A method to analyze allele-specific methylation.

We have developed a method to analyze the methylation patterns of individual alleles of a gene. The target gene must have alleles identifiable by restriction fragment length polymorphism analysis. The method involves separation of the alleles after digestion by restriction enzyme digestion and electrophoresis, followed by recovery from the gel on ion-exchange paper. Methylation analysis can be done on the separate alleles by Southern blot after digestion by methylation-sensitive enzymes. As an example, we studied human c-Ha-ras-1 and showed that the methylation patterns of different alleles are stable and inherited. The method can be applied to the study of inheritance and methylation in genes where alleles can be identified by restriction fragment length polymorphism.