The transformation from a single fertilized cell to a fully formed animal is one of the most amazing processes in nature. During this process, the developing embryo goes through numerous transitions as new tissues, organs and cell types are formed. Each transition is driven by a change in gene expression, and we are interested in understanding how gene expression is re-programmed to support the formation of new cells and tissues. A better understanding of these processes will allow us to trace the embryonic origin of birth defects and will also help inform experiments to grow various cell types in culture for future clinical use. We study these events in the zebrafish model system, which allows unprecedented access to early embryonic stages, and we apply various genome-wide approaches to define genetic and epigenetic programs that drive changes in cell fate.