Though much of what defines a human is encoded in the sequence of our DNA, many additional factors influence how this genetic information is manifest. For example, heritable epigenetic information contained within chromatin, the higher-order structure that packages the genome, has critical functions during embryonic development and can contribute to the pathogenesis of disease. Our laboratory applies high-throughput sequencing-based technologies to characterize chromatin structure genome-wide in human and mouse. In addition to advancing technology and providing unprecedented global views of mammalian chromatin, this work has led to an appreciation of the role of large-scale chromatin structures, or ‘domains', in regulating developmental genes. In differentiated cells, chromatin domains marked by either ‘active' or ‘repressive' histone modifications maintain expression or repression of key developmental genes (‘master regulators'). However, in pluripotent ES cells, chromatin domains enriched for both active and repressive modifications repress developmental genes while maintaining their potential for subsequent activation. Current projects in the lab are are focused on these 'bivalent' domains with the goals of understanding their initial establishment, their higher-order structure, and their roles in ES cell pluripotency and epigenetic regulation. Similar approaches are also being used to characterize chromatin modifications in adult stem cells and cancer models. Our long-term goal is to achieve a systems level understanding of chromatin regulation during development, and how chromatin mis-regulation contributes to human disease.