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

Frédéric Biemar, David A. Nix, Jessica Piel, Brant Peterson, Matthew Ronshaugen, Victor Sementchenko, Ian Bell, J. Robert Manak, Michael S. Levine

Research output: Contribution to journalArticlepeer-review

46 Scopus citations


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 ≈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.

Original languageEnglish (US)
Pages (from-to)12763-12768
Number of pages6
JournalProceedings of the National Academy of Sciences of the United States of America
Issue number34
StatePublished - Aug 22 2006
Externally publishedYes

All Science Journal Classification (ASJC) codes

  • General


  • Gene network
  • MicroRNA
  • Noncoding RNA


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