Seeking Sense in the Hox Gene Cluster.

The Hox gene cluster, responsible for patterning of the head-tail axis, is an ancestral feature of all bilaterally symmetrical animals (the Bilateria) that remains intact in a wide range of species. We can say that the Hox cluster evolved successfully only once since it is commonly the same in all groups, with labial-like genes at one end of the cluster expressed in the anterior embryo, and Abd-B-like genes at the other end of the cluster expressed posteriorly. This review attempts to make sense of the Hox gene cluster and to address the following questions. How did the Hox cluster form in the protostome-deuterostome last common ancestor, and why was this with a particular head-tail polarity? Why is gene clustering usually maintained? Why is there collinearity between the order of genes along the cluster and the positions of their expressions along the embryo? Why do the Hox gene expression domains overlap along the embryo? Why have vertebrates duplicated the Hox cluster? Why do Hox gene knockouts typically result in anterior homeotic transformations? How do animals adapt their Hox clusters to evolve new structural patterns along the head-tail axis?

Hox cluster genes and collinearities throughout the tree of animal life.

The discovery of Hox gene clusters, first in Drosophila (a protostome) and then as homologues in vertebrates (deuterostomes), was a major step in our understanding of both developmental and evolutionary biology. Hox genes in both species perform the same overall function: that is, organization of the body along its head-tail axis. The conclusion is that the protostome-deuterostome ancestor, founder of 99% of all described animal species, must already have had this same basic Hox cluster, and that it probably used it in the same way to establish its body plan. A striking feature of Hox genes is the spatial collinearity rule: that order of the genes along the chromosome corresponds with the order of their expression domains along the embryo. For vertebrates, though not Drosophila, there is also the temporal collinearity rule: that order of genes along the chromosome corresponds with timing of Hox expressions in the embryo. Although Hox genes are clearly recognized in pre-bilaterians (Cnidaria), it is only in bilaterians that the characteristic clustered Hox arrangement and function is commonly found. Spatial collinearity in expression is conserved widely throughout Bilateria but temporal collinearity is so far limited to vertebrates, cephalochordates, and some arthropods and annelids. In addition to conserved use of Hox genes to pattern the head-tail axis, some animal groups, particularly lophotrochozoans, have extensively co-opted Hox genes, outside collinearity rules, to regulate development of novel structures. Satisfactory understanding of Hox cluster function requires better understanding of the bilaterian last common ancestor (Urbilateria). Xenacoelomorpha may provide useful living models of the ancestral bilaterian condition.

Mouse embryo Hox gene enhancers assayed in cell culture: Hoxb4, b8 and a7 are activated by Cdx1 protein.

Mouse Hox gene enhancer elements have typically been identified and characterized using Hox/lacZ transgenic mouse embryos. Such studies have, for example, identified Cdx responsive binding motifs in the enhancers of Hoxb8 and Hoxa7. Production of transgenic mouse embryos involves issues of cost, welfare, and considerable technical skill. It would be of benefit if these studies could be performed, or advanced, in cell culture. It is shown here that Cdx1 activation of mouse Hoxb4, b8 and a7 embryo-active enhancers can be detected using a HepG2 cell culture model system. The technique employed uses co-transfection of an inducible Cdx1 expression construct together with a Hox enhancer/luciferase reporter construct. Cultures to be compared receive identical DNAs and differ only in whether or not they also receive inducer (doxycycline). Response of all three Hox enhancers to Cdx1 protein is inhibited by mutation of Cdx binding motifs which are conserved in sequence from fish or Xenopus to mammals. The magnitude of transfected chick Hoxa7 activation by Cdx1 is increased by multiple copies of its enhancer, but for maximum effect these must contain intact Cdx binding motifs. Cdx1 protein was found not to activate Hoxb4, b8 or a7 enhancers in P19 mouse pluripotential cells.

Gdf11/Smad signalling and Cdx proteins cooperate to activate the Hoxc8 early enhancer in HepG2 cells.

Developing anatomy along the head-tail axis of bilaterian embryos is specified, to a large extent, by the overlapping patterns of expression of the Hox genes. Hox gene enhancers respond to a variety of signals in order to regulate these discreet domains of expression. For mouse Hoxc8, the 399bp "early enhancer" plays a major role. Activation of this enhancer is now examined using luciferase expression constructs transfected into HepG2 cells. Constructs are activated by the combined actions of Gdf11/Smad and Cdx protein signalling pathways, both of which are functional in early embryos. Each of these pathways alone has little stimulatory effect. Stimulation by the two pathways together exceeds the sum of the effects of each pathway alone, indicating synergistic activity. By mutation analysis, two Smad binding motifs are identified as mediators of the Gdf11 effect and two Cdx binding motifs mediate the Cdx effect. The two Smad motifs and one of the Cdx sites are conserved from fish to mammals. Gdf11 stimulation is partially inhibited by Specific Inhibitor of Smad3, suggesting that Smad3 plays a part in signal transduction. Fgf2 increases luciferase activation by the Hoxc8 enhancer, but not, apparently, by specific interactions with either Gdf11 or Cdx effects.

Possible rules for the ancestral origin of Hox gene collinearity.

The Hox gene cluster is believed to have formed from a single ProtoHox gene by repeated cycles of the following events: tandem gene duplication, mutation to generate a new expression boundary along the embryonic axis, and acquisition of a new Hox patterning function. The Hox cluster in Bilateria evolved in compliance with the so-called collinearity rule. That is, the order of the genes along the chromosome corresponds with the order of their embryonic expression domains along the head-tail axis. Gaunt (2015) suggested that collinearity may have arisen as a mechanism to minimise the incidence of boundaries between active and inactive genes within the Hox cluster. We now attempt to clarify the model by presenting it in the form of three rules: 1) no two Hox genes may persist in the same cluster with the same anterior boundary of activity in the same tissue; 2) an inactive Hox gene must not be flanked by two active Hox genes; 3) an active Hox gene must not be flanked by two inactive genes. We provide evidence and illustrative computer simulations to show that these rules, which can apply only to partially overlapping patterns of Hox activity, may account for the ancestral origin of Hox gene collinearity.

The significance of Hox gene collinearity.

Arthropods and vertebrates inherited their Hox clusters from an ancestral cluster of at least six genes already present in their last common ancestor, Urbilateria. Clustering and a common transcriptional direction are both likely features of the way that the gene complex first arose in a process of tandem gene duplication. Spatial collinearity (correspondence between ordering of Hox genes along the chromosome and their expression patterns along the head-tail axis) has been conserved in many animal groups and is likely to have been already present in Urbilateria. It is not known why the Hox cluster evolved with spatial collinearity. Four models are discussed. These vary in the significance they place upon Hox chromatin structure, and also on whether they propose that collinearity is primarily concerned with establishment or maintenance of Hox expression. Published proposals to explain spatial collinearity, which invoke enhancer sharing, chromatin closing or chromatin opening, are either problematic or can offer only partial explanations. In an alternative proposal it is suggested here that spatial collinearity evolved principally to maximise physical segregation, and thereby minimise incidence of boundaries, between active and inactive genes within the Hox cluster. This is to minimise erroneous transfer of transcriptional activity, or inactivity, between adjacent Hox genes.

Synergistic action in P19 pluripotential cells of retinoic acid and Wnt3a on Cdx1 enhancer elements.

Cdx1 encodes a homeodomain protein that regulates expression of some Hox genes. Cdx1 itself is known to be regulated in the primitive streak/tailbud by both retinoic acid (RA) and Wnt3a. Cdx1 in eutherian mammals has two retinoic acid response elements (RAREs), located upstream and in the first intron, and each is adjacent to structural Lef/Tcf motifs. Upstream Lef/Tcf motifs respond to canonical Wnt signalling to activate Cdx1 synergistically with RA. By combined use of reporter assays, immunofluorescence and flow cytometry in mouse P19 embryonal carcinoma cells we show that the Cdx1 intron Lef/Tcf motif also responds to Wnt3a signalling. Synergy between individual Cdx1 RARE and Lef/Tcf motifs can occur whether they are adjacent or distant in the gene. Part, though not all, of the Cdx1 stimulation by RA (in absence of added Wnt3a) likely depends upon Wnt protein produced by the cells themselves, since it is inhibited by mutation of Lef/Tcf motifs, or by IWP-2, an inhibitor of Wnt production. RA and Wnt3a stimulate Cdx1 by increasing both the proportion of P19 cells that are expressing and also their mean level of expression. The expressing/non-expressing sub-populations do not simply correspond with those that express a marker of pluripotentiality, Nanog. We conclude that RA and Wnt3a activate Cdx1 synergistically by overlapping use of both upstream and intron enhancers, and that mouse embryonal carcinoma cell populations display heterogeneity in their response to these activators.

Ossification sequence and genetic patterning in the mouse axial skeleton.

We provide novel data on vertebral ontogeny in the mouse, the mammalian model-of-choice for developmental studies. Most previous studies on ossification sequences in mice have focused on pooled elements of the spine (cervicals, thoracics, lumbars, sacrals, and caudals). Here, we contribute data on ossification sequences in the neural arches and centra to provide a comparative basis upon which to evaluate mammalian diversity of the axial skeleton. In attempt to explain the ossification pattern observed, we compared our observations with the phenotype of Cdx over-expresser mice. We use high-resolution X-ray microtomography and clearing and staining techniques to quantify the precise sequential ossification pattern of the mouse spine. We show that micro-CT scans perform better in all cases whereas clearing and staining exhibit sensitivity to the presence of semi-opaque tissue. We observe that the centra of wild-type mice always ossify after neural arches and that the ossification of the neural arches proceeds from two loci. The ossification of the centra appears more complex, especially in the neck where ossification is delayed and does not just follow the order of the vertebrae along the anterior-posterior axis. Our findings also suggest that Cdx genes' expression levels may be involved in the delayed ossification in the neck centra.

Direct activation of a mouse Hoxd11 axial expression enhancer by Gdf11/Smad signalling.

A Hoxd11/lacZ reporter, expressed with a Hoxd11-like axial expression pattern in transgenic mouse embryos, is stimulated in tailbud fragments when cultured in presence of Gdf11, a TGF-ß growth/differentiation factor. The same construct is also stimulated by Gdf11 when transiently transfected into cultures of HepG2 cells. Stimulation of the reporter in HepG2 cells is enhanced where it contains only the 332 bp Hoxd11 enhancer region VIII upstream or downstream of a luciferase or lacZ reporter. This enhancer contains three elements conserved from fish to mice, one of which has the sequence of a Smad3/4 binding element. Mutation of this motif inhibits the ability of Gdf11 to enhance reporter activity in the HepG2 cell assay. Chromatin immunoprecipitation experiments show direct evidence of Smad2/3 protein binding to the Hoxd11 region VIII enhancer. The action of Gdf11 upon Hoxd11 in HepG2 cells is inhibited, at least in part, by SIS3, a specific inhibitor of Smad3. SIS3 also produces partial inhibition of Hoxd11/lacZ expression in cultured transgenic tailbuds, indicating that Smad3 may play a similar role in the embryonic expression of Hoxd11. Transgenic mouse experiments show that the Smad binding motif is essential for the axial expression of Hoxd11/lacZ reporter in the embryo tailbud, posterior mesoderm and neurectoderm.

Changes in Cis-regulatory Elements during Morphological Evolution.

How have animals evolved new body designs (morphological evolution)? This requires explanations both for simple morphological changes, such as differences in pigmentation and hair patterns between different Drosophila populations and species, and also for more complex changes, such as differences in the forelimbs of mice and bats, and the necks of amphibians and reptiles. The genetic changes and pathways involved in these evolutionary steps require identification. Many, though not all, of these events occur by changes in cis-regulatory (enhancer) elements within developmental genes. Enhancers are modular, each affecting expression in only one or a few tissues. Therefore it is possible to add, remove or alter an enhancer without producing changes in multiple tissues, and thereby avoid widespread (pleiotropic) deleterious effects. Ideally, for a given step in morphological evolution it is necessary to identify (i) the change in phenotype, (ii) the changes in gene expression, (iii) the DNA region, enhancer or otherwise, affected, (iv) the mutation involved, (v) the nature of the transcription or other factors that bind to this site. In practice these data are incomplete for most of the published studies upon morphological evolution. Here, the investigations are categorized according to how far these analyses have proceeded.

Origins of Cdx1 regulatory elements suggest roles in vertebrate evolution.

Cdx1, an upstream regulator of Hox genes, is best characterized for its homeotic effects upon the developing axial skeleton, particularly in the neck. It responds to retinoic acid (RA) in both mouse embryos and embryonal carcinoma (EC) cells. By use of beta-galactosidase chemiluminescence, we show that a mouse Cdx1/lacZ reporter expressed in P19 EC cells responds to RA by the combined activities of an intron retinoic acid response element (RARE) and an upstream RARE. In contrast, a chicken Cdx1/lacZ reporter responds only by activity of the intron RARE. Database analyses upon Cdx1 from twenty three vertebrate species reveal that the intron RARE is structurally conserved in amniotes (eutherian mammals, marsupials, birds and Anole lizard), but not in Xenopus or fish. The upstream RARE is structurally conserved only in eutherian mammals. We conclude that the intron RARE originated at around the amphibian/amniote division, and the upstream RARE appeared around the marsupial/eutherian mammal division. In view of the site of action of Cdx1, we propose that acquisition of the intron RARE may have facilitated the substantial changes that occurred in the neck and anterior thorax at the advent of the amniotes. We present evidence that Cdx1 is also a developmental regulator of the female urogenital system, and we suggest that acquisition of the upstream RARE may have contributed to morphological divergence of marsupial and eutherian mammals.

Down-regulation of Cdx2 in colorectal carcinoma cells by the Raf-MEK-ERK 1/2 pathway.

Cdx2 is a homeodomain transcription factor that regulates normal intestinal cell differentiation. Cdx2 is frequently lost during progression of colorectal cancer (CRC) and is widely viewed as a colorectal tumour suppressor. A previous study suggested that activation of protein kinase C (PKC) may be responsible for Cdx2 down-regulation in CRC cells. Here we show that activation of PKC does indeed promote down-regulation of Cdx2 at both the mRNA and protein levels. However, PKC-dependent loss of Cdx2 is dependent upon activation of the Raf-MEK-ERK1/2 pathway. Indeed, specific activation of the ERK1/2 pathway using the conditional kinase DeltaRaf-1:ER is sufficient to inhibit Cdx2 transcription. The Raf-MEK-ERK1/2 pathway is hyper-activated in a large fraction of colorectal cancers due to mutations in K-Ras and we show that treatment of CRC cell lines with MEK inhibitors causes an increase in Cdx2 expression. Furthermore, activation of the ERK1/2 pathway promotes the phosphorylation and proteasome-dependent degradation of the Cdx2 protein. The inhibitory effect of ERK1/2 upon Cdx2 in CRC cells is in sharp contrast to its stimulatory effect upon Cdx2 expression in trophectoderm and trophoblast stem cells. These results provide important new insights into the regulation of the Cdx2 tumour suppressor by linking it to ERK1/2, a pathway which is frequently activated in CRC.

Multiple regulatory regions control the complex expression pattern of the mouse Cdx2 homeobox gene.

BACKGROUND & AIMS: The Cdx2 homeobox gene exerts multiple functions including trophectoderm specification, antero-posterior patterning, and determination of intestinal identity. The aim of this study was to map genomic regions that regulate the transcription of Cdx2, with a particular interest in the gut. METHODS: Genomic fragments covering 13 kilobase (kb) of the mouse Cdx2 locus were analyzed in transgenic mice and in cell assays. RESULTS: No fragment was active in the trophectoderm. Fragments containing the first intron and extending up to -5-kb upstream of the transcription start site became active posteriorly at gastrulation and then inactive at midgestation in every tissue including the endoderm. Specific persistence of activity in the intestinal endoderm/epithelium beyond midgestation requires extending the genomic fragment up to -9 kb. We identified a 250-base pair segment around -8.5-kb binding and responding to endodermal factors, with a stimulatory effect exerted synergistically by HNF4alpha, GATA6, Tcf4, and beta-catenin. These factors were able to activate endogenous expression of Cdx2 in nonintestinal Hela cells. CONCLUSIONS: Multiple regulatory regions control the complex developmental pattern of Cdx2, including far upstream sequences required for the persistence of gene expression specifically in the gut epithelium throughout life. Cooperation between HNF4alpha, GATA6, beta-catenin, and Tcf4 contributes to the intestine-specific expression of Cdx2.

Increased Cdx protein dose effects upon axial patterning in transgenic lines of mice.

To investigate the link between Cdx protein concentration and axial patterning in embryos, we made lines of mice OE1, OE2 and OE4 that overexpress each of the Cdx genes Cdx1, Cdx2 and Cdx4, respectively. The lines carry Cdx transgenes under the transcriptional control of their own promoter/enhancer elements. Transgenic embryos show Cdx transcription at 8.5 to 8.7 days within normal spatial domains for Cdx expression (primitive streak/tailbud), yet, overall, they contain elevated levels of Cdx proteins. Increased doses of Cdx proteins result in homeotic shifts in vertebral types along most of the vertebral column, with transformations being most obvious within the cervical region. Most of the shifts are anterior-to-posterior transformations and the anterior limits of these are commonly skull/vertebra 1 (v1) for OE1, v1/v2 for OE2 and v7 for OE4. OE embryos display anterior shifts in the expression of a Hoxa7/lacZ reporter within neural, paraxial and lateral plate mesoderm tissues. Hoxa7/lacZ expression commences at the normal time in OE1 and OE4 embryos. OE2 embryos display a forward shift in the gradient of Cdx2 protein along the axis, suggesting that a Cdx morphogen gradient model could account, at least in part, for the homeotic shifts in vertebral types. OE mice display additional defects: forelimb deficiencies in OE1, multiple tail axes, vertebral mis-alignments and axial truncations in OE2.

cdx4/lacZ and cdx2/lacZ protein gradients formed by decay during gastrulation in the mouse.

Expression of the mouse caudal genes cdx4 and cdx2 is examined by use of lacZ reporter constructs expressed in transgenic mouse embryos. During early gastrulation, up to at least 8.5 days of development, reporter mRNA distributions are apparently similar to those of endogenous cdx mRNAs. By 8.25 to 8.8 days, cdx/lacZ protein activities have become distributed as posterior-to-anterior gradients along the neural and mesoderm tissues. The gradients form by decay of activity as cells become distanced from the regressing tailbud. In situ hybridization studies indicate that the decay is primarily in cdx/lacZ protein activities rather than mRNAs. As gastrulation proceeds, the locations of the gradients regress progressively posteriorly along the growing axis. Our results indicate how cdx4 and cdx2 protein gradients might be generated by decay during normal development. The smoothness of the gradients that we detect shows that there cannot be extensive mixing of cells once they leave the tailbud to contribute to the growing axis. An enhancer element located in the first intron of the cdx4 gene is essential for correct transgene expression.

Additional enhancer copies, with intact cdx binding sites, anteriorize Hoxa-7/lacZ expression in mouse embryos: evidence in keeping with an instructional cdx gradient.

Expression of a Hoxa-7/lacZ reporter construct in transgenic mouse embryos is shifted anteriorly when the upstream enhancer is multimerized. The shift occurs in spinal ganglia, neurectoderm and in both paraxial and lateral plate mesoderms. Much of the multimer effect is inhibited by destruction of a single caudal (cdx) binding motif in the additional copies of the enhancer. These observations are in agreement with earlier enhancer multimerization analyses made for Hoxb-8 (Charite et al., 1998). Our findings therefore provide further evidence that the anterior limit of a Hox gene's expression domain is normally dependent upon and is determined by, the dosage of transcription factor(s) which bind to its enhancer element(s) and that these factors may be, or must include, the cdx proteins. We consider these findings in terms of both instructional (morphogen-like) gradient and timing models for the establishment of Hox gene expression domains. Enhancer multimerization results in an earlier onset of Hoxa-7/lacZ activity in the embryo. In neurectoderm at 8.7 days and in mesoderm at 10.5 days, the anterior boundaries of expression are located posterior to those seen at some earlier stages of development. We discuss how these findings are in keeping with a model where Hox expression boundaries become set along instructional cdx gradients, formed by cdx decay in cells moving away from the primitive streak region.

Vertebrate caudal gene expression gradients investigated by use of chick cdx-A/lacZ and mouse cdx-1/lacZ reporters in transgenic mouse embryos: evidence for an intron enhancer.

The vertebrate caudal proteins, being upstream regulators of the Hox genes, play a role in establishment of the body plan. We describe analysis of two orthologous caudal genes (chick cdx-A and mouse cdx-1) by use of lacZ reporters expressed in transgenic mouse embryos. The expression patterns show many similarities to the expression of endogenous mouse cdx-1. At 8.7 days, cdx/lacZ activity within neurectoderm and mesoderm forms posterior-to-anterior gradients, and we discuss the possibility that similar gradients of cdx gene expression may function as morphogen gradients for the establishment of Hox gene expression boundaries. Our observations suggest that gradients form by decay of cdx/lacZ activity in cells that have moved anterior to the vicinity of the node. The cdx-A/lacZ expression pattern requires an intron enhancer that includes two functional control elements: a DR2-type retinoic acid response element and a Tcf/beta-catenin binding motif. These motifs are structurally conserved in mouse cdx-1.

Colinearity and non-colinearity in the expression of Hox genes in developing chick skin.

Hox genes are usually expressed temporally and spatially in a colinear manner with respect to their positions in the Hox complex. We found that these characteristics apply to several Hox genes expressed in developing chick skin (Hoxb-4, Hoxa-7 and Hoxc-8), and we classed this group of genes as regionally restricted. To our surprise, we found that most of the Hox genes we examined are regionally unrestricted in their expression in the embryonic chick skin. This second group includes the Hoxd genes, Hoxd-4 to Hoxd-13, Hoxa-11 and Hoxc-6. Temporally, the expression of the regionally restricted genes can be observed by E5 within the epidermis, whereas the spatially unrestricted genes are not expressed in the epidermis until E6.25. Unexpectedly, we found that all the unrestricted genes are expressed concomitantly and therefore do not conform to temporal colinearity. Moreover, the dermal expression for both groups occurs later, but maintains the same anteroposterior patterning to that seen previously in the epidermis. During embryonic day 7-8, expression for all genes is up-regulated within the dense dermis whilst being reduced within the inter-bud regions. Later expression within the bud mesenchyme is down-regulated whilst high levels of transcriptional activity are detectable within the epidermal sheath of each feather bud. These results indicate that the transcriptional activity of Hox genes in the developing chick skin could be important during embryonic skin patterning both by providing regionally restricted positional cues, and also by imparting generic signals necessary for feather morphology.