Methylation-sensitive genome scanning

Imprinted genes in mammals are expressed exclusively from one of the parental alleles (1-6). This is regulated by parental-allele-specific CpG methylation. For example, H19 is methylated exclusively on the paternal allele, which is repressed, and is expressed exclusively from the maternal allele, which is unmethylated. Therefore, one way to find imprinted genes is searching for parental-allele-specific CpG methylation. Southern analysis using methylation-sensitive restriction enzymes could be used for such a purpose. However, usually only one gene can be analyzed by one Southern analysis. Moreover, Southern analysis requires one DNA probe for each analysis. These facts indicate at least 300 Southern analyses using 300 different probes are required to find only one imprinted gene, because the population of imprinted genes is estimated to be 0.3%. Therefore, this kind of analysis is not appropriate for searching for new imprinted genes, and the development of a new method that can simultaneously analyze thousands of genes was required.