Studies on CpG distribution in genomes

Abstract

DNA methylation is an epigenetic modification that plays very important role in vertebrate genomes. In vertebrate genomes, DNA methylation occurs at CpG sites and leads to gene regulation, gene imprinting, X-chromosome inactivation and cancer. DNA methylation has resulted in depletion in CpG sites in vertebrate genome. CpG islands are the clusters of CpGs in regions of high GC content and are usually unmethylated. However all the clusters of CpGs are not CpG islands but seem to affects the DNA methylation levels in vertebrate genomes. The present study has used CpG gap size (number of nucleotides between two adjacent CpG) to investigate the distribution of CpGs in genomes. Mean CpG gap sizes have been observed to be larger in methylated genome while smaller values are associated with poorly and non-methylated genomes. Similarly, dispersion index of CpG gap values also shows higher value for methylated genomes and lower value in poorly or unmethylated genomes indicating relationship between DNA methylation and clustered distribution of CpGs in the genomes. A similar result was obtained when exon, intron and intergenic region of different organisms were studied separately. Further CpG gap analysis were compared against five other related dinucleotides gaps (GpC, TpG, GpT, CpA and ApC) in differently methylated genomes and higher value of mean CG gaps and dispersion index was found in methylated human genome in a pronounced manner.