TitleComprehensive identification of Drosophila dorsal-ventral patterning genes using a whole-genome tiling array.
Publication TypeJournal Article
Year of Publication2006
AuthorsBiemar, F, Nix, DA, Piel, J, Peterson, B, Ronshaugen, M, Sementchenko, V, Bell, I, J Manak, R, Levine, MS
JournalProc Natl Acad Sci U S A
Date Published2006 Aug 22
KeywordsAnimals, Body Patterning, Drosophila melanogaster, Embryo, Nonmammalian, Gene Expression Regulation, Developmental, Genome, Insect, Oligonucleotide Array Sequence Analysis

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 (miRNA) 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 approximately 100 protein-coding genes that were missed in earlier annotations. As many as nine intergenic uncharacterized transcription units were identified, including two that contain known microRNAs, miR-1 and -9a. We discuss the potential functions of these recently identified genes and suggest that intronic enhancers are a common feature of the DV gene network.

Alternate JournalProc. Natl. Acad. Sci. U.S.A.