Epigenetic alterations, including DNA methylation, histone modification and RNA mediated gene silencing, are defined as heritable changes in gene function that occur without an alteration of the underlying DNA sequence and which afford a level of transcriptional regulation above and beyond DNA sequence [8]. DNA methylation, which occurs at discrete CpG dinucleotide motifs, is believed to be an important mediator of gene expression; this observation has been most frequently linked to DNA methylation at CpG islands, regions of the genome that contain a high density of CpG sites, often proximal to gene promoter regions. A classical inverse relationship between the extent of DNA methylation at CpG islands and expression levels of the proximal gene product has been most often described [8]. To date the relationship between genetics, DNA methylation and gene expression is one that has been largely and necessarily confined to observations at single loci and transcripts in individual cell systems or tissues. The recent development of genome-scale technologies provides unprecedented opportunities to expand upon these experiments. The integration of genetic, epigenetic and expression data promises to provide general
