Human Molecular Genetics, 2000, Vol. 9, No. 18 2651-2663
© 2000 Oxford University Press
Large-scale methylation analysis of human genomic DNA reveals tissue-specific differences between the methylation profiles of genes and pseudogenes
1Department of Genome Analysis, Institute for Molecular Biotechnology, Beutenbergstrasse 11, D-07745 Jena, Germany, 2Friedrich-Schiller-University, Department of Pathology, Ziegelmühlenweg 1, D-07743 Jena, Germany and 3Department of Biology and Pharmacy, Friedrich-Schiller-University, D-07743 Jena, Germany
Cytosine in CpG dinucleotides is frequently found to be methylated in the DNA of higher eukaryotes and differential methylation has been proposed to be a key element in the organization of gene expression in man. To address this question systematically, we used bisulfite genomic sequencing to study the methylation patterns of three X-linked genes and one autosomal pseudogene in two adult individuals and across nine different tissues. Two of the genes, SLC6A8 and MSSK1, are tissue-specifically expressed. CDM is expressed ubiquitously. The pseudogene, 
SLC6A8, is exclusively expressed in the testis. The promoter regions of the SLC6A8, MSSK1 and CDM genes were found to be essentially unmethylated in all tissues, regardless of their relative expression level. In contrast, the pseudogene SLC6A8 shows high methylation of the CpG islands in all somatic tissues but complete demethylation in testis. Methylation profiles in different tissues are similar in shape but not identical. The data for the two investigated individuals suggest that methylation profiles of individual genes are tissue specific. Taken together, our findings support a model in which the bodies of the genes are predominantly methylated and thus insulated from the interaction with DNA-binding proteins. Only unmethylated promoter regions are accessible for binding and interaction. Based on this model we propose to use DNA methylation studies in conjunction with large-scale sequencing approaches as a tool for the prediction of cis-acting genomic regions, for the identification of cryptic and potentially active CpG islands and for the preliminary distinction of genes and pseudogenes.
+ Present address: Institute for Human Genetics, CNRS UPR 1142, Laboratoire de Séquences Répétées et Centromères Humains, Rue de la Cardonille, 34396 Montpellier, France
§ To whom correspondence should be addressed at: metaGen GmbH, Ihnestrasse 63, D-14195 Berlin-Dahlem, Germany. Tel: +49 30 8413 1673; Fax: +49 30 8413 1674; Email: andrex1x@aol.com
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