Transcriptional control of Hox genes in the vertebrate nervous system

Simultaneous detection of multiple mRNAs and proteins in bovine IVD cells and tissue with single cell resolution

OBJECTIVES

Interactions of cells with their neighbors and influences by the surrounding extracellular matrix (ECM) is reflected in a cells transcriptome and proteome. In tissues comprised of heterogeneous cell populations or cells depending on ECM signalling cues such as those of the intervertebral disc (IVD), this information is obscured or lost when cells are pooled for the commonly used transcript analysis by quantitative PCR or RNA sequencing. Instead, these cells require means to analyse RNA transcript and protein distribution at a single cell or subcellular level to identify different cell types and functions, without removing them from their surrounding signalling cues.

RESULTS

We developed a simple, sequential protocol combining RNA is situ hybridisation (RISH) and immunohistochemistry (IHC) for the simultaneous analysis of multiple transcripts alongside proteins. This allows one to characterize heterogeneous cell populations at the single cell level in the natural cell environment and signalling context, both in vivo and in vitro. This protocol is demonstrated on cells of the bovine IVD, for transcripts and proteins involved in mechanotransduction, stemness and cell proliferation.

CONCLUSIONS

A simple, sequential protocol combining RISH and IHC is presented that allows for simultaneous information on RNA transcripts and proteins to characterize cells within a heterogeneous cell population and complex signalling environments such as those of the IVD.

A quantitative and qualitative RNA expression profiling assay for cell culture with single cell resolution

Cells are often characterized by their gene expression profile. However, commonly used methods to detect mRNA require cell pooling and could therefore mask differences in gene expression within heterogeneous cell populations. q²PISH allows for the analysis of both qualitative and quantitative (q²) gene expression on cultured cells for quality control measures with single cell resolution. q²PISH was optimized for the subsequent use of two alkaline phosphatase substrates in combination with a cell nucleus count to allow for accurate quantification of gene expression per cell and simultaneously qualitative assessment of potential culture population drift or heterogeneity. As proof of principle the assay was applied to cell lines derived from different areas of the bovine intervertebral disc, showing significant difference in the expression of Col1a1, Col2a1, Acan and Sox9. Furthermore, the assay served to explore a potential impact on cultured cells when substituting a critical media component, fetal bovine serum (FBS), suggesting no significant difference in gene expression for the biomarkers analyzed. As a tool, q²PISH serves as an accurate quality control with single cell resolution for cultured cells.

An Integrative Developmental Genomics and Systems Biology Approach to Identify an In Vivo Sox Trio-Mediated Gene Regulatory Network in Murine Embryos

Embryogenesis is an intricate process involving multiple genes and pathways. Some of the key transcription factors controlling specific cell types are the Sox trio, namely, Sox5, Sox6, and Sox9, which play crucial roles in organogenesis working in a concerted manner. Much however still needs to be learned about their combinatorial roles during this process. A developmental genomics and systems biology approach offers to complement the reductionist methodology of current developmental biology and provide a more comprehensive and integrated view of the interrelationships of complex regulatory networks that occur during organogenesis. By combining cell type-specific transcriptome analysis and in vivo ChIP-Seq of the Sox trio using mouse embryos, we provide evidence for the direct control of Sox5 and Sox6 by the transcriptional trio in the murine model and by Morpholino knockdown in zebrafish and demonstrate the novel role of Tgfb2, Fbxl18, and Tle3 in formation of Sox5, Sox6, and Sox9 dependent tissues. Concurrently, a complete embryonic gene regulatory network has been generated, identifying a wide repertoire of genes involved and controlled by the Sox trio in the intricate process of normal embryogenesis.

The use of protein-DNA, chromatin immunoprecipitation, and transcriptome arrays to describe transcriptional circuits in the dehydrated male rat hypothalamus

The supraoptic nucleus (SON) of the hypothalamus is responsible for maintaining osmotic stability in mammals through its elaboration of the antidiuretic hormone arginine vasopressin. Upon dehydration, the SON undergoes a function-related plasticity, which includes remodeling of morphology, electrical properties, and biosynthetic activity. This process occurs alongside alterations in steady state transcript levels, which might be mediated by changes in the activity of transcription factors. In order to identify which transcription factors might be involved in changing patterns of gene expression, an Affymetrix protein-DNA array analysis was carried out. Nuclear extracts of SON from dehydrated and control male rats were analyzed for binding to the 345 consensus DNA transcription factor binding sequences of the array. Statistical analysis revealed significant changes in binding to 26 consensus elements, of which EMSA confirmed increased binding to signal transducer and activator of transcription (Stat) 1/Stat3, cellular Myelocytomatosis virus-like cellular proto-oncogene (c-Myc)-Myc-associated factor X (Max), and pre-B cell leukemia transcription factor 1 sequences after dehydration. Focusing on c-Myc and Max, we used quantitative PCR to confirm previous transcriptomic analysis that had suggested an increase in c-Myc, but not Max, mRNA levels in the SON after dehydration, and we demonstrated c-Myc- and Max-like immunoreactivities in SON arginine vasopressin-expressing cells. Finally, by comparing new data obtained from Roche-NimbleGen chromatin immunoprecipitation arrays with previously published transcriptomic data, we have identified putative c-Myc target genes whose expression changes in the SON after dehydration. These include known c-Myc targets, such as the Slc7a5 gene, which encodes the L-type amino acid transporter 1, ribosomal protein L24, histone deactylase 2, and the Rat sarcoma proto-oncogene (Ras)-related nuclear GTPase.

Genome wide expression profiling during spinal cord regeneration identifies comprehensive cellular responses in zebrafish

BACKGROUND

Among the vertebrates, teleost and urodele amphibians are capable of regenerating their central nervous system. We have used zebrafish as a model to study spinal cord injury and regeneration. Relatively little is known about the molecular mechanisms underlying spinal cord regeneration and information based on high density oligonucleotide microarray was not available. We have used a high density microarray to profile the temporal transcriptome dynamics during the entire phenomenon.

RESULTS

A total of 3842 genes expressed differentially with significant fold changes during spinal cord regeneration. Cluster analysis revealed event specific dynamic expression of genes related to inflammation, cell death, cell migration, cell proliferation, neurogenesis, neural patterning and axonal regrowth. Spatio-temporal analysis of stat3 expression suggested its possible function in controlling inflammation and cell proliferation. Genes involved in neurogenesis and their dorso-ventral patterning (sox2 and dbx2) are differentially expressed. Injury induced cell proliferation is controlled by many cell cycle regulators and some are commonly expressed in regenerating fin, heart and retina. Expression pattern of certain pathway genes are identified for the first time during regeneration of spinal cord. Several genes involved in PNS regeneration in mammals like stat3, socs3, atf3, mmp9 and sox11 are upregulated in zebrafish SCI thus creating PNS like environment after injury.

CONCLUSION

Our study provides a comprehensive genetic blue print of diverse cellular response(s) during regeneration of zebrafish spinal cord. The data highlights the importance of different event specific gene expression that could be better understood and manipulated further to induce successful regeneration in mammals.

Functional dissection of HOXD cluster genes in regulation of neuroblastoma cell proliferation and differentiation

Retinoic acid (RA) can induce growth arrest and neuronal differentiation of neuroblastoma cells and has been used in clinic for treatment of neuroblastoma. It has been reported that RA induces the expression of several HOXD genes in human neuroblastoma cell lines, but their roles in RA action are largely unknown. The HOXD cluster contains nine genes (HOXD1, HOXD3, HOXD4, and HOXD8-13) that are positioned sequentially from 3' to 5', with HOXD1 at the 3' end and HOXD13 the 5' end. Here we show that all HOXD genes are induced by RA in the human neuroblastoma BE(2)-C cells, with the genes located at the 3' end being activated generally earlier than those positioned more 5' within the cluster. Individual induction of HOXD8, HOXD9, HOXD10 or HOXD12 is sufficient to induce both growth arrest and neuronal differentiation, which is associated with downregulation of cell cycle-promoting genes and upregulation of neuronal differentiation genes. However, induction of other HOXD genes either has no effect (HOXD1) or has partial effects (HOXD3, HOXD4, HOXD11 and HOXD13) on BE(2)-C cell proliferation or differentiation. We further show that knockdown of HOXD8 expression, but not that of HOXD9 expression, significantly inhibits the differentiation-inducing activity of RA. HOXD8 directly activates the transcription of HOXC9, a key effector of RA action in neuroblastoma cells. These findings highlight the distinct functions of HOXD genes in RA induction of neuroblastoma cell differentiation.

The atypical homeoprotein Pbx1a participates in the axonal pathfinding of mesencephalic dopaminergic neurons

BACKGROUND

The pre B-cell leukemia transcription factor 1 (Pbx1) genes belong to the three amino acid loop extension family of homeodomain proteins that form hetero-oligomeric complexes with other homeodomain transcription factors, thereby modulating target specificity, DNA binding affinity and transcriptional activity of their molecular associates.

RESULTS

Here, we provide evidence that Pbx1 is expressed in mesencephalic dopaminergic neurons from embryonic day 11 into adulthood and determines some of the cellular properties of this neuronal population. In Pbx1-deficient mice, the mesencephalic dopaminergic axons stall during mid-gestation at the border between di- and telencephalon before entering the ganglionic eminence, leading to a loose organization of the axonal bundle and partial misrouting. In Pbx1-deficient dopaminergic neurons, the high affinity netrin-1 receptor, deleted in colon cancer (DCC), is down-regulated. Interestingly, we found several conserved Pbx1 binding sites in the first intron of DCC, suggesting a direct regulation of DCC transcription by Pbx1.

CONCLUSIONS

The expression of Pbx1 in dopaminergic neurons and its regulation of DCC expression make it an important player in defining the axonal guidance of the midbrain dopaminergic neurons, with possible implications for the normal physiology of the nigro-striatal system as well as processes related to the degeneration of neurons during the course of Parkinson's disease.

Hox clusters of the bichir (Actinopterygii, Polypterus senegalus) highlight unique patterns of sequence evolution in gnathostome phylogeny

Teleost fishes have extra Hox gene clusters owing to shared or lineage-specific genome duplication events in rayfinned fish (actinopterygian) phylogeny. Hence, extrapolating between genome function of teleosts and human or even between different fish species is difficult. We have sequenced and analyzed Hox gene clusters of the Senegal bichir (Polypterus senegalus), an extant representative of the most basal actinopterygian lineage. Bichir possesses four Hox gene clusters (A, B, C, D); phylogenetic analysis supports their orthology to the four Hox gene clusters of the gnathostome ancestor. We have generated a comprehensive database of conserved Hox noncoding sequences that include cartilaginous, lobe-finned, and ray-finned fishes (bichir and teleosts). Our analysis identified putative and known Hox cis-regulatory sequences with differing depths of conservation in Gnathostoma. We found that although bichir possesses four Hox gene clusters, its pattern of conservation of noncoding sequences is mosaic between outgroups, such as human, coelacanth, and shark, with four Hox gene clusters and teleosts, such as zebrafish and pufferfish, with seven or eight Hox gene clusters. Notably, bichir Hox gene clusters have been invaded by DNA transposons and this trend is further exemplified in teleosts, suggesting an as yet unrecognized mechanism of genome evolution that may explain Hox cluster plasticity in actinopterygians. Taken together, our results suggest that actinopterygian Hox gene clusters experienced a reduction in selective constraints that surprisingly predates the teleost-specific genome duplication.

Prospectively isolated CD133/CD24-positive ependymal cells from the adult spinal cord and lateral ventricle wall differ in their long-term in vitro self-renewal and in vivo gene expression

In contrast to ependymal cells located above the subventricular zone (SVZ) of the adult lateral ventricle wall (LVW), adult spinal cord (SC) ependymal cells possess certain neural stem cell characteristics. The molecular basis of this difference is unknown. In this study, antibodies against multiple cell surface markers were applied to isolate pure populations of SC and LVW ependymal cells, which allowed a direct comparison of their in vitro behavior and in vivo gene expression profile. Isolated CD133(+)/CD24(+)/CD45(-)/CD34(-) ependymal cells from the SC displayed in vitro self-renewal and differentiation capacity, whereas those from the LVW did not. SC ependymal cells showed a higher expression of several genes involved in cell division, cell cycle regulation, and chromosome stability, which is consistent with a long-term self-renewal capacity, and shared certain transcripts with neural stem cells of the embryonic forebrain. They also expressed several retinoic acid (RA)-regulated genes and responded to RA exposure. LVW ependymal cells showed higher transcript levels of many genes regulated by transforming growth factor-β family members. Among them were Dlx2, Id2, Hey1, which together with Foxg1 could explain their potential to turn into neuroblasts under certain environmental conditions.

Retracted: Gene duplication and functional evolution of Hox genes in fishes

With their power to shape animal morphology, few genes have captured the imagination of biologists as much as the evolutionarily conserved members of the Hox clusters. Hox genes encode transcription factors that play a key role in specifying the body plan in metazoans and are therefore essential in explaining patterns of evolutionary diversity. While each Hox cluster contains the same genes among the different mammalian species, this does not happen in ray-finned fish, in which both the number and organization of Hox genes and even Hox clusters are variable. Teleost fishes provide the first unambiguous support for ancient whole-genome duplication (third round) in an animal lineage. The number of genes differs in each cluster as a result of increased freedom to mutate after duplication. This has also allowed them to diverge and to adopt novel developmental roles. In this review, the authors have firstly focused on broadly outlining the duplication of Hoxgenes in fishes and discussing how comparative genomics is elucidating the molecular changes associated with the evolution of Hox genes expression and developmental function in the teleost fishes.Additional related research aspects, such as imaging of roles of microRNAs, chromatin regulation and evolutionary findings are also discussed.

Effect of excessive iodine exposure on the placental deiodinase activities and Hoxc8 expression during mouse embryogenesis

Excessive iodine induces thyroid dysfunction. However, the effect of excessive iodine exposure on maternal-fetal thyroid hormone metabolism and on the expression of genes involved in differentiation, growth and development is poorly understood. Since a thyroid hormone receptor response element was found in the Hoxc8 promoter region, Hoxc8 expression possibly regulated by excessive iodine exposure was firstly investigated. In the present study, Balb/C mice were given different doses of iodine in the form of potassium iodate (KIO3) at the levels of 0 (sterile water), 1.5, 3.0, 6.0, 12.0 and 24.0 microg/ml in drinking water for 4 months, then were mated. On 12.5 d postcoitum, placental type 2 and type 3 deiodinase activities and fetal Hoxc8 expression were determined. The results showed that excessive iodine exposure above 1.5 microg/ml resulted in an increase of total thyroxine and a decrease of total triiodothyronine in the serum of maternal mice, which was mainly associated with the inhibition of type 1 deiodinase activity in liver and kidney. Placental type 2 deiodinase activity decreased, showing an inverse relationship with maternal thyroxine level. Hoxc8 mRNA and protein expression at 12.5 d postcoitum embryos were down regulated. Because Hoxc8 plays an important role in normal skeletal development, this finding provides a possible explanation for the skeletal malformation induced by excessive iodine exposure and also provides a new clue to study the relationship between iodine or thyroid hormones and Hox gene expression pattern.

Hox gene clusters in blunt snout bream, Megalobrama amblycephala and comparison with those of zebrafish, fugu and medaka genomes

Hox genes encode transcription factors that play a key role in specifying the body plan in metazoans and are therefore essential in explaining patterns of evolutionary diversity. While each Hox cluster contains the same genes among the different mammalian species, this does not happen in ray-finned fish, in which both the number and organization of Hox genes and even Hox clusters are variables. Here we reveal the organization of Hox genes loci in blunt snout bream. Forty-nine Hox genes including a pseudogene A9b in total have been found in seven clusters as follows: 8 Hox genes in the Aa cluster; 5 in Ab; 10 in Ba; 4 in Bb; 11 in Ca; 4 in Cb; and 7 in Da. In terms of gene content, clusters organization and sequence similarities of putative amino acids, blunt snout bream is more closely related to zebrafish than to fugu and medaka. In contrast to the situation in fugu and medaka, both blunt snout bream and zebrafish have duplicated HoxC cluster but only a single copy of the HoxD cluster. The result implies that the loss of the second HoxD cluster might be a shared feature of the Ostariophysi, to which zebrafish and blunt snout bream both belong. Phylogenetic analysis bases on the paralogous genes from twin clusters supports the duplication-first model, i.e., four original clusters may have duplicated in an event before the divergence of the blunt snout bream-plus-zebrafish lineage and the fugu-plus-medaka lineage. Additionally, the relationship between the decrease of GC level and the loss of conservation and function of one of the paralogous genes from twin clusters is discussed.

Identification of a murine methyl cytosine phosphate guanine binding domain-containing factor 3 (MBD3) promoter segment sufficient for driving reporter gene expression in neurons in vitro and in vivo

In this study, we characterize the functional properties of a segment of the murine methyl cytosine phosphate guanine binding domain-containing factor 3 (MBD3) promoter region. Transient transfection of a chimera consisting of a 1072 base pair region extending upstream from the MBD3 initiation codon fused to a luciferase complementary DNA (cDNA) confirmed the presence of a functional promoter unit. Primer extension analysis failed to identify a single predominant transcription initiation site, but rather detected multiple transcription initiation sites in both brain tissue and cultured neuroblastomaxglioma cell line (NG108-15) and rat pheochromocytoma cell line (PC12) cells. Reporter gene assays revealed that this 1072 base pair fragment efficiently drives expression in transfected NG108-15 cells, PC12 cells, cultured primary neurons, and in neurons of a transgenic mouse brain. Deletion analysis mapped the critical region for promoter activity to a segment of approximately 518 base pairs, located from positions -585 to -68 relative to the translational start codon. Taken together, these data indicate that a 1072 base pair fragment of the MBD3 promoter is sufficient to drive expression in cell lines and primary cultured neurons, and is able to direct transgene expression in the mouse brain in a pattern with spatial similarity to that of native MBD3.

Shifting boundaries of retinoic acid activity control hindbrain segmental gene expression

Retinoic acid (RA) generated by Raldh2 in paraxial mesoderm is required for specification of the posterior hindbrain, including restriction of Hoxb1 expression to presumptive rhombomere 4 (r4). Hoxb1 expression requires 3' and 5' RA response elements for widespread induction up to r4 and for r3/r5 repression, but RA has previously been detected only from r5-r8, and vHnf1 is required for repression of Hoxb1 posterior to r4 in zebrafish. We demonstrate in mouse embryos that an RA signal initially travels from the paraxial mesoderm to r3, forming a boundary next to the r2 expression domain of Cyp26a1 (which encodes an RA-degrading enzyme). After Hoxb1 induction, the RA boundary quickly shifts to r4/r5, coincident with induction of Cyp26c1 in r4. A functional role for Cyp26c1 in RA degradation was established through examination of RA-treated embryos. Analysis of Raldh2-/- and vHnf1-/- embryos supports a direct role for RA in Hoxb1 induction up to r4 and repression in r3/r5, as well as an indirect role for RA in Hoxb1 repression posterior to r4 via RA induction of vHnf1 up to the r4/r5 boundary. Our findings suggest that Raldh2 and Cyp26 generate shifting boundaries of RA activity, such that r3-r4 receives a short pulse of RA and r5-r8 receives a long pulse of RA. These two pulses of RA activity function to establish expression of Hoxb1 and vHnf1 on opposite sides of the r4/r5 boundary.

Comparative cis-regulatory analyses identify new elements of the mouse Hoxc8 early enhancer

The Hoxc8 early enhancer is a 200 bp region that controls the early phase of Hoxc8 expression during mouse embryonic development. This enhancer defines the domain of Hoxc8 expression in the neural tube and mesoderm of the posterior regions of the developing embryo. Five distinct cis-acting elements, A-E, were previously shown to govern early phase Hoxc8 expression. Significant divergence between mammalian and fish Hoxc8 early enhancer sequences and activities suggested additional cis-acting elements. Here we describe four additional cis-acting elements (F-I) within the 200 bp Hoxc8 early enhancer region identified by comparative regulatory analysis and transgene-mutation studies. These elements affect posterior neural tube and mesoderm expression of the reporter gene, either singly or in combination. Surprisingly, these new elements are missing from the zebrafish and Fugu Hoxc8 early enhancer sequences. Considering that fish enhancers direct robust reporter expression in transgenic mouse embryos, it is tempting to postulate that fish and mammalian Hoxc8 early enhancers utilize different sets of elements to direct Hoxc8 early expression. These observations reveal a remarkable plasticity in the Hoxc8 early enhancer, suggesting different modes of initiation and establishment of Hoxc8 expression in different species. We postulate that extensive restructuring and remodeling of Hox cis-regulatory regions occurring in different taxa lead to relatively different Hox expression patterns, which in turn may act as a driving force in generating diverse axial morphologies.

Bichir HoxA cluster sequence reveals surprising trends in ray-finned fish genomic evolution

The study of Hox clusters and genes provides insights into the evolution of genomic regulation of development. Derived ray-finned fishes (Actinopterygii, Teleostei) such as zebrafish and pufferfish possess duplicated Hox clusters that have undergone considerable sequence evolution. Whether these changes are associated with the duplication(s) that produced extra Hox clusters is unresolved because comparison with basal lineages is unavailable. We sequenced and analyzed the HoxA cluster of the bichir (Polypterus senegalus), a phylogenetically basal actinopterygian. Independent lines of evidence indicate that bichir has one HoxA cluster that is mosaic in its patterns of noncoding sequence conservation and gene retention relative to the HoxA clusters of human and shark, and the HoxAalpha and HoxAbeta clusters of zebrafish, pufferfish, and striped bass. HoxA cluster noncoding sequences conserved between bichir and euteleosts indicate that novel cis-sequences were acquired in the stem actinopterygians and maintained after cluster duplication. Hence, in the earliest actinopterygians, evolution of the single HoxA cluster was already more dynamic than in human and shark. This tendency peaked among teleosts after HoxA cluster duplication.

Retinoic acid regulates the expression of PBX1, PBX2, and PBX3 in P19 cells both transcriptionally and post-translationally

Pre-B cell leukemia transcription factors (PBXs) are important co-factors for the transcriptional regulation mediated by a number of Hox proteins during embryonic development. It was previously shown that the expression of several Pbx genes is elevated in mouse embryo limb buds and embryonal carcinoma P19 cells upon retinoic acid (RA) treatment although the mechanism of this induction is not well understood. In this report, we demonstrate that PBX1a, PBX1b, PBX2, and PBX3 mRNAs and PBX1/2/3 proteins are induced during endodermal and neuronal differentiation of P19 cells in a RAR-dependent subtype-unspecific manner following RA treatment. The increases in both PBX1 mRNA and PBX3 mRNA levels are secondary responses to RA treatment requiring new proteins synthesis while the increase in PBX2 mRNA is a primary response. The RA-dependent increases in PBX1 mRNA, PBX2 mRNA, and PBX3 mRNA levels are likely to be transcriptionally regulated since the stability of these mRNAs does not change. In addition, the half-lives of PBX1/2/3 proteins are significantly extended by RA treatment. Two possible mechanisms could contribute to the stabilization of PBX proteins: PBX proteins associate with RA-dependent increased levels of MEIS proteins, and RA may decrease the proteasome dependent degradation of PBX proteins.

Signal transduction and the control of gene expression

More than 2000 transcription factors are encoded in the human genome. Such proteins have often been classified according to common structural elements. But because transcription factors evolved in the service of biologic function, we propose an alternative grouping of eukaryotic transcription factors on the basis of characteristics that describe their roles within cellular regulatory circuits.

Neural patterning in the vertebrate embryo

The embryonic central nervous system (CNS) is patterned along its antero-posterior, dorsal-ventral, and left-right axes. Along the dorsal-ventral axis, cell fate determination occurs during and following neural tube closure and involves the action of two opposing signaling pathways: SHH ventrally from the notochord and BMP/GDF dorsally from the boundary of neural and nonneural ectoderm and later from the roof plate. In addition, Wnt and retinoic acid signaling have been shown to act in dorsal-ventral patterning; however, their roles are understood in less detail. Along the antero-posterior axis, signals divide the neural tube into four major divisions: forebrain, midbrain, hindbrain, and spinal cord, and these differences can be detected soon after the formation of the neural plate. The FGF, Wnt, and retinoic acid signaling pathways have been implicated in the caudalization of neural tissue. Boundaries of Hox gene expression are observed along the anteroposterior axis and have been suggested to be involved in establishing different identities in the hindbrain and spinal cord. Complex gene expression patterns in the brain suggest the development of neuromeres dividing the brain into different regions that are elaborated further during development. Patterning along the left-right axis occurs concurrently with antero-posterior and dorsal-ventral patterning during gastrulation. A leading candidate for initiating asymmetry is activin, which acts through Nodal and Lefty before any morphological differences are observed. The big challenge will be understanding how these diverse signaling pathways interact both temporally and spatially to generate the complex adult nervous system.

FTZ-Factor1 and Fushi tarazu interact via conserved nuclear receptor and coactivator motifs

To activate transcription, most nuclear receptor proteins require coactivators that bind to their ligand-binding domains (LBDs). The Drosophila FTZ-Factor1 (FTZ-F1) protein is a conserved member of the nuclear receptor superfamily, but was previously thought to lack an AF2 motif, a motif that is required for ligand and coactivator binding. Here we show that FTZ-F1 does have an AF2 motif and that it is required to bind a coactivator, the homeodomain-containing protein Fushi tarazu (FTZ). We also show that FTZ contains an AF2-interacting nuclear receptor box, the first to be found in a homeodomain protein. Both interaction motifs are shown to be necessary for physical interactions in vitro and for functional interactions in developing embryos. These unexpected findings have important implications for the conserved homologs of the two proteins.

Activation of neurospecific gene expression by antennapedia homeobox peptide

Antennapedia homeobox peptide has been reported to enhance neurite outgrowth and branching. Thus it is of interest to investigate whether antennapedia peptide is capable of modulating the expression of genes related to different events of neuronal development. In this paper we report the enhancement of a 68 KDa neurofilament subunit, choline acetyltransferase and acetylcholinesterase expression in spinal cord neurons, elicited by antennapedia peptide. Modulation of gene expression is different with respect to each gene product analyzed, suggesting a specific action of the peptide on diverse genes controlling different events of neuronal differentiation.

Patterning the ascidian nervous system: structure, expression and transgenic analysis of the CiHox3 gene

Hox genes play a fundamental role in the establishment of chordate body plan, especially in the anteroposterior patterning of the nervous system. Particularly interesting are the anterior groups of Hox genes (Hox1-Hox4) since their expression is coupled to the control of regional identity in the anterior regions of the nervous system, where the highest structural diversity is observed. Ascidians, among chordates, are considered a good model to investigate evolution of Hox gene, organisation, regulation and function. We report here the cloning and the expression pattern of CiHox3, a Ciona intestinalis anterior Hox gene homologous to the paralogy group 3 genes. In situ hybridization at the larva stage revealed that CiHox3 expression was restricted to the visceral ganglion of the central nervous system. The presence of a sharp posterior boundary and the absence of transcript in mesodermal tissues are distinctive features of CiHox3 expression when compared to the paralogy group 3 in other chordates. We have investigated the regulatory elements underlying CiHox3 neural-specific expression and, using transgenic analysis, we were able to isolate an 80 bp enhancer responsible of CiHox3 activation in the central nervous system (CNS). A comparative study between mouse and Ciona Hox3 promoters demonstrated that divergent mechanisms are involved in the regulation of these genes in vertebrates and ascidians.

On the homology of structures and Hox genes: the vertebral column

Research on expression patterns of Hox genes has revealed a surprisingly high conservation among vertebrates. In agreement with this conservation, a correlation has been found between the anterior limits of expression areas of certain Hox genes and the borders between morphological regions of the vertebral axis. These similarities are striking and important, but also counterintuitive, unless there are strong selection pressures to protect this conservatism. It is important to identify the selective forces that maintain these conservative networks. These selective forces can be due to pleiotropy or to internal selection. Discussed are the selective factors that are involved in the evolutionary constraint on the number of cervical vertebral numbers in mammals. Factors involved are due to internal selection and involve susceptibility to cancer, stillbirths and neuronal problems. It is intriguing how similar genetic networks can lead to fundamentally different animals. Clearly the same genes are used for different purposes. It is therefore important to try to find these differences. The search, for homology between organisms, and the enthusiasm about similarities that come with it, at times impedes the discovery of such differences. I have searched the literature for differences within vertebrates in the functioning and expression patterns of Hox genes during the development of the vertebral axis. The ensuing implications for homology of structures and genes are discussed. The vertebral column is a promising model system for the evaluation of the relationship between homologous Hox genes and homologous structures because of the large conservation of Hox gene expression patterns along the anterior axis. However, extensive remodelling of the vertebrate column indicates that important changes in the genetic basis must have taken place. A survey of the literature indicates that the correlation between Hox gene expression areas and vertebral regions is not such that one can predict the borders between vertebral regions on the basis of Hox gene expression patterns. The involvement of Hox genes in the development of identity of vertebrae is complex and the problems regarding the value of gene expression patterns for the determination of anatomical homology are discussed.

Multiple cis-acting regulatory regions are required for restricted spatio-temporal Hoxa5 gene expression

Genetic analyses have revealed the essential role of the murine Hoxa5 gene for the correct specification of the cervical and upper thoracic region of the skeleton, and for the normal organogenesis and function of the respiratory tract, both structures expressing Hoxa5 during embryogenesis. To understand how the expression domains of the Hoxa5 gene are established during development, we have analyzed the cis-acting control regions mediating Hoxa5 gene expression using a transgenic approach. Four transcripts are derived from the Hoxa5 locus. The shortest and most abundant one displays a specific spatio-temporal profile of expression at earlier stages and in more anterior structures along the embryonic axis than the larger forms. We established that an 11.1 kilobase pair (kb) genomic fragment, extending from position -3.8 kb to +7.3 kb relative to Hoxa5 transcription initiation site, was sufficient to reproduce the temporal expression and substantially reconstitute the spatial pattern of the major Hoxa5 transcript. By deletion analyses, we identified a 2.1 kb fragment located downstream of the Hoxa5 gene that possesses mesodermal enhancer activity. Overall, the findings demonstrate that cis-acting regulatory elements essential for the correct expression of the major Hoxa5 transcript are located both upstream and downstream of the Hoxa5 coding sequences.

Distinct functions for Aldh1 and Raldh2 in the control of ligand production for embryonic retinoid signaling pathways

During vertebrate embryogenesis retinoic acid (RA) synthesis must be spatiotemporally regulated in order to appropriately stimulate various retinoid signaling pathways. Various forms of mammalian aldehyde dehydrogenase (ALDH) have been shown to oxidize the vitamin A precursor retinal to RA in vitro. Here we show that injection of Xenopus embryos with mRNAs for either mouse Aldh1 or mouse Raldh2 stimulates RA synthesis at low and high levels, respectively, while injection of human ALDH3 mRNA is unable to stimulate any detectable level of RA synthesis. This provides evidence that some members of the ALDH gene family can indeed perform RA synthesis in vivo. Whole-mount immunohistochemical analyses of mouse embryos indicate that ALDH1 and RALDH2 proteins are localized in distinct tissues. RALDH2 is detected at E7.5-E10.5 primarily in trunk tissue (paraxial mesoderm, somites, pericardium, midgut, mesonephros) plus transiently from E8.5-E9.5 in the ventral optic vesicle and surrounding frontonasal region. ALDH1 is first detected at E9.0-E10. 5 primarily in cranial tissues (ventral mesencephalon, dorsal retina, thymic primordia, otic vesicles) and in the mesonephros. As previous findings indicate that embryonic RA is more abundant in trunk rather than cranial tissues, our findings suggest that Raldh2 and Aldh1 control distinct retinoid signaling pathways by stimulating high and low RA biosynthetic activities, respectively, in various trunk and cranial tissues.

Recombinogenic targeting: a new approach to genomic analysis--a review

Currently, recombinational cloning procedures based upon methods developed for yeast, Saccharomyces cerevisiae, are being exploited for targeted cloning and in-vivo modification of genomic clones. In this review, we will discuss the development of large-insert vectors, homologous recombination-based techniques for cloning and modification, and their application towards functional analysis of genes using transgenic mouse model systems.

Vax1 is a novel homeobox-containing gene expressed in the developing anterior ventral forebrain

The vertebrate forebrain is formed at the rostral end of the neural plate under the regulation of local and specific signals emanating from both the endomesoderm and neuroectoderm. The development of the rostral and ventral forebrain in particular was difficult to study, mainly because no specific markers are available to date. Here, we report the identification of Vax1, a novel homeobox-containing gene identified in mouse, Xenopus and human. It is closely related to members of the Not and Emx gene families, all of which are required for the formation of structures where they are expressed. In mouse and Xenopus, Vax1 expression first occurs in the rostral neural plate, in the medial anterior neural ridge and adjacent ectoderm. Later, at midgestation in the mouse and tadpole stage in Xenopus, the expression remains confined in the derivatives of this territory which differentiate into rostromedial olfactory placode, optic nerve and disc, and anterior ventral forebrain. Together, these observations suggest that Vax1 could have an early evolutionary origin and could participate in the specification and formation of the rostral and ventral forebrain in vertebrates. Comparison of the limits of the expression territory of Vax1 with that of Dlx1, Pax6 and Emx1 indicates that the corticostriatal ridge is a complex structure with distinct identifiable genetic compartments. Besides, the study of Vax1 expression in Pax6-deficient homozygous brains indicates that its regulation is independent of Pax6, although the expression patterns of these two genes appear complementary in wild-type animals. Vax1 chromosomal location is mapped at the distal end of the mouse chromosome 19, linked with that of Emx2. These two genes may have arisen by tandem duplication. The Vax1 gene is thus an interesting new tool to study the rostral ventral forebrain patterning, morphogenesis and evolution as well as the terminal differentiation of the forebrain in mouse and Xenopus.

Zebrafish hox genes: genomic organization and modified colinear expression patterns in the trunk

The Hox genes are implicated in conferring regional identity to the anteroposterior axis of the developing embryo. We have characterized the organization and expression of hox genes in the teleost zebrafish (Danio rerio), and compared our findings with those made for the tetrapod vertebrates. We have isolated 32 zebrafish hox genes, primarily via 3′RACE-PCR, and analyzed their linkage relationships using somatic cell hybrids. We find that in comparison to the tetrapods, zebrafish has several additional hox genes, both within and beyond the expected 4 hox clusters (A-D). For example, we have isolated a member of hox paralogue group 8 lying on the hoxa cluster, and a member of hox paralogue group 10 lying on the b cluster, no equivalent genes have been reported for mouse or human. Beyond the 4 clusters (A-D) we have isolated a further 3 hox genes (the hoxx and y genes), which according to their sequence homologies lie in paralogue groups 4, 6, and 9. The hoxx4 and hoxx9 genes occur on the same set of hybrid chromosomes, hinting at the possibility of an additional hox cluster for the zebrafish. Similar to their tetrapod counterparts, zebrafish hox genes (including those with no direct tetrapod equivalent) demonstrate colinear expression along the anteroposterior (AP) axis of the embryo. However, in comparison to the tetrapods, anterior hox expression limits are compacted over a short AP region; some members of adjacent paralogue groups have equivalent limits. It has been proposed that during vertebrate evolution, the anterior limits of Hox gene expression have become dispersed along the AP axis allowing the genes to take on novel patterning roles and thus leading to increased axial complexity. In the teleost zebrafish, axial organization is relatively simple in comparison to that of the tetrapod vertebrates; this may be reflected by the less dispersed expression domains of the zebrafish hox genes.

Molecular evolution of Hox gene regulation: cloning and transgenic analysis of the lamprey HoxQ8 gene

The mammalian Hox clusters arose by duplication of a primordial cluster. The duplication of Hox clusters created redundancy within cognate groups, allowing for change in function over time. The lamprey, Petromyzon marinus, occupies an intermediate position within the chordates, both in terms of morphologic complexity and possibly cluster number. To determine the extent of divergence among Hox genes after duplication events within vertebrates, we analyzed Hox genes belonging to cognate group 8. Here we report characterization of the HoxQ8 gene, which shows conservation with mammalian genes in its amino-terminal, homeobox and hexapeptide sequences, and in the position of its splice sites. A beta-galactosidase reporter gene was introduced in the HoxQ8 genomic region by targeted recombinational cloning using a yeast-bacteria shuttle vector, pClasper. These reporter gene constructs were tested for their ability to direct region-specific expression patterns in transgenic mouse embryos. Lamprey enhancers direct expression to posterior neural tube but not to mesoderm, suggesting conservation of neuronal enhancers. In the presence of the mouse heat shock promoter, lamprey enhancers could also direct expression to the posterior mesoderm suggesting that there has been some divergence in promoter function. Our results suggest that comparative studies on Hox gene structure and analysis of regulatory elements may provide insights into changes concomitant with Hox cluster duplications in the chordates.

Molecular cloning, chromosomal mapping and developmental expression of BAPX1, a novel human homeobox-containing gene homologous to Drosophila bagpipe

We describe here the cloning of the human BAPX1 gene, a homologue of the Drosophila bagpipe gene which has 87% aa identity within the homeodomain relative to the fly gene. We recently have identified the murine bagpipe homolog. The predicted aa sequence of the human gene has 85% overall identity to the murine gene, with 100% identity in the homeodomain. In mouse, this gene maps to the proximal portion of chromosome 5. We show that the human gene maps to 4p16.1, the human region syntenic with mouse chromosome 5. Expression of BAPX1 was evaluated during human embryonic development by RT-PCR analysis and by RNA in situ hybridization. RT-PCR analysis showed that BAPX1 is expressed in embryo tissues, particularly the limb, and at a lower level in an embryonic lung cell line. RNA in situ hybridization revealed that BAPX1 is predominantly expressed in mesenchymal condensations of the fetal limb and axial skeleton, and in lateral plate mesoderm giving rise to visceral muscle. The expression pattern of BAPX1 combined with the chromosomal localization to 4p16.1, where several human genetic diseases involving dysmorphology of the skeleton have been assigned, raises the potential of it being a candidate gene for one of these disorders. O

Bapx1: an evolutionary conserved homologue of the Drosophila bagpipe homeobox gene is expressed in splanchnic mesoderm and the embryonic skeleton

In Drosophila, the visceral mesoderm giving rise to gut musculature is specified by the bagpipe homeobox gene. We have isolated, from both mouse and human, homologues of the bagpipe gene designated Bapx1 and BAPX1, respectively. Bapx1 encodes a predicted protein of 333 amino acids, and has significant regions of homology outside the homeodomain with members of the NK homeobox gene superfamily. Bapx1 maps to the proximal end of chromosome 5 in mouse, near the Msx1 gene. The syntenic region in human corresponds to a chromosomal region containing loci for several skeletal disorders. Bapx1 is first detectable in embryos just prior to axis rotation in lateral plate mesoderm (splanchnic mesoderm) adjacent to the endodermal lining of the prospective gut, and in the most newly formed somites in the region corresponding to the presclerotome, the precursor of the vertebrae. Thus, Bapx1 is one of the earliest developmental markers for the sclerotome portion of the somite and the gut mesentery. Bapx1 continues to be expressed well into organogenesis in lateral plate mesoderm surrounding the mid- and hindgut, and in essentially all cartilaginous condensations which will subsequently undergo endochondral bone formation. The expression pattern of Bapx1 in murine embryos suggests that there are evolutionary conserved mechanisms of visceral mesoderm development across the animal kingdom, and that the mammalian Bapx1 gene may have recently acquired an additional developmental role in skeletal patterning.