Abstract
BackgroundHomeobox genes are a superclass of transcription factors with diverse developmental regulatory functions, which are found in plants, fungi and animals. In animals, several Antennapedia (ANTP)-class homeobox genes reside in extremely ancient gene clusters (for example, the Hox, ParaHox, and NKL clusters) and the evolution of these clusters has been implicated in the morphological diversification of animal bodyplans. By contrast, similarly ancient gene clusters have not been reported among the other classes of homeobox genes (that is, the LIM, POU, PRD and SIX classes).ResultsUsing a combination of in silico queries and phylogenetic analyses, we found that a cluster of three PRD-class homeobox genes (Homeobrain (hbn), Rax (rx) and Orthopedia (otp)) is present in cnidarians, insects and mollusks (a partial cluster comprising hbn and rx is present in the placozoan Trichoplax adhaerens). We failed to identify this 'HRO' cluster in deuterostomes; in fact, the Homeobrain gene appears to be missing from the chordate genomes we examined, although it is present in hemichordates and echinoderms. To illuminate the ancestral organization and function of this ancient cluster, we mapped the constituent genes against the assembled genome of a model cnidarian, the sea anemone Nematostella vectensis, and characterized their spatiotemporal expression using in situ hybridization. In N. vectensis, these genes reside in a span of 33 kb with the same gene order as previously reported in insects. Comparisons of genomic sequences and expressed sequence tags revealed the presence of alternative transcripts of Nv-otp and two highly unusual protein-coding polymorphisms in the terminal helix of the Nv-rx homeodomain. A population genetic survey revealed the Rx polymorphisms to be widespread in natural populations. During larval development, all three genes are expressed in the ectoderm, in non-overlapping territories along the oral-aboral axis, with distinct temporal expression.ConclusionWe report the first evidence for a PRD-class homeobox cluster that appears to have been conserved since the time of the cnidarian-bilaterian ancestor, and possibly even earlier, given the presence of a partial cluster in the placozoan Trichoplax. Very similar clusters comprising these three genes exist in Nematostella and diverse protostomes. Interestingly, in chordates, one member of the ancestral cluster (homeobrain) has apparently been lost, and there is no linkage between rx and orthopedia in any of the vertebrates. In Nematostella, the spatial expression of these three genes along the body column is not colinear with their physical order in the cluster but the temporal expression is, therefore, using the terminology that has been applied to the Hox cluster genes, the HRO cluster would appear to exhibit temporal but not spatial colinearity. It remains to be seen whether the mechanisms responsible for the evolutionary conservation of the HRO cluster are the same mechanisms responsible for cohesion of the Hox cluster and other ANTP-class homeobox clusters that have been widely conserved throughout animal evolution.
Highlights
Homeobox genes are a superclass of transcription factors with diverse developmental regulatory functions, which are found in plants, fungi and animals
Since the pioneering studies by Ed Lewis and co-workers on the Antennapedia (ANTP) and Bithorax complexes of Drosophila [22], comparative genomic studies have revealed (i) that certain homeobox clusters are widely conserved throughout the animal kingdom, (ii) that clustering may influence gene expression and (iii) that clustering may be conserved by stabilizing selection if disrupting the cluster has deleterious effects on the spatiotemporal expression of linked genes [23,24,25,26,27,28]
We identified four additional expressed sequence tags (ESTs) sequences for Nematostella rx, two that were previously deposited at the National Center for Biotechnology Information (NCBI) (CAGN10625 and DV088198) and two that were generated by the Joint Genome Institute (JGI) as part of the Nematostella genome sequencing initiative (2664141-1 and 2664141-2)
Summary
Homeobox genes are a superclass of transcription factors with diverse developmental regulatory functions, which are found in plants, fungi and animals. Clustering can contribute to coordinated transcriptional regulation of linked genes if the local chromatin structure affects several genes in the same chromosomal neighborhood or if shared regulatory elements drive the expression of neighboring genes, such as the gene clusters of the human cardiac transcriptome [8]. Since the pioneering studies by Ed Lewis and co-workers on the Antennapedia (ANTP) and Bithorax complexes of Drosophila [22], comparative genomic studies have revealed (i) that certain homeobox clusters are widely conserved throughout the animal kingdom, (ii) that clustering may influence gene expression and (iii) that clustering may be conserved by stabilizing selection if disrupting the cluster has deleterious effects on the spatiotemporal expression of linked genes [23,24,25,26,27,28]
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