DNA methylation profiles of human ECRs.

<p>The bisulfite-converted DNA of human normal tissues (left) and matched pair sets (right) were amplified, and subsequently analyzed with COBRA (Combine Bisulfite Restriction Analysis). The normal DNA was from brain, testis, lung and liver. The matched pair sets of normal (N) and adjacent cancer (C) were from breast and lung. Each PCR product from a given ECR was digested with a restriction enzyme, resulting in a mixture of digested and undigested products. Depending upon each enzyme, the status of digestion indicates either unmethylation (U) or methylation (M) of the particular CpG site, which is part of the recognition site of the enzyme. Digestion by two enzymes, <i>Fok</i>I and <i>Hph</i>I, indicate Unmethylation since these enzymes recognize TG. In contrast, the other remaining enzymes recognize CG, thus indicating Methylation. The ECRs with boxes are the ones showing dramatic changes in their DNA methylation levels in the matched pair sets. DNA methylation levels of these ECRs were estimated through calculating the density of DNA bands with the ImageJ program. Compared to the levels of the normal samples, the observed changes in the cancer samples are indicated with either hypomethylation (green) or hypermethylation (red).