Epigenetic systems play crucial roles in the differentiation of a mammalian fertilized egg into hundreds of cell types exhibiting distinct phenotypes, using a set of DNA molecules comprising about 3 billion nucleotides. Genomewide analyses of epigenetic marks have revealed the remarkably well-established and well-maintained structure of the epigenome, consisting of DNA methylation and histone modifications that vary their state in a tissue type-and developmental stage-specific manner at numerous genomic loci. DNA methylation profiles comprising numerous tissuedependent and differentially methylated regions (T-DMRs), found at such loci, are unique to every type of cell and tissue, and illuminate molecular networks that represent their phenotypes. T-DMRs are located in not only genic but also nongenic regions—including transposable genetic elements, such as short interspersed transposable element. Epigenetic studies indicate that the molecules that perform these modifications directly, such as DNA methyltransferases and eukaryotic histone methyltransferases, or indirectly, such as CpG-binding protein and noncoding RNAs—and combinations of these—contribute to the DNA methylation profile. It remains to be addressed how these molecules precisely find their target genomic loci.