Detection of homeobox genes in development and evolution

Expansion of the Hox gene family and the evolution of chordates

Homeobox genes encode DNA-binding transcription regulators that participate in the formation of embryonic pattern or contribute to cell-type specificity during metazoan development. Homeobox genes that regulate axial patterning and segmental identity (Hox/HOM genes) share a conserved clustered genomic organization. Mammals have four clusters that have likely arisen from the duplication of a single ancestral cluster. The number of Hox-type genes in other deuterostomes was estimated by using a polymerase chain reaction sampling method. Increased Hox gene complements are associated with the appearance of chordate and vertebrate characters. Our data suggest the presence of one Hox cluster in the acorn worm, a hemichordate; two Hox clusters in amphioxus, a cephalochordate; and three in the lamprey, a primitive vertebrate.

The phylogenetic position of the zebrafish (Danio rerio), a model system in developmental biology: an invitation to the comparative method

The zebrafish, Danio (Brachydanio) rerio, has become one of the most widely studied model systems in developmental biology. We present a DNA-based phylogeny of zebrafish and other species of the genus Danio, and the genera Rasbora, Puntius and Cyprinus. Homologous regions of the large (16S) mitochondrial ribosomal RNA gene were amplified by the polymerase chain reaction and directly sequenced. The phylogeny revealed: (i) the zebrafish, Danio (Brachydanio) rerio, is identical in its 16S sequence to its aquarium breeding morph, the leopard danio; (ii) the pearl danio (Danio albolineatus) is more closely related to the zebrafish than the giant danio (Danio aequipinnatus); and (iii) species of the genus Rasbora (hetermorpha, trilineata, elegans, pauciperforata, dorsiocellata) are more closely related to the danios than members of the genus Puntius (tetrazona, conchonius) and Cyprinus, the carp. All of these species are readily available in the aquarium trade, easily kept and bred in captivity, and amenable to developmental work. It is hoped that this molecular phylogeny will invite developmental biologists to use the comparative method to ask questions about function (e.g. cellular and genetic aspects) and evolution of zebrafish developmental biology in a phylogenetic context.

Ancestry and diversity of the HMG box superfamily

The HMG box is a novel type of DNA-binding domain found in a diverse group of proteins. The HMG box superfamily comprises a.o. the High Mobility Group proteins HMG1 and HMG2, the nucleolar transcription factor UBF, the lymphoid transcription factors TCF-1 and LEF-1, the fungal mating-type genes mat-Mc and MATA1, and the mammalian sex-determining gene SRY. The superfamily dates back to at least 1,000 million years ago, as its members appear in animals, plants and yeast. Alignment of all known HMG boxes defined an unusually loose consensus sequence. We constructed phylogenetic trees connecting the members of the HMG box superfamily in order to understand their evolution. This analysis led us to distinguish two subfamilies: one comprising proteins with a single sequence-specific HMG box, the other encompassing relatively non sequence-specific DNA-binding proteins with multiple HMG boxes. By studying the extent of diversification of the superfamily, we found that the speed of evolution was very different within the various groups of HMG-box containing factors. Comparison of the evolution of the two boxes of ABF2 and of mtTF1 implied different diversification models for these two proteins. Finally, we provide a tree for the highly complex group of SRY-like ('Sox' genes), clustering at least 40 different loci that rapidly diverged in various animal lineages.

The HOX11 gene encodes a DNA-binding nuclear transcription factor belonging to a distinct family of homeobox genes

A translocation involving human chromosome 10, band q24, in a subset of T-cell acute leukemias disrupts a region surrounding the putative oncogene HOX11, which encodes a protein with a homeodomain. The HOX11 protein binds to a specific DNA sequence, it localizes to the cell nucleus, and it transactivates transcription of a reporter gene linked to a cis-regulatory element, suggesting that HOX11 functions in vivo as a positive transcription activator. PCR analysis shows that the HOX11 homeodomain is a member of a distinct class of homeodomains, representatives of which occur in murine and Drosophila genomes. These all contain a threonine residue in place of the more common isoleucine or valine in helix 3 of the homeodomain. HOX11 therefore appears to belong to a family of DNA-binding transactivators of transcription.

Expression of a novel human homeobox-containing gene that maps to chromosome 7q36.1 in hematopoietic cells

A homeobox is a DNA sequence of 180 base pairs that encodes a DNA-binding domain known as a homeodomain. The polymerase chain reaction (PCR) has been used to prepare probes of homeobox-containing genes. We cloned and sequenced the amplified products of PCR that was performed with human genomic DNA and two primers that correspond to well-conserved regions in homeoboxes. Fifteen kinds of homeobox gene were identified and 13 of them were assigned to HOX genes that have already been reported. Two others represented novel homeobox genes and one of them, GBX1, was mapped to chromosome 7q36.1 by fluorescence in situ hybridization. Northern hybridization of mRNA for various kinds of hematopoietic cell showed that the newly identified GBX1 gene is expressed in K562 cells and Daudi cells.

Organization and expression of mouse Hox3 cluster genes

We determined the physical linkage of six mouse Hox3 homeobox sequences, including a new homeobox sequence (Hox3.5), by analysis of overlapping genomic clones. Additionally, we defined the locations of Hox1.7 and Hox1.8 in the Hox1 cluster. Analysis of the expression patterns of Hox3.6 and Hox3.5 during embryogenesis revealed that the relationship between relative position in the Hox3 cluster and expression domain along antero-posterior axis appears similar to that seen for members of the other Hox clusters.

A homeobox gene of the Antennapedia class is required for human adult erythropoiesis

In this report we investigate the role of homeobox genes of the Antennapedia class in adult erythropoiesis, the process by which erythrocytes are formed in the bone marrow. We initially identified Hox genes expressed in mouse erythroleukemia cells by a PCR technique using degenerate primers capable of detecting most of the known genes in Hox clusters 1-4. Four different transcripts, Hox-3.3, -3.5, -3.6, and -4.3 were identified. An antisense oligonucleotide directed against HOX3C (human homologue of Hox-3.3) was used to study the effect of the colony formation by human erythroid progenitor cells. The oligonucleotide inhibited the formation of colony-forming unit erythroid-derived colonies but did not affect the size or degree of hemoglobinization. The more primitive erythroid burst-forming unit colonies or myeloid colonies were not affected. These results show that Hox-3.3 is involved in an early step in the proliferation of the erythroid colony-forming unit subset of progenitor cells.

Homeobox genes are expressed in the retina and brain of adult goldfish

The goldfish (Carassius auratus) visual pathway displays continuous growth and plasticity throughout life. Since homeobox genes are important transcriptional regulators in development, we searched for homeobox genes in the adult goldfish retina and brain. Using the PCR, we discovered a repertoire of homeobox sequences expressed in these tissues. In addition to isolating homeodomain sequences found in the vertebrate Hox gene clusters, a sequence identical to the chicken CHox7 homeodomain was characterized. Furthermore, a sequence with significant homologies to the Xenopus XIHbox8 and leech Htr-A2 homeodomains was identified, and these sequences may define an additional class of homeodomain. Finally, a sequence belonging to the paired class (prd) of homeodomains is reported. Homeobox gene expression in the adult goldfish retina and brain may be associated with the persistent developmental features of these tissues.

Expression of Cnox-2, a HOM/HOX homeobox gene in hydra, is correlated with axial pattern formation

Cnox-2 is a HOM/HOX homeobox gene that we have identified in the simple metazoan Hydra vulgaris (Cnidaria: Hydrozoa). Cnox-2 is most closely related to anterior members of the Antennapedia gene complex from Drosophila, with the greatest similarity to Deformed. The Cnox-2 protein is expressed in the epithelial cells of adult hydra polyps in a region-specific pattern along the body axis, at a low level in the head and at a high level in the body column and the foot. The expression pattern of Cnox-2 is consistent with a role in axial pattern formation. Alteration of hydra axial patterning by treatment with diacylglycerol (DAG) results in an increase of head activation down the body column and in a coordinate reduction of Cnox-2 expression in epithelial cells in ‘head-like’ regions. These results suggest that Cnox-2 expression is negatively regulated by a signaling pathway acting through protein kinase C (PKC), and that the varying levels of expression of Cnox-2 along the body axis have the potential to result in differential gene expression which is important for hydra pattern formation.

Colinearity in the Xenopus laevis Hox-2 complex

Here we describe experiments detailing the developmental expression, and the inducibility by all-trans retinoic acid (RA) of six members of the Xenopus Hox-2 complex of homeobox-containing genes. We first report the cloning and characterisation of two novel Xenopus Hox-2 genes (Xhox2.7 and Xhox2.9), and provide evidence that the six genes studied are indeed closely linked in the same chromosomal complex. We next show that all six genes are expressed in a spatial sequence which is colinear with their putative 3' to 5' chromosomal sequence and that five of them are also expressed in a 3' to 5' colinear temporal sequence. The sixth gene (Xhox2.9) has an exceptional spatial and temporal expression pattern. The six genes all respond to RA by showing altered spatiotemporal expression patterns, and are also hyperinduced by RA, with a sequence of magnitudes which is colinear with their 3' to 5' chromosomal sequence and with their spatial and temporal expression sequences. Our data also suggest a pre-existing anteroposterior polarity in the embryo's competence to respond to RA. These results complement and extend previous findings made using murine and avian embryos and mammalian cell lines. They suggest a mechanism whereby an endogenous retinoid could help to provide positional information in the early embryo.

The Antennapedia-type homeobox genes have evolved from three precursors separated early in metazoan evolution

The developmental control genes containing an Antennapedia-type homeobox are clustered in insects and vertebrates. The evolution of these genes was studied by the construction of evolutionary trees and by statistical geometry in sequence space. The comparative analysis of the homeobox sequences reveals the subdivision of the Antennapedia-type homeobox genes into three classes early in metazoan evolution. This observation suggests an important function of these genes even in the most primitive metazoans. Subsequent duplication events generated a cluster of at least five homeobox genes in the last common ancestor of insects and vertebrates. These genes later independently gave rise to the 13 groups of paralogous genes in vertebrates and to the 11 Antennapedia-type genes in the Drosophila complexes.

A novel murine homeobox gene isolated by a tissue specific PCR cloning strategy

We have identified a novel homeobox gene, designated K-2, using a reverse transcription PCR cloning strategy. Sequence analysis reveals that the homeobox of K-2 is 77.6% homologous at the nucleotide level and 97% identical at the amino acid sequence level to another murine gene, S8. Homeodomain sequence comparisons indicate that K-2 and S8 represent a distinct subclass of paired type homeobox genes. Northern blot analysis of RNA from murine embryos and adult tissues identified multiple transcripts that are expressed in a developmentally specific and tissue restricted manner. Alternate splicing of K-2 at the 3-coding region leads to the inclusion of a chain terminating sequence. In addition, the developmental expression pattern of this gene at day 12 of gestation was determined by in situ hybridization. Expression was observed in diverse mesenchymal cells in craniofacial, pericardial, primitive dermal, prevertebral, and genital structures.

Expression pattern of a murine homeobox gene, Dbx, displays extreme spatial restriction in embryonic forebrain and spinal cord

Homeobox genes specify regional identity during development. A homeobox sequence that we have named Dbx was isolated from 13.5-day embryonic mouse telencephalon cDNA. The Dbx homeodomain shows highest sequence homology to Drosophila H2.0 and chicken CHox E. We report here the expression pattern of Dbx during mouse embryogenesis. In situ hybridization analyses indicate that Dbx is expressed exclusively within the embryonic central nervous system in a highly restricted manner. Dbx transcripts are detected within a region of the prospective cerebral cortex of the midgestation telencephalon. Dbx is also expressed in the diencephalon as well as in two thin continuous columns of neuroblasts within the hindbrain and spinal cord. This expression is limited to regions of active mitosis. Dbx may act to specify subsets of neuroblasts during the development of the central nervous system.

Sequence and embryonic expression of the murine Hox-3.5 gene

The murine Hox-3.5 gene has been mapped and linked genomically to a position 18 kb 3′ of its most 5′ locus neighbour, Hox-3.4, on chromosome 15. The sequence of the Hox-3.5 cDNA, together with the position of the gene within the locus, show it to be a paralogue of Hox-2.6, Hox-1.4 and Hox-4.2. The patterns of embryonic expression for the Hox-3.5 gene are examined in terms of three rules, proposed to relate a Hox gene's expression pattern to its position within the locus. The anterior boundaries of Hox-3.5 expression in the hindbrain and prevertebral column lie anterior to those of Hox-3.4 and all other, more 5′-located Hox-3 genes. Within the hindbrain, the Hox-3.5 boundary is seen to lie posterior to that of its paralogue, Hox-2.6, by a distance equal to about the length of one rhombomere. Patterns of Hox-3.5 expression within the oesophagus and spinal cord, but not the testis, are similar to those of other Hox-3 genes, Hox-3.3 and Hox-3.4.

Identification of a homeobox-containing gene located between lin-45 and unc-24 on chromosome IV in the nematode Caenorhabditis elegans

Using two primers corresponding to helix 1 and helix 3 regions in the homeodomain, we subjected genomic DNA from Caenorhabditis elegans to amplification by the polymerase chain reaction. Sequence analysis of the amplified products revealed a new homeobox-containing gene, designated ceh-19. This gene was located between lin-45 and unc-24 on chromosome IV where no homeogene has previously been mapped.

Repression of the beta-amyloid gene in a Hox-3.1-producing cell line

Mammalian homeobox genes are widely expressed in the developing central nervous system and are postulated to control developmental processes by regulating gene expression at the transcriptional level. In vitro studies have identified consensus DNA sequences that contain an ATTA core as sites for interaction with homeodomain proteins. Such elements have been found in the upstream regulatory region of the gene encoding beta-amyloid precursor protein, which is associated with the neurological disorder Alzheimer disease. As the beta-amyloid precursor protein gene is also expressed in the developing central nervous system and appears to play a role in cellular regulatory processes, we have examined the possibility that a homeobox gene product can regulate its transcription. We demonstrate by Northern blot analyses and transfection experiments that the expression of the beta-amyloid precursor protein gene is decreased in cultured cells expressing the mouse homeobox gene Hox-3.1.