Dynamic and Differential Regulation of Stem Cell Factor FoxD3 in the Neural Crest Is Encrypted in the Genome

FoxD3 is an important stem cell factor expressed in many types of embryonic cells including neural crest cells. In the embryo, neural crest cells are a type of stem cell that forms diverse derivatives, including nerve cells, pigment cells, and facial structures. To better understand neural crest development and differentiation, we have explored how FoxD3 expression is regulated in these cells. By examining non-coding DNA, we have identified distinct genomic regions that mediate expression of green fluorescent protein (GFP) in a pattern that recapitulates FoxD3 expression. Interestingly, we find two genomic “on–off” switches or enhancers, called NC1 and NC2, that drive GFP expression in a pattern that recapitulates FoxD3 expression at different times and places during neural crest development. We find that Pax and Msx proteins turn on both NC1 and NC2 enhancers by directly binding to them. In addition, cranial expression driven by NC1 requires a protein called Ets1, whereas trunk expression of NC2 requires a different protein called Zic1. The results show that FoxD3 in differentially regulated in distinct neural crest cell populations in a manner that is specifically encoded in the genome. These enhancers provide valuable tools for understanding neural crest development in birds and mammals.