Genes constitute only a small proportion of the mammalian genome, the majority of which is composed of non-genic repetitive elements including interspersed repeats and satellites. A unique feature of the mammalian genome is that there are numerous tissue-dependent, differentially methylated regions (T-DMRs) in the non-repetitive sequences, which include genes and their regulatory elements. The epigenetic status of T-DMRs varies from that of repetitive elements and constitutes the DNA methylation profile genome-wide. Since the DNA methylation profile is specific to each cell and tissue type, much like a fingerprint, it can be used as a means of identification. The formation of DNA methylation profiles is the basis for cell differentiation and development in mammals. The epigenetic status of each T-DMR is regulated by the interplay between DNA methyltransferases, histone modification enzymes, histone subtypes, non-histone nuclear proteins and non-coding RNAs. In this review, we will discuss how these epigenetic factors cooperate to establish cell-and tissue-specific DNA methylation profiles.
KEY WORDS: epigenetics, DNA methylation, T-DMR, histone modification, chromatin remodeling
Epigenetic systems in mammalian developmentIn unicellular organisms, each individual cell uses almost all of the genomic information and displays an essentially identical phenotype. In contrast, in mammals there are at least a few hundred different cell types based on a variety of physiological and morphological criteria. All of these cell types are derived from a single fertilized egg. The differentiation of each cell type is achieved without changes in DNA sequence, but through the coordinated utilization of subsets of genes. In order to achieve the proper temporal and spatial regulation of these genes throughout development, a set of epigenetic mechanisms are employed, which includes histone modifications and DNA methylation (Shiota, 2004;Lieb et al., 2006).In mammals, DNA methylation occurs through DNA methyltransferases (Dnmts) that operate within 5'-CG-3' dinucleInt.