Homeogene expression patterns and chromosomal imprinting

In both mouse and Drosophila, Antennapedia-like homeobox-containing genes (homeogenes) display a strict correspondence between the order of genes (3' to 5') along the chromosome and the order of their expression domains (anterior to posterior) in the developing embryo. We show here how this, and other points of similarity, may indicate that both species use a common mechanism of chromosomal imprinting in order to retain cellular memory of homeogene expression patterns throughout embryonic development.     

The structural and functional organization of the murine HOX gene family resembles that of Drosophila homeotic genes.

This paper reports the cloning of the fourth major murine homeogene complex, HOX-5. The partial characterization of this gene cluster revealed the presence of two novel genes (Hox-5.2, Hox-5.3) located at the 5' extremity of this complex. In situ hybridization experiments showed that these two genes are transcribed in very posterior domains during embryonic and foetal development. We also show that Hox-1.6, the gene located at the 3' most position in the HOX-1 complex, has a very anterior expression boundary during early development. These results clearly support the recently proposed hypothesis that the expression of murine Antp-like homeobox-containing genes along the antero-posterior developing body axis follows a positional hierarchy which reflects their respective physical positions within the HOX clusters, similar to that which is found for the Drosophila homeotic genes. Such a structural and functional organization is likely conserved in most vertebrates. Moreover, on the basis of sequence comparisons, we propose that the ordering of homeobox-containing genes within clusters has been conserved between Drosophila and the house mouse. Thus, very different body plans might be achieved, both in insects and vertebrates, by evolutionarily conserved gene networks possibly displaying similar regulatory interactions.     

Heads and tails: evolution of antero-posterior patterning in insects

In spite of their varied appearances, insects share a common body plan whose layout is established by patterning genes during embryogenesis. We understand in great molecular detail how the Drosophila embryo patterns its segments. However, Drosophila has a type of embryogenesis that is highly derived and varies extensively as compared to most insects. Therefore, the study of other insects is invaluable for piecing together how the ancestor of all insects established its segmented body plan, and how this process can be plastic during evolution. In this review, we discuss the evolution of Antero-Posterior (A-P) patterning mechanisms in insects. We first describe two distinct modes of insect development - long and short germ development - and how these two modes of patterning are achieved. We then summarize how A-P patterning occurs in the long-germ Drosophila, where most of our knowledge comes from, and in the well-studied short-germ insect, Tribolium. Finally, using examples from other insects, we highlight differences in patterns of expression, which suggest foci of evolutionary change.     

Murine genes related to the Drosophila AbdB homeotic genes are sequentially expressed during development of the posterior part of the body.

The cloning, characterization and developmental expression patterns of two novel murine Hox genes, Hox-4.6 and Hox-4.7, are reported. Structural data allow us to classify the four Hox-4 genes located in the most upstream (5') position in the HOX-4 complex as members of a large family of homeogenes related to the Drosophila homeotic gene Abdominal B (AbdB). It therefore appears that these vertebrate genes are derived from a selective amplification of an ancestral gene which gave rise, during evolution, to the most posterior of the insect homeotic genes so far described. In agreement with the structural colinearity, these genes have very posteriorly restricted expression profiles. In addition, their developmental expression is temporally regulated according to a cranio-caudal sequence which parallels the physical ordering of these genes along the chromosome. We discuss the phylogenetic alternative in the evolution of genetic complexity by amplifying either genes or regulatory sequences, as exemplified by this system in the mouse and Drosophila. Furthermore, the possible role of 'temporal colinearity' in the ontogeny of all coelomic (metamerized) metazoans showing a temporal anteroposterior morphogenetic progression is addressed.     

The murine and Drosophila homeobox gene complexes have common features of organization and expression

In situ hybridization analysis of mouse embryos shows the seven members of the Hox-2 complex to be differentially expressed in the central and peripheral nervous system and in mesodermal derivatives (somites and lung). Beginning at the 5' end of the cluster, each successive gene displays a more anterior boundary of expression in the central nervous system. A gene's position in the Hox-2 cluster therefore reflects its relative domain of expression along the anteroposterior axis of the embryo, a feature observed with Drosophila homeotic genes. Sequence comparisons of the Hox-2 cluster with other mouse and Drosophila homeobox genes have defined subgroups of related genes; in the mouse there are four clusters related by duplication and divergence. Alignment shows a clear relationship among genes in the mouse and Drosophila complexes, based on relative position, sequence identity, and domains of expression along the rostral-caudal axis. Our results argue that these complexes arose from a common ancestor, present before the divergence of lineages that gave rise to arthropods and vertebrates.     

Phylogenetic tests of the hypothesis of block duplication of homologous genes on human chromosomes 6, 9, and 1

There are 10 gene families that have members on both human chromosome 6 (6p21.3, the location of the human major histocompatibility complex [MHC]) and human chromosome 9 (mostly 9q33-34). Six of these families also have members on mouse chromosome 17 (the mouse MHC chromosome) and mouse chromosome 2. In addition, four of these families have members on human chromosome 1 (1q21-25 and 1p13), and two of these have members on mouse chromosome 1. One hypothesis to explain these patterns is that members of the 10 gene families of human chromosomes 6 and 9 were duplicated simultaneously as a result of polyploidization or duplication of a chromosome segment ("block duplication"). A subsequent block duplication has been proposed to account for the presence of representatives of four of these families on human chromosome 1. Phylogenetic analyses of the 9 gene families for which data were available decisively rejected the hypothesis of block duplication as an overall explanation of these patterns. Three to five of the genes on human chromosomes 6 and 9 probably duplicated simultaneously early in vertebrate history, prior to the divergence of jawed and jawless vertebrates, and shortly after that, all four of the genes on chromosomes 1 and 9 probably duplicated as a block. However, the other genes duplicated at different times scattered over at least 1.6 billion years. Since the occurrence of these clusters of related genes cannot be explained by block duplication, one alternative explanation is that they cluster together because of shared functional characteristics relating to expression patterns.      

Evidence for 14 homeobox gene clusters in human genome ancestry

The arrangement of Hox genes into physical clusters is fundamental to the patterning of animal body plans. Other homeobox genes are often described as dispersed, with only occasional examples of linkage reported, such as the amphioxus ParaHox and Drosophila 93D/E clusters. This clustering is unlikely to be the derived condition, as the genes of the ParaHox and 93D/E clusters are phylogenetically widespread. To assess whether clustering is retained in mammals, and to infer its history, we considered the distribution of ANTP superclass homeobox genes in human and mouse genomes. We postulate four ancient arrays of ANTP superclass genes in animal genomes, denoted 'extended Hox' (Hox, Evx and Mox), NKL (including NK1, NK3, NK4, Lbx, Tlx, Emx, Vax, Hmx, NK6, Msx), ParaHox (Cdx, Xlox, Gsx) and EHGbox (En, HB9, Gbx). Each of these duplicated in the ancestry of the human genome to yield four Hox, four NKL, four ParaHox and at least two EHGbox clusters or arrays. Two of the human NKL clusters (four in mouse) have subsequently been split by chromosome rearrangement, as has one human EHGbox array. We date all cluster duplications to early chordate evolution and infer that three clusters (Hox, NKL, EHGbox) resided on the same chromosome before duplication.     

Evolution of the echinoderm Hox gene cluster

SUMMARY Extant echinoderms are members of an ancient and highly derived deuterostome phylum. The composition and arrangement of their Hox gene clusters are consequently of interest not only from the perspective of evolution of development, but also in terms of metazoan phylogeny and body plan evolution. Over the last decade numerous workers have reported partial Hox gene sequences from a variety of echinoderms. In this paper we used a combined methods approach to analyze phylogenetic relationships between 68 echinoderm Hox homeodomain fragments, from species of five extant classes—two asteroids, one crinoid, one ophiuroid, one holothuroid, and three echinoids. This analysis strengthens Mito and Endo's (2000) proposition that the ancestral echinoderm's Hox gene cluster contained at least eleven genes, including at least four posterior paralogous group genes. However, representatives of all paralogous groups are not known from all echinoderm classes. In particular, these data suggest that echinoids may have lost a posterior group Hox gene subsequent to the divergence of the echinoderm classes. Evolution of the highly derived echinoderm body plan may have been accompanied by class-specific duplication, diversification and loss of Hox genes.     

The Hox Paradox: More complex(es) than imagined

An understanding of the origin of different body plans requires knowledge of how the genes and genetic pathways that control embryonic development have evolved. The Hox genes provide an appealing starting point for such studies because they play a well-understood causal role in the regionalization of the body plan of all bilaterally symmetric animals. Vertebrate evolution has been characterized by gene, and possibly genome, duplication events, which are believed to have provided raw genetic material for selection to act upon. It has recently been established that the Hox gene organization of ray-finned fishes, such as the zebrafish, differs dramatically from that of their lobe-finned relatives, a group that includes humans and all the other widely used vertebrate model systems. This unusual Hox gene organization of zebrafish is the result of a duplication event within the ray-finned fish lineage. Thus, teleosts, such as zebrafish, have more Hox genes arrayed over more clusters (or "complexes") than do tetrapod vertebrates. Here, I review our understanding of Hox cluster architecture in different vertebrates and consider the implications of gene duplication for Hox gene regulation and function and the evolution of different body plans.     

Genome Duplications and Accelerated Evolution of Hox Genes and Cluster Architecture in Teleost Fishes

The early origin of four vertebrate Hox gene clusters duringthe evolution of gnathostomes was likely caused by two consecutiveduplications of the entire genome and the subsequent loss ofindividual genes. The presumed conserved and important rolesof these genes in tetrapods during development led to the generalassumption that Hox cluster architecture had remained unchangedsince the last common ancestor of all jawed vertebrates. Butrecent data from teleost fishes reveals that this is not thecase. Here, we present an analysis of the evolution of vertebrateHox genes and clusters, with emphasis on the differences betweenthe Hox A clusters of fish (actinopterygian) and tetrapod (sarcopterygian)lineages. In contrast to the general conservation of genomicarchitecture and gene sequence observed in sarcopterygians,the evolutionary history of actinopterygian Hox clusters likelyincludes an additional (third) genome duplication that initiallyincreased the number of clusters from four to eight. We document,for the first time, higher rates of gene loss and gene sequenceevolution in the Hox genes of fishes compared to those of landvertebrates. These two observations might suggest that two differentmolecular evolutionary strategies exist in the two major vertebratelineages. Preliminary data from the African cichlid fish Oreochromisniloticus compared to those of the pufferfish and zebrafishreveal important differences in Hox cluster architecture amongfishes and, together with genetic mapping data from Medaka,indicate that the third genome duplication was not zebrafish-specific,but probably occurred early in the history of fishes. Each descendingfish lineage that has been characterized so far, distinctivelymodified its Hox cluster architecture through independent secondarylosses. This variation is related to the large body plan differencesobserved among fishes, such as the loss of entire sets of appendagesand ribs in some lineages.     

Selective maintenance of Drosophila tandemly arranged duplicated genes during evolution

Background

The physical organization and chromosomal localization of genes within genomes is known to play an important role in their function. Most genes arise by duplication and move along the genome by random shuffling of DNA segments. Higher order structuring of the genome occurs in eukaryotes, where groups of physically linked genes are co-expressed. However, the contribution of gene duplication to gene order has not been analyzed in detail, as it is believed that co-expression due to recent duplicates would obscure other domains of co-expression.

Results

We have catalogued ordered duplicated genes in Drosophila melanogaster, and found that one in five of all genes is organized as tandem arrays. Furthermore, among arrays that have been spatially conserved over longer periods than would be expected on the basis of random shuffling, a disproportionate number contain genes encoding developmental regulators. Using in situ gene expression data for more than half of the Drosophila genome, we find that genes in these conserved clusters are co-expressed to a much higher extent than other duplicated genes.

Conclusions

These results reveal the existence of functional constraints in insects that retain copies of genes encoding developmental and regulatory proteins as neighbors, allowing their co-expression. This co-expression may be the result of shared cis-regulatory elements or a shared need for a specific chromatin structure. Our results highlight the association between genome architecture and the gene regulatory networks involved in the construction of the body plan.     

Voltage-Gated Potassium Channel Genes Are Clustered in Paralogous Regions of the Mouse Genome

Cloning of the Drosophila Shaker gene established that a neurological phenotype including locomotor dysfunction can be caused by a mutation in a voltage-gated potassium (K) channel gene. Shaker sequences have been used to isolate a large family of related K channel genes from both flies and mammals. Toward elucidating the evolutionary relationship between loci and the potential causal connection that K channels may have to mammalian genetic disorders, we report here the genetic mapping of 12-16 different murine, voltage-gated K channel genes. We find that multiple genes, in some cases from distantly related K channel subfamilies, occur in clusters in the mouse genome. These mapping results suggest that the K channel gene subfamilies arose through ancient localized gene duplication events, followed by chromosomal duplications and rearrangements as well as further gene duplication. We also note that several neurologic disorders of both mouse and human are associated with the chromosomal regions containing K channel genes.     

HYPERMUTABILITY OF HOXA13A AND FUNCTIONAL DIVERGENCE FROM ITS PARALOG ARE ASSOCIATED WITH THE ORIGIN OF A NOVEL DEVELOPMENTAL FEATURE IN ZEBRAFISH AND RELATED TAXA (CYPRINIFORMES)

Gene duplication is widely regarded as the predominant mechanism by which genes with new functions and associated phenotypic novelties arise. A whole genome duplication occurred shortly before the most recent common ancestor of teleosts, the most diverse chordate group, resulting in duplication and retention of many Hox cluster genes. Because they play a key role in determination of body plan morphology, it has been widely assumed that Hox genes play a key role in the evolution of diverse metazoan body plans. However, it is not clear whether certain aspects of molecular evolution, such as asymmetric divergence and neofunctionalization, contribute to the initial retention of paralogs. We investigate the molecular evolution and functional divergence of the duplicated HoxA13 paralogs in zebrafish to determine when asymmetric divergence and functional divergence occurred after the duplication event. Our findings demonstrate the contribution of gene duplication to the evolution of novel features through evolutionary mechanisms other than those traditionally investigated, such as positive selection occurring immediately after gene duplication. Rather, we find a latent build up of molecular changes in a gene associated with the development of a novel feature in a very diverse group of fishes.