Nature Genetics
37, 853 - 862 (2005)
Published online: 10 July 2005; | doi:10.1038/ng1598
Chromosome-wide and promoter-specific analyses identify sites of differential DNA methylation in normal and transformed human cellsMichael Weber1, Jonathan J Davies2, David Wittig1, Edward J Oakeley1, Michael Haase3, Wan L Lam2
& Dirk Schübeler11
Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland. 2
British Columbia Cancer Research Center, Vancouver, British Columbia, Canada. 3
Department of Pathology, Dresden University of Technology, Dresden, Germany.
Correspondence should be addressed to Dirk Schübeler dirk@fmi.ch Cytosine methylation is required for mammalian development and is often perturbed in human cancer. To determine how this epigenetic modification is distributed in the genomes of primary and transformed cells, we used an immunocapturing approach followed by DNA microarray analysis to generate methylation profiles of all human chromosomes at 80-kb resolution and for a large set of CpG islands. In primary cells we identified broad genomic regions of differential methylation with higher levels in gene-rich neighborhoods. Female and male cells had indistinguishable profiles for autosomes but differences on the X chromosome. The inactive X chromosome (Xi) was hypermethylated at only a subset of gene-rich regions and, unexpectedly, overall hypomethylated relative to its active counterpart. The chromosomal methylation profile of transformed cells was similar to that of primary cells. Nevertheless, we detected large genomic segments with hypomethylation in the transformed cell residing in gene-poor areas. Furthermore, analysis of 6,000 CpG islands showed that only a small set of promoters was methylated differentially, suggesting that aberrant methylation of CpG island promoters in malignancy might be less frequent than previously hypothesized.
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