Targeting Drosophila eye development

The Drosophila retinal determination gene network (RDGN) consists of seven transcription factors, conserved from flies to humans, that cooperate to regulate cell specification and determination during eye development. At the top of this network are the master regulators Twin of Eyeless (Toy) and Eyeless (Ey), homologs of vertebrate Pax6, which activate expression of the genes for the conserved downstream transcription factors Eyes Absent (Eya), Sine Oculis (So), Optix and Dachshund (Dac) (Figure 1). The transcription factor Eyegone (Eyg) is also a retinal determination protein, but has not yet been positioned within the pathway. At present only a small number of direct targets of any of these transcription factors have been identified (see Figure 1). An elegant strategy integrating bioinformatics and microarray-based expression profiling with in vivo genetics has recently been used by Ostrin et al. [1] to isolate and validate transcriptional targets of Ey.The strength of a large-scale screen lies in its design and in the implementation of effective secondary tests to distinguish the desired output from the inevitable background. Standard microarray analysis results in long lists of genes whose expression changes under different experimental conditions, but does not reveal which genes reflect direct transcriptional targets. For example, a previous study by Michaut et al. [2] compared expression profiles of wild-type eye and leg imaginal discs (the larval tissues from which the adult structures develop) from third-instar larvae, as well as leg discs ectopically expressing eyeless (ey), and identified 371 genes relevant to eye specification and development; which of these genes actually represent direct transcriptional targets of Ey remained an open question, however [2]. Ostrin et al. [1] have taken a novel approach, utilizing microarray-based epistasis analysis to identify genes expressed in a spatial and temporal pattern consistent with that of direct Ey targets. Ep