Genome-wide analysis of chromatin state in extended pluripotent stem cells, primed pluripotent stem cells, and naïve pluripotent stem cells

Among all known cultured stem cell types, pluripotent stem cells (PSCs) sit atop the landscape of developmental potency and are characterized by their unrestricted developmental potential, able to generate all cell types of an adult organism. However, PSCs show limited contribution to the extraembryonic (ExEm) tissues, in particular, those giving rise to the placenta in vivo. To date, it remains unknown whether stem cells with both embryonic and extraembryonic developmental potency can be captured and maintained in vitro. Here, we identify a new chemical cocktail that allows for the generation of stem cells with extended developmental potency from mouse and human, designated as extended pluripotent stem (EPS) cells, which is capable of chimerizing both embryonic and extraembryonic tissues. Importantly, a single mouse EPS (mEPS) cell shows widespread contribution to both embryonic and extraembryonic lineages in chimeric mouse conceptuses at late-gestation stages, and permits generation of high-grade germline competent chimeras as well as single EPS-derived viable mice by tetraploid complementation. Furthermore, human EPS (hEPS) cells contribute to embryonic and extraembryonic tissues in interspecies chimeric mouse conceptuses. Compared to known PSCs, EPS cells show unique gene modules that upregulate in embryonic cells from early preimplantation development. Further analysis shows that PARP1 inhibition is required for maintaining EPS potency. Our findings constitute a first step towards capturing pluripotent stem cells with extraembryonic developmental potentials in culture, and open new avenues for generating mammalian PSCs with robust chimeric competency for basic and translational research. Overall design: Examination of histone modifications H3K4me3 and H3K27me3 in extended pluripotent stem cells, primed pluripotent stem cells and naïve pluripotent stem cells.