Studies on Relation between DNA Methylation Levels and Sequence Characteristics of Mammalian DNA

Abstract

DNA methylation is an epigenetic modification that occurs at N6 position of Adenine and N4 and C5 positions of Cytosine in prokaryotes while, in higher eukaryotes it occurs at C5 position of Cytosine. DNA methylation is performed by DNA methyltransferases, maintenance methyltransferases Dnmt1 that has preference for hemimethylated CpG sites and de novo methyltransferases Dnmt3a Dnmt3b which do not discriminate between hemimethylated and unmethylated CpG sites. Target CpG sites are known to be differentially methylated in the genome and the phenomenon has been shown to be influenced by the local DNA sequence characteristics. In the present study it has been attempted to investigate effects of sequence composition such as homopolymeric stretches of purines, pyrimidines, poly H, V, D and B on DNA methylation. Recently published bisulphite sequence analysis based methylation data of 297 amplicones of chromosome 21 of 5 human cell types has been used to compare mean methylation levels with above mentioned DNA sequence characteristics.