Comparison of NCGN Tetranucleotide Frequencies in Vertebrate and Invertebrate Genomes

Abstract

DNA methylation, a DNA modification which occurs at the N6 position of adenine and the N4 and C5 positions of cytosine in prokaryotes while only C5 methylation is found in higher eukaryotes. It is an epigenetic mechanism which plays critical role in gene silencing, X chromosome inactivation, imprinting and silencing of intragenomic parasites. In mammals DNA cytosines are methylated by DNA methyltransferases in CpG dinucleotide context and the flanking regions of CpG dinucleotides affect the activity of the enzymes. CG methylation results in mutation (CG→TG/CA) which is responsible for CG dinucleotide suppression in vertebrate genome. In this study, we have investigated if flanking base preference of DNA methyltransferases is reflected in frequency distribution of NCGN frequencies of different genomes as a result of mutations of NCGN. We have compared tetranucleotide frequencies in randomly selected representative genomic sequences of different organisms with initial relative velocities of DNA methylation by Dnmt3a.