Females contain two copies of the X chromosome. Silencing one of these two copies is essential for normal development. Methylation of the DNA is the mechanism by which the second X chromosome is silenced. The normally nonmethylated “CpG islands” become methylated as part of this silencing process.

A similar strategy is utilized to silence one of two copies of genes other than those on the X chromosome. In these cases the inactivated (or imprinted) gene that is inactivated by methylation can be of either maternal or paternal origin. Loss of normal imprinting as a result of decreased methylation contributes to a number of inherited diseases including Beckwith-Wiedemann, Prader-Willi and Angelman syndromes, among others.