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Nucleic Acids Research 2005 33(8):e73; doi:10.1093/nar/gni072
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Published online 28 April 2005

© The Author 2005. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions{at}oupjournals.org

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Array-based analysis of genomic DNA methylation patterns of the tumour suppressor gene p16INK4A promoter in colon carcinoma cell lines

Cora Mund, Verena Beier1,*, Peter Bewerunge2, Michael Dahms3, Frank Lyko and Jörg D. Hoheisel1

Division of Epigenetics, Deutsches Krebsforschungszentrum Im Neuenheimer Feld 580, 69120 Heidelberg, Germany 1Division of Functional Genome Analysis, Deutsches Krebsforschungszentrum Im Neuenheimer Feld 580, 69120 Heidelberg, Germany 2Division of Intelligent Bioinformatics Systems, Deutsches Krebsforschungszentrum Im Neuenheimer Feld 580, 69120 Heidelberg, Germany 3febit AG Käfertaler Strasse 190, 68167 Mannheim, Germany

*To whom correspondence should be addressed. Tel: +49 6221 42 4882; Fax: +49 6221 42 4687; Email: v.beier{at}dkfz.de

Received December 28, 2004. Revised April 1, 2005. Accepted April 1, 2005.

Aberrant DNA methylation at CpG dinucleotides can result in epigenetic silencing of tumour suppressor genes and represents one of the earliest events in tumourigenesis. To date, however, high-throughput tools that are capable of surveying the methylation status of multiple gene promoters have been restricted to a limited number of cytosines. Here, we present an oligonucleotide microarray that permits the parallel analysis of the methylation status of individual cytosines, thus combining high throughput and high resolution. The approach was used to study the CpG island in the promoter region of the tumour suppressor gene p16INK4A. In total, 876 oligonucleotide probes of 21 nt in length were used to inspect the methylation status of 53 CpG dinucleotides, producing correct signals in colorectal cancer cell lines as well as control samples with a defined methylation status. The information was validated by established alternative methods. The overall methylation pattern was consistent for each cell line, while different between them. At the level of individual cytosines, however, significant variations between individual cells of the same type were found, but also consistencies across the panel of cancer cell lines were observed.

The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors


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