Shadow Enhancers Mediate Dynamic Shifts of Gap Gene Expression in the Drosophila Embryo

Drosophila patterning genes often contain pairs of primary and shadow enhancers that possess overlapping activities [1-5]. It has been suggested that this regulatory "redundancy'' helps ensure reliable activation of gene expression under stressful conditions such as increases in temperature [4, 5]. There is also evidence that shadow enhancers help produce sharp on/off boundaries of gene expression in response to small changes in the levels of regulatory factors, such as the maternal Bicoid gradient [6, 7]. Here, we use live-imaging methods to visualize the temporal dynamics of the gap genes Kruppel and knirps, which are essential for the patterning of the thorax and abdomen, respectively [8, 9]. Previous analyses of fixed embryos suggested anterior shifts of the Kruppel and knirps expression patterns [10]. Here, we use computational visualization methods to reveal the precise temporal dynamics of these shifts and further suggest that shadow enhancers are crucial for this process. We discuss potential mechanisms for enhancer dominance, whereby one enhancer represses the other to foster temporal dynamics.