Trimethylation of histone 3 lysine 27 (H3K27me3) is a critical epigenetic mark for the maintenance of gene silencing. Additional accumulation of DNA methylation in target loci is thought to cooperatively support this epigenetic silencing during tumorigenesis. However, molecular mechanisms underlying the complex interplay between the two marks remain to be explored. Here we show that activation of PI3K/AKT signaling can be a trigger of this epigenetic processing at many downstream target genes. We also find that DNA methylation can be acquired at the same loci in cancer cells, thereby reinforcing permanent repression in those losing the H3K27me3 mark. Because of a link between PI3K/AKT signaling and epigenetic alterations, we conducted epigenetic therapies in conjunction with the signaling-targeted treatment. These combined treatments synergistically relieve gene silencing and suppress cancer cell growth in vitro and in xenografts. The new finding has important implications for improving targeted cancer therapies in the future. Cancer Res; 71(5);

Metastable and somatically heritable patterns of DNA methylation provide an important level of genomic regulation. In this article, we review methods for analyzing these genome-wide epigenetic patterns and offer a perspective on the ever-expanding literature, which we hope will be useful for investigators who are new to this area. The historical aspects that we cover will be helpful in interpreting this literature and we hope that our discussion of the newest analytical methods will stimulate future progress. We emphasize that no single approach can provide a complete view of the overall methylome, and that combinations of several modalities applied to the same sample set will give the clearest picture. Given the unexpected epigenomic patterns and new biological principles, as well as new disease markers, that have been uncovered in recent studies, it is likely that important discoveries will continue to be made using genome-wide DNA methylation profiling.Keywords bisulfite sequencing; CpG island; differential methylation hybridization; DNA methylation; methylation profiling; methylated CpG island recovery assay; methylated DNA immunoprecipitation; methylation-sensitive SNP chip analysis; next-generation DNA sequencing In 1942, Waddington defined epigenetics as the development of phenotypes from genotypes [1]. Since then, the term has taken on a specific molecular meaning, mostly referring to the patterning of DNA methylation and histone modifications in chromosomes. Epigenetic patterns are largely maintained during somatic cell proliferation, and are important in diverse physiological and pathophysiological phenomena. Among the various types of epigenetic modifications of the genome, DNA methylation is certainly one of the most stable. Methylation of DNA in mammalian cells is generally restricted to the 5 position of the pyrimidine ring of cytosine residues located in CpG dinucleotides (5-methylcytosine [5-mC]). In mammalian genomes, CpG dinucleotides are somewhat depleted on average, but are found densely clustered within sequences known as CpG islands (CGIs). These CGIs are typically in the range of 0.5-2 kb in size and located within 1 kb of transcription start sites. Under normal Financial & competing interests disclosureThe authors have no relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript. This includes employment, consultancies, honoraria, stock ownership or options, expert testimony, grants or patents received or pending, or royalties. No writing assistance was utilized in the production of this manuscript NIH Public Access Author ManuscriptEpigenomics. Author manuscript; available in PMC 2010 October 1. [6,7]). As shown in experiments with knockout mice, each of these enzymes is essential for viability of the conceptus to term. Once established, the faithful transmission of methylation patterns to daughter cells is thought to be primarily due to DNMT1...