Homeobox-containing Gene Research Articles

Identification and expression pattern of zebrafish prox2 during embryonic development

Prox2, together with the previously isolated Prox1, is the vertebrate homolog of the Drosophila homeobox-containing gene prospero, the founder member of a family of transcription factors which have been shown to play critical roles in many developmental events. We have isolated a cDNA which encodes a putative protein that shares a high degree of homology with mammalian Prox1, Prox2, and zebrafish Prox1. Comparative genomic analysis revealed that this protein corresponds to the zebrafish Prox2 homolog being the gene syntenic with the chromosome region hosting mouse Prox2. Whole-mount in situ experiments demonstrated that prox2 is expressed, during zebrafish embryonic development, in defined structures of the central nervous system and the eye, as previously reported in mouse. Additionally, reverse transcriptase-polymerase chain reaction analysis disclosed prox2 expression in several adult organs. Finally, prox1 loss- and gain-of-function assays have been carried out to search for regulative effects on prox2 expression.

Expression Profile of Selected HOX Genes in Different Childhood ALL Subtypes

Homeobox-containing (HOX) genes represent a large family of transcription factors that are involved in anteroposterior pattern formation during embryonic organogenesis. Besides their role in ontogenesis, various HOX genes have been associated with haematologic disorders including leukaemia. Multiple studies revealed that dysregulation of HOX genes is relevant to AML, ALL and CML; in addition, HOX genes are rearranged in some cases of human leukaemia and make part of fusion proteins such as NUP98-HOXA9, PBX1-E2A, etc. We have previously studied the pattern of HOX gene expression in chromosomally defined subsets of acute myeloid leukaemia and have shown that HOX genes exhibit a specific expression pattern throughout the AML subsets that can be related to the patient outcome. In this study, we studied the expression profile of various HOX genes in childhood acute lymphoblastic leukaemia (ALL) subtypes. We analysed mRNA levels of 23 different homeobox-containing genes in 59 children patients with ALL that were divided into six groups based on cytogenetic abnormalities and prednisone responsiveness: BCR/ABL, hyperdiploid ALL, TEL/AML1, MLL/AF4, T-ALL, prednisone good responders (PGR) and prednisone poor responders (PPR). Patient cDNA samples were analyzed using SYBRGreen I real-time quantitative PCR (qRT-PCR) and data obtained were normalized to the expression of ABL control gene. Our data indicate that certain HOX genes including HOXA3, HOXA4, HOXA5, HOXA6, HOXA9, HOXA10, HOXB2 or HOXB3 are differentially expressed throughout the ALL subtypes. Most notably, HOXA4, HOXA9, HOXB2 and HOXB3 mRNA levels appear to be elevated in T-ALL patients; hyperdiploid ALL patients display increased HOXA5 mRNA levels and HOXA3, HOXA6, HOXA9 and HOXA10 expression is higher in patients bearing the MLL/AF4 fusion gene. A relatively high level of HOXA5, HOXB2 and HOXB3 expression was observed in all patient groups. Furthermore, HOX gene expression distinguishes PGR from PPR group of patients; this divergence is most apparent in the case of HOXB2, HOXB3 and HOXB7. This study shows potential prognostic relevance of HOX gene levels in patients with childhood ALL. Data also confirm the differential HOX gene expression in various childhood ALL subtypes and underline the importance of certain HOX genes in leukemogenesis.

Timing of Genome Duplications Relative to the Origin of the Vertebrates: Did Cyclostomes Diverge before or after?

Two rounds of whole-genome duplications are thought to have played an important role in the establishment of gene repertoires in vertebrates. These events occurred during chordate evolution after the split of the urochordate and cephalochordate lineages but before the radiation of extant gnathostomes (jawed vertebrates). During this interval, diverse agnathans (jawless fishes), including cyclostomes (hagfishes and lampreys), diverged. However, there is no solid evidence for the timing of these genome duplications in relation to the divergence of cyclostomes from the gnathostome lineage. We conducted cDNA sequencing in diverse early vertebrates for members of homeobox-containing (Dlx and ParaHox) and other gene families that would serve as landmarks for genome duplications. Including these new sequences, we performed a molecular phylogenetic census using the maximum likelihood method for 55 gene families. In most of these gene families, we detected many more gene duplications before the cyclostome-gnathostome split, than after. Many of these gene families (e.g., visual opsins, RAR, Notch) have multiple paralogs in conserved, syntenic genomic regions that must have been generated by large-scale duplication events. Taken together, this indicates that the genome duplications occurred before the cyclostome-gnathostome split. We propose that the redundancy in gene repertoires possessed by all vertebrates, including hagfishes and lampreys, was introduced primarily by genome duplications. Apart from subsequent lineage-specific modifications, these ancient genome duplication events might serve generally to distinguish vertebrates from invertebrates at the genomic level.

Eye formation in the absence of retina

Eye development is a complex process that involves the formation of the retina and the lens, collectively called the eyeball, as well as the formation of auxiliary eye structures such as the eyelid, lacrimal gland, cornea and conjunctiva. The developmental requirements for the formation of each individual structure are only partially understood. We have shown previously that the homeobox-containing gene Rx is a key component in eye formation, as retinal structures do not develop and retina-specific gene expression is not observed in Rx-deficient mice. In addition, Rx−/− embryos do not develop any lens structure, despite the fact that Rx is not expressed in the lens. This demonstrates that during normal mammalian development, retina-specific gene expression is necessary for lens formation. In this paper we show that lens formation can be restored in Rx-deficient embryos experimentally, by the elimination of β-catenin expression in the head surface ectoderm. This suggests that β-catenin is involved in lens specification either through Wnt signaling or through its function in cell adhesion. In contrast to lens formation, we demonstrate that the development of auxiliary eye structures does not depend on retina-specific gene expression or retinal morphogenesis. These results point to the existence of two separate developmental processes involved in the formation of the eye and its associated structures. One involved in the formation of the eyeball and the second involved in the formation of the auxiliary eye structures.

Identification and characterization of cryptic SHOX intragenic deletions in three Japanese patients with Léri–Weill dyschondrosteosis

Although short-stature homeobox-containing gene (SHOX ) haploinsufficiency is responsible for Léri-Weill dyschondrosteosis (LWD), the molecular defect has not been identified in approximately 20% of Japanese LWD patients. Furthermore, although high prevalence of microdeletions affecting SHOX is primarily ascribed to the presence of repeat sequences such as Alu elements around SHOX, it remains to be determined whether microdeletions are actually mediated by repeat sequences. We performed multiple ligation probe amplification (MLPA) assay in six Japanese LWD patients with apparently normal SHOX, followed by fluorescent in situ hybridization (FISH) analysis and sequencing for polymerase chain reaction (PCR) products encompassing the deletion junctions in patients with abnormal MLPA patterns. Consequently, heterozygous intragenic deletions were identified in three cases, i.e., a 5,906-bp deletion involving exons 4-5 in case 1, a 5,594-bp deletion involving exons 4-6a in case 2, and a 50,199-bp deletion involving exons 4-6b in case 3. The deletion breakpoints of cases 1 and 2 were present in nonrepeat sequences, whereas those of case 3 resided within Alu elements. The results suggest that cryptic SHOX intragenic deletions account for a small fraction of LWD and that microdeletions affecting SHOX can be generated by repeat-sequence-mediated aberrant recombinations and by nonhomologous end joining.

Clinical Indicators for

Mutations or deletions of the short stature homeobox-containing gene (SHOX, which is found on the short arm of the X and Y chromosomes in the

Involvement of hormones and KNOXI genes in early Arabidopsis seedling development

Plant hormones control plant development by modulating the expression of regulatory genes, including homeobox-containing KNOXI genes. However, much remains to be elucidated about the interactions involved. Therefore, hormonal regulation of KNOXI gene expression was investigated using hormone applications and an inducible transgenic ipt expression system to increase endogenous cytokinin (CK) levels. Treatments with auxin, abscisic acid (ABA), cytokinins, ethylene, and gibberellin (GA) did not result in ectopic expression of the BP (BREVIPEDICELLUS) gene. However, BP expression was strongly reduced by ABA, increased by auxin treatment (correlating with the initiation of lateral root meristems, which strongly express BP), and did not significantly respond to short-term treatments with the other hormones in whole seedlings. Following short-term ipt activation, organ-specific differential regulation of KNOXI gene expression was observed. While several KNOXI genes were transiently up-regulated to low levels, STM was selectively repressed (especially at low light) in hypocotyls. In cotyledons, activation of CK-responsive genes preceded ipt induction, suggesting that CKs are transported more rapidly than the inducing agent (dexamethasone). Long-term increases in CK levels induced raised levels of several KNOXI transcripts in hypocotyls, correlating with the radial expansion of vascular tissues, the main domains of KNOXI gene expression, suggesting that CKs had little effect on KNOXI promoter activity. No alterations in hormone sensitivity were observed in a bp null mutant. Constitutive BP overexpression caused reductions in the length and number of lateral roots, while the primary root remained unaffected. The transgenic seedlings displayed weak, but significant, alterations in sensitivity to ABA, CK, and 1-amino-cyclopropane-1-carboxylic acid.

Formation and patterning of the avian neuraxis: one dozen hypotheses.

Formation of the neuraxis is dependent on cell-cell interactions and cell movements beginning during stages of gastrulation. Cell movements bring together new combinations of cells, allowing sequential inductive interactions to occur and leading to the specification of the neural plate and to its ultimate mediolateral (subsequently dorsoventral) and rostrocaudal patterning. Formation of the neural plate involves changes in the shape of its constituent cells and the first appearance of neural-specific cell markers. Shortly after the neural plate forms it undergoes 'shaping', in which the pseudostratified columnar epithelium constituting the neural plate thickens apicobasally, narrows transversely and extends longitudinally. Shaping is driven by three principal intrinsic types of cell behaviour: changes in cell shape, position and number. The next stage of neurulation begins while shaping is underway--bending of the neural plate. Bending involves two main processes, furrowing and folding. Furrowing of the neural plate is associated with the formation of the hinge points; these are localized, longitudinal areas where the neuroepithelium is attached to adjacent tissues and where wedging of neuroepithelial cells occurs. Cell wedging in the median hinge point occurs as a result of inductive interactions with the notochord; such wedging drives furrowing, thereby facilitating subsequent folding. Folding of the neural plate requires extrinsic forces generated largely by the surface ectoderm. Types of cell behaviour that could provide such forces include changes in cell shape, position and number. As a result of shaping and bending of the neural plate, the neural folds are brought into apposition in the dorsal midline. Final closure of the neural groove is mediated by cell surface glycoconjugates coating the apical surfaces of the neural folds. Patterning of the neuraxis begins during shaping of the neural plate and continues throughout stages of neurulation and into early postneurula stages. Patterning probably involves inductive interactions with adjacent tissues and the expression of putative positional identity genes such as homeobox-containing genes.

A high-throughput method for monitoring changes in homeobox gene expression

Members of the homeobox gene superfamily of transcription factors are essential determinants of cellular identity during development. Their regulation and downstream gene targets are not well understood, however. This is due, in part, to the large number of genes that need to be analyzed simultaneously. A method has been developed for the rapid and simultaneous detection of changes in the expression of homeobox-containing genes, including members of the developmentally important Hox gene family. The method selectively amplifies and labels homeobox-containing mRNAs using a 3′-RACE procedure in combination with a degenerate forward primer that targets a highly conserved region of the homeobox found in all vertebrate Hox genes and many non- Hox homeobox-containing genes. The amplified sequences are identified by hybridization to a membrane-based array of covalently bound Hox and non- Hox homeobox gene sequences of interest. The method has been used here to demonstrate previously undetected changes in the expression of homeobox genes during retinoic acid-induced nerve cell differentiation in mouse pluripotent P19 cells.

Mutations in HOXD13 Underlie Syndactyly Type V and a Novel Brachydactyly-Syndactyly Syndrome

HOXD13, the homeobox-containing gene located at the most 5' end of the HOXD cluster, plays a critical role in limb development. It has been shown that mutations in human HOXD13 can give rise to limb malformations, with variable expressivity and a wide spectrum of clinical manifestations. Polyalanine expansions in HOXD13 cause synpolydactyly, whereas amino acid substitutions in the homeodomain are associated with brachydactyly types D and E. We describe two large Han Chinese families with different limb malformations, one with syndactyly type V and the other with limb features overlapping brachydactyly types A4, D, and E and mild syndactyly of toes 2 and 3. Two-point linkage analysis showed LOD scores >3 (theta =0) for markers within and/or flanking the HOXD13 locus in both families. In the family with syndactyly type V, we identified a missense mutation in the HOXD13 homeodomain, c.950A-->G (p.Q317R), which leads to substitution of the highly conserved glutamine that is important for DNA-binding specificity and affinity. In the family with complex brachydactyly and syndactyly, we detected a deletion of 21 bp in the imperfect GCN (where N denotes A, C, G, or T) triplet-containing exon 1 of HOXD13, which results in a polyalanine contraction of seven residues. Moreover, we found that the mutant HOXD13 with the p.Q317R substitution was unable to transactivate the human EPHA7 promoter. Molecular modeling data supported these experimental results. The calculated interactions energies were in agreement with the measured changes of the activity. Our data established the link between HOXD13 and two additional limb phenotypes--syndactyly type V and brachydactyly type A4--and demonstrated that a polyalanine contraction in HOXD13, most likely, led to other digital anomalies but not to synpolydactyly. We suggest the term "HOXD13 limb morphopathies" for the spectrum of limb disorders caused by HOXD13 mutations.

Different skeletal phenotypes in a mother and two daughters with short stature homeobox-containing haploinsufficiency.

Haploinsufficiency of the short stature homeobox-containing (SHOX) gene causes Turner skeletal features such as short metacarpals, cubitus valgus, and Madelung deformity. We report the clinical findings of a Japanese family consisting of two daughters with SHOX haploinsufficiency (46, X, del(X) (p.22.3)) and their mother with 45,X [9]/ 46, X, del(X) (p22.3) [11] karyotype. Physical and auxological examinations revealed a mesomelic appearance, cubitus valgus, a short neck and short stature in the daughters, but on the other hand, only a short neck and short stature in the mother. Radiological studies indicated markedly curved radii in the daughters, but only mild curvature of the radii in the mother. Regular menstruation had taken place since the age of 12 yr in the elder daughter, but the mother had irregular menstruation and she had received fertility treatment for pregnancy. The different skeletal phenotypes of the mother and her daughters with SHOX haploinsufficiency might be due to the mild gonadal estrogen deficiency found in the mother, which was caused by mosaic Turner syndrome, and the phenotypic variability of SHOX haploinsufficiency.

A mechanism for the sharp transition of morphogen gradient interpretation in Xenopus

BackgroundOne way in which positional information is established during embryonic development is through the graded distribution of diffusible morphogens. Unfortunately, little is known about how cells interpret different concentrations of morphogen to activate different genes or how thresholds are generated in a morphogen gradient.ResultsHere we show that the concentration-dependent induction of the T-box transcription factor Brachyury (Xbra) and the homeobox-containing gene Goosecoid (Gsc) by activin in Xenopus can be explained by the dynamics of a simple network consisting of three elements with a mutual negative feedback motif that can function to convert a graded signal (activin) into a binary output (Xbra on and Gsc off, or vice versa). Importantly, such a system can display sharp thresholds. Consistent with the predictions of our model, Xenopus ectodermal cells display a binary response at the single cell level after treatment with activin.ConclusionThis kind of simple network with mutual negative feedback might provide a general mechanism for selective gene activation in response to different levels of a single external signal. It provides a mechanism by which a sharp boundary might be created between domains of different cell types in response to a morphogen gradient.

Genotypes and phenotypes in children with short stature: clinical indicators of SHOX haploinsufficiency

Background: Short stature affects approximately 2% of children, representing one of the more frequent disorders for which clinical attention is sought during childhood. Despite assumed genetic heterogeneity, mutations or deletions...

Growth Hormone Is Effective in Treatment of Short Stature Associated with Short Stature Homeobox-Containing Gene Deficiency: Two-Year Results of a Randomized, Controlled, Multicenter Trial

The short stature homeobox-containing gene, SHOX, located on the distal ends of the X and Y chromosomes, encodes a homeodomain transcription factor responsible for a significant proportion of long-bone growth. Patients with mutations or deletions of SHOX, including those with Turner syndrome (TS) who are haplo-insufficient for SHOX, have variable degrees of growth impairment, with or without a spectrum of skeletal anomalies consistent with dyschondrosteosis. Our objective was to determine the efficacy of GH in treating short stature associated with short stature homeobox-containing gene deficiency (SHOX-D). Fifty-two prepubertal subjects (24 male, 28 female; age, 3.0-12.3 yr) with a molecularly proven SHOX gene defect and height below the third percentile for age and gender (or height below the 10th percentile and height velocity below the 25th percentile) were randomized to either a GH-treatment group (n = 27) or an untreated control group (n = 25) for 2 yr. To compare the GH treatment effect between subjects with SHOX-D and those with TS, a third study group, 26 patients with TS aged 4.5-11.8 yr, also received GH. Between-group comparisons of first-year and second-year height velocity, height sd score, and height gain (cm) were performed using analysis of covariance accounting for diagnosis, sex, and baseline age. The GH-treated SHOX-D group had a significantly greater first-year height velocity than the untreated control group (mean +/- se, 8.7 +/- 0.3 vs. 5.2 +/- 0.2 cm/yr; P < 0.001) and similar first-year height velocity to GH-treated subjects with TS (8.9 +/- 0.4 cm/yr; P = 0.592). GH-treated subjects also had significantly greater second-year height velocity (7.3 +/- 0.2 vs. 5.4 +/- 0.2 cm/yr; P < 0.001), second-year height sd score (-2.1 +/- 0.2 vs.-3.0 +/- 0.2; P < 0.001) and second-year height gain (16.4 +/- 0.4 vs. 10.5 +/- 0.4 cm; P < 0.001) than untreated subjects. This large-scale, randomized, multicenter clinical trial in subjects with SHOX-D demonstrates marked, highly significant, GH-stimulated increases in height velocity and height SDS during the 2-yr study period. The efficacy of GH treatment in subjects with SHOX-D was equivalent to that seen in subjects with TS. We conclude that GH is effective in improving the linear growth of patients with various forms of SHOX-D.

A murine specific expansion of the Rhox cluster involved in embryonic stem cell biology is under natural selection

BackgroundThe rodent specific reproductive homeobox (Rhox) gene cluster on the X chromosome has been reported to contain twelve homeobox-containing genes, Rhox1-12.ResultsWe have identified a 40 kb genomic region within the Rhox cluster that is duplicated eight times in tandem resulting in the presence of eight paralogues of Rhox2 and Rhox3 and seven paralogues of Rhox4. Transcripts have been identified for the majority of these paralogues and all but three are predicted to produce full-length proteins with functional potential. We predict that there are a total of thirty-two Rhox genes at this genomic location, making it the most gene-rich homoeobox cluster identified in any species. From the 95% sequence similarity between the eight duplicated genomic regions and the synonymous substitution rate of the Rhox2, 3 and 4 paralogues we predict that the duplications occurred after divergence of mouse and rat and represent the youngest homoeobox cluster identified to date. Molecular evolutionary analysis reveals that this cluster is an actively evolving region with Rhox2 and 4 paralogues under diversifying selection and Rhox3 evolving neutrally. The biological importance of this duplication is emphasised by the identification of an important role for Rhox2 and Rhox4 in regulating the initial stages of embryonic stem (ES) cell differentiation.ConclusionThe gene rich Rhox cluster provides the mouse with significant biological novelty that we predict could provide a substrate for speciation. Moreover, this unique cluster may explain species differences in ES cell derivation and maintenance between mouse, rat and human.

Rx‐Cre, a tool for inactivation of gene expression in the developing retina

Rx is a homeobox-containing gene that is critical for vertebrate eye development. Its expression domain delineates a field of cells from which the retina and the ventral hypothalamus develop. The 5' upstream regulatory sequences of the medaka fish Rx gene are functionally conserved during evolution to a degree that they direct gene expression into the Rx-expressing field of cells in mice. Using these sequences, we made a Cre line that can be used for inactivation of gene expression in the developing retina.

Expression of the short stature homeobox gene Shox is restricted by proximal and distal signals in chick limb buds and affects the length of skeletal elements

SHOX is a homeobox-containing gene, highly conserved among species as diverse as fish, chicken and humans. SHOX gene mutations have been shown to cause idiopathic short stature and skeletal malformations frequently observed in human patients with Turner, Leri–Weill and Langer syndromes. We cloned the chicken orthologue of SHOX, studied its expression pattern and compared this with expression of the highly related Shox2. Shox is expressed in central regions of early chick limb buds and proximal two thirds of later limbs, whereas Shox2 is expressed more posteriorly in the proximal third of the limb bud. Shox expression is inhibited distally by signals from the apical ectodermal ridge, both Fgfs and Bmps, and proximally by retinoic acid signaling. We tested Shox functions by overexpression in embryos and micromass cultures. Shox-infected chick limbs had normal proximo-distal patterning but the length of skeletal elements was consistently increased. Primary chick limb bud cell cultures infected with Shox showed an initial increase in cartilage nodules but these did not enlarge. These results fit well with the proposed role of Shox in cartilage and bone differentiation and suggest chick embryos as a useful model to study further the role of Shox in limb development.

Conservation and Phylogeny of a Novel Family of Non-Hox Genes of the Antp Class in Demospongiae (Porifera)

A survey across the most basal animal phylum, the Porifera, for the presence of homeobox-containing genes led to the isolation of 24 partial or complete homeobox sequences from 21 sponge species distributed in 15 families and 6 orders of Demospongiae. All the new sequences shared a high identity/similarity with EmH-3 (Ephydatia muelleri), a non-Hox gene from the Antp class. The Demox sequences, EmH-3, and related homeodomains formed a well-supported clade with no true affinity with any known bilaterian family, including the Tlx/Hox11 family, suggesting that the EmH-3 family of genes, comprising 31 members, represents a novel family of non-Hox genes, called the Demox family, widespread among Demospongiae. The presence of the Tlx/Hox11 specific signature in the Demox family and common regulatory elements suggested that the Demox and Tlx/Hox11 families are closely related. In the phylogenetic analyses, freshwater Haplosclerida appeared as monophyletic, and Haplosclerida and Halichondrida as polyphyletic, with a clade comprising Agelas species and Axinella corrugata. As for their expression, high levels of Demox transcripts were found in adult tissues. Our data add to the number of published poriferan homeobox sequences and provide independent confirmation of the current Demospongiae phylogenies.

Short stature and dysmorphology associated with defects in the SHOX gene

Since its discovery in 1997, knowledge about the SHOX gene ( Short stature HOmeoboX-containing gene) has rapidly advanced. Although originally described as causing idiopathic short stature, SHOX mutations are also responsible for growth retardation in Léri-Weill dyschondrosteosis, Langer mesomelic dysplasia and Turner syndrome. Furthermore, SHOX has a broad functional scope and leads to a variety of different morphological-skeletal stigmata associated with these syndromes. This article reviews clinical and molecular data associated SHOX gene defects. Functional ongoing studies are expected to improve our understanding of the SHOX gene as comprising part of a genetic process responsible for normal growth and bone development.

A novel maternally transcribed homeobox gene, Eso‐1, is preferentially expressed in oocytes and regulated by cytoplasmic polyadenylation

The homeobox gene families play important roles in the transcriptional regulation of gene expression prior to and during embryo development. To identify novel homeobox genes expressed in early embryonic development, we conducted a degenerated oligonucleotide polymerase chain reaction (PCR) to screen a mouse embryonic stem (ES) cell cDNA library. A novel homeobox-containing gene, Eso-1, which is preferentially expressed in ES cells and ovaries, was identified. The full-length Eso-1 cDNA was found to be 1,710 bp with a predicted homeodomain that has no significant homology to previously reported homeodomain proteins. Eso-1 was mapped to chromosome 14A3. Reverse transcription-polymerase chain reaction (RT-PCR) analyses showed that Eso-1 was expressed through oogenesis and continuing to be expressed through to the blastocyst stage. De novo expression of Eso-1 started at 13.5 days postcoitum in the ovaries, which coincides with the initiation of oogenesis. Northern blot analyses demonstrated that Eso-1 is preferentially expressed in both ovaries and ES cells as a 1.7-kb transcript. Results from whole mount in situ hybridization revealed that Eso-1 in oocytes showed increased expression from primordial to antral follicles. The 3'-untranslated region of Eso-1 transcripts contained cytoplasmic polyadenylation sequences while the length of poly (A) tails changed during oocyte maturation, indicating that Eso-1 expression is controlled by time-dependent translational activation. We suggest that the novel homeodomain protein, Eso-1, plays a role during oocyte maturation and early embryonic development.