In past years, much attention has focused on the gene networks that regulate 
early developmental processes, but less attention has been paid to how multiple 
networks and processes are temporally coordinated. Recently the discovery of the 
transcriptional activator Zelda (Zld), which binds to CAGGTAG and related 
sequences present in the enhancers of many early-activated genes in Drosophila, 
hinted at a mechanism for how batteries of genes could be simultaneously 
activated. Here we use genome-wide binding and expression assays to identify Zld 
target genes in the early embryo with the goal of unraveling the gene circuitry 
regulated by Zld. We found that Zld binds to genes involved in early 
developmental processes such as cellularization, sex determination, 
neurogenesis, and pattern formation. In the absence of Zld, many target genes 
failed to be activated, while others, particularly the patterning genes, 
exhibited delayed transcriptional activation, some of which also showed weak 
and/or sporadic expression. These effects disrupted the normal sequence of 
patterning-gene interactions and resulted in highly altered spatial expression 
patterns, demonstrating the significance of a timing mechanism in early 
development. In addition, we observed prevalent overlap between Zld-bound 
regions and genomic "hotspot" regions, which are bound by many developmental 
transcription factors, especially the patterning factors. This, along with the 
finding that the most over-represented motif in hotspots, CAGGTA, is the Zld 
binding site, implicates Zld in promoting hotspot formation. We propose that Zld 
promotes timely and robust transcriptional activation of early-gene networks so 
that developmental events are coordinated and cell fates are established 
properly in the cellular blastoderm embryo.