DNA methylation is known to be abnormal in all forms of cancer, but it is not really understood how this occurs and what is its role in tumorigenesis. In this review, we take a wide view of this problem by analyzing the strategies involved in setting up normal DNA methylation patterns and understanding how this stable epigenetic mark works to prevent gene activation during development. Aberrant DNA methylation in cancer can be generated either prior to or following cell transformation through mutations. Increasing evidence suggests, however, that most methylation changes are generated in a programmed manner and occur in a subpopulation of tissue cells during normal aging, probably predisposing them for tumorigenesis. It is likely that this methylation contributes to the tumor state by inhibiting the plasticity of cell differentiation processes. Cancer Res; 76(12); 3446-50. Ó2016 AACR.

Following erasure in the blastocyst, the entire genome undergoes de novo methylation at the time of implantation, with CpG islands being protected from this process. This bimodal pattern is then preserved throughout development and the lifetime of the organism. Using mouse embryonic stem cells as a model system, we demonstrate that the binding of an RNA polymerase complex on DNA before de novo methylation is predictive of it being protected from this modification, and tethering experiments demonstrate that the presence of this complex is, in fact, sufficient to prevent methylation at these sites. This protection is most likely mediated by the recruitment of enzyme complexes that methylate histone H3K4 over a local region and, in this way, prevent access to the de novo methylation complex. The topological pattern of H3K4me3 that is formed while the DNA is as yet unmethylated provides a strikingly accurate template for modeling the genomewide basal methylation pattern of the organism. These results have far-reaching consequences for understanding the relationship between RNA transcription and DNA methylation. development | epigenetics | inheritance | histomodification I n animals, the genome-wide DNA methylation pattern is initially erased in the early embryo and then reestablished in each individual at about the time of implantation. This is carried out by a process in which almost all of the DNA is subject to de novo methylation while CpG island-like regions are protected on the basis of underlying sequence motifs (1), but the biological logic and molecular mechanism of this process are still unknown. Analysis of these CpG-rich sites indicates that they are highly enriched for transcription start sites and characterized by the presence of binding motifs for many transcription factors (2). This close correlation suggested the possibility that protection from de novo methylation may actually be dictated by the binding of transcription complexes at recognized sites in the preimplantation embryo. In this work, we have used bioinformatic tools as well as genetic techniques to test this idea. The results of these experiments lead to a concept for how DNA methylation functions during development. ResultsEmbryonic stem (ES) cells represent an excellent system for studying the process of global de novo methylation that takes place at the time of implantation. Although initially derived from the blastocyst stage of development, these cells harbor a DNA methylation pattern that is almost identical to the implantationstage embryo (∼E6.5) (3, 4). Furthermore, unlike somatic cells in culture, ES cells constantly maintain the ability to actively de novo methylate newly introduced DNA sequences while at the same time protecting CpG islands (5-7). Since we were interested in characterizing the factors that may play a role in the formation of this pattern, we needed a model of the genomic landscape as it existed before de novo methylation. To this end, we took advantage of ES cells carrying knockouts (TKO) for all three DNA methyl...