Checklist: vertebrate homeobox genes

Transcriptional interferences at the Hoxa4/Hoxa5 locus: importance of correct Hoxa5 expression for the proper specification of the axial skeleton

We have previously described a Hoxa5 mutant mouse line in which specification of axial identity is perturbed and viability is markedly reduced. In the present study, we assay the Hoxa5 mutation in different genetic backgrounds and carry out a complete analysis of skeletal transformations. Although Hoxa5 is expressed over a large domain during embryogenesis, homeotic transformations of the axial skeleton are confined between cervical vertebra C3 and thoracic vertebra T2, which corresponds to the specific expression domain of the major Hoxa5 transcript. Loss of Hoxa5 function also affects the formation of the acromion in the appendicular skeleton. Disruption of the adjacent Hoxa4 gene leads to similar homeotic transformations of the cervicothoracic vertebrae. To discriminate the respective role of each gene, we generated transheterozygous animals carrying inactivated Hoxa4 and Hoxa5 alleles on different chromosomes. Compound heterozygous mutants exhibit homeotic transformations in the cervicothoracic transition region more reminiscent to those observed in Hoxa5 homozygous mutants. Although the Hoxa5 mutation does not significantly affect Hoxa4 expression, the pattern of Hoxa5 expression is impaired in cis by the Hoxa4 mutation, specifically in the cervicothoracic region of the prevertebral column. The expression of Hoxa5 in this particular domain is also perturbed by the Hoxa5 mutation itself, raising the possibility of regional autoregulation. Altogether, these results demonstrate the crucial role of Hoxa5 in the specification of the cervical and upper thoracic region of the skeleton and establish the importance of its correct expression for the proper patterning of the embryo.

A distal-less class homeobox gene, DLX4, is a candidate for regulating epithelial-mesenchymal cell interactions in the human placenta

Homeobox genes of the Distal-less (Dlx) family are expressed in the vertebrate embryo in regions where epithelial cell layers contact adjacent mesenchymal cells. This study shows that the human Dlx family member, DLX4, is expressed in the placenta, primarily in regions where epithelial and mesenchymal cell layers contact. In situ hybridization studies at first trimester human placental sections revealed that DLX4 was expressed predominantly in the cytotrophoblast stem cell layer. In term placenta, DLX4 was expressed in the syncytiotrophoblast. Northern analysis revealed two DLX4 transcripts in first trimester placenta of 2.8 and 3.0 kb. Elevated levels of DLX4 mRNA were detected in a choriocarcinoma derived cell line when compared with a cytotrophoblast cell line and normal placenta. This is the first study to show that a member of the Dlx family of homeobox genes is expressed in regions of epithelial and mesenchymal cell layer contact in the human. Accumulated evidence from several studies suggest that a combinatorial code of homeobox genes is required to regulate epithelial-mesenchymal cell interactions in the vertebrate embryo. It is predicted that a similar combination of homeobox genes, that includes DLX4, is involved in regulating epithelial-mesenchymal cell interactions in extraembryonic tissues. DLX4 may also have a role in the regulation of the genes important for trophoblast invasion since the level of expression in trophoblast cell lines reflects invasive potential.

Early postnatal lethality in Hoxa-5 mutant mice is attributable to respiratory tract defects

To uncover roles for the Hoxa-5 gene during embryogenesis, we have focused on identifying structural and functional defects in organ systems underlying the perinatal lethality in Hoxa-5 homozygous mutants. Analysis of the mutant phenotype shows that Hoxa-5 is essential for normal organogenesis and function of the respiratory tract. In homozygous newborn mutants, improper tracheal and lung morphogenesis can lead to tracheal occlusion, and to respiratory distress associated with a marked decrease in the production of surfactant proteins. Collectively, these defects likely underlie the pronounced mortality of homozygous mutant pups. Furthermore, the loss of Hoxa-5 function results in altered TTF-1, HNF-3 beta, and N-myc gene expression in the pulmonary epithelium. Since expression of Hoxa-5 is confined to the mesenchymal component of the developing trachea and lung, the effects observed in epithelial cells may result from a disruption of normal epithelial-mesenchymal interactions.

Molecular cloning, chromosomal mapping and developmental expression of BAPX1, a novel human homeobox-containing gene homologous to Drosophila bagpipe

We describe here the cloning of the human BAPX1 gene, a homologue of the Drosophila bagpipe gene which has 87% aa identity within the homeodomain relative to the fly gene. We recently have identified the murine bagpipe homolog. The predicted aa sequence of the human gene has 85% overall identity to the murine gene, with 100% identity in the homeodomain. In mouse, this gene maps to the proximal portion of chromosome 5. We show that the human gene maps to 4p16.1, the human region syntenic with mouse chromosome 5. Expression of BAPX1 was evaluated during human embryonic development by RT-PCR analysis and by RNA in situ hybridization. RT-PCR analysis showed that BAPX1 is expressed in embryo tissues, particularly the limb, and at a lower level in an embryonic lung cell line. RNA in situ hybridization revealed that BAPX1 is predominantly expressed in mesenchymal condensations of the fetal limb and axial skeleton, and in lateral plate mesoderm giving rise to visceral muscle. The expression pattern of BAPX1 combined with the chromosomal localization to 4p16.1, where several human genetic diseases involving dysmorphology of the skeleton have been assigned, raises the potential of it being a candidate gene for one of these disorders. O

The expression domain of two related homeobox genes defines a compartment in the chicken inner ear that may be involved in semicircular canal formation

Homeobox-containing genes encode a class of proteins that control patterning in developing systems, in some cases by acting as selector genes that define compartment identity. In an effort to demonstrate a similar role for such genes during ear development in the chicken, we present a detailed expression study of two related homeobox-containing genes, SOHo-1 and GH6, using in situ hybridization. At otocyst stages the two genes define a broad lateral domain of expression, which may represent a developmental compartment. Three-dimensional computer reconstructions of SOHo-1 expression at these and later stages revealed that the lateral domain becomes progressively restricted to the three semicircular canals. Thus, SOHo-1 and GH6 are among a small group of markers for a specific structural component of the inner ear. The gene expression domain initially includes the sensory regions of the semicircular canals, known as the cristae ampullaris, but none of the other four sensory organs which were recognizable by BMP4 expression during early morphogenesis (stages 19-24). Significantly, two of the sensory organs (the superior and posterior cristae) were found at the limits, or boundaries, of the SOHo-1/GH6 expression domain, suggesting that compartment boundaries may be involved in specifying sensory organ location as well as identity. Maintained expression at the boundaries may aid in specifying the location of canal outgrowth. These concepts are presented as a formal model which emphasizes that patterning information could be provided at the boundaries of gene expression domains in the inner ear.

Embryonic expression and characterization of a Ptx1 homolog in Drosophila

We describe the molecular characterization of the paired-type homeobox gene D-Ptx1 of Drosophila, a close homolog of the mouse pituitary homeobox gene Ptx1 and the unc-30 gene of C. elegans, characterized by a lysine residue at position 9 of the third alpha-helix of the homeodomain. D-Ptx1 is expressed at various restricted locations throughout embryogenesis. Initial expression of D-Ptx1 in the posterior-most region of the blastoderm embryo is controlled by fork head activity in response to the activated Ras/Raf signaling pathway. During later stages of embryonic development. D-Ptx1 transcripts and protein accumulate in the posterior portion of the midgut, in the developing Malpighian tubules, in a subset of ventral somatic muscles, and in neural cells. Phenotypic analysis of gain-of-function and lack-of-function mutant embryos show that the D-Ptx1 gene is not involved in morphologically apparent differentiation processes. We conclude that D-Ptx1 is more likely to control physiological cell functions than pattern formation during Drosophila embryogenesis.

Anf: a novel class of vertebrate homeobox genes expressed at the anterior end of the main embryonic axis

Five novel genes homologous to the homeobox-containing genes Xanf-1 and Xanf-2 of Xenopus and Hesx-1/Rpx of mouse have been identified as a result of a PCR survey of cDNA in sturgeon, zebrafish, newt, chicken and human. Comparative analysis of the homeodomain primary structure of these genes revealed that they belong to a novel class of homeobox genes, which we name Anf. All genes of this class investigated so far have similar patterns of expression during early embryogenesis, characterized by maximal transcript levels being present at the anterior extremity of the main embryonic body axis. The data obtained also suggest that, despite considerable high structural divergence between their homeodomains, all known Anf genes may be orthologues, and thus represent one of the most quickly evolving classes of vertebrate homeobox genes.

Homeobox genes in embryogenesis and pathogenesis

The homeobox, a 60-amino acid-encoding DNA sequence, originally discovered in the genome of the fruit fly Drosophila, was subsequently identified throughout the three kingdoms of multicellular organisms. Homeobox-containing genes encode DNA-binding proteins that regulate gene expression and control various aspects of morphogenesis and cell differentiation. In particular, the Hox family of clustered homeobox genes plays a fundamental role in the morphogenesis of the vertebrate embryo, providing cells with regional information along the main body axis. The nonclustered or divergent homeobox genes include a large number of genes scattered throughout the genome that, nevertheless, can be organized in distinct families based on their homologies and functional similarities. This review will provide the reader with a brief overview on some recent studies aimed at understanding the functional role of homeobox genes in normal mammalian development as well as their involvement in congenital malformations and oncogenesis.

Gastrulation and homeobox genes in chick embryos

We review the early stages of chick embryogenesis, in particular the formation of the hypoblast, and the ingression of endoderm and mesoderm through the primitive streak. The formation of a trilaminar embryo during gastrulation is accompanied by the specification of body axes. The first axis is already present in the unfertilized egg and runs from the cytoplasmatic animal to the yolk rich vegetal pole. Already within the uterus a second axis conveys bilateral symmetry to the embryo. It extends from a dorsal/anterior to a ventral/posterior position. These axial poles segregate during gastrulation to form the classical coordinates, a dorsal-ventral and an anterior-posterior axis. The establishment of axes is accompanied by the expression of specific combinations of homeobox genes during gastrulation in the chick, as in other metazoa. We review the avian specific information and compare it with findings in other species. A combinatorial homeobox code for the specification of identities during development is discussed.

Chicken Nkx-2.8: a novel homeobox gene expressed in early heart progenitor cells and pharyngeal pouch-2 and -3 endoderm

Members of the NK family of homeobox transcription factors regulate critical steps of organogenesis during vertebrate development. In the studies described in this report, we have isolated and functionally characterized the chicken Nkx-2.8 (cNkx-2.8) cDNA and protein and defined the temporal and spatial pattern of cNkx-2.8 gene expression during chicken development. cNkx-2.8 transcripts are first detectable at HH stage 7 in the splanchnopleura. At stage 10(+), the cNkx-2.8 gene is expressed in the linear heart tube and the dorsal half of the vitelline vein. However, after looping, HH stage 13, cNkx-2.8 is no longer expressed in the looped heart tube, but is expressed in the ventral pharyngeal endoderm. At stage 15, in addition to the pharyngeal expression pattern, cNkx-2.8 is expressed in the ectoderm of the pharyngeal arches and the aortic sac. By HH Stage 17, cNkx-2.8 expression is detectable in lateral endoderm of the second and third pharyngeal pouches, the posterior portion of the aortic sac, and the sinus venosus. cNkx-2.8 binds to previously characterized Nkx2-1 and Nkx2-5 DNA-binding sites and overexpression of cNkx-2.8 transactivates a minimal promoter which contains multimerized Nkx-2 DNA-binding sites. In addition, cNkx-2.8 and serum response factor can coactivate a minimal cardiac alpha-actin promoter. These data are consistent with a model in which cNkx-2.8 performs a unique temporally and spatially restricted function in the developing embryonic heart and pharyngeal region. Moreover, the coexpression of cNkx-2.5 and -2.8 raises the possibility that cNkx-2. 8 may have a redundant role with cNkx-2.5 in the coalescing heart tube and may play an important role in the transcriptional program(s) that underlies thymus formation. The existence of multiple NK-2 family members and their partially overlapping patterns of expression are discussed within the framework of a "Nkx code."

The signaling pathway mediated by the type IIB activin receptor controls axial patterning and lateral asymmetry in the mouse

Vertebrate animals exhibit segmented axial skeletons and lateral asymmetry of the visceral organs. The segment identity of individual vertebrae is believed to be determined by a combination of functionally active Hox genes that have defined expression boundaries along the anteroposterior axis (known as the axial Hox code). Disturbance of the Hox code by ectopic expression or mutation of Hox genes often leads to homeotic transformation of the vertebrae. Largely unknown, however, are the signaling molecules that provide the positional cues for the precise establishment and maintenance of the Hox code. In this study we show that disruption of the type IIB activin receptor (ActRIIB) by gene targeting results in altered expression of multiple Hox genes and abnormal patterning of the vertebrae, similar to but severer than retinoic acid (RA)-induced anterior transformation. We further show that RA and ActRIIB mutation have synergistic effects on vertebral patterning. Activin, Vg-1 and, type II activin receptors have been implicated in regulation of lateral asymmetry during chick and Xenopus development. We show here that the ActRIIB-/- mice die after birth with complicated cardiac defects including randomized heart position, malposition of the great arteries, and ventricular and atrial septal defects. In addition, the heart anomalies are associated with right pulmonary isomerism and splenic abnormalities, recapitulating the clinical symptoms of the human asplenia syndrome. These findings provide genetic evidence that the ActRIIB-mediated signaling pathway plays a critical role in patterning both anteroposterior and left-right axes in vertebrate animals.

Two Otx proteins generated from multiple transcripts of a single gene in Strongylocentrotus purpuratus

Orthodenticle-related (Otx) proteins are a highly conserved class of homeobox-containing transcription factors found in a wide range of organisms. They function in numerous developmental events, most prominently, anterior head patterning in insects and vertebrates. In the sea urchin, Strongylocentrotus purpuratus, an orthodenticle-related protein called SpOtx is believed to direct the activation of the aboral ectoderm-specific Spec2a gene and more generally the differentiation of aboral ectoderm cells. To learn more about the structure, expression, and function of SpOtx and compare its properties with those of orthologs from other species, we isolated cDNA and genomic clones containing SpOtx sequences. Here, we report that SpOtx exists in two forms (alpha and beta) that are generated by alternative RNA splicing from a single SpOtx gene. SpOtx(alpha) and SpOtx(beta) had identical C-termini and homeoboxes but were entirely different in their N-terminal domains. SpOtx(alpha) mRNAs were transcribed from a single start site and accumulated in all cells during cleavage, but were gradually concentrated in oral ectoderm and vegetal plate territories during gastrulation. In contrast, three distinct SpOtx(beta) mRNAs resulted from two separate transcriptional initiation events, and these transcripts began to accumulate at mesenchyme blastula stage primarily in ectoderm and then later were largely restricted to oral ectoderm and vegetal plate territories. DNA-binding activity for SpOtx(beta) appeared later in development than SpOtx(alpha). Overexpression of SpOtx(alpha) and SpOtx(beta) induced in sea urchin embryos by mRNA injection demonstrated that SpOtx(alpha) was able to repress the accumulation of SpOtx(beta) transcripts, whereas SpOtx(beta) had no effect on the accumulation of SpOtx(alpha) transcripts. These results demonstrate that novel forms of Otx are produced in sea urchins by differential promoter utilization and alternative splicing. It may be that similar regulatory mechanisms lead to diverse forms of Otx in vertebrates.

Spx1, a novel X-linked homeobox gene expressed during spermatogenesis

Spx1, a novel mouse homeobox gene, encodes a homeodomain characteristic of the paired-like class of homeobox genes and has been mapped to the distal end of the X chromosome. Northern blot hybridization of adult tissues detected high levels of a single Spx1 transcript in the testis. Further analysis by in situ hybridization revealed predominant Spx1 expression within the spermatogonia/preleptotene spermatocytes and round spermatids of spermatogenic stages IV-VII. These expression data suggest SPX1 may play a role in the regulation of spermatogenesis.

Homeobox genes and disease

To date, not many disorders have been associated with homeobox genes, especially with those belonging to the HOX family. This is particularly surprising, considering the body of evidence accumulated for a role of these genes in the control of mammalian development. Recently, this situation has changed and some congenital or somatic defects have been demonstrated to involve mutations in homeobox genes of the HOX, EMX, PAX, and MSX families, as well as in other novel genes containing either a paired- or bicoid-type homeobox.

Patterning of the mammalian dentition in development and evolution

The mammalian dentition is a segmented organ system with shape differences among its serially homologous elements (individual teeth). It is believed to have evolved from simpler precursors with greater similarities in shape among teeth, and a wealth of descriptive data exist on changes to the dentition that have occurred within mammals. Recent progress has been made in determining the genetic basis of the processes that form an individual tooth, but patterning of the dentition as a whole (i.e. the number, location and shape of the teeth) is less well understood. In contrast to similarly organized systems, such as the vertebral column and limb, Hox genes are not involved in specifying differences among elements. Nevertheless, recent work on a variety of systems is providing clues to the transcription factors and extracellular signalling molecules involved.

Salivary glands: a paradigm for diversity of gland development

The major salivary glands of mammals are represented by three pairs of organs that cooperate functionally to produce saliva for the oral cavity. While each type of gland produces a signature secretion that complements the secretions from the other glands, there is also redundancy as evidenced by secretion of functionally similar and, in some cases, identical products in the three glands. This, along with their common late initiation of development, in fetal terms, their similarities in developmental pattern, and their proximate sites of origin, suggests that a common regulatory cascade may have been shared until shortly before the onset of overt gland development. Furthermore, occasional ectopic differentiation of individual mature secretory cells in the "wrong" gland suggests that control mechanisms responsible for the distinctive cellular composition of each gland also share many common steps, with only minor differences providing the impetus for diversification. To begin to address this area, we examine here the origins of the salivary glands by reviewing the expression patterns of several genes with known morphogenetic potential that may be involved based on developmental timing and location. The possibility that factors leading to determination of the sites of mammalian salivary gland development might be homologous to the regulatory cascade leading to salivary gland formation in Drosophila is also evaluated. In a subsequent section, cellular phenotypes of neonatal and adult glands are compared and evaluated for insights into the mechanisms and lineages leading to cellular diversification. Finally, the phenomena of proliferation, repair, and regeneration in adult salivary glands are reviewed, with emphasis on the extent to which the cellular diversity is reversible and which cell type other than stem cells has the ability to redifferentiate into other cell types.

Prostate-specific and androgen-dependent expression of a novel homeobox gene

A new member of the mouse NK family of homeobox genes that is related to Drosophila NK-3 has been identified. Expression of this gene, termed Nkx-3.1, is largely restricted to the prostate gland in adult animals. The level of Nkx-3.1 mRNA decreases markedly in response to castration, suggesting that its expression is androgen-dependent. In situ hybridization analyses demonstrated that expression of Nkx-3.1 in the prostate is confined to epithelial cells. In newborns, Nkx-3.1 mRNA is detected in the urethral epithelium that is being induced by the surrounding mesenchyme to invaginate to form prostatic buds. Together, these observations suggest that the Nkx-3.1 protein, which likely functions as a transcription factor, plays a prominent role both in the initiation of prostate development and in the maintenance of the differentiated state of prostatic epithelial cells.

Pancreatic-duodenal homeobox 1 -role in gastric endocrine patterning

The gastrointestinal tract is subdivided into regions with different roles in digestion and absorption. How this patterning is established is unknown. We now report that the pancreatic-duodenal homeobox 1 gene (pdx1) is also expressed in cells of the distal stomach. Positive cells include subpopulations of the three main endocrine (gastrin, somatostatin and serotonin) cell types of this region. Pdx1 deficient mice were virtually devoid of gastrin cells, had normal numbers of somatostatin cells and increased numbers of serotonin cells. Pdx1 is thus important for development of the gastrin cells of the antropyloric mucosa of the stomach and probably acts by controlling the fate of gastrin/serotonin precursor cells.

The caudal-related homeodomain protein Cdx-2/3 regulates glucagon gene expression in islet cells

Glucagon gene transcription in the endocrine pancreas is regulated by at least four cis-acting DNA control elements. We showed previously that G1 is critical for alpha cell-specific expression. G1 contains three AT-rich sequences important for promoter function, which represent candidate binding sites for homeodomain transcription factors. Performing reverse transcription-polymerase chain reaction amplifications with degenerate oligonucleotide primers homologous to the Antennapedia homeobox, cDNA clones corresponding to the caudal-related gene cdx-2/3 were predominantly obtained from glucagon-producing cells and primary non-beta cells. From RNase protection and polymerase chain reaction analyses, cdx-2/3 turned out to be the only caudal-related gene that is expressed at significant levels in cells of the endocrine pancreas. Cdx-2/3 binds with high affinity to an AT-rich motif of G1, which matches the consensus binding site of caudal-related proteins. In the glucagon-producing hamster cell line InR1G9, Cdx-2/3 is a subunit of complex B3 formed on G1. Alternative splicing generates two cdx-2/3 transcripts in islet cells, coding for a full-length protein and an amino-terminally truncated isoform. Although both isoforms bind G1 with similar affinity, only the full-length Cdx-2/3 A protein activates glucagon gene transcription in non-glucagon-producing cells, transcriptional activation being dose-dependent. We therefore conclude that the caudal-related gene cdx-2/3 is implicated in the transcriptional control of glucagon gene expression in the alpha cells of the islets of Langerhans.

Cloning and characterization of four murine homeobox genes

Four novel murine homeobox genes, Uncx-4.1, OG-2, OG-9, and OG-12, were cloned and partially sequenced. The amino acid sequence of the mouse Uncx-4.1 homeodomain is closely related to the sequence of the unc-4 homeodomain of Caenorhabditis elegans. However, the OG-2, OG-9, and OG-12 homeodomains are relatively diverged and are not closely related to any previously described homeodomain. Northern blot analyses revealed multiple bands of Uncx-4.1, OG-2, OG-9, and OG-12 poly(A)+ RNA in RNA from mouse embryos and adults that change during development and showed that each gene is expressed in a tissue-specific manner. OG-12 cDNAs were cloned that correspond to two alternatively spliced species of OG-12 mRNA. Three major bands of Uncx-4.1 poly(A)+ RNA were found only in RNA from adult mouse brain, but an additional band was observed in RNA from all of the other tissues tested. Major bands of OG-9 and OG-2 poly(A)+ RNA were found only in RNA from striated muscle; however, trace bands were detected in RNA from other tissues.