DNA methylation is the modification of DNA molecule, transferring methy group to the 5th position of the cytosine pyrimidine ring. This biochemical process plays a crucial role in many cellular processes of higher organisms. For example, people have found distinct patterns of DNA methylation during cellular differentiation and tissue development. The differential DNA methylation profiles are often associated with gene expression. In addition, DNA methylation reveals genomic imprinting and affects on chromatin remodeling and cellular homeostasis. Such epigenetic modification has also been proven to be involved in nearly all cancer-related signaling pathways. However, the mechanism and process against how DNA methylation regulates gene expression are still not clear. The study of DNA methylation and its regulation on gene expression provides fundamental and new insights into the genetic heritability.