Methylation of DNA is the most studied epigenetic modification. Many restriction enzymes are sensitive to the DNA methylation states. Cleavage may be blocked, or impaired, when a particular base in the enzyme's recognition site is modified.
Methylation sensitive restriction enzymes can be used to generate fragments for further epigenetic analysis. When used in conjunction with an isoschizomer that has the same recognition site, but is methylation insensitive, information about methylation status can be obtained. Examples of methylation-sensitive restriction enzymes important in epigenetics include:
- DpnI (NEB #R0176) and DpnII (NEB #R0543) for N6-methyladenine detection within GATC recognition site
- HpaII (NEB #R0171) and MspI (NEB #R0106) for C5-methylcytosine detection within CCGG recognition site