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Chromosome-wide and promoter-specific analyses identify sites of differential DNA methylation in normal and transformed human cells

Abstract

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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Figure 1: Methylation analysis by DNA immunoprecipitation (MeDIP).
Figure 2: Chromosomal profile of DNA methylation using a tiled whole human genome BAC array.
Figure 3: Methylated cytosines are more abundant in gene-rich regions.
Figure 4: Chromosomal profiles of DNA methylation in colon cancer cells.
Figure 5: CpG island methylation profile in colon cancer cells versus primary fibroblasts and normal colon mucosa.
Figure 6: New targets for aberrant methylation in colon cancer.

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Acknowledgements

We thank members of the laboratory of D.S. and W.L.L., C. Alvarez, C. MacAuly and U. Platzbecker for advice; C. Wirbelauer for technical assistance; P. Svoboda for advice on bisulfite genomic sequencing; A. Peters, M. Groudine, M. Lorincz and C. Brown for comments on the manuscript; T. Forné for sharing genomic DNA from hybrid mice; S. Der for access to CpG island sequence reads; B. van Steensel for help in gene annotation; and M. Rebhan for assistance in data analysis. This work was supported by funds from the Novartis Research foundation to D.S.; the Canadian Institute for Health Research, National Institute of Dental Cranial Research, and Genome Canada/British Columbia to W.L.L.; and National Sciences and Engineering Research Council of Canada and Michael Smith Foundation for Health Research Scholarships to J.J.D.

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Correspondence to Dirk Schübeler.

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Supplementary information

Supplementary Fig. 1

Profile of DNA methylation for the human genome. (PDF 264 kb)

Supplementary Fig. 2

Differences in methylation levels between male and female fibroblasts. (PDF 46 kb)

Supplementary Fig. 3

Genomic features of methylated DNA on the level of chromosomes and individual BAC probes. (PDF 119 kb)

Supplementary Fig. 4

Profile of DNA methylation in SW48 colon cancer cells. (PDF 246 kb)

Supplementary Table 1

Primer sequences. (PDF 12 kb)

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Weber, M., Davies, J., Wittig, D. et al. Chromosome-wide and promoter-specific analyses identify sites of differential DNA methylation in normal and transformed human cells. Nat Genet 37, 853–862 (2005). https://doi.org/10.1038/ng1598

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