title: Analysis of the transcriptomes downstream of Eyeless and the Hedgehog, Decapentaplegic and Notch signaling pathways in Drosophila melanogaster.
abstract: Tissue-specific transcription factors are thought to cooperate with signaling pathways to promote patterned tissue specification, in part by co-regulating transcription. The Drosophila melanogaster Pax6 homolog Eyeless forms a complex, incompletely understood regulatory network with the Hedgehog, Decapentaplegic and Notch signaling pathways to control eye-specific gene expression. We report a combinatorial approach, including mRNAseq and microarray analyses, to identify targets co-regulated by Eyeless and Hedgehog, Decapentaplegic or Notch. Multiple analyses suggest that the transcriptomes resulting from co-misexpression of Eyeless+signaling factors provide a more complete picture of eye development compared to previous efforts involving Eyeless alone: (1) Principal components analysis and two-way hierarchical clustering revealed that the Eyeless+signaling factor transcriptomes are closer to the eye control transcriptome than when Eyeless is misexpressed alone; (2) more genes are upregulated at least three-fold in response to Eyeless+signaling factors compared to Eyeless alone; (3) based on gene ontology analysis, the genes upregulated in response to Eyeless+signaling factors had a greater diversity of functions compared to Eyeless alone. Through a secondary screen that utilized RNA interference, we show that the predicted gene CG4721 has a role in eye development. CG4721 encodes a neprilysin family metalloprotease that is highly up-regulated in response to Eyeless+Notch, confirming the validity of our approach. Given the similarity between D. melanogaster and vertebrate eye development, the large number of novel genes identified as potential targets of Ey+signaling factors will provide novel insights to our understanding of eye development in D. melanogaster and humans.
authors.affiliation: Department of Biology, New Mexico State University, Las Cruces, New Mexico, USA.
authors.forename: Landry E
authors.initials: LE
authors.lastname: Nfonsam
authors.forename: Carlos
authors.initials: C
authors.lastname: Cano
authors.forename: Joann
authors.initials: J
authors.lastname: Mudge
authors.forename: Faye D
authors.initials: FD
authors.lastname: Schilkey
authors.forename: Jennifer
authors.initials: J
authors.lastname: Curtiss
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D057506:Arthropod Antennae / Q000378:metabolism; D004268:DNA-Binding Proteins / Q000378:metabolism; D015536:Down-Regulation / Q000235:genetics; D029721:Drosophila Proteins / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism*; D004331:Drosophila melanogaster / Q000166:cytology / Q000235:genetics* / Q000254:growth & development; D005123:Eye / Q000166:cytology / Q000378:metabolism; D020869:Gene Expression Profiling; D018507:Gene Expression Regulation, Developmental; D049750:Genome, Insect / Q000235:genetics; D053823:Hedgehog Proteins / Q000378:metabolism; D008969:Molecular Sequence Data; D015260:Neprilysin / Q000737:chemistry / Q000378:metabolism; D009928:Organ Specificity / Q000235:genetics; D017956:Photoreceptor Cells, Invertebrate / Q000378:metabolism; D034622:RNA Interference; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D051880:Receptors, Notch / Q000378:metabolism; D015398:Signal Transduction / Q000235:genetics*; D014158:Transcription, Genetic; D059467:Transcriptome / Q000235:genetics*; D015854:Up-Regulation / Q000235:genetics; D014921:Wings, Animal / Q000166:cytology / Q000378:metabolism
chemical_list: D004268:DNA-Binding Proteins; D029721:Drosophila Proteins; D053823:Hedgehog Proteins; C497759:N protein, Drosophila; D012333:RNA, Messenger; D051880:Receptors, Notch; C064196:dpp protein, Drosophila; C113278:ey protein, Drosophila; C077245:hh protein, Drosophila; D015260:Neprilysin