Effect of CpG methylation on Msp I.

The restriction enzyme Msp I is inhibited by the presence of a methyl moiety at the external cytosine of the sequence CCGG, but is generally unaffected by methylation at the internal cytosine. At specific subsets of this sequence such as the hexanucleotide CCGGCC, however, methylation of the internal cytosine strongly inhibits Msp I digestion, leading to artifacts in the interpretation of DNA methylation analyses. Our results show, for instance, that the CCGG site at the 5' end of the human gamma globin gene, which was thought to be methylated at both the internal and external cytosines, is actually methylated only at the internal CpG residue.