Various types of pluripotent stem cell lines have been established from mouse early embryo. These stem cell lines comprise a small number of cells with a distinct state of pluripotency, termed a subpopulation. We use EC (embryonal carcinoma) cells from teratocarcinomas to study how such subpopulations emerged from a clonal EC cell population and how structural changes of heterochromatin occur in the subpopulation cells. Through these investigations, we aim to understand the epigenetic alternations of chromosomal structure and gene expression during mammalian early development.