Aberrant DNA methylation at CpG dinucleotide islands, the major epigenetic modification of mammalian genomes, is frequent during tumor progression. For example, inactivation by DNA methylation is the cause for down-regulation of tumor suppressors, apoptotic factors, DNA repair enzymes, and adhesion molecules involved in malignant progression to melanoma and other cancers. In addition, a panel of melanoma antigens, known as cancer/testis-antigens is aberrantly re-expressed due to DNA demethylation of CpG promoter islands. In this project normal human melanocytes and primary melanoma cells will be employed to assess changes in CpG methylation patterns and the genes they affect in a high throughput manner. This will be accomplished by probing promoter chip arrays and genomic tiling arrays employing modified DNA and ChIP on chip procedures. The information will be used to assess CpG island methylation as a marker for tumor progression of early melanocytic lesion.
The specific aims are:
Aim 1 : To establish a procedure to probe promoter chip and chromosome tiling arrays for analysis of the methylation status of CpG rich islands on a genome-wide basis, determine the methylation status of CpG island regions in normal melanocytes versus primary melanoma cells.
Aim 2 : To employ chromatin immunoprecipitation procedure to identify binding regions of methyl-CpG-binding domain proteins (MBP) in the promoter region of these genes (Chip/chip).
Aim 3 : To validate the results of these two procedures by the bisulfite DNA modification method combined with sequencing of specific DNA regions and gene expression analysis. The information derived from these experiments will reveal the identity of a large fraction of genes whose expression is modulated by CpG island methylation/demethylation events and the extent of changes in CpG island methylation in the early progression of melanocytes to melanomas. The data will then be used to design a simpler and cheaper CpG island microarray chip that can be sed to probe the status of DNA methylation in melanocytic lesions as markers for malignancy.
| Cheng, Elaine; Trombetta, Sergio E; Kovacs, Daniela et al. (2006) Rab33A: characterization, expression, and suppression by epigenetic modification. J Invest Dermatol 126:2257-71 |
| Liu, Meng-Min; Weissman, Sherman M; Tang, Ling (2006) Identification of coding single nucleotide polymorphisms and mutations by combination of genome tiling arrays and enrichment/depletion of mismatch cDNAs. Anal Biochem 356:117-24 |
