Search for binding sites for micro RNA in cis-regulatory sequences and in SNP in the lipid, carbohydrate metabolism, oxidative and anti-inflammatory homeostasis genes
Background: Polymorphisms and disruption of the expression profile of miRNA genes are associated with systemic diseases (autoimmune and cardiovascular diseases). The aim of the study: To study the localization of miRNA binding sites to mRNA in cis-regulatory regions of genes and in the coding sequences of DNA (CDS) associated in our studies with early and late atherosclerosis, and to search for possible localization of binding sites to microRNAs with gene sites (PPARGC1A; LIPC; PON1; APOE; LPL; APOC3; EDN; TNFα; SERPINE1). Materials and methods: The search for homologous micro RNA motifs was carried out in the cis-regulatory regions of the studied genes with the help of the bio-information package MEME Suite. Known miRNAs were taken from the miRBase database (http://mirbase.org/). Nucleotide sequences of cis-regulatory regions and gene introns were obtained from the NCBI database (http://www.ncbi.nlm.nih.gov/) using a set of scripts, IFITCH, designed to automatically retrieve data from NCBI sequences. The "miRBase" database was analyzed using automated search for binding sites in the original sequence using the MScanner classifier. 28645 microRNAs were registered (http://www.mirbase.org). Results: The results of the bioinformational search for the localization of motifs homologous to known microRNAs before and after the gene, as well as in the coding protein sequences and introns of the following genes: PON1, APOC3, LIPC, LPL, APOE, PPARGC1A, TNF, EDN, SERPIN showed that in genes and intergenic spaces there are a large number of motifs homologous to mature micro-RNA. The greatest absolute number of motifs is localized within the PPARGC1A gene – 22 microRNAs. However, if we consider the relative frequency of microRNA localization calculated for 100,000 bp, then the largest number of microRNAs is localized in the PON1 gene and is 7.6 × 10-5. While for the PPARGS1 gene the frequency is 3.2 × 10-5. Conclusion: Thus, the microRNAs we detected localized in large numbers inside and near the studied genes, may indicate their functional role in the pathogenesis of atherosclerosis.