Differential Methylation Hybridization Using CpG Island Arrays

Differential hybridization and its related techniques have been developed to identify genes whose expressions are altered during different physiological conditions or in dissimilar cell or tissue types (1 –3 ). High-throughput DNA array technologies have further advanced these analyses, providing for simultaneous examinations of expressions of thousands of genes between two different cell types in a single experiment (4 –6 ). Recently, we have adapted the hybridization approach to devise an array-based technique, called differential methylation hybridization (DMH), to identify changes in DNA methylation patterns commonly observed in cancer (7 ). Methylation of DNA is the addition of a methyl group to the 5th carbon position of cytosine that is 5′ to a guanine in GC-rich regions known as CpG islands, which are frequently located in the 5′-end of regulatory regions of genes (8 ,9 ) This epigenetic reaction does not usually change nucleotide sequences nor affect the specificity of DNA base pairing, but it can have inhibitory effects on gene expression (8 ,9 ).