Table 2.

DNA methylation in different genomic compartments in normal and cancer and its consequence.

Compartment	Methylation in normal	Methylation in cancer	Consequence
Promoter CpG island	1–2% methylated, corresponding to X-inactivation, imprinting and germ cell specific expression	Increase methylation of 1–10% of loci	Gene silencing
Non-promoter CpG island	Variably methylated, often tissue specific	Increased methylation	Unknown
non-CpG island promoter	Methylated or unmethylated	Methylated or unmethylated	Associated with expression but may be secondary to transcription programs
Gene body	Methylated in active genes	Poorly studied	May be secondary to transcription programs
Retrotransposons	Mostly methylated	Frequently hypomethylated	Chromosome instability