Comparative analysis of Hox downstream genes inDrosophila

Abstract

Functional diversification of body parts is dependent on the formation of specialized structures along the various body axes. In animals, region-specific morphogenesis along the anteroposterior axis is controlled by a group of conserved transcription factors encoded by the Hox genes. Although it has long been assumed that Hox proteins carry out their function by regulating distinct sets of downstream genes, only a small number of such genes have been found, with very few having direct roles in controlling cellular behavior. We have quantitatively identified hundreds of Hox downstream genes in Drosophila by microarray analysis, and validated many of them by in situ hybridizations on loss-and gain-of-function mutants. One important finding is that Hox proteins, despite their similar DNA-binding properties in vitro, have highly specific effects on the transcriptome in vivo, because expression of many downstream genes respond primarily to a single Hox protein. In addition, a large fraction of downstream genes encodes realizator functions, which directly affect morphogenetic processes, such as orientation and rate of cell divisions, cell-cell adhesion and communication, cell shape and migration, or cell death. Focusing on these realizators, we provide a framework for the morphogenesis of the maxillary segment. As the genomic organization of Hox genes and the interaction of Hox proteins with specific co-factors are conserved in vertebrates and invertebrates, and similar classes of downstream genes are regulated by Hox proteins across the metazoan phylogeny, our findings represent a first step toward a mechanistic understanding of morphological diversification within a species as well as between species.

Hox transcriptional specificity despite a single class of cofactors: Are flexible interaction modes the key?

“…In addition, the AbdA protein has been shown to use various combinations of at least three different protein motifs for accomplishing PBCdependent functions in vivo [25]. Interestingly, the capacity of AbdA to diversify its interaction mode with PBC coincides with the observation that this Hox protein regulates the larger set of target genes in the Drosophila embryo [26].…”

“…Our comparison of ChIP and transcriptome analyses performed with the Drosophila Dfd and Ubx proteins [26,27] demonstrates that a small proportion of target genes contain a corresponding binding peak of the Hox protein in their vicinity (Fig. 1A and B).…”

“…2). These are distinct from semi-instructive sites since they allow different transcriptional responses, depending on the Hox protein con- [27]) and the transcriptome (in green, [26]) of Dfd (upper case) or Ubx (lower case) in the Drosophila embryo. B: Comparison between the ChIP of Ubx (in blue, [27]) and the transcriptome (in green, [26]) of Ubx (upper case) or Dfd (lower case) in the Drosophila embryo.…”

“…These are distinct from semi-instructive sites since they allow different transcriptional responses, depending on the Hox protein con- [27]) and the transcriptome (in green, [26]) of Dfd (upper case) or Ubx (lower case) in the Drosophila embryo. B: Comparison between the ChIP of Ubx (in blue, [27]) and the transcriptome (in green, [26]) of Ubx (upper case) or Dfd (lower case) in the Drosophila embryo. A small proportion of Dfd (35) and Ubx (59) downstream genes show a corresponding binding peak of the Hox protein in their vicinity (by considering 10,000 bases upstream and downstream of the binding pic) [26,27].…”

“…B: Comparison between the ChIP of Ubx (in blue, [27]) and the transcriptome (in green, [26]) of Ubx (upper case) or Dfd (lower case) in the Drosophila embryo. A small proportion of Dfd (35) and Ubx (59) downstream genes show a corresponding binding peak of the Hox protein in their vicinity (by considering 10,000 bases upstream and downstream of the binding pic) [26,27]. These genes are considered as direct (or primary) target genes.…”