Figure 7.

Examples of applications using a CpG island microarray. (A) Hybridization of the unmethylated fraction of placenta DNA and post mortem brain DNA to a CpG island array. Two pools of CpG island elements could be identified, which display extensively different methylation levels between these tissues (Note: some of the identified differences could be due to DNA sequence variation). (B) To validate the identified methylation differences, several CpG islands were subjected to bisulfite modification based mapping of methylated cytosines as exemplified for CpG island clones 22_B_12 (promoter region of Galectin-1) and 52_C_03 (promoter region of a brain-specific transcript, CR606704). The top sequence shows the reverse strand (−) of the original restriction sites, the bottom sequence displays the bisulfite-modified DNA. For each bisulfite-modified CpG-island, 8–10 clones were sequenced per tissue. Sequence 52_C_03 revealed several fully methylated CpG's in placenta, which were unmethylated in brain. In contrast, clone 22_B_12 showed subtler methylation differences (15–100%), depending on the position of CpG-dinucleotide. (C) Methylation patterns of clones 22B_12 and 52_C_03 derived from bisulfite sequencing of 10–12 clones per tissue. The yellow boxes indicate CpG dinucleotides that are shown in the sequenced graph (Figure 7B).