Multicellular organisms are made up of diverse populations of many different types of cells, each of which contains an identical set of genetic information coded in its DNA. Cell differentiation and the process of development itself depend on the ability of individual cells to maintain the expression of different genes, and for their progeny to do so through multiple cycles of cell division. In recent years, we have begun to understand that the maintenance of specific patterns of gene expression does not rely on the DNA sequence, but rather takes place in a heritable, “epigenetic” manner. DNA methylation, chromatin modifications, and RNA silencing are some of the best known epigenetic phenomena. Our team investigates how modifications to the structure and configuration of chromatin (complexes of nuclear DNA and proteins) contribute to epigenetic gene regulation by studying events at the molecular scale in the model organism, fission yeast, ciliate Tetrahymena, and in cultured mammalian cells.