Studies on the Effect of Flanking bases on the Distribution of CGs in Methylated Genomes

Abstract

DNA methylation is an epigenetic modification that plays very important role in vertebrate genomes as it is involved in number of important events that include gene regulation, gene imprinting, X-chromosome inactivation and even in diseases like cancer. In vertebrate genomes DNA methylation occurs at CG sites in both the strands of DNA. In the present studies the effect of flanking bases on the distribution of CG dinucleotides in the methylated as well as non methylated genomes is studied. In order to analyse the effect of flanking bases i.e. flanking sequence preference on the distribution of CG dinucleotides so as to understand the effect on rate of methylation we have designed various permutation sets ranging from a simple sets of NCG, CGN, NCGN, NCGNN, NNCGN, NNCG, CGNN, to complex ones i.e. NNCGNN, NNNCGNNN and NNNNCGNNNN. The consensuses sequences are derived based on NNNNCGNNNN (65536 permutations). Results of consensus sequences derived from high methylation group and low methylation group agrees with YCGR and RCGY observations repectively. There is appreciable overlap observed between the frequency based consensus sequences and those obtained by physiological data based on methylation levels which is very exhilarating.