Isolation and regional localization of the murine homeobox-containing gene Hox-3.3 to mouse chromosome region 15E

A role for phosphorylation by casein kinase II in modulating Antennapedia activity in Drosophila

We present evidence that the in vivo activity of the HOX protein Antennapedia (ANTP) is modified because of phosphorylation by the serine/threonine kinase casein kinase II (CKII). Using an in vivo assay a form of ANTP that has alanine substitutions at its CKII target sites has, in addition to wild-type ANTP functions, the ability to alter severely thoracic and abdominal development. The novel functions of this protein suggest that this form of ANTP is not suppressed phenotypically by the more posterior homeotic proteins. In contrast, the in vivo activity of a form of ANTP that contains acidic amino acid substitutions at its CKII target sites, thereby mimicking a constitutively phosphorylated ANTP protein, is greatly reduced. This hypoactive form of ANTP, but not the alanine-substituted form, is also reduced in its ability to bind to DNA cooperatively with the homeodomain protein Extradenticle. Our results suggest that phosphorylation of ANTP by CKII is important for preventing inappropriate activities of this homeotic protein during embryogenesis.

Analysis of Hox gene expression in the chick limb bud

The vertebrate Hox genes have been shown to be important for patterning the primary and secondary axes of the developing vertebrate embryo. The function of these genes along the primary axis of the embryo has been generally interpreted in the context of positional specification and homeotic transformation of axial structures. The way in which these genes are expressed and function during the development of the secondary axes, particularly the limb, is less clear. In order to provide a reference for understanding the role of the Hox genes in limb patterning, we isolated clones of 23 Hox genes expressed during limb development, characterized their expression patterns and analyzed their regulation by the signalling centers which pattern the limb. The expression patterns of the Abd-B-related Hoxa and Hoxd genes have previously been partially characterized; however, our study reveals that these genes are expressed in patterns more dynamic and complex than generally appreciated, only transiently approximating simple, concentric, nested domains. Detailed analysis of these patterns suggests that the expression of each of the Hoxa and Hoxd genes is regulated in up to three independent phases. Each of these phases appears to be associated with the specification and patterning of one of the proximodistal segments of the limb (upper arm, lower arm and hand). Interestingly, in the last of these phases, the expression of the Hoxd genes violates the general rule of spatial and temporal colinearity of Hox gene expression with gene order along the chromosome. In contrast to the Abd-B-related Hoxa and Hoxd genes, which are expressed in both the fore and hind limbs, different sets of Hoxc genes are expressed in the two limbs. There is a correlation between the relative position of these genes along the chromosome and the axial level of the limb bud in which they are expressed. The more 3′ genes are expressed in the fore limb bud while the 5′ genes are expressed in the hind limb bud; intermediate genes are transcribed in both limbs. However, there is no clear correlation between the relative position of the genes along the chromosome and their expression domains within the limb. With the exception of Hoxc-11, which is transcribed in a posterior portion of the hind limb, Hoxc gene expression is restricted to the anterior/proximal portion of the limb bud. Importantly, comparison of the distributions of Hoxc-6 RNA and protein products reveals posttranscriptional regulation of this gene, suggesting that caution must be exercised in interpreting the functional significance of the RNA distribution of any of the vertebrate Hox genes. To understand the genesis of the complex patterns of Hox gene expression in the limb bud, we examined the propagation of Hox gene expression relative to cell proliferation. We find that shifts in Hox gene expression cannot be attributed to passive expansion due to cell proliferation. Rather, phase-specific Hox gene expression patterns appear to result from a context-dependent response of the limb mesoderm to Sonic hedgehog. Sonic hedgehog (the patterning signal from the Zone of Polarizing Activity) is known to be able to activate Hoxd gene expression in the limb. Although we find that Sonic hedgehog is capable of initiating and polarizing Hoxd gene expression during both of the latter two phases of Hox gene expression, the specific patterns induced are not determined by the signal, but depend upon the temporal context of the mesoderm receiving the signal. Misexpression of Sonic hedgehog also reveals that Hoxb-9, which is normally excluded from the posterior mesenchyme of the leg, is negatively regulated by Sonic hedgehog and that Hoxc-11, which is expressed in the posterior portion of the leg, is not affected by Sonic hedgehog and hence is not required to pattern the skeletal elements of the lower leg.

Theoretical approaches to the analysis of homeobox gene evolution

The homeobox gene system presents a unique model for experimental and theoretical analyses of gene evolution. Homeobox genes play a role in patterning the embryonic development of diverse organisms and as such are likely to have been fundamental to the evolution of the specialized body plans of many animal species. The organization of Hox-genes in chromosomal, clusters in many species implicates gene duplication as a prominent mechanism in the evolution of this multigene family. I review here various theoretical analyses that have contributed to our understanding of the molecular evolution of this class of developmental control genes. This article also illustrates relationships between theoretical predictions and experimental studies and outlines future avenues for the evolutionary analysis of developmental systems.

Checklist: vertebrate homeobox genes

Up to now around 170 different homeobox genes have been cloned from vertebrate genomes. A compilation of the various isolates from mouse, chick, frog, fish and man is presented in the form of a concise checklist, including the designations from the original publications. Putative homologs from different species are aligned, and key characteristics of embryonic or adult expression domains, as well as mutant phenotypes are briefly indicated.

Identification of homeobox genes expressed during the process of rat liver regeneration after partial hepatectomy

Homeobox (HBox) genes are well-known to be involved in development and differentiation. To ascertain a role of HBox genes in the process of liver regeneration, we identified HBox genes expressed at various times after partial hepatectomy in rats (at 0 hr, 1 hr, 2 days, and 4 days) by using reverse transcription-polymerase chain reaction (RT-PCR), cloning, and sequencing techniques. By the competitive RT-PCR method using generic primers, expression levels of HBox genes in regenerating livers were estimated at as low as only 0.4-2% of that in 14-day embryonic liver; however, we identified multiple HBox genes at different stages. Comparing sets of HBox genes identified at different stages, we could find two candidates of stage specifically expressed HBox genes (one rat caudal-related gene, RCdx-3, stimulated at 1 hr, and one rat Hox gene, RHoxB5, repressed after hepatectomy) and continuous expression of five Hox genes (RHoxA1, A4, A5, B2, and B3) before and after hepatectomy. These HBox genes are considered to correlate with the process of liver regeneration.

Organization and expression of mouse Hox3 cluster genes

We determined the physical linkage of six mouse Hox3 homeobox sequences, including a new homeobox sequence (Hox3.5), by analysis of overlapping genomic clones. Additionally, we defined the locations of Hox1.7 and Hox1.8 in the Hox1 cluster. Analysis of the expression patterns of Hox3.6 and Hox3.5 during embryogenesis revealed that the relationship between relative position in the Hox3 cluster and expression domain along antero-posterior axis appears similar to that seen for members of the other Hox clusters.

Hox-3.6: isolation and characterization of a new murine homeobox gene located in the 5′ region of the Hox-3 cluster

Most members of the murine Hox gene system can be grouped into two subclasses based on their structural similarity to either one of the Drosophila homeotic genes Antennapedia (Antp) or Abdominal B (AbdB). All the AbdB-like genes reported thus far are located in the 5' region of their respective cluster. We describe here the isolation, structural characterization and spatio-temporal expression pattern of a new AbdB-like homeobox gene designated Hox-3.6 that is located in the 5' region of the Hox-3 cluster. Hox-3.6 has an extreme posterior expression domain in embryos of 12.5 days of gestation, a feature that has thus far only been observed for the 5' most genes of the Hox-4 cluster. Like the other members of the AbdB subfamily, Hox-3.6 exhibits spatially restricted expression in the hindlimb bud, but the expression domain is antero-proximal in contrast to the postero-distal domain reported for its cognate gene Hox-4.5. Structural analysis of the 5' region revealed the presence of a 35 bp sequence which shares homology and relative 5' position with an upstream sequence present in its two nearest downstream neighbors, Hox-3.2 and -3.1.

Characterization of mouse-hamster somatic cell hybrids by PCR: a panel of mouse-specific primers for each chromosome

Mouse/hamster somatic cell hybrids form a valuable resource for mouse gene mapping. Characterization of these hybrids by isozyme analysis can be technically demanding and time-consuming. Species-specific polymerase chain reaction (PCR), where a mouse gene but not its homolog in the hamster is amplified, can provide an alternative means of characterization. Mouse-specific primers have been designed for at least one gene on each of the mouse autosomes and the X Chromosome (Chr). Primers are chosen to correspond to untranslated regions of the mouse gene concerned, in order to decrease the chance of cross-hybridization with the homologous hamster gene. These primer sequences are presented, together with the conditions for their use.

Molecular cloning, chromosomal assignment, and nucleotide sequence of the feline homeobox HOX3A

The feline homolog to the mammalian homeobox locus, HOX3A, was isolated by screening a domestic cat genomic library with the murine Hox-3.1 probe. The nucleotide sequence similarity of the feline homeobox was 96% to human HOX3A, 94% to mouse Hox-3.1, and 94% to rat R4. The deduced amino acid sequence (homeodomain) of this feline homeobox was identical to all homeodomains of these cognate genes. Using a panel of feline x rodent somatic cell hybrids, the HOX3A locus was assigned to feline chromosome B4. Human HOX3A and mouse Hox-3.1 have been mapped previously to human chromosome 12 and mouse chromosome 15, respectively, both of which share syntenic homology to feline chromosome B4. These data demonstrate evolutionary conservation of both HOX3A gene sequences and chromosomal location during mammalian evolution.

Disruption of the Hox-1.6 homeobox gene results in defects in a region corresponding to its rostral domain of expression

The Hox-1.6 gene disrupted in embryonic stem cells by homologous recombination was introduced into the mouse germline. Heterozygous mice were normal, but homozygous mice died at birth from anoxia and had numerous defects that were centered at the level of rhombomeres 4 to 7 and included delayed hindbrain neural tube closure, absence of certain cranial nerves and ganglia, and malformed inner ears and bones of the skull. Thus, Hox-1.6 is involved in regional specification along the rostrocaudal axis, but only in its most rostral domain of expression. Hox-1.6 appears to specify neurogenic neural crest cells prior to specification of mesenchymal neural crest cells by Hox-1.5. Thus, within the same region of the presumptive hindbrain, two HOX-1 genes are involved in the patterning of two different populations of neural crest cells. The implication of these results for the function of the Hox network during mouse embryogenesis is discussed.

Characterisation of the murine Hox-3.3 gene and its promoter

The murine Hox-3.3 homeobox containing gene and its Xenopus homologue (XlHbox 1) produce two embryonic transcripts from two distinct promoters located approximately 9 kb apart. In order to begin to characterise one of these promoter regions (PRII), we have sequenced 3 kb of DNA immediately upstream of the transcription start site of the PRII transcript and analyzed the sequence for sequences known to bind transcription factors. Within this region are located a number of sequences that match known cis-elements. We have analysed the ability of two of these sequences that match to the Drosophila hunchback and Antennapedia/fushi-tarazu consensus binding sequences to specifically bind proteins extracted from embryos and from adult tissues. Using gel retention assays with oligonucleotides derived from these sequences, we show that both sequences specifically bind proteins present in extracts of mouse embryos and some, but not all extracts of various adult tissues. Protein binding cannot, however, be correlated with the known spatial domains of Hox-3.3 expression, suggesting that binding to these sequences is not simply related to activation of Hox-3.3 expression. A two base pair change in the most conserved region of the hunchback-like binding sequence completely abolishes protein binding. The presence of these highly conserved cis-acting elements that are known to be involved in regulation of the hunchback, even-skipped and engrailed genes in Drosophila suggests that these sequences may also be involved in the regulation of expression of Hox-3.3 and furthermore that regulation may in part at least involve binding of hunchback-like proteins (i.e. zinc-finger proteins) and Antennapedia-like homeobox-containing proteins.

Structural analysis of the Hox-3.1 transcription unit and the Hox-3.2--Hox-3.1 intergenic region

The mouse Hox gene family is a set of mammalian homeobox genes that may represent developmental control genes. Complete information about the primary structure of these genes is a prerequisite for a systematic analysis of the mechanisms that determine their complex tempero-spatial expression patterns. In this report we describe the complete sequence of the Hox-3.1 locus and provide evidence for several closely spaced transcriptional start sites. Sequence analysis of the 5' region of the Hox-3.1 gene extending to its nearest upstream neighbor, Hox-3.2, allowed us to identify sequences known to be capable of interactions with transcription factors. Several of these sequence motifs are similar to cis-regulatory elements found in the regulatory regions of other known developmentally regulated genes.

A yeast artificial chromosome containing the mouse homeobox cluster Hox-2

We have isolated two genes, Hox-2.8 and Hox-2.9, from the mouse homeobox cluster Hox-2, located on chromosome 11. A 120-kilobase yeast artificial chromosome (YAC) containing a large region of the murine Hox-2 cluster, including 45 kilobases of sequence upstream of the most 5' gene, was cloned. The DNA sequence of the YAC is unrearranged relative to the genomic map. We have subcloned from the YAC insert a homeobox gene, Hox-2.8, whose homeodolmain is highly related to that of the Drosophila homeotic gene proboscopedia (pb). The expression pattern of Hox-2.8 during embryogenesis extends the trend established by genes from Hox-2.5 to -2.7 of successively anterior domains of expression in the neural tube. We have also subcloned and sequenced from a cosmid the labial (lab)-related Hox-2.9, the most 3' member of the cluster to date. These data lend further support to the idea of a common evolutionary origin of the mouse Hox and Drosophila HOM clusters. The YAC will enable us to construct modified forms of the Hox-2 cluster in yeast and to identify their effect on the phenotype of the animal in transgenic mouse strains.

Chromosome assignment of the murine Hox-4.1 gene

The murine homebox gene 4.1 was assigned to chromosome 2 by Southern analysis of somatic cell hybrids and by in situ hybridization. This assignment and the report of Featherstone et al. (M. S. Featherstone, A. Baron, S. J. Gaunt, M. G. Mattei, and D. Duboule, 1988, Proc. Natl. Acad. Sci. USA, 85, 4760-4764) indicate that a fourth group of homeobox genes is located on chromosome 2 in the mouse (in addition to the homeobox gene clusters on chromosomes 6, 11, and 15).

Duplication of large genomic regions during the evolution of vertebrate homeobox genes

The phylogenetic relationships of 21 murine Antp-class (Drosophila mutation Antennapedia-type class) homeobox genes have been analyzed, and several groups of related genes have been identified. The murine Antp-class homeobox genes are localized within four gene clusters. The similar structural organization of the four gene clusters strongly suggests that genes within a group of related Antp-class homeobox genes are derived from duplications of large genomic regions. After the duplication, the gross structures of the homeobox gene clusters have been maintained over a long period of evolutionary time, indicating that the specific organization of genes within a cluster may be of functional importance.

The murine and Drosophila homeobox gene complexes have common features of organization and expression

In situ hybridization analysis of mouse embryos shows the seven members of the Hox-2 complex to be differentially expressed in the central and peripheral nervous system and in mesodermal derivatives (somites and lung). Beginning at the 5' end of the cluster, each successive gene displays a more anterior boundary of expression in the central nervous system. A gene's position in the Hox-2 cluster therefore reflects its relative domain of expression along the anteroposterior axis of the embryo, a feature observed with Drosophila homeotic genes. Sequence comparisons of the Hox-2 cluster with other mouse and Drosophila homeobox genes have defined subgroups of related genes; in the mouse there are four clusters related by duplication and divergence. Alignment shows a clear relationship among genes in the mouse and Drosophila complexes, based on relative position, sequence identity, and domains of expression along the rostral-caudal axis. Our results argue that these complexes arose from a common ancestor, present before the divergence of lineages that gave rise to arthropods and vertebrates.