Identification of candidate downstream genes for the homeodomain transcription factor Labial in Drosophila through oligonucleotide-array transcript imaging

Ronny Leemans¹, Thomas Loop¹, Boris Egger¹, Haiqiong He¹, Lars Kammermeier¹, Beate Hartmann¹, Ullrich Certa², Heinrich Reichert¹ and Frank Hirth¹

¹Institute of Zoology, Biocenter/Pharmacenter, University of Basel, Klingelbergstrasse 50, CH-4056 Basel, Switzerland

²PRGT, Hoffmann-La Roche Ltd, CH-4070 Basel, Switzerland

author email corresponding author email

Genome Biology 2001, 2:research0015.1-0015.9doi:10.1186/gb-2001-2-5-research0015


Published:	24 April 2001

Subject areas: Genome studies, Development, Molecular biology

Abstract

Background

Homeotic genes are key developmental regulators that are highly conserved throughout evolution. Their encoded homeoproteins function as transcription factors to control a wide range of developmental processes. Although much is known about homeodomain-DNA interactions, only a small number of genes acting downstream of homeoproteins have been identified. Here we use a functional genomic approach to identify candidate target genes of the Drosophila homeodomain transcription factor Labial.

Results

High-density oligonucleotide arrays with probe sets representing 1,513 identified and sequenced genes were used to analyze differential gene expression following labial overexpression in Drosophila embryos. We find significant expression level changes for 96 genes belonging to all functional classes represented on the array. In accordance with our experimental procedure, we expect that these genes are either direct or indirect targets of labial gene action. Among these genes, 48 were upregulated and 48 were downregulated following labial overexpression. This corresponds to 6.3% of the genes represented on the array. For a selection of these genes, we show that the data obtained with the oligonucleotide arrays are consistent with data obtained using quantitative RT-PCR.

Conclusions

Our results identify a number of novel candidate downstream target genes for Labial, suggesting that this homeoprotein differentially regulates a limited and distinct set of embryonically expressed Drosophila genes.