One of the great paradoxes in cellular differentiation is how cells with identical DNA sequences differentiate into so many different cell types. The mechanisms underlying this process involve epigenetic regulation mediated by alterations in DNA methylation, histone posttranslational modifications, and nucleosome remodeling. It is becoming increasingly clear that disruption of the "epigenome" as a result of alterations in epigenetic regulators is a fundamental mechanism in cancer. This has major implications for the future of both molecular diagnostics as well as cancer chemotherapy. Epigenetics is a rapidly evolving field focused on explaining how heritable changes in gene expression occur that do not involve changes in nucleotide sequence.1 Epigenetic regulation of transcription can be mediated through DNA methylation, histone modifications including histone acetylation, phosphorylation, methylation, ubiquitination, and proteolysis, and alterations in chromatin remodeling. Importantly, increasing evidence shows that epigenetic deregulation is a common mechanism in cancer. The role of DNA methylation in cancer has been extensively studied, and a number of excellent reviews have been published on this topic.2-4 More recently, it has become clear that histone modifications, as well as disruption of chromatin remodeling machinery, play a fundamental role in cancer, and this is our primary focus in this review. It is important to recognize that these three types of epigenetic regulation are highly interdependent. For example, patterns of histone methylation are important for establishing patterns of DNA methylation. Chromatin remodeling, in turn, is programmed in part by changes in DNA methylation and histone modifications.
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DNA MethylationCpG-rich sequences are generally rare in the mammalian genome except for in so-called CpG islands, which are associated with centromeres, microsatellite sequences, and the proximal promoter regions of approximately half of all genes. CpG-containing sequences are cytosine methylated by a family of DNA methyltransferases or DNMTs (to date, unequivocal evidence for DNA demethylases is lacking). These methyltransferases generally exempt promoter-associated CpG islands, where Ͻ20% are CpG methylated.