Using transcriptomics to identify targets of eyeless and signaling pathways in Drosophila eye development

Tissue-specific transcription factors cooperate with signaling pathways to promote specification, in part by co-regulating transcription. The Drosophila melanogaster Pax6 homolog Eyeless forms a complex, incompletely understood regulatory network with signaling pathways to control eye-specific gene expression. I employed mRNAseq and microarray approaches to identify targets co-regulated by Eyeless and Hedgehog, Decapentaplegic or Notch signals, to further understand the Drosophila eye network. The gene encoding the neprilysin family peptidase 'Abnormally blistered and morphologically misshapen eyes' Abams and the Drosophila class II 'Myosin heavy chain' protein, Mhc, were expressed at higher levels in the eye tissues versus wing tissues, and were highly expressed in eye tissues in response to Ey+N. Thus, both abams and Mhc were predicted to have roles in eye development. Whereas wild type eyes have a regular array of ommatidia interspersed with regularly occurring sensory bristles, using RNA interference (RNAi), I showed that reduction of abams function resulted in smaller eyes that consisted of patches of individual ommatidia surrounded by numerous bristles. Photoreceptor development was disrupted when abams function was reduced in eye precursors. Loss of function analyses and RNAi of Mhc revealed disruptions in the eye lattice and the mis-positioning of photoreceptor nuclei within the eye precursor epithelium. My results suggest that Abams is involved in cell-cell signaling while Mhc regulates cell morphology and/or cell-cell adhesion during eye development. Transcription factor binding site (BS) analyses using computational modeling revealed ≥94 other candidate genes as potential direct targets of Ey or Ey+Hh, Dpp or N. These included genes with already known roles in Drosophila eye development, as well as genes with unknown function, thus providing potential new directions to pursue to further understand the mechanism of interaction between Ey and Hh, Dpp or Notch during Drosophila eye development. Given the similarity between D. melanogaster and vertebrate eye development, further study of Abams and Mhc in Drosophila eye development will provide novel insights into our understanding of eye development in D. melanogaster and humans.