Embryonic stem (ES) cells offer insight into early developmental fate decisions, 
and their controlled differentiation may yield vast regenerative potential. The 
molecular determinants supporting ES cell self-renewal are incompletely 
understood. The homeodomain proteins Nanog and Oct4 are essential for mouse ES 
cell self-renewal. Using a high-throughput approach, we discovered DNaseI 
hypersensitive sites and potential regulatory elements along a 160-kb region of 
the genome that includes GDF3, Dppa3, and Nanog. We analyzed gene expression, 
chromatin occupancy, and higher-order chromatin structure throughout this gene 
locus and found that expression of the reprogramming factor Oct4 is required to 
maintain its integrity.