5'-CG-3', 5'-CNG-3', 5'-GC-3' and 5'-GNC-3' site localization in microRNA sequences

Abstract

Aim. Discovery of localization pattern of 5'-CG-3' dinucleotide and 5'-CNG-3' trinucleotide in microRNA (miRNA) sequences. Methods. Bioinformatic and statistic analysis of mature miRNA sequences. Results. One of the highest peaks of 5'-CG-3' dinucleotides concentration is located close to the nucleotide 10 from 5'-end of miRNA. The level of 5'-CG-3' in this peak exceeds more than four times the average genomic frequency of this dinucleotide. Other evolutionary conservative peaks are located around the nucleotides 16 and 21 in miRNA sequence. Peaks of 5'-CNG-3' trinucleotides concentration correspond to the nucleotides 4 and 8. Approximately 50 % of miRNA sequences contain two or more 5'-CG-3' or 5'CNG-3' sites. The distance between these sites amounts mostly to 1 or 3–9 nucleotides. Conclusions. The peaks of 5'-CG-3' and 5'CNG-3' sites concentration are located not only within seed region, but also along the full length of miRNA sequence. Nevertheless, these sites are disposed in the same miRNA molecule mainly within one turn of double helix. Such site localization pattern may be an evidence of participation of the whole miRNA sequence in miRNAdependent DNA methylation