Comprehensive identification of Drosophila dorsal-ventral patterning genes using a whole-genome tiling array

Dorsal-ventral (DV) patterning of the Drosophila embryo is initiated by Dorsal, a sequence specific transcription factor distributed in a broad nuclear gradient in the precellular embryo.Previous studies have identified as many as 70 protein-coding genes and one microRNA gene that are directly or indirectly regulated by this gradient. A gene regulation network, or circuit diagram, including the functional interconnections among 40 Dorsal target genes and 20 associated tissue-specific enhancers, has been determined for the initial stages of gastrulation. Here, we attempt to extend this analysis by identifying additional DV patterning genes using a recently developed whole-genome tiling array. This analysis led to the identification of another 30 protein-coding genes, including the Drosophila homolog of Idax, an inhibitor of Wnt signaling. In addition, remote 5' exons were identified for at least 10 of the ~100 protein-coding genes that were missed in earlier annotations. As many as 9 intergenic, uncharacterized transcription units were identified, including two that contain known microRNAs, miR-1 and miR-9a. We discuss the potential functions of these newly identified genes, and suggest that intronic enhancers are a common feature of the DV gene network. Keywords: gene expression, dorsal-ventral pattern genes, tiling array 3 samples where analyzed (Tollrm9/Tollrm10, pipe386/pipe664, Toll10B/+), 3 technical replicates