Antony J. Durston

MiR-10 represses HoxB1a and HoxB3a in zebrafish.

Background The Hox genes are involved in patterning the anterior-posterior axis. In addition to the protein coding Hox genes, the miR-10, miR-196 and miR-615 families of microRNA genes are conserved within the vertebrate Hox clusters. The members of the miR-10 family are located at positions associated with Hox-4 paralogues. No function is yet known for this microRNA family but the genomic positions of its members suggest a role in anterior-posterior patterning. Methodology/Principal Findings Using sensor constructs, overexpression and morpholino knockdown, we show in Zebrafish that miR-10 targets HoxB1a and HoxB3a and synergizes with HoxB4 in the repression of these target genes. Overexpression of miR-10 also induces specific phenotypes related to the loss of function of these targets. HoxB1a and HoxB3a have a dominant hindbrain expression domain anterior to that of miR-10 but overlap in a weaker expression domain in the spinal cord. In this latter domain, miR-10 knockdown results in upregulation of the target genes. In the case of a HoxB3a splice variant that includes miR-10c within its primary transcript, we show that the microRNA acts in an autoregulatory fashion. Conclusions/Significance We find that miR-10 acts to repress HoxB1a and HoxB3a within the spinal cord and show that this repression works cooperatively with HoxB4. As with the previously described interactions between miR-196 and HoxA7 and Hox-8 paralogues, the target genes are located in close proximity to the microRNA. We present a model in which we postulate a link between the clustering of Hox genes and post-transcriptional gene regulation. We speculate that the high density of transcription units and enhancers within the Hox clusters places constraints on the precision of the transcriptional control that can be achieved within these clusters and requires the involvement of post-transcriptional gene silencing to define functional domains of genes appropriately.

Expression of retinoic acid 4-hydroxylase (CYP26) during mouse and Xenopus laevis embryogenesis.

Retinoids are important signal molecules during vertebrate embryonic development and their synthesis as well as catabolism should therefore be strictly regulated. The retinoic acid (RA) 4-hydroxylase, belonging to the cytochrome P450 family CYP26, is an enzyme catalyzing the 4-hydroxylation of RA, thereby regulating RA homeostasis. Here we describe the temporal and spatial expression patterns of mouse (mCYP26) and Xenopus laevis (xCYP26) homologues. In mouse, expression is detected in uterine crypt, around differentiating cartilage, several regions of the head, regions of the pharynx, the neural retina, and several regions of the trunk. In Xenopus, Northern blot analysis shows presence of xCYP26 transcripts before the MBT and an increased expression level during gastrulation. Whole-mount in situ hybridization shows a specific expression pattern arising at onset of gastrulation, with a ring around the blastopore. By mid gastrulation there is an anterior and a posterior expression domain, each of which gets more complex later in development. There are some important similarities and differences in expression pattern between Xenopus and mouse.

Extensive Polycistronism and Antisense Transcription in the Mammalian Hox Clusters

The Hox clusters play a crucial role in body patterning during animal development. They encode both Hox transcription factor and micro-RNA genes that are activated in a precise temporal and spatial sequence that follows their chromosomal order. These remarkable collinear properties confer functional unit status for Hox clusters. We developed the TranscriptView platform to establish high resolution transcriptional profiling and report here that transcription in the Hox clusters is far more complex than previously described in both human and mouse. Unannotated transcripts can represent up to 60% of the total transcriptional output of a cluster. In particular, we identified 14 non-coding Transcriptional Units antisense to Hox genes, 10 of which (70%) have a detectable mouse homolog. Most of these Transcriptional Units in both human and mouse present conserved sizeable sequences (>40 bp) overlapping Hox transcripts, suggesting that these Hox antisense transcripts are functional. Hox clusters also display at least seven polycistronic clusters, i.e., different genes being co-transcribed on long isoforms (up to 30 kb). This work provides a reevaluated framework for understanding Hox gene function and dys-function. Such extensive transcriptions may provide a structural explanation for Hox clustering.

Knockdown of the complete Hox paralogous group 1 leads to dramatic hindbrain and neural crest defects

The Hox paralogous group 1 (PG1) genes are the first and initially most anterior Hox genes expressed in the embryo. In Xenopus, the three PG1 genes, Hoxa1, Hoxb1 and Hoxd1, are expressed in a widely overlapping domain, which includes the region of the future hindbrain and its associated neural crest. We used morpholinos to achieve a complete knockdown of PG1 function. When Hoxa1, Hoxb1 and Hoxd1 are knocked down in combination, the hindbrain patterning phenotype is more severe than in the single or double knockdowns, indicating a degree of redundancy for these genes. In the triple PG1 knockdown embryos the hindbrain is reduced and lacks segmentation. The patterning of rhombomeres 2 to 7 is lost, with a concurrent posterior expansion of the rhombomere 1 marker, Gbx2. This effect could be via the downregulation of other Hox genes, as we show that PG1 function is necessary for the hindbrain expression of Hox genes from paralogous groups 2 to 4. Furthermore, in the absence of PG1 function, the cranial neural crest is correctly specified but does not migrate into the pharyngeal arches. Embryos with no active PG1 genes have defects in derivatives of the pharyngeal arches and, most strikingly, the gill cartilages are completely missing. These results show that the complete abrogation of PG1 function in Xenopus has a much wider scope of effect than would be predicted from the single and double PG1 knockouts in other organisms.

Axial patterning in snakes and caecilians: Evidence for an alternative interpretation of the Hox code

It is generally assumed that the characteristic deregionalized body plan of species with a snake-like morphology evolved through a corresponding homogenization of Hox gene expression domains along the primary axis. Here, we examine the expression of Hox genes in snake embryos and show that a collinear pattern of Hox expression is retained within the paraxial mesoderm of the trunk. Genes expressed at the anterior and most posterior, regionalized, parts of the skeleton correspond to the expected anatomical boundaries. Unexpectedly however, also the dorsal (thoracic), homogenous rib-bearing region of trunk, is regionalized by unconventional gradual anterior limits of Hox expression that are not obviously reflected in the skeletal anatomy. In the lateral plate mesoderm we also detect regionalized Hox expression yet the forelimb marker Tbx5 is not restricted to a rudimentary forelimb domain but is expressed throughout the entire flank region. Analysis of several Hox genes in a caecilian amphibian, which convergently evolved a deregionalized body plan, reveals a similar global collinear pattern of Hox expression. The differential expression of posterior, vertebra-modifying or even rib-suppressing Hox genes within the dorsal region is inconsistent with the homogeneity in vertebral identity. Our results suggest that the evolution of a deregionalized, snake-like body involved not only alterations in Hox gene cis-regulation but also a different downstream interpretation of the Hox code.

4 Retinoids and Related Signals in Early Development of the Vertebrate Central Nervous System

Publisher Summary This chapter discusses the evidence that active metabolites of vitamin A (retinoids) and related hormonal signals act as morphogens during the early vertebrate development. It then concentrates on their potential functions in patterning the early vertebrate central nervous system (CNS). The teratogenic effects of acidic retinoids show resemblance to the action of the neural transformation signal, but also differ from this in retinoids that are particularly active in transforming within the fore/mid/hindbrain part of the CNS rather than the spinal cord. An involvement of retinoids in patterning the more anterior part of the CNS is supported, by the results of loss of function experiments, and elements of a potential mechanism are provided, by the identification of RAREs regulating 3′(hindbrain-expressed) hox genes. It is likely that retinoids cooperate, with other pathways, to pattern the whole neural plate. The identification of active acidic retinoids provides candidates for putative retinoid morphogens mediating neural transformation. Hox gene-mediated modulation of the dorsoventral program of growth and neurogenesis provides an elegant mechanism, whereby retinoids and other signals could affect or generate positional information.

Graded retinoid responses in the developing hindbrain

The purpose of this study was to make an explicit test of the idea that a retinoid could act as a morphogen, differentially activating genes and specifying anteroposterior (a‐p) level in the developing vertebrate central nervous system (CNS). Our approach was to characterize the concentration‐dependent effects of retinoic acid (RA) on the neural expression of a set of a‐p patterning genes, both in vivo and in an in vitro system for neural patterning. Our results indicate that a retinoid is unlikely to specify a‐p level along the entire CNS. Instead, our data support the idea that the developing hindbrain may be patterned by a retinoid gradient. Sequentially more posterior hindbrain patterning genes were induced effectively by sequentially higher RA concentration windows. The most posterior CNS level induced under our RA treatment conditions corresponded to the most posterior part of the hindbrain. Dev. Dyn. 1998;213:39–49.© 1998 Wiley‐Liss, Inc.

Developmental expression and differential regulation by retinoic acid ofXenopus COUP-TF-A andCOUP-TF-B

COUP-TFs (Chicken Ovalbumin Upstream Promoter Transcription Factors) have been proposed to be negative regulators of retinoid receptor-mediated transcriptional activation. In a previous paper we reported the cloning of aXenopus (x) COUP-TF (Matharu, P.J. and Sweeney, G.E. (1992) Biochim. Biophys. Acta 1129, 331–334). Here we describe the cloning of a secondxCOUP-TF. Amino acid sequence comparison between these twoXenopus COUP-TFs revealed a high level of similarity. Extensive amino acid sequence conservation was found among allDrosophila, Xenopus, zebrafish and mammalianCOUP-TF genes examined. Phylogenetic tree analyses indicate that the vertebrate COUP-TFs fall into three classes. The twoXenopus COUP-TF genes show similar temporal expression patterns: both are expressed from the end of gastrulation. In situ hybridization studies reveal complex expression patterns in the developing central nervous system (CNS), besides expression in the eye and in some mesodermal tissues. Retinoic acid (RA) treatment enhancesxCOUP-TF-A expression in neurula stage embryos, whereas the expression ofxCOUP-TF-B is inhibited during the same developmental period. The strictly conserved amino acid sequences and the strong similarities between the expression patterns of the two differentxCOUP-TFs on the one hand, and other vertebrateCOUP-TF homologues on the other, make it likely that COUP-TFs have a conserved role in patterning the nervous system.

A position-dependent organisation of retinoid response elements is conserved in the vertebrate Hox clusters.

Unlike the genetic code, the protein-DNA recognition modalities are degenerate in both directions. Consequently, how do transcription factors achieve their considerable specificity and selectivity in regulating the genetic programs that they ultimately influence? Here, we discuss the fact that different Hox gene-specific variants of retinoid response elements are not equivalent. Each particular variant occurs at a precise position along the vertebrate Hox clusters and this organization was present before the time when the ancestral vertebrate Hox cluster was duplicated.

Comparative functional analysis provides evidence for a crucial role for the homeobox gene Nkx2.1/Titf‐1 in forebrain evolution

Knockout of the Nkx2.1 (Titf‐1) homeobox gene in the mouse leads to severe malformation and size reduction of the basal telencephalon/preoptic area and basal hypothalamus, indicating an important role of this gene in forebrain patterning. Here we show that abrogation of the orthologous gene in the frog Xenopus laevis by way of morpholino knockdown also affects the relative size of major regions in both the telencephalon (subpallium versus pallium) and diencephalon (hypothalamus versus thalamus). Remarkably, while a similar effect on the telencephalon was noted previously in Nkx2.1‐knockout mice, the effect on the diencephalon seems to be specific for Xenopus. This difference may be explained by the partially dissimilar expression of the orthologous genes in the forebrain of Xenopus and mouse. In both species Nkx2.1 is expressed in the basal telencephalon/preoptic area and basal hypothalamus, but in Xenopus this gene is additionally expressed in the alar hypothalamus. Phylogenetic comparison of Nkx2.1 expression in the forebrain suggests that the expression in the basal telencephalon‐preoptic region and alar hypothalamus appeared in the transition from jawless to jawed vertebrates, but the alar hypothalamic expression was later dramatically reduced during evolution to birds and mammals. Our study suggests that changes in the regulation of Nkx2.1 expression have played an important role on the evolution of forebrain development, and emphasizes the potential of the combined analysis of expression and function of master control genes in different vertebrates for unraveling the origin of brain complexity and diversity. J. Comp. Neurol. 506:211–223, 2008.