Creating a functional organism requires reproducible developmental patterning. A nuclear gradient of the NF-κB transcription factor, Dorsal, provides positional information necessary to specify the mesoderm, neurogenic ectoderm, dorsal ectoderm and amnioserosa along the dorsal-ventral axis in Drosophila melanogaster embryos. In this work we investigate the role that Dorsal and other transcription factors play in these crucial patterning events. We focus primarily on the gene regulation that controls patterning of the presumptive neurogenic ectoderm that is specified in lateral regions of the embryo. We investigate this early patterning event in two ways: first, by studying a known regulatory element for this region, and second, by examining the levels of Dorsal in the nuclei. We find that Dorsal can function with Zelda, a maternally deposited ubiquitous activator, to specify the neurogenic ectoderm. We then ask if the levels of Dorsal in wild type embryos are predictive of the gene expression outputs, as suggested by existing models. We measure the amount of Dorsal protein able to activate target gene expression in mutants, where the levels of Dorsal protein have been genetically manipulated. Our measurements indicate that Dorsal does not regulate gene expression in a concentration-dependent fashion. Instead, our data support the idea that Dorsal functions with other proteins to establish gene expression boundaries. These studies jointly suggest that regulation of differential gene expression requires combinatorial interactions between spatially localized and uniformly distributed transcription factors
