title: Comprehensive identification of Drosophila dorsal-ventral patterning genes using a whole-genome tiling array.
abstract: 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.
authors.affiliation: Division of Genetics and Development, Department of Molecular Cell Biology, Center for Integrative Genomics, University of California, Berkeley, CA 94720, USA.
authors.forename: Frédéric
authors.initials: F
authors.lastname: Biemar
authors.forename: David A
authors.initials: DA
authors.lastname: Nix
authors.forename: Jessica
authors.initials: J
authors.lastname: Piel
authors.forename: Brant
authors.initials: B
authors.lastname: Peterson
authors.forename: Matthew
authors.initials: M
authors.lastname: Ronshaugen
authors.forename: Victor
authors.initials: V
authors.lastname: Sementchenko
authors.forename: Ian
authors.initials: I
authors.lastname: Bell
authors.forename: J Robert
authors.initials: JR
authors.lastname: Manak
authors.forename: Michael S
authors.initials: MS
authors.lastname: Levine
mesh_terms: D000818:Animals; D019521:Body Patterning / Q000235:genetics*; D004331:Drosophila melanogaster / Q000196:embryology* / Q000235:genetics*; D004625:Embryo, Nonmammalian / Q000196:embryology / Q000378:metabolism; D018507:Gene Expression Regulation, Developmental; D049750:Genome, Insect / Q000235:genetics*; D020411:Oligonucleotide Array Sequence Analysis