Serial deletions and duplications suggest a mechanism for the collinearity of Hoxd genes in limbs

Altering enhancer-promoter linear distance impacts promoter competition in cis and in trans

In Drosophila, pairing of maternal and paternal homologs can permit trans-interactions between enhancers on one homolog and promoters on another, an example of a phenomenon called transvection. When chromosomes are paired, promoters in cis and in trans to an enhancer can compete for the enhancer's activity, but the parameters that govern this competition are as yet poorly understood. To assess how the linear spacing between an enhancer and promoter can influence promoter competition in Drosophila, we employed transgenic constructs wherein the eye-specific enhancer GMR is placed at varying distances from a heterologous hsp70 promoter driving a fluorescent reporter. While GMR activates the reporter to a high degree when the enhancer and promoter are spaced by a few hundred base pairs, activation is strongly attenuated when the enhancer is moved 3 kilobases away. By examining transcription of endogenous genes near the point of transgene insertion, we show that linear spacing of 3 kb between GMR and the hsp70 promoter results in elevated transcription of neighboring promoters, suggesting a loss of specificity between the enhancer and its intended transgenic target promoter. Furthermore, increasing spacing between GMR and hsp70 by just 100 bp can enhance transvection, resulting in increased activation of a promoter on a paired homolog at the expense of a promoter in cis to the enhancer. Finally, cis-/trans-promoter competition assays in which one promoter carries mutations to key core promoter elements show that GMR will skew its activity toward a wild type promoter, suggesting that an enhancer is in a balanced competition between its potential target promoters in cis and in trans.

Essay the (unusual) heuristic value of Hox gene clusters; a matter of time?

Ever since their first report in 1984, Antennapedia-type homeobox (Hox) genes have been involved in such a series of interesting observations, in particular due to their conserved clustered organization between vertebrates and arthropods, that one may legitimately wonder about the origin of this heuristic value. In this essay, I first consider different examples where Hox gene clusters have been instrumental in providing conceptual advances, taken from various fields of research and mostly involving vertebrate embryos. These examples touch upon our understanding of genomic evolution, the revisiting of 19th century views on the relationships between development and evolution and the building of a new framework to understand long-range and pleiotropic gene regulation during development. I then discuss whether the high value of the Hox gene family, when considered as an epistemic object, is related to its clustered structure (and the absence thereof in some animal species) and, if so, what is it in such particular genetic oddities that made them so generous in providing the scientific community with interesting information.

Theories, laws, and models in evo-devo

Evolutionary developmental biology (evo-devo) is the study of the evolution of developmental mechanisms. Here, I review some of the theories, models, and laws in evo-devo, past and present. Nineteenth-century evo-devo was dominated by recapitulation theory and archetypes. It also gave us germ layer theory, the vertebral theory of the skull, floral organs as modified leaves, and the "inverted invertebrate" theory, among others. Newer theories and models include the frameshift theory, the genetic toolkit for development, the ABC model of flower development, the developmental hourglass, the zootype, Urbilateria, and the hox code. Some of these new theories show the influence of archetypes and recapitulation. Interestingly, recent studies support the old "primordial leaf," "inverted invertebrate," and "segmented head" theories. Furthermore, von Baer's first three laws may now need to be rehabilitated, and the hourglass model modified, in view of what Abzhanov has pointed out about the maternal-zygotic transition. There are many supposed "laws" of evo-devo but I argue that these are merely generalizations about trends in particular lineages. I argue that the "body plan" is an archetype, and is often used in such a way that it lacks any scientific meaning. Looking to the future, one challenge for evo-devo will be to develop new theories and models to accommodate the wealth of new data from high-throughput sequencing, including single-cell sequencing. One step in this direction is the use of sophisticated in silico analyses, as in the "transcriptomic hourglass" models.

Role of vertebrate GAGA associated factor (vGAF) in early development of zebrafish

Homeotic genes and their genomic organization show remarkable conservation across bilaterians. Consequently, the regulatory mechanisms, which control hox gene expression, are also highly conserved. The crucial presence of conserved GA rich motifs between Hox genes has been previously observed but what factor binds to these is still unknown. Previously we have reported that the vertebrate homologue of Drosophila Trl-GAF preferentially binds to GA rich regions in Evx2-hoxd13 intergenic region of vertebrate HoxD cluster. In this study, we show that the vertebrate-GAF (v-GAF) binds at known cis-regulatory elements in the HoxD complex of zebrafish and mouse. We further used morpholino based knockdown and CRISPR-cas9 knockout technique to deplete the v-GAF in zebrafish. We checked expression of the HoxD genes and found gain of the HoxD4 gene in GAF knockout embryos. Further, we partially rescued the morphological phenotypes in GAF depleted embryos by providing GAF mRNA. Our results show that GAF binds at intergenic regions of the HoxD complex and is important for maintaining the spatial domains of HoxD4 expression during embryonic development.

Proximo-distal positional information encoded by an Fgf-regulated gradient of homeodomain transcription factors in the vertebrate limb

The positional information theory proposes that a coordinate system provides information to embryonic cells about their position and orientation along a patterning axis. Cells interpret this information to produce the appropriate pattern. During development, morphogens and interpreter transcription factors provide this information. We report a gradient of Meis homeodomain transcription factors along the mouse limb bud proximo-distal (PD) axis antiparallel to and shaped by the inhibitory action of distal fibroblast growth factor (FGF). Elimination of Meis results in premature limb distalization and HoxA expression, proximalization of PD segmental borders, and phocomelia. Our results show that Meis transcription factors interpret FGF signaling to convey positional information along the limb bud PD axis. These findings establish a new model for the generation of PD identities in the vertebrate limb and provide a molecular basis for the interpretation of FGF signal gradients during axial patterning.

Geminin is required for Hox gene regulation to pattern the developing limb

Development of the complex structure of the vertebrate limb requires carefully orchestrated interactions between multiple regulatory pathways and proteins. Among these, precise regulation of 5' Hox transcription factor expression is essential for proper limb bud patterning and elaboration of distinct limb skeletal elements. Here, we identified Geminin (Gmnn) as a novel regulator of this process. A conditional model of Gmnn deficiency resulted in loss or severe reduction of forelimb skeletal elements, while both the forelimb autopod and hindlimb were unaffected. 5' Hox gene expression expanded into more proximal and anterior regions of the embryonic forelimb buds in this Gmnn-deficient model. A second conditional model of Gmnn deficiency instead caused a similar but less severe reduction of hindlimb skeletal elements and hindlimb polydactyly, while not affecting the forelimb. An ectopic posterior SHH signaling center was evident in the anterior hindlimb bud of Gmnn-deficient embryos in this model. This center ectopically expressed Hoxd13, the HOXD13 target Shh, and the SHH target Ptch1, while these mutant hindlimb buds also had reduced levels of the cleaved, repressor form of GLI3, a SHH pathway antagonist. Together, this work delineates a new role for Gmnn in modulating Hox expression to pattern the vertebrate limb.

Accelerated Evolution of Limb-Related Gene Hoxd11 in the Common Ancestor of Cetaceans and Ruminants (Cetruminantia)

Reduced numbers of carpal and tarsal bones (wrist and ankle joints) are extensively observed in the clade of Cetacea and Ruminantia (Cetruminantia). Homebox D11 (Hoxd11) is one of the important genes required for limb development in mammals. Mutations in Hoxd11 can lead to defects in particular bones of limbs, including carpus and tarsus. To test whether evolutionary changes in Hoxd11 underlie the loss of these bones in Cetruminantia, we sequenced and analyzed Hoxd11 coding sequences and compared them with other 5' HoxA and HoxD genes in a taxonomic coverage of Cetacea, Ruminantia and other mammalian relatives. Statistical tests on the Hoxd11 sequences found an accelerated evolution in the common ancestor of cetaceans and ruminants, which coincided with the reduction of carpal and tarsal bones in this clade. Five amino acid substitutions (G222S, G227A, G229S, A240T and G261V) and one amino acid deletion (G254Del) occurred in this lineage. In contrast, other 5' HoxA and HoxD genes do not show this same evolutionary pattern, but instead display a highly conserved pattern of evolution in this lineage. Accelerated evolution of Hoxd11, but not other 5' HoxA and HoxD genes, is probably related to the reduction of the carpal and tarsal bones in Cetruminantia. Moreover, we found two amino acid substitutions (G110S and D223N) in Hoxd11 that are unique to the lineage of Cetacea, which coincided with hindlimb loss in the common ancestor of cetaceans. Our results give molecular evidence of Hoxd11 adaptive evolution in cetaceans and ruminants, which could be correlated with limb morphological adaptation.

The regulatory landscapes of developmental genes

Regulatory landscapes have been defined in vertebrates as large DNA segments containing diverse enhancer sequences that produce coherent gene transcription. These genomic platforms integrate multiple cellular signals and hence can trigger pleiotropic expression of developmental genes. Identifying and evaluating how these chromatin regions operate may be difficult as the underlying regulatory mechanisms can be as unique as the genes they control. In this brief article and accompanying poster, we discuss some of the ways in which regulatory landscapes operate, illustrating these mechanisms using genes important for vertebrate development as examples. We also highlight some of the techniques available to researchers for analysing regulatory landscapes.

The formation of the thumb requires direct modulation of Gli3 transcription by Hoxa13

In the tetrapod limb, the digits (fingers or toes) are the elements most subject to morphological diversification in response to functional adaptations. However, despite their functional importance, the mechanisms controlling digit morphology remain poorly understood. Here we have focused on understanding the special morphology of the thumb (digit 1), the acquisition of which was an important adaptation of the human hand. To this end, we have studied the limbs of the Hoxa13 mouse mutant that specifically fail to form digit 1. We show that, consistent with the role of Hoxa13 in Hoxd transcriptional regulation, the expression of Hoxd13 in Hoxa13 mutant limbs does not extend into the presumptive digit 1 territory, which is therefore devoid of distal Hox transcripts, a circumstance that can explain its agenesis. The loss of Hoxd13 expression, exclusively in digit 1 territory, correlates with increased Gli3 repressor activity, a Hoxd negative regulator, resulting from increased Gli3 transcription that, in turn, is due to the release from the negative modulation exerted by Hox13 paralogs on Gli3 regulatory sequences. Our results indicate that Hoxa13 acts hierarchically to initiate the formation of digit 1 by reducing Gli3 transcription and by enabling expansion of the 5'Hoxd second expression phase, thereby establishing anterior-posterior asymmetry in the handplate. Our work uncovers a mutual antagonism between Gli3 and Hox13 paralogs that has important implications for Hox and Gli3 gene regulation in the context of development and evolution.

Two modes of transvection at the eyes absent gene of Drosophila demonstrate plasticity in transcriptional regulatory interactions in cis and in trans

For many genes, proper gene expression requires coordinated and dynamic interactions between multiple regulatory elements, each of which can either promote or silence transcription. In Drosophila, the complexity of the regulatory landscape is further complicated by the tight physical pairing of homologous chromosomes, which can permit regulatory elements to interact in trans, a phenomenon known as transvection. To better understand how gene expression can be programmed through cis- and trans-regulatory interactions, we analyzed transvection effects for a collection of alleles of the eyes absent (eya) gene. We find that trans-activation of a promoter by the eya eye-specific enhancers is broadly supported in many allelic backgrounds, and that the availability of an enhancer to act in trans can be predicted based on the molecular lesion of an eya allele. Furthermore, by manipulating promoter availability in cis and in trans, we demonstrate that the eye-specific enhancers of eya show plasticity in their promoter preference between two different transcriptional start sites, which depends on promoter competition between the two potential targets. Finally, we show that certain alleles of eya demonstrate pairing-sensitive silencing resulting from trans-interactions between Polycomb Response Elements (PREs), and genetic and genomic data support a general role for PcG proteins in mediating transcriptional silencing at eya. Overall, our data highlight how eya gene regulation relies upon a complex but plastic interplay between multiple enhancers, promoters, and PREs.

Gene regulation requires interactions between regions of DNA known as regulatory elements, which, in combination, determine where and when a gene will be active or silenced. Some genes use just a few regulatory elements, whereas others rely on highly complex interactions between many different elements that are poorly understood. While we typically imagine regulatory elements interacting with one another along the length of a single chromosome, in a curious phenomenon called transvection, elements can communicate between two different chromosomes that are held in close proximity. Here, we use the study of transvection to better understand how different regulatory elements contribute to the expression of eyes absent (eya), a gene required for proper eye development in Drosophila. Our data show that a class of elements that initiate eya gene expression, called promoters, will compete with one another for activation by eya’s enhancers, a second class of regulatory element, with the promoter that is closest to the enhancers being the favored target for activation. Furthermore, our study of transvection uncovers an important role for a silencing element, called a PRE, in opposing eya gene expression. Overall, our study sheds new light on how different elements combine to produce patterned expression of eya.

Heterogeneous combinatorial expression of Hoxd genes in single cells during limb development

BACKGROUND

Global analyses of gene expression during development reveal specific transcription patterns associated with the emergence of various cell types, tissues, and organs. These heterogeneous patterns are instrumental to ensure the proper formation of the different parts of our body, as shown by the phenotypic effects generated by functional genetic approaches. However, variations at the cellular level can be observed within each structure or organ. In the developing mammalian limbs, expression of Hox genes from the HoxD cluster is differentially controlled in space and time, in cells that will pattern the digits and the forearms. While the Hoxd genes broadly share a common regulatory landscape and large-scale analyses have suggested a homogenous Hox gene transcriptional program, it has not previously been clear whether Hoxd genes are expressed together at the same levels in the same cells.

RESULTS

We report a high degree of heterogeneity in the expression of the Hoxd11 and Hoxd13 genes. We analyzed single-limb bud cell transcriptomes and show that Hox genes are expressed in specific combinations that appear to match particular cell types. In cells giving rise to digits, we find that the expression of the five relevant Hoxd genes (Hoxd9 to Hoxd13) is unbalanced, despite their control by known global enhancers. We also report that specific combinatorial expression follows a pseudo-time sequence, which is established based on the transcriptional diversity of limb progenitors.

CONCLUSIONS

Our observations reveal the existence of distinct combinations of Hoxd genes at the single-cell level during limb development. In addition, we document that the increasing combinatorial expression of Hoxd genes in this developing structure is associated with specific transcriptional signatures and that these signatures illustrate a temporal progression in the differentiation of these cells.

Distal Limb Patterning Requires Modulation of cis-Regulatory Activities by HOX13

The combinatorial expression of Hox genes along the body axes is a major determinant of cell fate and plays a pivotal role in generating the animal body plan. Loss of HOXA13 and HOXD13 transcription factors (HOX13) leads to digit agenesis in mice, but how HOX13 proteins regulate transcriptional outcomes and confer identity to the distal-most limb cells has remained elusive. Here, we report on the genome-wide profiling of HOXA13 and HOXD13 in vivo binding and changes of the transcriptome and chromatin state in the transition from the early to the late-distal limb developmental program, as well as in Hoxa13^−/−; Hoxd13^−/−limbs. Our results show that proper termination of the early limb transcriptional program and activation of the late-distal limb program are coordinated by the dual action of HOX13 on cis-regulatory modules.

John Saunders' ZPA, Sonic hedgehog and digit identity - How does it really all work?

Among John Saunders' many seminal contributions to developmental biology, his discovery of the limb 'zone of polarizing activity' (ZPA) is arguably one of the most memorable and ground-breaking. This discovery introduced the limb as a premier model for understanding developmental patterning and promoted the concept of patterning by a morphogen gradient. In the 50 years since the discovery of the ZPA, Sonic hedgehog (Shh) has been identified as the ZPA factor and the basic components of the signaling pathway and many aspects of its regulation have been elucidated. Although much has also been learned about how it regulates growth, the mechanism by which Shh patterns the limb, how it acts to instruct digit 'identity', nevertheless remains an enigma. This review focuses on what has been learned about Shh function in the limb and the outstanding puzzles that remain to be solved.

Genetics of clubfoot; recent progress and future perspectives

Clubfoot or talipes equinovarus (TEV) is an inborn three-dimensional deformity of leg, ankle and foot. It results from structural defects of several tissues of foot and lower leg leading to abnormal positioning of foot and ankle joints. TEV can lead to long-lasting functional disability, malformation and discomfort if left untreated. Substantial progress has been achieved in the management and diagnosis of limb defects; however, not much is known about the molecular players and signalling pathways underlying TEV disorder. The homeostasis and development of the limb depends on the complex interactions between the lateral plate mesoderm cells and outer ectoderm. These complex interactions include HOX signalling and PITX1-TBX4 pathways. The susceptibility to develop TEV is determined by a number of environmental and genetic factors, although the nature and level of interplay between them remains unclear. Familial occurrence and inter and intra phenotypic variability of TEV is well documented. Variants in genes that code for contractile proteins of skeletal myofibers might play a role in the aetiology of TEV but, to date, no strong candidate genes conferring increased risk have emerged, although variants in TBX4, PITX1, HOXA, HOXC and HOXD clusters genes, NAT2 and others have been shown to be associated with TEV. The mechanisms by which variants in these genes confer risk and the nature of the physical and genetic interaction between them remains to be determined. Elucidation of genetic players and cellular pathways underlying TEV will certainly increase our understanding of the pathophysiology of this deformity.

Analysis of transcription factors expressed at the anterior mouse limb bud

Limb bud patterning, outgrowth, and differentiation are precisely regulated in a spatio-temporal manner through integrated networks of transcription factors, signaling molecules, and downstream genes. However, the exact mechanisms that orchestrate morphogenesis of the limb remain to be elucidated. Previously, we have established EMBRYS, a whole-mount in situ hybridization database of transcription factors. Based on the findings from EMBRYS, we focused our expression pattern analysis on a selection of transcription factor genes that exhibit spatially localized and temporally dynamic expression patterns with respect to the anterior-posterior axis in the E9.5–E11.5 limb bud. Among these genes, Irx3 showed a posteriorly expanded expression domain in Shh^-/- limb buds and an anteriorly reduced expression domain in Gli3^-/- limb buds, suggesting their importance in anterior-posterior patterning. To assess the stepwise EMBRYS-based screening system for anterior regulators, we generated Irx3 transgenic mice in which Irx3 was expressed in the entire limb mesenchyme under the Prrx1 regulatory element. The Irx3 gain-of-function model displayed complex phenotypes in the autopods, including digit loss, radial flexion, and fusion of the metacarpal bones, suggesting that Irx3 may contribute to the regulation of limb patterning, especially in the autopods. Our results demonstrate that gene expression analysis based on EMBRYS could contribute to the identification of genes that play a role in patterning of the limb mesenchyme.

Transcriptomic insights into the genetic basis of mammalian limb diversity

Background

From bat wings to whale flippers, limb diversification has been crucial to the evolutionary success of mammals. We performed the first transcriptome-wide study of limb development in multiple species to explore the hypothesis that mammalian limb diversification has proceeded through the differential expression of conserved shared genes, rather than by major changes to limb patterning. Specifically, we investigated the manner in which the expression of shared genes has evolved within and among mammalian species.

Results

We assembled and compared transcriptomes of bat, mouse, opossum, and pig fore- and hind limbs at the ridge, bud, and paddle stages of development. Results suggest that gene expression patterns exhibit larger variation among species during later than earlier stages of limb development, while within species results are more mixed. Consistent with the former, results also suggest that genes expressed at later developmental stages tend to have a younger evolutionary age than genes expressed at earlier stages. A suite of key limb-patterning genes was identified as being differentially expressed among the homologous limbs of all species. However, only a small subset of shared genes is differentially expressed in the fore- and hind limbs of all examined species. Similarly, a small subset of shared genes is differentially expressed within the fore- and hind limb of a single species and among the forelimbs of different species.

Conclusions

Taken together, results of this study do not support the existence of a phylotypic period of limb development ending at chondrogenesis, but do support the hypothesis that the hierarchical nature of development translates into increasing variation among species as development progresses.

Electronic supplementary material

The online version of this article (doi:10.1186/s12862-017-0902-6) contains supplementary material, which is available to authorized users.

Integration of Shh and Fgf signaling in controlling Hox gene expression in cultured limb cells

During embryonic development, fields of progenitor cells form complex structures through dynamic interactions with external signaling molecules. How complex signaling inputs are integrated to yield appropriate gene expression responses is poorly understood. In the early limb bud, for instance, Sonic hedgehog (Shh) is expressed in the distal posterior mesenchyme, where it acts as a mediator of anterior to posterior (AP) patterning, whereas fibroblast growth factor 8 (Fgf8) is produced by the apical ectodermal ridge (AER) at the distal tip of the limb bud to direct outgrowth along the proximal to distal (PD) axis. Here we use cultured limb mesenchyme cells to assess the response of the target Hoxd genes to these two factors. We find that they act synergistically and that both factors are required to activate Hoxd13 in limb mesenchymal cells. However, the analysis of the enhancer landscapes flanking the HoxD cluster reveals that the bimodal regulatory switch observed in vivo is only partially achieved under these in vitro conditions, suggesting an additional requirement for other factors.

Genome-Wide Binding of Posterior HOXA/D Transcription Factors Reveals Subgrouping and Association with CTCF

Homeotic genes code for key transcription factors (HOX-TFs) that pattern the animal body plan. During embryonic development, Hox genes are expressed in overlapping patterns and function in a partially redundant manner. In vitro biochemical screens probing the HOX-TF sequence specificity revealed largely overlapping sequence preferences, indicating that co-factors might modulate the biological function of HOX-TFs. However, due to their overlapping expression pattern, high protein homology, and insufficiently specific antibodies, little is known about their genome-wide binding preferences. In order to overcome this problem, we virally expressed tagged versions of limb-expressed posterior HOX genes (HOXA9-13, and HOXD9-13) in primary chicken mesenchymal limb progenitor cells (micromass). We determined the effect of each HOX-TF on cellular differentiation (chondrogenesis) and gene expression and found that groups of HOX-TFs induce distinct regulatory programs. We used ChIP-seq to determine their individual genome-wide binding profiles and identified between 12,721 and 28,572 binding sites for each of the nine HOX-TFs. Principal Component Analysis (PCA) of binding profiles revealed that the HOX-TFs are clustered in two subgroups (Group 1: HOXA/D9, HOXA/D10, HOXD12, and HOXA13 and Group 2: HOXA/D11 and HOXD13), which are characterized by differences in their sequence specificity and by the presence of cofactor motifs. Specifically, we identified CTCF binding sites in Group 1, indicating that this subgroup of HOX-proteins cooperates with CTCF. We confirmed this interaction by an independent biological assay (Proximity Ligation Assay) and demonstrated that CTCF is a novel HOX cofactor that specifically associates with Group 1 HOX-TFs, pointing towards a possible interplay between HOX-TFs and chromatin architecture.

Hox genes encode transcription factors that determine the vertebrate body plan and pattern structures and organs in the developing embryo. Despite decades of effort and research on Hox genes, little is known about the HOX-DNA binding properties in vivo. This lack of knowledge is mainly due to the absence of appropriate antibodies to distinguish between different HOX transcription factors. Here, we adapt a cell culture system that allows us to investigate HOX-DNA binding on a genome-wide scale. With this approach, we define and directly compare the genome-wide binding sites of nine posterior HOXA and HOXD transcription factors. We report that the in vivo HOX binding specificity differs from the in vitro specificity and find that HOX-TFs largely rely on co-factor binding and not only on direct HOX-DNA binding. Finally, we identify a novel HOX co-factor, a genome architecture protein, CTCF suggesting a possible interplay between HOX-TF function and chromatin architecture.

The Shh Topological Domain Facilitates the Action of Remote Enhancers by Reducing the Effects of Genomic Distances

Gene expression often requires interaction between promoters and distant enhancers, which occur within the context of highly organized topologically associating domains (TADs). Using a series of engineered chromosomal rearrangements at the Shh locus, we carried out an extensive fine-scale characterization of the factors that govern the long-range regulatory interactions controlling Shh expression. We show that Shh enhancers act pervasively, yet not uniformly, throughout the TAD. Importantly, changing intra-TAD distances had no impact on Shh expression. In contrast, inversions disrupting the TAD altered global folding of the region and prevented regulatory contacts in a distance-dependent manner. Our data indicate that the Shh TAD promotes distance-independent contacts between distant regions that would otherwise interact only sporadically, enabling functional communication between them. In large genomes where genomic distances per se can limit regulatory interactions, this function of TADs could be as essential for gene expression as the formation of insulated neighborhoods.

Evolution of Hoxa11 regulation in vertebrates is linked to the pentadactyl state

The fin-to-limb transition represents one of the major vertebrate morphological innovations associated with the transition from aquatic to terrestrial life and is an attractive model for gaining insights into the mechanisms of morphological diversity between species. One of the characteristic features of limbs is the presence of digits at their extremities. Although most tetrapods have limbs with five digits (pentadactyl limbs), palaeontological data indicate that digits emerged in lobed fins of early tetrapods, which were polydactylous. How the transition to pentadactyl limbs occurred remains unclear. Here we show that the mutually exclusive expression of the mouse genes Hoxa11 and Hoxa13, which were previously proposed to be involved in the origin of the tetrapod limb, is required for the pentadactyl state. We further demonstrate that the exclusion of Hoxa11 from the Hoxa13 domain relies on an enhancer that drives antisense transcription at the Hoxa11 locus after activation by HOXA13 and HOXD13. Finally, we show that the enhancer that drives antisense transcription of the mouse Hoxa11 gene is absent in zebrafish, which, together with the largely overlapping expression of hoxa11 and hoxa13 genes reported in fish, suggests that this enhancer emerged in the course of the fin-to-limb transition. On the basis of the polydactyly that we observed after expression of Hoxa11 in distal limbs, we propose that the evolution of Hoxa11 regulation contributed to the transition from polydactyl limbs in stem-group tetrapods to pentadactyl limbs in extant tetrapods.

Hox Gene Collinearity: From A-P Patterning to Radially Symmetric Animals

Hox gene collinearity relates the gene order of the Hox cluster in the chromosome (telomeric to centromeric end) with the serial activation of these genes in the ontogenetic units along the Anterior-Posterior embryonic axis. Although this collinearity property is well respected in bilaterians (e.g. vertebrates), it is violated in other animals. The A-P axis is established in the early embryo of the sea urchin. Subsequently, rotational symmetry is superimposed when the vestibula larva is formed. In analogy to the linear A-P case, it is here hypothesized that the circular topology of the ontogenetic modules is associated to the architectural restructuring of the Hox loci where the two discrete ends of the Hox cluster approach each other so that an almost circular DNA contour is created. In the evolutionary process the circular mode undergoes double strand breaks and the generated cluster ends are attached to the open ends of the flanking chromosome. This event may lead to a novel gene ordering associated with an evolutionary innovation. For example, the loss of Hox4 is followed by the formation of a shorter gene circular arrangement. The opening of this contour at the missing Hox4 location and its connection to the chromosomal flanking ends leads to a new diversification namely the creation of the unusual gene order of the sea urchin Hox cluster.

A genome-wide association study identifies a genomic region for the polycerate phenotype in sheep (Ovis aries)

Horns are a cranial appendage found exclusively in Bovidae, and play important roles in accessing resources and mates. In sheep (Ovies aries), horns vary from polled to six-horned, and human have been selecting polled animals in farming and breeding. Here, we conducted a genome-wide association study on 24 two-horned versus 22 four-horned phenotypes in a native Chinese breed of Sishui Fur sheep. Together with linkage disequilibrium (LD) analyses and haplotype-based association tests, we identified a genomic region comprising 132.0–133.1 Mb on chromosome 2 that contained the top 10 SNPs (including 4 significant SNPs) and 5 most significant haplotypes associated with the polycerate phenotype. In humans and mice, this genomic region contains the HOXD gene cluster and adjacent functional genes EVX2 and KIAA1715, which have a close association with the formation of limbs and genital buds. Our results provide new insights into the genetic basis underlying variable numbers of horns and represent a new resource for use in sheep genetics and breeding.

Generation of an 870 kb deletion encompassing the Skt/Etl4 locus by combination of inter- and intra-chromosomal recombination

Background

Etl4^lacZ (Enhancer trap locus 4) and Skt^Gt (Sickle tail) are lacZ reporter gene integrations into the same locus on mouse chromosome 2 targeting a gene that is expressed in the notochord of early embryos and in multiple epithelia during later development. Both insertions caused recessive mutations that resulted exclusively in mild defects in the caudal vertebral column. Since notochord-derived signals are essential for formation of the vertebral column the phenotypes suggested that the lacZ insertions interfered with some notochord-dependent aspect of vertebral development. As both insertions occurred in introns it was unclear whether they represent hypomorphic alleles or abolish gene function. Here, we have generated a definitive null allele of the Skt/Etl4 gene and analysed homozygous mutants.

Results

We have introduced loxP sites into three positions of the gene based on additional upstream exons that we identified, and deleted approximately 870 kb of the locus by a combination of inter- and intra-chromosomal Cre-mediated recombinations in the female germ line of mice. This deletion removes about 90 % of the coding region and results in the loss of the SKT/ETL4 protein. Similar to the Etl4^lacZ and Skt^Gt alleles our deletion mutants are viable and fertile and show only mild defects in caudal vertebrae due to abnormal intervertebral disc development, although with higher penetrance. No other tissue with Skt/Etl4 expression that we analysed showed obvious defects.

Conclusion

The complete loss of Skt/Etl4 function affects only development of caudal notochord derivatives and is compensated for in its other expression domains.

Electronic supplementary material

The online version of this article (doi:10.1186/s12863-015-0302-0) contains supplementary material, which is available to authorized users.

Key pathways regulated by HoxA9,10,11/HoxD9,10,11 during limb development

Background

The 39 mammalian Hox genes show problematic patterns of functional overlap. In order to more fully define the developmental roles of Hox genes it is necessary to remove multiple combinations of paralogous and flanking genes. In addition, the downstream molecular pathways regulated by Hox genes during limb development remain incompletely delineated.

Results

In this report we examine limb development in mice with frameshift mutations in six Hox genes, Hoxa9,10,11 and Hoxd9,10,11. The mice were made with a novel recombineering method that allows the simultaneous targeting of frameshift mutations into multiple flanking genes. The Hoxa9,10,11^−/−/Hoxd9,10,11^−/− mutant mice show a reduced ulna and radius that is more severe than seen in Hoxa11^−/−/Hoxd11^−/− mice, indicating a minor role for the flanking Hox9,10 genes in zeugopod development, as well as their primary function in stylopod development. The mutant mice also show severe reduction of Shh expression in the zone of polarizing activity, and decreased Fgf8 expression in the apical ectodermal ridge, thereby better defining the roles of these specific Hox genes in the regulation of critical signaling centers during limb development. Importantly, we also used laser capture microdissection coupled with RNA-Seq to characterize the gene expression programs in wild type and mutant limbs. Resting, proliferative and hypertrophic compartments of E15.5 forelimb zeugopods were examined. The results provide an RNA-Seq characterization of the progression of gene expression patterns during normal endochondral bone formation. In addition of the Hox mutants showed strongly altered expression of Pknox2, Zfp467, Gdf5, Bmpr1b, Dkk3, Igf1, Hand2, Shox2, Runx3, Bmp7 and Lef1, all of which have been previously shown to play important roles in bone formation.

Conclusions

The recombineering based frameshift mutation of the six flanking and paralogous Hoxa9,10,11 and Hoxd9,10,11 genes provides a resource for the analysis of their overlapping functions. Analysis of the Hoxa9,10,11^−/−/Hoxd9,10,11^−/− mutant limbs confirms and extends the results of previous studies using mice with Hox mutations in single paralogous groups or with entire Hox cluster deletions. The RNA-Seq analysis of specific compartments of the normal and mutant limbs defines the multiple key perturbed pathways downstream of these Hox genes.

Electronic supplementary material

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Hox genes control vertebrate body elongation by collinear Wnt repression

In vertebrates, the total number of vertebrae is precisely defined. Vertebrae derive from embryonic somites that are continuously produced posteriorly from the presomitic mesoderm (PSM) during body formation. We show that in the chicken embryo, activation of posterior Hox genes (paralogs 9–13) in the tail-bud correlates with the slowing down of axis elongation. Our data indicate that a subset of progressively more posterior Hox genes, which are collinearly activated in vertebral precursors, repress Wnt activity with increasing strength. This leads to a graded repression of the Brachyury/T transcription factor, reducing mesoderm ingression and slowing down the elongation process. Due to the continuation of somite formation, this mechanism leads to the progressive reduction of PSM size. This ultimately brings the retinoic acid (RA)-producing segmented region in close vicinity to the tail bud, potentially accounting for the termination of segmentation and axis elongation.

DOI:http://dx.doi.org/10.7554/eLife.04379.001

In humans and other vertebrates, the number of bones (vertebrae) in the spine is determined early in development. The vertebrae form from blocks of tissue called somites that make segments along the body axis—a virtual line running from the head to the tail-end—of the embryo. The somites form as the embryo increases in length, with new somites forming periodically at the back near the embryo's tail-end.

A family of genes called the Hox genes are involved in controlling the formation of the somites. However, it is not known whether they directly control the number of somites that form, or whether they control the length of the body of the embryo.

Denans et al. studied the Hox genes in chicken embryos. The experiments suggest that the activation of some of the Hox genes in a structure called the tail-bud, which is found at the tail-end of the embryo, slow down the elongation of the body. The Hox genes achieve this by repressing the activity of a signaling pathway called Wnt so that Wnt activity in the tail-bud progressively decreases as the embryo develops.

The elongation of the body stops when the levels of a molecule called retinoic acid increase in the tail-bud, which causes the loss of the stem cells that are needed to make the somites. Denans et al.'s findings suggest that Hox genes influence the timing of the halt in elongation, which in turn is important for determining the total number of somites that form. Understanding how Hox genes control the formation of the cells that will make up the somites and influence Wnt signaling is a major challenge for the future.

DOI:http://dx.doi.org/10.7554/eLife.04379.002

A discrete transition zone organizes the topological and regulatory autonomy of the adjacent tfap2c and bmp7 genes

Despite the well-documented role of remote enhancers in controlling developmental gene expression, the mechanisms that allocate enhancers to genes are poorly characterized. Here, we investigate the cis-regulatory organization of the locus containing the Tfap2c and Bmp7 genes in vivo, using a series of engineered chromosomal rearrangements. While these genes lie adjacent to one another, we demonstrate that they are independently regulated by distinct sets of enhancers, which in turn define non-overlapping regulatory domains. Chromosome conformation capture experiments reveal a corresponding partition of the locus in two distinct structural entities, demarcated by a discrete transition zone. The impact of engineered chromosomal rearrangements on the topology of the locus and the resultant gene expression changes indicate that this transition zone functionally organizes the structural partition of the locus, thereby defining enhancer-target gene allocation. This partition is, however, not absolute: we show that it allows competing interactions across it that may be non-productive for the competing gene, but modulate expression of the competed one. Altogether, these data highlight the prime role of the topological organization of the genome in long-distance regulation of gene expression.

The specificity of enhancer-gene interactions is fundamental to the execution of gene regulatory programs underpinning embryonic development and cell differentiation. However, our understanding of the mechanisms conferring specificity to enhancers and target gene interactions is limited. In this study, we characterize the cis-regulatory organization of a large genomic locus consisting of two developmental genes, Tfap2c and Bmp7. We show that this locus is structurally partitioned into two distinct domains by the constitutive action of a discrete transition zone located between the two genes. This separation restricts selectively the functional action of enhancers to the genes present within the same domain. Interestingly, the effects of this region as a boundary are relative, as it allows some competing interactions to take place across domains. We show that these interactions modulate the functional output of a brain enhancer on its primary target gene resulting in the spatial restriction of its expression domain. These results support a functional link between topological chromatin domains and allocation of enhancers to genes. They further show that a precise adjustment of chromatin interaction levels fine-tunes gene regulation by long-range enhancers.

Genetic interactions between Shox2 and Hox genes during the regional growth and development of the mouse limb

The growth and development of the vertebrate limb relies on homeobox genes of the Hox and Shox families, with their independent mutation often giving dose-dependent effects. Here we investigate whether Shox2 and Hox genes function together during mouse limb development by modulating their relative dosage and examining the limb for nonadditive effects on growth. Using double mRNA fluorescence in situ hybridization (FISH) in single embryos, we first show that Shox2 and Hox genes have associated spatial expression dynamics, with Shox2 expression restricted to the proximal limb along with Hoxd9 and Hoxa11 expression, juxtaposing the distal expression of Hoxa13 and Hoxd13. By generating mice with all possible dosage combinations of mutant Shox2 alleles and HoxA/D cluster deletions, we then show that their coordinated proximal limb expression is critical to generate normally proportioned limb segments. These epistatic interactions tune limb length, where Shox2 underexpression enhances, and Shox2 overexpression suppresses, Hox-mutant phenotypes. Disruption of either Shox2 or Hox genes leads to a similar reduction in Runx2 expression in the developing humerus, suggesting their concerted action drives cartilage maturation during normal development. While we furthermore provide evidence that Hox gene function influences Shox2 expression, this regulation is limited in extent and is unlikely on its own to be a major explanation for their genetic interaction. Given the similar effect of human SHOX mutations on regional limb growth, Shox and Hox genes may generally function as genetic interaction partners during the growth and development of the proximal vertebrate limb.

Hox gene regulation and timing in embryogenesis

Hox genes are critical regulators of embryonic development in bilaterian animals. They exhibit a unique mode of transcriptional regulation where the position of the genes along the chromosome corresponds to the time and place of their expression during development. The sequential temporal activation of these genes in the primitive streak helps determining their subsequent pattern of expression along the anterior-posterior axis of the embryo, yet the precise correspondence between these two collinear processes is not fully understood. In addition, vertebrate Hox genes evolved similar modes of regulation along secondary body axes, such as the developing limbs. We review the current understanding of the mechanisms operating during activation, maintenance and silencing of Hox gene expression in these various contexts, and discuss the evolutionary significance of their genomic organization.

Unique expression patterns of multiple key genes associated with the evolution of mammalian flight

Bats are the only mammals capable of true flight. Critical adaptations for flight include a pair of dramatically elongated hands with broad wing membranes. To study the molecular mechanisms of bat wing evolution, we perform genomewide mRNA sequencing and in situ hybridization for embryonic bat limbs. We identify seven key genes that display unique expression patterns in embryonic bat wings and feet, compared with mouse fore- and hindlimbs. The expression of all 5'HoxD genes (Hoxd9-13) and Tbx3, six known crucial transcription factors for limb and digit development, is extremely high and prolonged in the elongating wing area. The expression of Fam5c, a tumour suppressor, in bat limbs is bat-specific and significantly high in all short digit regions (the thumb and foot digits). These results suggest multiple genetic changes occurred independently during the evolution of bat wings to elongate the hand digits, promote membrane growth and keep other digits short. Our findings also indicate that the evolution of limb morphology depends on the complex integration of multiple gene regulatory networks and biological processes that control digit formation and identity, chondrogenesis, and interdigital regression or retention.

Homeotic gene regulation: a paradigm for epigenetic mechanisms underlying organismal development

The organization of eukaryotic genome into chromatin within the nucleus eventually dictates the cell type specific expression pattern of genes. This higher order of chromatin organization is established during development and dynamically maintained throughout the life span. Developmental mechanisms are conserved in bilaterians and hence they have body plan in common, which is achieved by regulatory networks controlling cell type specific gene expression. Homeotic genes are conserved in metazoans and are crucial for animal development as they specify cell type identity along the anterior-posterior body axis. Hox genes are the best studied in the context of epigenetic regulation that has led to significant understanding of the organismal development. Epigenome specific regulation is brought about by conserved chromatin modulating factors like PcG/trxG proteins during development and differentiation. Here we discuss the conserved epigenetic mechanisms relevant to homeotic gene regulation in metazoans.

Clustering of tissue-specific sub-TADs accompanies the regulation of HoxA genes in developing limbs

HoxA genes exhibit central roles during development and causal mutations have been found in several human syndromes including limb malformation. Despite their importance, information on how these genes are regulated is lacking. Here, we report on the first identification of bona fide transcriptional enhancers controlling HoxA genes in developing limbs and show that these enhancers are grouped into distinct topological domains at the sub-megabase scale (sub-TADs). We provide evidence that target genes and regulatory elements physically interact with each other through contacts between sub-TADs rather than by the formation of discreet “DNA loops”. Interestingly, there is no obvious relationship between the functional domains of the enhancers within the limb and how they are partitioned among the topological domains, suggesting that sub-TAD formation does not rely on enhancer activity. Moreover, we show that suppressing the transcriptional activity of enhancers does not abrogate their contacts with HoxA genes. Based on these data, we propose a model whereby chromatin architecture defines the functional landscapes of enhancers. From an evolutionary standpoint, our data points to the convergent evolution of HoxA and HoxD regulation in the fin-to-limb transition, one of the major morphological innovations in vertebrates.

Hox genes encode transcription factors with crucial roles during development. These genes are grouped in four different clusters names HoxA, B, C, and D. Mutations in genes of the HoxA and D clusters have been found in several human syndromes, affecting in some cases limb development. Despite their essential role and contrary to the genes of the HoxD cluster, little is known about how the HoxA genes are regulated. Here, we identified a large set of regulatory elements controlling HoxA genes during limb development. By studying spatial chromatin organization at the HoxA region, we found that the regulatory elements are spatially clustered regardless of their activity. Clustering of enhancers define tissue-specific chromatin domains that interact specifically with each other and with active genes in the limb. Our findings give support to the emerging concept that chromatin architecture defines the functional properties of genomes. Additionally, our study suggests a common constraint of the chromatin topology in the evolution of HoxA and HoxD regulation in the emergence of the hand/foot, which is one of the major morphological innovations in vertebrates.

Evolutionary constraints favor a biophysical model explaining hox gene collinearity

The Hox gene collinearity enigma has often been approached using models based on biomolecular mechanisms. The biophysical model is an alternative approach based on the hypothesis that collinearity is caused by physical forces pulling the Hox genes from a territory where they are inactive to a distinct spatial domain where they are activated in a step by step manner. Such Hox gene translocations have recently been observed in support of the biophysical model. Genetic engineering experiments, performed on embryonic mice, gave rise to several unexpected mutant expressions that the biomolecular models cannot predict. On the contrary, the biophysical model offers convincing explanation. Evolutionary constraints consolidate the Hox clusters and as a result, denser and well organized clusters may create more efficient physical forces and a more emphatic manifestation of gene collinearity. This is demonstrated by stochastic modeling with white noise perturbing the expression of Hox genes. As study cases the genomes of mouse and amphioxus are used. The results support the working hypothesis that vertebrates have adopted their comparably more compact Hox clustering as a tool needed to develop more complex body structures. Several experiments are proposed in order to test further the physical forces hypothesis.

"Self-regulation," a new facet of Hox genes' function

BACKGROUND

Precise temporal and spatial expression of the clustered Hox genes is essential for patterning the developing embryo. Temporal activation of Hox genes was shown to be cluster-autonomous. However, gene clustering appears dispensable for spatial colinear expression. Generally, a set of Hox genes expressed in a group of cells instructs these cells about their fate such that the differential expression of Hox genes results in morphological diversity. The spatial colinearity is considered to rely both on local and long-range cis regulation.

RESULTS

Here, we report on the global deregulation of HoxA and HoxD expression patterns upon inactivation of a subset of HOXA and HOXD proteins.

CONCLUSIONS

Our data suggest the existence of a "self-regulation" mechanism, a process by which HOX proteins establish and/or maintain the spatial domains of the Hox gene family and we propose that the functionally dominant HOX proteins could contribute to generating the spatial parameters of Hox expression in a given tissue, i.e., HOX controlling the establishment of the ultimate HOX code.

Hox genes regulation in vertebrates

Hox genes encode transcription factors defining cellular identities along the major and secondary body axes. Their coordinated expression in both space and time is critical for embryonic patterning. Accordingly, Hox genes transcription is tightly controlled at multiple levels, and involves an intricate combination of local and long-range cis-regulatory elements. Recent studies revealed that in addition to transcription factors, dynamic patterns of histone marks and higher-order chromatin structure are important determinants of Hox gene regulation. Furthermore, the emerging picture suggests an involvement of various species of non-coding RNA in targeting activating and repressive complexes to Hox clusters. I review these recent developments and discuss their relevance to the control of Hox gene expression in vivo, as well as to our understanding of transcriptional regulatory mechanisms.

mRNA fluorescence in situ hybridization to determine overlapping gene expression in whole-mount mouse embryos

BACKGROUND

Whole-mount in situ hybridization (ISH) is a prevalent tool to examine the spatial distribution of gene transcripts in intact embryos. Chromogenic-based methods of signal development are commonly used in mouse embryos because of their high sensitivity. Fluorescence techniques, however, offer several advantages over chromogenic methods including the ability to visualize multiple signals in a specimen at once.

RESULTS

We describe a procedure for fluorescence in situ hybridization (FISH) for whole mouse embryos up to embryonic day 13.5. We show that this approach successfully produces a bright expression signal for several genes, validating the procedure in multiple tissues. Further, we show that double FISH can be used to visualize the expression of two genes in a single embryo by determining that Hoxd13 and Shh are co-expressed in both the limb bud and the hindgut. Finally, we demonstrate that FISH can be paired with confocal microscopy to take optical sections of interior regions of the embryo.

CONCLUSIONS

FISH is a valid alternative to chromogenic-based ISH for visualizing gene expression in whole mouse embryos. This work provides a framework to add additional fluorescence signals in the mouse such as visualizing both mRNA and protein by pairing the procedure with immunofluorescence.

Tracing the evolution of avian wing digits

It is widely accepted that birds are a subgroup of dinosaurs, but there is an apparent conflict: modern birds have been thought to possess only the middle three fingers (digits II-III-IV) of an idealized five-digit tetrapod hand based on embryological data, but their Mesozoic tetanuran dinosaur ancestors are considered to have the first three digits (I-II-III) based on fossil evidence. How could such an evolutionary quirk arise? Various hypotheses have been proposed to resolve this paradox. Adding to the confusion, some recent developmental studies support a I-II-III designation for avian wing digits whereas some recent paleontological data are consistent with a II-III-IV identification of the Mesozoic tetanuran digits. A comprehensive analysis of both paleontological and developmental data suggests that the evolution of the avian wing digits may have been driven by homeotic transformations of digit identity, which are more likely to have occurred in a partial and piecemeal manner. Additionally, recent genetic studies in mouse models showing plausible mechanisms for central digit loss invite consideration of new alternative possibilities (I-II-IV or I-III-IV) for the homologies of avian wing digits. While much progress has been made, some advances point to the complexity of the problem and a final resolution to this ongoing debate demands additional work from both paleontological and developmental perspectives, which will surely yield new insights on mechanisms of evolutionary adaptation.

Females and males contribute in opposite ways to the evolution of gene order in Drosophila

An intriguing association between the spatial layout of chromosomes within nuclei and the evolution of chromosome gene order was recently uncovered. Chromosome regions with conserved gene order in the Drosophila genus are larger if they interact with the inner side of the nuclear envelope in D. melanogaster somatic cells. This observation opens a new door to understand the evolution of chromosomes in the light of the dynamics of the spatial layout of chromosomes and the way double-strand breaks are repaired in D. melanogaster germ lines. Chromosome regions at the nuclear periphery in somatic cell nuclei relocate to more internal locations of male germ line cell nuclei, which might prefer a gene order-preserving mechanism to repair double-strand breaks. Conversely, chromosome regions at the nuclear periphery in somatic cells keep their location in female germ line cell nuclei, which might be inaccessible for cellular machinery that causes gene order-disrupting chromosome rearrangements. Thus, the gene order stability for genome regions at the periphery of somatic cell nuclei might result from the active repair of double-strand breaks using conservative mechanisms in male germ line cells, and the passive inaccessibility for gene order-disrupting factors at the periphery of nuclei of female germ line cells. In the present article, I find evidence consistent with a DNA break repair-based differential contribution of both D. melanogaster germ lines to the stability/disruption of gene order. The importance of germ line differences for the layout of chromosomes and DNA break repair strategies with regard to other genomic patterns is briefly discussed.

Chromatin organization and global regulation of Hox gene clusters

During development, a properly coordinated expression of Hox genes, within their different genomic clusters is critical for patterning the body plans of many animals with a bilateral symmetry. The fascinating correspondence between the topological organization of Hox clusters and their transcriptional activation in space and time has served as a paradigm for understanding the relationships between genome structure and function. Here, we review some recent observations, which revealed highly dynamic changes in the structure of chromatin at Hox clusters, in parallel with their activation during embryonic development. We discuss the relevance of these findings for our understanding of large-scale gene regulation.

Engineering of large deletions and duplications in vivo

Gene targeting in embryonic stem (ES) cells coupled with the site-specific Cre/loxP recombination system offers unique opportunities to identify and analyze the roles of cis-acting sequences in the regulation of imprinted gene expression. Although several different approaches have been described to engineer large chromosomal rearrangements in ES cells, these strategies can be labor-intensive and often require several subcloning of the original stem cells, therefore limiting the chances of obtaining germ line transmission of the mutation introduced. Here we describe an alternative approach which is based on in vivo recombination, therefore limiting the number of steps performed in ES cells and allowing to take advantage of the growing number of loxP insertional mutations already available in transgenic mice.

Hox genes regulate digit patterning by controlling the wavelength of a Turing-type mechanism

The formation of repetitive structures (such as stripes) in nature is often consistent with a reaction-diffusion mechanism, or Turing model, of self-organizing systems. We used mouse genetics to analyze how digit patterning (an iterative digit/nondigit pattern) is generated. We showed that the progressive reduction in Hoxa13 and Hoxd11-Hoxd13 genes (hereafter referred to as distal Hox genes) from the Gli3-null background results in progressively more severe polydactyly, displaying thinner and densely packed digits. Combined with computer modeling, our results argue for a Turing-type mechanism underlying digit patterning, in which the dose of distal Hox genes modulates the digit period or wavelength. The phenotypic similarity with fish-fin endoskeleton patterns suggests that the pentadactyl state has been achieved through modification of an ancestral Turing-type mechanism.

Hoxa11 and Hoxd11 regulate chondrocyte differentiation upstream of Runx2 and Shox2 in mice

During limb development, posterior Hox genes of the Hoxa- and Hoxd cluster provide positional information along the limb axis. Here we report a new function for Hoxa11 and Hoxd11 in regulating the early steps of chondrocyte differentiation. We analyzed forelimbs of Hoxa11^−/−;d11^−/− and Ulnaless mice, which are characterized by specifically shortened zeugopods. By detailed morphological and molecular analyses, we show that loss of Hoxa11 and Hoxd11 in the ulna of both mutants leads to an arrest of chondrocyte differentiation at a step before the separation into round and columnar cells takes place. Furthermore, we demonstrate that Hoxa11 and Hoxd11 act upstream of Runx2 and Shox2, two key regulators of chondrocyte differentiation. We hypothesize that Runx2 activates Shox2 in early chondrocytes, which at later stages induces Runx2 expression to regulate hypertrophic differentiation. These results give insight into mechanisms by which positional information might be translated into a specific bone pattern.