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Drosophila melanogaster has one of the best characterized metazoan genomes in terms of functionally annotated regulatory elements. To explore how these elements contribute to gene regulation in the context of gene regulatory networks, we need convenient tools to identify the proteins that bind to them. Here, we present the development and validation of a highly automated protein-DNA interaction detection method, enabling the high-throughput yeast one-hybrid-based screening of DNA elements versus an array of full-length, sequence-verified clones containing 647 (over 85%) of predicted Drosophila transcription factors (TFs). Using six well-characterized regulatory elements (82 bp – 1kb), we identified 33 TF-DNA interactions of which 27 are novel. To simultaneously validate these interactions and locate their binding sites of involved TFs, we implemented a novel microfluidics-based approach that enables us to conduct hundreds of gel shift-like assays at once, thus allowing the retrieval of DNA occupancy data for each TF throughout the respective target DNA elements. Finally, we biologically validate several interactions and specifically identify two novel regulators of sine oculis gene expression and hence eye development.

There are two Pax6 genes in Drosophila melanogaster; eyeless (ey) and twin-of-eyeless (toy), due to a duplication, which most likely occurred in the insect lineage. They encode transcription factors important for head development. Misexpression of either toy or ey can induce formation of ectopic compound eyes. Toy regulates the ey gene by binding to an eye-specific enhancer in its second intron. However, Toy can induce ectopic eyes also in an ey− background, which indicates a redundancy between the two Pax6 copies in eye formation. To elucidate to what extent these two genes are interchangeable, we first generated toy-Gal4 constructs capable of driving the Pax6 genes in a toy-specific manner. Genetic dissection of the promoter proximal region of toy identified a 1,300-bp region around the canonical transcription start that is sufficient to drive toy expression in embryonic brain and eye primorida and in larval eye-antennal discs. We find that exogenous expression of toy can partially rescue the lethality and eye phenotype caused by lethal mutations in ey and vice versa. We therefore conclude that Toy and Ey, to some extent, can substitute for each other. Nevertheless, the phenotypes of the rescued flies indicate that the two Pax6 genes are specialized to regulate defined structures of the fly head. Electronic supplementary material The online version of this article (doi:10.1007/s00438-009-0458-2) contains supplementary material, which is available to authorized users.