From Genome to Life:

BLAGITKO Nadja

Genomic Technologies, Janssen Research Foundation, Turnhoutseweg 30, B-2340 Beerse, Belgium

title: GENE EXPRESSION PROFILING OF CELLS OVEREXPRESSING DNA METHYLTRANSFERASE 1 (DNMT1)

N. Blagitko, I. Van den Wyngaert, H. Goehlmann, S. Kass Department of Genomic Technologies, Janssen Research Foundation, Beerse, Belgium

In mammals, DNA methylation is essential for transcriptional silencing of genes on the inactive X chromosome, imprinted genes and parasitic DNAs. In many tumors, aberrant methylation of CpG islands in the promoter region of tumor suppressor genes results in their silencing, indicating a role for DNA methylation in tumorigenesis. However, the extent and identity of the methylation-regulated targets is largely unknown. Cell lines have been generated that stably overexpress DNA methyltransferase 1 (DNMT1), an enzyme playing a pivotal role in methylation-mediated gene silencing. Cells were either untreated, or treated with the DNMT1 inhibitor 5-aza-deoxycitidine (5-aza-dC), the histone deacetylase inhibitor trichostatin A (TSA) or with a combination of both. We used high-density oligonucleotide gene expression microarrays to identify downstream targets of DNMT1 and to examine the effects of 5-aza-dC and/or TSA treatment in DNMT1 overexpressing cells. A number of differentially expressed genes have been identified. The greatest differences in gene expression were observed between untreated control and overexpressor cell lines, and between untreated and TSA-treated overexpressor cell lines. Overexpression of DNMT1 induced numerous members of histone H1 and H2 gene families and several other chromatin-relevant genes. Genes that were downregulated upon DNMT1 overexpression included among others extracellular matrix proteins (fibronectin, fibrillin, procollagens, etc.) and a number of cyclin-dependent kinase inhibitors. To understand whether the identified expression changes are a direct consequence of DNA methylation or a secondary effect, we selected a number of deregulated genes for further methylation analysis. Methylation status of promoter CpG islands from six representative genes has been assessed using genomic sequencing of the bisufite treated DNA.