In vertebrates, genomic DNA is often methylated at the 5th position of cytosine in the sequence of CpG, and this is the only chemical modification that genomic DNA of vertebrates allows under physiological conditions. During evolution, vertebrates acquired CpG methylation as a new tool for controlling gene expression in addition to the varieties of transcription factors. In mammals, the methylation pattern of genomic DNA is erased and reset in germ line and at the early stage of embryogenesis. Maintenance-type methylation activity ensures clonal transmission of the lineage-specific methylation pattern in somatic cells. The methylation pattern is dynamic and changes during cell differentiation. Prior to the expression of tissue-specific genes, specific sites of the promoters are demethylated. In general, the methylation of a gene suppresses its expression. However, not much is known about the mechanisms that regulate the methylation state and the gene expression by DNA methylation.