ΔG/ΔGm ratios equal to 85 % and more. The mRNAs of PDGFA and LDLRgenes have miR-4258 binding sites. The binding sites, containing CGG repeats are located in 5'UTRs and 3'UTRs. The 3'UTR mRNA of the human GDNF gene has six miR-1281 binding sites containing AGG repeats. The mRNA of EGFR gene has two binding sites for miR-3960 located consecutively in the 5’UTR. The mRNA of ADCYAP1R1 gene binds with 28 miRNAs in 3’UTR, 5’UTR and CDS. The majority of miRNAs binding sites are located in the CDSs of mRNAs of target genes. The miR- 4291 binds with mRNA of CYP4F3 gene in the CDS; binding sites contain CUG repeats, which encode polyleucine. The miR-191-5p binding site is located in the CDS of the TNFRSF18gene and contains CUG trinucleotide repeats. The mRNA of SEMA3Fgene has binding sites for ten miRNAs in 5′UTR, CDS and 3′UTR. The miR-4443 binding sites in 3'UTR mRNA of ADRB2 has 11C nucleotide repeat.

In this study, we have shown that 356 human miRNAs have binding sites on mRNAs of 35 target genes with nucleotide repeats. The features of miRNA binding with mRNA genes with nucleotide repeats were studied.

 

References:

  1. Cardoso I.L, Marques V., “Trinucleotide repeat diseases - anticipation diseases,“ J clin gen genomics. March-2018; 1(1):4-9.
  2. Ling-Bo Li, Nancy M Bonini., “Roles of trinucleotide repeat RNA in neurological disease and degeneration,” Trends Neurosci. 2010 Jun; 33(6):292-8. Doi: 10.1016/j.tins.2010.03.004.
  3. Krzyzosiak W.J, Sobczak K, Wojciechowska M., et al. “Triplet repeat RNA structure and its role as pathogenic agent and therapeutic target,” Nucleic Acids Res 2012; 40:11-26.
  4. Atambayeva Sh.A, Niyazova R.E, Ivashchenko A.T, Pyrkova A.Y, Pinsky I.V, Akimniyazova A.N, Labeit S., “The Binding Sites of miR-619-5p in the mRNAs of Human and Orthologous Genes,” BMC Genomics 2017. 18:428. Doi: 10.1186/s12864-017-3811-6.
  5. Ivashchenko A.T, Pyrkova A.Y, Niyazova R.Y, Alybayeva, A, Baskakov K., “Prediction of miRNA binding sites in mRNA”, Bioinformation 2016; 12:237-240.
Year: 2018
City: Shymkent
Category: Medicine