Nomenclature for homoeobox-containing genes

The 5' end sequences and exon organization in rat regucalcin gene

The 5'-flanking region of the gene for a Ca(2+)-binding protein regucalcin was cloned from a rat genomic library which was constructed in lambda EMBL3 SP6/T7 vector. The genomic library was screened by using the radiolabeled probe with the 5' region (0.5 kb) of rat regucalcin complementary deoxyribonucleic acid (cDNA). Positive clone had the 5.5 kb fragment which was hybridized with the 5'-probe. This fragment contained three exons (I-III) of the gene coding for a rat regucalcin. The nucleotide sequence of exons completely agreed with that of a rat regucalcin cDNA clone. A supposed translational initiation site existed in the exon II. Homology analysis showed that a putative transcription start site in the rat regucalcin gene was located at position 26 downstream from a TATA-box. Another upstream element, a CCAAT box-like sequence, was located at -170. Moreover, there were many regulatory elements (Hox, AP-1, AP-2 and AP-4) in the 5'-flanking region of the rat regucalcin gene. The organization of rat regucalcin gene seemed to be about 18 kb in size and consisted of seven exons and six introns.

Protein product of the somatic-type transcript of the Hoxa-4 (Hox-1.4) gene binds to homeobox consensus binding sites in its promoter and intron

The murine Hoxa-4 gene encodes a protein with a homeodomain closely related to those produced by the Antennapedia-like class of Drosophila genes. Drosophila homeodomain proteins can function as transcription factors, binding to several specific DNA sequences. One sequence that is frequently encountered contains a core ATTA motif within a larger consensus sequence, such as CAATTAA. The in vitro synthesized protein product of Hoxa-4 was shown to bind to a subset of restriction fragments of the Hoxa-4 gene itself as determined by gel retardation experiments. Direct examination of the sequences of the fragments bound by Hoxa-4 protein revealed the presence of four regions containing the core ATTA motif. Two regions contained sequences of the CAATTAA class and were located approximately 1 kb upstream from the putative somatic Hoxa-4 promoter and within the intron. Two additional binding sites containing the consensus target sequence involved in autoregulation of Drosophila Deformed gene were identified: one immediately downstream of the putative embryonic transcription start site and one within the intron, respectively. Specific binding of the in vitro produced Hoxa-4 protein to oligonucleotides corresponding to these sequences was observed in gel retardation assays. The same results were obtained with Hoxa-4 protein produced in a Baculovirus expression system. Experiments using oligonucleotides containing base substitutions in positions 1, 3, 4, and 5 in the sequence CAATTAA showed severely reduced binding. The use of truncated mutant Hoxa-4 proteins in gel retardation assays and in transient co-transfection experiments revealed that the intact homeodomain was required for the binding. These results also suggested that the Hoxa-4 gene has the potential to auto-regulate its expression by interacting with the homeodomain binding sites present in the promoter as well as in the intron.

Sequences 5′ of the homeobox of the Hox-1.4 gene direct tissue-specific expression of lacZ during mouse development

The murine homeobox-containing gene Hox-1.4 is expressed in restricted patterns during embryogenesis and in male germ cells. To begin identification of the cis-acting elements regulating this expression, transgenic mice were generated carrying a chimeric construct that contained approx. 4 kb of 5′ flanking sequence and approx. 1 kb of structural gene, fused in frame to the E. coli lacZ gene. This construct directed expression of the resulting Hox-1.4, beta-galactosidase fusion protein in a pattern that reproduced virtually the complete embryonic and adult sites of expression of the endogenous gene. Embryonic expression of the fusion protein was first detected in mesoderm at day 8.0 of gestation (E 8.0). Between gestational ages E 8.5 to E 12.5, beta-gal expression was observed in the somites, the lateral walls of the posterior myelencephalon, the dorsal region and ventral wall of the spinal cord, spinal ganglia and prevertebrae and their surrounding mesenchyme, between presumptive ribs, as well as in mesenchymal layers in the lung, kidney and portions of the gut. Expression was also noted in the pancreas and in the supporting cells and sheath around subsets of peripheral nerves, sites that had not been detected previously. Adult expression was observed in testes, specifically in meiotic and post-meiotic male germ cells. In contrast, transgenic mice carrying 5′ deletions of the construct which leave approx. 1.2 kb or approx. 2.0 kb of Hox-1.4 sequence 5′ to the embryonic promoter, did not exhibit beta-gal staining. These deletion experiments defined at least one cis-acting control element necessary for the expression of the Hox-1.4 gene to a 2 kb region located 2 to 4 kb 5′ of the embryonic transcription start site.

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.

Molecular mechanisms for generation of neural diversity and specificity: roles of polypeptide factors in development of postmitotic neurons

Development of postmitotic neurons is influenced by two groups of polypeptide factors. Neurotrophic factors promote neuronal survival both in vivo and in vitro. Neuronal differentiation factors influence transmitter phenotypes without affecting neuronal survival. The list of neurotrophic factors is increasing partly because certain growth factors and cytokines have been shown to possess neurotrophic activities and also because new neurotrophic factors including new members of the nerve growth factor (NGF) family have been identified at the molecular level. In vitro assays using recombinant neurotrophic factors and distributions of their mRNAs and proteins have indicated that members of a neurotrophic gene family may play sequential and complementary roles during development and in the adult nervous system. Most of the receptors for neurotrophic factors contain tyrosine kinase domains, suggesting the importance of tyrosine phosphorylation and subsequent signal transduction for their effects. Molecules such as LIF (leukemia inhibitory factor) and CNTF (ciliary neurotrophic factor) have been identified as neuronal differentiation factors in vitro. At the moment, however, it remains to be determined whether or not the receptors for a group of neuronal differentiation factors constitute a gene family or contain domains of kinase or phosphatase activity. Synergetic combinations of neurotrophic and neuronal differentiation factors as well as their receptors may contribute to the generation of neural specificity and diversity.

HOX11, a homeobox-containing T-cell oncogene on human chromosome 10q24

A common chromosomal abnormality in childhood T-cell acute leukemia is a translocation, t(10;14) (q24;q11), that together with the variant t(7;10)(q35;q24) is present in up to 7% of this tumor type. The gene adjacent to the 10q24 region is transcriptionally activated after translocation to either TCRD (14q11) or TCRB (7q35). It encodes a homeobox gene closely related to the developmentally regulated homeotic genes of flies and mammals. The coding capacity of this activated gene, designated HOX11, is undisturbed in a T-cell line carrying the translocation t(7;10)(q35;q24). Therefore, the HOX11 homeobox gene seems to be involved in T-cell tumorigenesis.

Regionally restricted developmental defects resulting from targeted disruption of the mouse homeobox gene hox-1.5

Gene targeting in mouse embryo-derived stem cells has been used to disrupt the homeobox gene hox-1.5. Mice heterozygous at the hox-1.5 locus appear normal, whereas hox-1.5-/hox-1.5- mice die at or shortly after birth. These homozygotes are athymic, aparathyroid, have reduced thyroid and submaxillary tissue and exhibit a wide range of throat abnormalities. In addition, they often feature defects of the heart and arteries as well as craniofacial abnormalities. These deficiencies are remarkably similar to the pathology of the human congenital disorder DiGeorge's syndrome.

Expression of HOX homeogenes in human neuroblastoma cell culture lines

Mammalian genes containing a class-I homeobox (HOX genes) are highly expressed in the embryonic nervous system. As a first step towards the molecular analysis of the role these genes play in neural cells, we studied the expression of four human HOX genes in five neuroblastoma (NB) cell lines - SK-N-BE, CHP-134, IMR-32, SK-N-SH and LAN-1 - during the process of differentiation induced by treatment with retinoic acid (RA). The four genes, HOX1D, 2F, 3E and 4B, located at corresponding positions in the four HOX loci, share a high degree of sequence similarity with the Drosophila Deformed homeotic gene and constitute a homology group, group 10. One of these genes, HOX1D, is not expressed in the cells used, whereas the other three are highly expressed in untreated and RA-induced NB cells, even though the expression pattern in the various lines is slightly different for the three genes. Our analysis reveals a complex and specific expression pattern in these lines, paving the way to an identification of different NB-cell populations by means of specific HOX gene expression schemes. On the other hand, in every line studied, morphological maturation toward a neuronal differentiated phenotype appears to be associated with increased HOX gene expression.

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).

Remarkable intron and exon sequence conservation in human and mouse homeobox Hox 1.3 genes

A high degree of conservation exists between the Hox 1.3 homeobox genes of mice and humans. The two genes occupy the same relative positions in their respective Hox 1 gene clusters, they show extensive sequence similarities in their coding and noncoding portions, and both are transcribed into multiple transcripts of similar sizes. The predicted human Hox 1.3 protein differs from its murine counterpart in only 7 of 270 amino acids. The sequence similarity in the 250 base pairs upstream of the initiation codon is 98%, the similarity between the two introns, both 960 base pairs long, is 72%, and the similarity in the 3' noncoding region from termination codon to polyadenylation signal is 90%. Both mouse and human Hox 1.3 introns contain a sequence with homology to a mating-type-controlled cis element of the yeast Ty1 transposon. DNA-binding studies with a recombinant mouse Hox 1.3 protein identified two binding sites in the intron, both of which were within the region of shared homology with this Ty1 cis element.

Expression of a large family of POU-domain regulatory genes in mammalian brain development

A novel region referred to as the POU-domain is present in two tissue-specific transcription factors, Pit-1 and Oct-2, that activate expression of genes specifying pituitary and lymphocyte phenotypes. We report the identification of multiple new members of a large family of POU-domain genes expressed in adult brain, and document that all the known mammalian POU-domain genes, including Pit-1 and Oct-2, are expressed widely in the developing nervous system.

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

A murine homeobox-containing cDNA clone has been isolated from an adult spinal cord library. Using in situ hybridization and somatic cell genetics techniques, the newly isolated homeobox gene has been mapped to mouse chromosome region 15E. Because of its chromosomal location, we called this gene locus Hox-3.3. Nucleotide sequence analysis revealed that the Hox-3.3 gene represents the murine cognate of the human homeobox gene c8. The presumptive organization of the murine Hox-3 homeobox gene cluster is discussed.

Differential expression of human HOX-2 genes along the anterior-posterior axis in embryonic central nervous system

We have investigated the structure of the human HOX-2 locus, which encompasses a 90-kb region on chromosome 17q21. Five new human HOX-2 homeoboxes, termed HOX-2.5, 2.4, 2.6, 2.7 and 2.8, have been identified, and their nucleotide sequences are reported. They have the same 5'-3' transcriptional orientation and are clustered with three previously described HOX-2 homeoboxes (5'-2.5-2.4-2.3-2.2-2.1-2.6-2.7-2.8-3'). We have also investigated the region-specific expression of HOX-2 genes in human embryonic-fetal life by Northern-blot analysis. All genes are expressed in whole embryos and fetuses at 5-9 weeks from conception. Their major site of expression lies within the central nervous system (CNS), although they are transcribed at a lower level in body structures other than the CNS. Their relatively abundant expression in CNS has been analyzed along the anterior-posterior axis by dissecting the brain, the medulla oblongata and the spinal cord proper. HOX-2.5, 2.4 and 2.3 transcripts are markedly more abundant in spinal cord than in medulla, whereas 2.2, 2.1, 2.6 and 2.7 mRNAs are progressively more abundant in the medulla. Additionally, expression in brain was detected, although at lower level, for HOX-2.1, 2.6, 2.7, 2.8. Thus, the relative position of HOX-2 homeobox genes along the chromosome in the 5'-3' direction appears to correlate with the relative position of their expression domains along the CNS longitudinal axis in the caudal-cephalic direction.

Complementary homeo protein gradients in developing limb buds

A new human homeo box-containing gene designated Hox-5.2 was cloned and mapped to human chromosome 2. This homeo box is related in sequence to Abdominal-B, a Drosophila homeotic gene that specifies identity of posterior segments. An antibody probe was made using a human Hox-5.2 fusion protein and was found to stain posterior regions of mouse, chicken, and Xenopus embryos. Unexpectedly, when the distribution of Hox-5.2 antigen was compared with that of X1Hbox 1 antigen, a non-overlapping and mutually exclusive pattern was detected (e.g., in developing limb buds, intestine, and somites). Regions expressing Hox-5.2 do not express X1Hbox 1 protein, and vice versa. Hox-5.2 antigen is detected strongly in developing fore- and hindlimb buds, where it forms a gradient of nuclear protein throughout most of the mesenchyme. This gradient is maximal in distal and posterior regions. Hox-5.2 expression is activated in Xenopus limb regeneration blastemas, as expected for any gene involved in pattern formation. As described previously, a gradient of X1Hbox 1 protein can be detected in the forelimb. The latter gradient has the opposite polarity to that of Hox-5.2. i.e., maximal in anterior and proximal mesoderm. These two opposing gradients (and possibly others) could be involved in determining positional values in developing limb buds.

Remarkable intron and exon sequence conservation in human and mouse homeobox Hox 1.3 genes

A high degree of conservation exists between the Hox 1.3 homeobox genes of mice and humans. The two genes occupy the same relative positions in their respective Hox 1 gene clusters, they show extensive sequence similarities in their coding and noncoding portions, and both are transcribed into multiple transcripts of similar sizes. The predicted human Hox 1.3 protein differs from its murine counterpart in only 7 of 270 amino acids. The sequence similarity in the 250 base pairs upstream of the initiation codon is 98%, the similarity between the two introns, both 960 base pairs long, is 72%, and the similarity in the 3' noncoding region from termination codon to polyadenylation signal is 90%. Both mouse and human Hox 1.3 introns contain a sequence with homology to a mating-type-controlled cis element of the yeast Ty1 transposon. DNA-binding studies with a recombinant mouse Hox 1.3 protein identified two binding sites in the intron, both of which were within the region of shared homology with this Ty1 cis element.

Early retinoic acid-induced F9 teratocarcinoma stem cell gene ERA-1: alternate splicing creates transcripts for a homeobox-containing protein and one lacking the homeobox

Retinoic acid (RA), the natural acidic derivative of vitamin A, can modulate the expression of specific genes and can induce some cell types, such as the murine F9 teratocarcinoma stem cell line, to differentiate in culture. As an initial step toward understanding the molecular mechanism(s) by which RA exerts these effects, we previously isolated cDNA clones for a gene, ERA-1, which has the characteristics of an early, direct target for RA. We demonstrated that RA causes a rapid, dose-dependent, and protein synthesis-independent expression of the ERA-1 gene (G. J. LaRosa and L. J. Gudas, Proc. Natl. Acad. Sci. USA 85:329-333, 1988). We now report the full-length cDNA sequence and the further characterization of this gene. The data indicate that the RA-induced 2.2- to 2.4-kilobase ERA-1 RNA species that we previously detected consists of two alternately spliced messages. One mRNA encodes a protein with a predicted mass of about 36 kilodaltons (kDa) that possesses the Hox 1.6 homeobox domain. The other mRNA encodes a truncated protein of about 15 kDa which is identical to the 36-kDa protein for 114 amino acids at the amino-terminal end but which lacks the homeobox amino acid sequence. The RA-associated increase in the ERA-1 mRNA level does not appear to be due to message stabilization, suggesting that the response is at the level of transcription. By Northern (RNA) blot analysis, the usual 2.2- to 2.4-kilobase mRNA species was also rapidly expressed in P19 teratocarcinoma cells during their differentiation to fibroblastic cells in response to RA and was detected in day 10.5 and day 13.5 mouse embryos. This result indicates that the expression of this gene is not limited to the endodermal differentiation of F9 cells.

Expression of Hox-2.4 homeobox gene directed by proviral insertion in a myeloid leukemia

The presence of an altered Hox-2.4 gene in the WEHI3B murine myeloid leukemia suggests that homeobox genes may contribute to neoplasia. A survey of 31 leukemia cell lines of the myeloid, lymphoid and erythroid lineages revealed that Hox-2.4 was expressed only in WEHI3B and the pre-B lymphoid line 70Z/3, in which no DNA rearrangement was observed. To clarify the WEHI3B alteration and normal Hox-2.4 structure, we have sequenced near full length cDNA clones from WEHI3B and 70Z/3, and the 5' portion of the normal Hox-2.4 gene. A WEHI3B cDNA clone demonstrates that an intracisternal A-particle (IAP) provirus has inserted within the first exon of the gene and generated a Hox-2.4 mRNA with a 5' sequence derived from the IAP long terminal repeat. A remarkable degree of similarity found between the amino acid sequences of Hox-2.4 and Hox-3.1, which reside on different chromosomes, supports the notion that an ancient homeobox gene cluster has been duplicated and dispersed early in vertebrate evolution.

Chromosomal localization of the human homeo box-containing genes, EN1 and EN2

The human homologs of the mouse homeo box-containing genes, En-1 and En-2, which show homology to the Drosophila engrailed gene, have been isolated. The human EN1 gene was mapped to chromosome 2 by analysis of mouse-human somatic cell hybrids. The human EN2 gene was localized to chromosome 7, 7q32-7qter, by analysis of rodent-human somatic cell hybrids and cell lines carrying portions of chromosome 7.

Homeobox genes and development of the vertebrate CNS

The discovery of homeobox genes in vertebrates may allow analysis of a basic problem in developmental neurobiology: how regional differences in CNS organization are specified during development. This view is based on the roles defined for homologous genes in Drosophila development, and is supported by studies of the patterns of homeobox gene expression in vertebrate embryos. Homeobox genes comprise a multigene family, members of which are expressed in different spatially restricted domains along the anterior-posterior axis of the CNS. These observations are consistent with homeobox genes having roles in the positional specification of CNS organization, and experimental tests of this should be forthcoming shortly.

A new family of mouse homeo box-containing genes: molecular structure, chromosomal location, and developmental expression of Hox-7.1

Two families of homeo box-containing genes have been identified in mammals to date, the Antennapedia- and engrailed-like homeo boxes, based on the sequence similarity to those from Drosophila. Here, we report the isolation of a homeo box-containing gene that belongs to a new family of which there are at least three related genes in the mouse genome. The homeo box of this new gene shows remarkable similarity to the Drosophila Msh homeo box that we designate as the prototype for this family. The gene maps to the proximal end of mouse chromosome 5 and does not cosegregate with any known homeo box-containing gene. We designate this locus Hox-7.1. In situ hybridizations to mouse embryos at different stages show a unique pattern of expression, as compared to other homeo box-containing genes described thus far. Hox-7.1 transcripts are detected in 9.5-day-old embryos in the neural crest, developing limb bud, and visceral arches. Later, this gene is expressed in regions of the face that are derived from neural crest and in the interdigital mesenchymal tissues in both the fore- and hindlimbs.

Posttranscriptional control of human homeobox gene expression in induced NTERA-2 embryonal carcinoma cells

We have studied the expression of four human homeobox genes representative of four different clusters (i.e., HOX-1, HOX-2, HOX-3 and HOX-5) in the embryonal carcinoma (EC) cell line NT2/D1. Following treatment with retinoic acid (RA), these cells differentiate into several cell types, including neurons, and steadily accumulate polyadenylated transcripts derived from the genes in a period ranging from 18 hr to 14 days of RA treatment. The sizes of major transcripts in differentiated EC cells coincide with those previously detected by the same probes in human embryos. Nuclear run-on transcriptional analysis showed no difference in the transcription rate of the four homeobox genes in differentiated vs. undifferentiated EC cells. Inhibition of protein synthesis by 5-18 hr of treatment of undifferentiated cells with cycloeximide causes accumulation of some homeobox transcripts at levels comparable to those observed after 18 hr of RA induction, although it does not cause superinduction in fully differentiated cells. These data suggest that the activation of homeobox gene expression in RA-induced EC cells is controlled, at least in part, by posttranscriptional mechanisms.

Structure and neural expression of a zebrafish homeobox sequence

A genomic library of zebrafish was constructed and screened with homeobox-containing probes. One of the positive clones contains a transcribed region which shares extensive sequence homology with the murine Hox-1.4 and Hox-2.6 genes and the human HHO.c13 gene. Characterization of this zebrafish homologue (ZF-13) with respect to expression demonstrated that it is transcribed during embryogenesis where a major RNA species of 2.5 kb and a minor transcript of 4.6 kb are detected. The highest concentration of both transcripts was found in embryos at the stage of somite formation. By in situ hybridization the spatial localization of expression was analysed in hatching embryos. Hybridization signals were mainly detected throughout the neural tube and in the brain. A small amount of RNA derived from ZF-13 was localized in differentiated muscle cells. Our results suggest that homeobox genes of distantly related vertebrate species are very similar with respect to structure and function.

Expression of the homeobox gene, Hox 2.1, during mouse embryogenesis

This article reviews recent studies on the expression of the homeobox gene, Hox 2.1, during mouse embryogenesis, using the technique of in situ hybridization. Differential hybridization of radiolabelled antisense versus sense strand RNA is first clearly detected in sections of 8.5 day post coitum (p.c.) early somite embryos. At 12.5 days p.c., higher levels of Hox 2.1 expression are seen in the spinal cord, extending into the base of the hind brain. Hybridization of antisense Hox 2.1 RNA is also seen in the spinal ganglia, in the nodose ganglia of the Xth cranial nerve (which contains derivatives of the neural crest arising from the posterior hind brain), and in the myenteric plexus. Mesodermal cells of certain visceral organs also express Hox 2.1 RNA, in particular the mesoderm of the lung, stomach and meso- and meta-nephric kidney. Comparison of the spatial domains of expression of mouse homeobox genes reveals a pattern consistent with the idea that they play a role in anteroposterior positional specification during embryogenesis.

A human protein specific for the immunoglobulin octamer DNA motif contains a functional homeobox domain

The homeobox domain is shared by Drosophila homeotic proteins, yeast mating type proteins, and some functionally uncharacterized mammalian proteins. A lymphoid-restricted human protein that binds to the immunoglobulin octamer regulatory motif was shown to contain an amino acid sequence that has 33% amino acid identity with the consensus sequence of the previously cloned homebox domains. This homeobox gene was localized to chromosome 19, thus mapping separately from other human homebox genes. A mutant protein containing amino acid substitutions within a putative helix-turn-helix motif in the homeobox domain did not bind DNA detectably. This human homeobox protein was shown to bind the same DNA sequence as the homeobox domains of the yeast mating type proteins and Drosophila homeotic protein, suggesting that homeobox proteins may have closely related DNA binding characteristics.

Differential antero-posterior expression of two proteins encoded by a homeobox gene in Xenopus and mouse embryos

The X.laevis XlHbox 1 gene uses two functional promoters to produce a short and a long protein, both containing the same homeodomain. In this report we use specific antibodies to localize both proteins in frog embryos. The antibodies also recognize the homologous proteins in mouse embryos. In both mammalian and amphibian embryos, expression of the long protein starts more posteriorly than that of the short protein. This difference in spatial expression applies to the nervous system, the segmented mesoderm and the internal organs. This suggests that each promoter from this gene has precisely restricted regions of expression along the anterior-posterior axis of the embryo. Because the long and short proteins share a common DNA-binding specificity but differ by an 82 amino acid domain, their differential distribution may have distinct developmental consequences.

Gene organization of murine homeobox-containing gene clusters

A chromosomal walk which links a previously described and a new homeobox to the Hox-2 murine homeobox gene cluster is described, and the nucleotide sequence of the new homeobox is presented. With these new data the Hox-2 gene cluster contains seven loci on an approximately 100-kb-long physical map. Homology comparisons reveal that a significant number of vertebrate homeoboxes are in fact analogous. We also find that the linear order of homologous homeoboxes is similar in the two murine gene complexes, Hox-1 and Hox-2, and among the human homeobox loci on chromosome 17. Conservation of the homeo-domain and the linear gene order of homeobox-containing genes in vertebrates is discussed in light of the interactions and the anteroposterior linear order of homeotic loci in insects.

Early retinoic acid-induced F9 teratocarcinoma stem cell gene ERA-1: alternate splicing creates transcripts for a homeobox-containing protein and one lacking the homeobox

Retinoic acid (RA), the natural acidic derivative of vitamin A, can modulate the expression of specific genes and can induce some cell types, such as the murine F9 teratocarcinoma stem cell line, to differentiate in culture. As an initial step toward understanding the molecular mechanism(s) by which RA exerts these effects, we previously isolated cDNA clones for a gene, ERA-1, which has the characteristics of an early, direct target for RA. We demonstrated that RA causes a rapid, dose-dependent, and protein synthesis-independent expression of the ERA-1 gene (G. J. LaRosa and L. J. Gudas, Proc. Natl. Acad. Sci. USA 85:329-333, 1988). We now report the full-length cDNA sequence and the further characterization of this gene. The data indicate that the RA-induced 2.2- to 2.4-kilobase ERA-1 RNA species that we previously detected consists of two alternately spliced messages. One mRNA encodes a protein with a predicted mass of about 36 kilodaltons (kDa) that possesses the Hox 1.6 homeobox domain. The other mRNA encodes a truncated protein of about 15 kDa which is identical to the 36-kDa protein for 114 amino acids at the amino-terminal end but which lacks the homeobox amino acid sequence. The RA-associated increase in the ERA-1 mRNA level does not appear to be due to message stabilization, suggesting that the response is at the level of transcription. By Northern (RNA) blot analysis, the usual 2.2- to 2.4-kilobase mRNA species was also rapidly expressed in P19 teratocarcinoma cells during their differentiation to fibroblastic cells in response to RA and was detected in day 10.5 and day 13.5 mouse embryos. This result indicates that the expression of this gene is not limited to the endodermal differentiation of F9 cells.

Differential expression of the homeobox gene Hox-1.3 in F9 embryonal carcinoma cells

The Hox-1.3 gene is located on mouse chromosome 6 and has been previously shown to be expressed in mouse embryos and adults. In this study, we have examined the steady-state levels of the Hox-1.3 transcripts in undifferentiated and differentiated F9 embryonal carcinoma cells. We find that there is a rapid increase of Hox-1.3 transcripts after differentiation induction of F9 cells. The level of the major 1.85-kilobase (kb) transcript peaks at 16-24 hr after differentiation induction of F9 cells. By using primer extension techniques the 5' ends of the major 1.85-kb transcript have been mapped to two sites in induced F9 cells. Cellular fractionation of RNA and transfer blot gel analysis has localized one minor transcript to the nucleus, whereas the major transcript and two additional minor transcripts appear in the nucleus and the cytoplasm of induced F9 cells. The results of nuclear run-off experiments with uninduced and induced F9 cell nuclei indicate that there is a substantial increase in the rate of Hox-1.3 transcription upon induction of F9 cells with retinoic acid.

Hox-5.1 defines a homeobox-containing gene locus on mouse chromosome 2

We have isolated a murine homeobox-containing gene, Hox-5.1, by virtue of its relatedness to the Hox-1.4 gene. In situ hybridization to metaphase spreads mapped Hox-5.1 to band D of mouse chromosome 2. Sequence comparisons indicate that Hox-5.1 is the murine homolog of the human C13 homeobox-containing gene. Hox-5.1 also bears significant similarity to the Xenopus Xhox-1A homeobox-containing gene and the Drosophila deformed homeotic gene at N-terminal and homeobox regions. Hox-5.1 transcripts were detected in mouse embryos, in adult mouse testis, kidney, heart, and intestine, and in mouse embryonal carcinoma cells treated with retinoic acid. In situ hybridization to sections from whole mouse embryos revealed Hox-5.1 expression in spinal cord and prevertebrae.

Expression of homeo box genes during mouse development: a review

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Differential utilization of the same reading frame in a Xenopus homeobox gene encodes two related proteins sharing the same DNA-binding specificity

Xenopus XlHbox 1 produces two transcripts during early development. One encodes a long open reading frame (ORF) and the other a short ORF sharing the same homeodomain, but differing by an 82 amino acid domain at the amino terminus. The long protein amino terminus is conserved with many other homeodomain proteins, and its absence from the short protein could have functional consequences. Some viral genes also utilize a single ORF to encode transcription factors of antagonistic functions. The overall organization of the homologous genes in frog and man is similar, supporting the notion that both transcripts are of functional significance. Studies on XlHbox 1 function show that the region common to the long and short proteins has a sequence-specific DNA-binding activity, and that microinjection of specific antibodies into embryos results in the loss of structures derived from cells normally expressing XlHbox 1.

At least three human homeoboxes on chromosome 12 belong to the same transcription unit

Mammalian homeoboxes show a clustered chromosomal organization. In the mouse, at least seven homeoboxes on chromosome 6 and at least six on chromosome 11 identify the murine Hox-1 and Hox-2 loci, respectively. A number of homeoboxes on chromosome 7 define the human HOX-1 locus and homeoboxes on chromosome 17 define the human HOX-2 locus. We studied the genomic organization of three homeobox sequences of the HOX-3 locus on chromosome 12 and analyzed transcripts from this region. Structural characterization and sequencing of several cDNA clones reveal that the three homeobox sequences present in this chromosomal region identify a single transcription unit. Primary transcripts are alternatively processed to give mature messengers with a common 5' noncoding exon encoding different proteins containing one of the three homeodomains.

Pax 1, a member of a paired box homologous murine gene family, is expressed in segmented structures during development

The mouse genome contains at least three copies of sequences homologous to the "paired box", a conserved domain in several Drosophila segmentation genes of the pair-rule and segment polarity classes. Overlapping phages were isolated from two different genomic libraries using the Drosophila gooseberry distal paired box as a probe. The hybridizing sequences are highly homologous to the conserved Drosophila paired box sequences. A single 3.1 kb Pax 1 (paired box gene) transcript was detected during embryonic development, whereas no transcripts were detected in adult tissues. Detailed in situ hybridization analyses with frozen embryonic sections demonstrated Pax 1 transcripts in the perichordal zone of the developing vertebral column. The expression pattern suggests a role for this gene in the formation of segmented structures of the mouse embryo.

A zebrafish engrailed-like homeobox sequence expressed during embryogenesis

The zebrafish genome was found to contain two sequences which cross-hybridize strongly with the engrailed gene of Drosophila. Several independent clones containing one of these cross-hybridizing sequences were isolated from a zebrafish genomic library. Characterization of this region (ZF-EN) by DNA sequencing showed that it shares about 70% sequence identity with the engrailed homeobox. More extensive homeobox homology (greater than 90%) was found relative to the murine En genes. The closest relationship exists between ZF-EN and En-2 where the C-terminal domains (104 amino acids) encoded by these genes are almost identical. We also observed that ZF-EN and En-2 are very similar with respect to their transcript sizes and temporal expression patterns.

A zebrafish homologue of the murine Hox-2.1 gene

Homeobox-containing sequences were isolated from a genomic library of zebrafish (Brachydanio rerio). A lambda clone containing two homeobox cross-hybridizing regions was characterized. DNA sequencing of one of these regions (ZF-21) revealed that it contains a homeobox closely related to the Antennapedia class of Drosophila homeobox sequences. Moreover, the deduced amino acid sequence of the C-terminal end (81 residues including the homeobox) is identical to the corresponding part of the murine Hox-2.1 protein. Similar to Hox-2.1, a ZF-21 derived transcript of 2.3 kb is present in embryos at the somite forming stages.

Expression of the homeo box-containing gene En-2 delineates a specific region of the developing mouse brain

We have examined the pattern of expression of the homeo box-containing gene En-2 during mouse embryogenesis using in situ hybridization. Transcripts were first detected in the neural folds of 8.0-day, 5-somite embryos, and expression continued throughout development into adulthood. Hybridization occurred only in the central nervous system (CNS) and was limited to one band of the neural tube and to parts of those structures that later developed from it; the cerebellum, pons, periaqueductal gray, and colliculi. Expression in the germinal zone of the CNS was uniform within the hybridizing band. However, later in development, once cells had migrated out of the germinal zone, there was a reduction in the extent of hybridization and an increase in its spatial complexity. In the adult, expression of En-2 appeared to be limited to specific groups of neurons. The early, localized expression of En-2 within an apparently homogeneous tissue is consistent with the hypothesis that En-2 plays a role in defining a spatial domain within the developing brain.

Molecular cloning and characterization of homeo-box-containing genes from Atlantic salmon

As the most primitive group among vertebrates, fish might serve as a model system when studying the genetic regulation of embryogenesis in higher animals. To identify genes important for early development, we have constructed a genomic library from Atlantic salmon (Salmo salar) and screened it with homeobox-containing probes from Drosophila melanogaster. Five different salmon homeoboxes were isolated. Two of these were located in the same clone, separated by only 7.5 kb. This demonstrates the presence of clustered homeobox genes in fish. The two clustered homeoboxes were sequenced and shown to be closely related to the ANT-C/BX-C class of Drosophila, being about 80% homologous to the Ultrabithorax gene (Ubx) homeobox. One of the clustered genes appears to be the salmon equivalent of the mouse Hox-2.1 gene, indicating that some of the vertebrate homeobox-containing genes are conserved in evolution. A more diverged homeobox that shares only 60% homology with Ubx, was also sequenced. In analogy to Drosophila, therefore, the salmon genome contains more than one class of homeoboxes. In addition, Northern-blot experiments demonstrated that two of the homeobox genes are expressed in salmon embryos, suggesting their importance for proper development.

Murine Hox-1.7 homeo-box gene: cloning, chromosomal location, and expression

A new murine homeo-box, called Hox-1.7, has been identified in a rare cDNA from F9 teratocarcinoma stem cells. The Hox-1.7 homeo-box is 68 and 72% homologous to the Drosophila antennapedia (Antp) and iab-7 homeo-boxes, respectively. A major 2.5-kilobase transcript and several minor transcripts were detected by Northern blot (RNA blot) analysis in adult tissues as well as in midgestational embryos. The posterior spinal cord was found to be a major site of Hox-1.7 expression in 12.5-day-old embryos. Somatic cell hybrids were used to map the Hox-1.7 gene to mouse chromosome 6. Restriction fragment length polymorphisms associated with either the Hox-1.7 gene or the previously known Hox-1 complex were identified. Their distribution patterns in recombinant inbred mouse strains were used to determine the linkage between the two loci as well as to other loci on chromosome 6. This maps Hox-1 and Hox-1.7 close to two mouse loci that affect morphogenesis, postaxial hemimelia (px) and hypodactyly (Hd).

The murine homeo box gene product, Hox 1.1 protein, is growth-controlled and associated with chromatin

In order to gain insight into the function of the Hox 1.1 gene, we studied the expression of the murine homeo box gene product, the Hox 1.1 protein. Monoclonal antibodies were raised against synthetic peptides of the Hox 1.1 protein to study the localization and expression pattern of this protein under various culture conditions. By means of indirect immunofluorescence we localized the Hox 1.1 protein to the nucleus in differentiated F9 and NIH 3T3 cells. During mitosis the protein was found to be associated with chromatin. Confluent NIH 3T3 cells harbored little if any Hox 1.1 protein. After "wounding" the cells in this confluent monolayer, we observed an induction of the expression of the Hox 1.1 protein. However, addition of insulin to F9 and contact-inhibited NIH 3T3 cells led to an increase of the Hox 1.1 RNA and protein expression. Thus, the induction of the Hox 1.1 protein is associated not only with the differentiation of embryonal carcinoma (EC) cells, but may also correlate with stages of cell growth.

Post-transcriptional regulation of a murine homeobox gene transcript in F9 embryonal carcinoma cells

A 2.4 kb RNA encoded by the murine Hox 1.1 (m6) homeobox gene is induced when F9 stem cells are differentiated with retinoic acid and dibutyryl cyclic AMP. The regulation of Hox 1.1 expression was probed by using cycloheximide, an inhibitor of protein synthesis. Production of the Hox 1.1 RNA in differentiating F9 cells was not blocked by treatment with cycloheximide, indicating that new protein synthesis is not required for its induction. On the contrary, this transcript was detected in F9 stem cells treated with cycloheximide, anisomycin, or emetine alone. Nuclear transcription assays indicated that the Hox 1.1 gene was transcribed in F9 stem cells and that the rate of transcription did not change early in the differentiation of F9 cells. These observations indicate that the induction of Hox 1.1 transcripts in F9 stem cells during differentiation is not regulated at the level of transcription initiation but results from stabilization of the transcript.

Murine Hox-1.7 homeo-box gene: cloning, chromosomal location, and expression

A new murine homeo-box, called Hox-1.7, has been identified in a rare cDNA from F9 teratocarcinoma stem cells. The Hox-1.7 homeo-box is 68 and 72% homologous to the Drosophila antennapedia (Antp) and iab-7 homeo-boxes, respectively. A major 2.5-kilobase transcript and several minor transcripts were detected by Northern blot (RNA blot) analysis in adult tissues as well as in midgestational embryos. The posterior spinal cord was found to be a major site of Hox-1.7 expression in 12.5-day-old embryos. Somatic cell hybrids were used to map the Hox-1.7 gene to mouse chromosome 6. Restriction fragment length polymorphisms associated with either the Hox-1.7 gene or the previously known Hox-1 complex were identified. Their distribution patterns in recombinant inbred mouse strains were used to determine the linkage between the two loci as well as to other loci on chromosome 6. This maps Hox-1 and Hox-1.7 close to two mouse loci that affect morphogenesis, postaxial hemimelia (px) and hypodactyly (Hd).