A high resolution oligonucleotide CpG island microarray

A56 CpG islands are stretches of high GC content DNA containing multiple CpG dinucleotides. When CpG dinucleotides within these islands are methylated, especially in promoter regions, expression of the corresponding downstream genes is often repressed. Aberrant CpG island methylation is implicated in cancer.
 We have developed an oligonucleotide microarray that specifically represents the CpG islands in the human genome. This microarray contains ~230,000 oligo probes tiling the 21 megabases of 27,800 CpG islands, with an average spacing between probes of 95 base pairs. The microarray is designed to be compatible with several published methods for the genome-wide detection of methylated CpG islands. To demonstrate the ability of this microarray to accurately detect methylated DNA, we performed analysis of human genomic DNA samples after methylated DNA immunoprecipitation (mDIP). Additionally, we developed and tested “spike-in” control DNA that was in vitro methylated to varying degrees.
 The mDIP method combined with CpG island microarray analysis accurately differentiated between partially and fully methylated spike-in DNAs. We then applied the whole-genome assay to the prostate cancer cell line PC3, where we detected methylated CpG islands upstream of cancer related genes including CDKN2A/p16. We extended the study to other cancer cell lines and determined relative methylation at multiple cancer related genes. Finally, using male and female embryonic lung fibroblast cell lines, we demonstrate that many CpG islands on the female X chromosome are more methylated than the corresponding islands on the male X chromosome. In comparison, methylation of CpG islands on the autosomes is essentially the same for both the male and female.