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doi: 10.1242/10.1242/dev.00348

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Development 130, 1243-1254 (2003)
Copyright © 2003 The Company of Biologists Limited

Genome-wide identification of in vivo Drosophila Engrailed-binding DNA fragments and related target genes

Pascal Jean Solano1,*, Bruno Mugat1,*, David Martin2, Franck Girard1, Jean-Marc Huibant1, Conchita Ferraz1, Bernard Jacq2, Jacques Demaille1 and Florence Maschat1,{dagger}

1 Institut de Génétique Humaine (UPR 1142). 141 rue de la Cardonille, 34396 Montpellier, France
2 Laboratoire de Génétique et Physiologie du Développement (UMR 6545), IBDM, Parc Scientifique de Luminy, 13288 Marseille, Cedex 9, France

{dagger} Author for correspondence (e-mail: fmaschat{at}igh.cnrs.fr)

Accepted 18 December 2002

Chromatin immunoprecipitation after UV crosslinking of DNA/protein interactions was used to construct a library enriched in genomic sequences that bind to the Engrailed transcription factor in Drosophila embryos. Sequencing of the clones led to the identification of 203 Engrailed-binding fragments localized in intergenic or intronic regions. Genes lying near these fragments, which are considered as potential Engrailed target genes, are involved in different developmental pathways, such as anteroposterior patterning, muscle development, tracheal pathfinding or axon guidance. We validated this approach by in vitro and in vivo tests performed on a subset of Engrailed potential targets involved in these various pathways. Finally, we present strong evidence showing that an immunoprecipitated genomic DNA fragment corresponds to a promoter region involved in the direct regulation of frizzled2 expression by engrailed in vivo.

Key words: Engrailed, Chromatin immunoprecipitation, In vivo targets, Drosophila


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