Summary: SOX3 is one of the earliest neural markers in vertebrates and is thought to play a role in specifying neuronal fate. To investigate the regulation of Sox3 expression we identified cis‐regulatory regions in the Sox3 promoter that... more
Summary: SOX3 is one of the earliest neural markers in vertebrates and is thought to play a role in specifying neuronal fate. To investigate the regulation of Sox3 expression we identified cis‐regulatory regions in the Sox3 promoter that direct tissue‐specific heterologous marker gene expression in transgenic mice. Our results show that an 8.3 kb fragment, comprising 3 kb upstream and 3 kb downstream of the Sox3 transcriptional unit, is sufficient in a lacZ reporter construct to reproduce most aspects of Sox3 expression during CNS development from headfold to midgestation stages. The apparently uniform expression of Sox3 in the neural tube depends, however, on the combined action of distinct regulatory modules within this 8.3 kb region. Each of these gives expression in a subdomain of the complete expression pattern. These are restricted along both the rostral‐caudal and dorso‐ventral axes and can be quite specific, one element giving expression largely confined to V2 interneuron precursors. We also find that at least some of the regulatory sequences are able to drive expression of the transgene in the CNS Xenopus laevis embryos in a manner that reflects the endogenous Sox3 expression pattern. These results imply that the underlying mechanism regulating early CNS patterning is conserved, despite several substantial differences in neurogenesis between mammals and amphibians. genesis 36:12–24, 2003. © 2003 Wiley‐Liss, Inc.
Research Interests: Genetics, Biology, Immunohistochemistry, Cell Biology, Transcription Factors, and 14 moreMedicine, Gene expression, In Situ Hybridization, Transgenic Mice, Xenopus, Mice, Animals, Central Nervous System, Genesis, DNA binding proteins, Biochemistry and cell biology, Gene Expression Regulation, High mobility group proteins, and Paediatrics and reproductive medicine
Frogs are an ecologically diverse and phylogenetically ancient group of living amphibians that include important vertebrate cell and developmental model systems, notably the genusXenopus. Here we report a high-quality reference genome... more
Frogs are an ecologically diverse and phylogenetically ancient group of living amphibians that include important vertebrate cell and developmental model systems, notably the genusXenopus. Here we report a high-quality reference genome sequence for the western clawed frog,Xenopus tropicalis, along with draft chromosome-scale sequences of three distantly related emerging model frog species,Eleutherodactylus coqui,Engystomops pustulosusandHymenochirus boettgeri. Frog chromosomes have remained remarkably stable since the Mesozoic Era, with limited Robertsonian (i.e., centric) translocations and end-to-end fusions found among the smaller chromosomes. Conservation of synteny includes conservation of centromere locations, marked by centromeric tandem repeats associated with Cenp-a binding, surrounded by pericentromeric LINE/L1 elements. We explored chromosome structure across frogs, using a dense meiotic linkage map forX. tropicalisand chromatin conformation capture (HiC) data for all spec...
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Several aspects of the structure of the chicken thymidine kinase gene (tk) have been resolved as a result of genetic experiments and nucleotide sequencing. Deletion mapping established the locations of two functional boundaries in a... more
Several aspects of the structure of the chicken thymidine kinase gene (tk) have been resolved as a result of genetic experiments and nucleotide sequencing. Deletion mapping established the locations of two functional boundaries in a region thought to correspond to the 5' terminus of the gene. One such boundary coincides with a transcriptional promoter, and the other coincides with the translation start codon of the chicken tk polypeptide. Similar deletion mapping assays identified a functional boundary at the 3' terminus of the gene. DNA sequence analysis confirms the prediction that this 3' region encodes the carboxyl terminus of the tk polypeptide. A recombinant cDNA clone complementary to genomic tk sequences was isolated. A comparison between genomic and cDNA sequences reveals the locations of six intervening sequences and allows prediction of the complete amino acid sequence of the chicken tk polypeptide.
Research Interests: Genetics, Molecular Biology, Biology, Medicine, Recombinant DNA Technology, and 15 moreBiological Sciences, Molecular and cellular biology, Mice, Animals, Nucleic acid hybridization, Gene, Genes, Molecular cloning, Chickens, Thymidine Kinase, Amino Acid Sequence, Base Sequence, Chromosome deletion, DNA Restriction Enzymes, and Medical and Health Sciences
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Research Interests: Genome assembly, Computational Biology, Statistical Analysis, Biology, Medicine, and 15 moreSequence Analysis, Next generation sequencing, Biological Sciences, DNA, Dna Sequencing, Humans, Animals, Genome, Physical chromosome mapping, High Resolution, Whole Genome Sequencing, Genome sequence, Genome Mapping, Contig, and gene amplification
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Proteins that recognize the core sequence GATA are important regulators of hematopoietic-specific gene transcription. We have characterized cDNAs encoding the Xenopus laevis homologues of three related transcription factors, designated... more
Proteins that recognize the core sequence GATA are important regulators of hematopoietic-specific gene transcription. We have characterized cDNAs encoding the Xenopus laevis homologues of three related transcription factors, designated GATA-1, -2, and -3. Comparative sequence analysis reveals strong conservation of the zinc-finger DNA-binding domain among all vertebrate GATA-binding proteins. GATA-2 and GATA-3 polypeptides are homologous throughout their entire sequences, whereas GATA-1 sequence is conserved only in the region responsible for DNA binding. In Xenopus, RNAs encoding GATA-binding proteins are expressed in both larval and adult erythroid cells. GATA-1, -2, and -3 RNAs are first detectable in early gastrula (Nieuwkoop developmental stage 11). This is earlier than the appearance of the early larval alpha T1 globin RNA (stage 15), beta T1 globin RNA (stage 26), or blood island formation (stage 30). The expression of GATA-1, -2, and -3 in early development may signal an ear...
Research Interests: Comparative sequence analysis, Biology, Cell Biology, Medicine, Gene expression, and 15 moreMultidisciplinary, Hematopoiesis, DNA, Animals, Embryonic Stem Cell, Polymerase Chain Reaction, Early development, Haematopoiesis, Transcription Factor, Embryonic Development, DNA binding, Amino Acid Sequence, DNA binding proteins, Molecular Sequence Data, and Nucleotide sequence
The expression of cloned tRNA genes has been studied by injecting single-stranded and double-stranded DNA templates into Xenopus oocyte nuclei. In both forms the genes are faithfully transcribed after injection. Some single-stranded DNA... more
The expression of cloned tRNA genes has been studied by injecting single-stranded and double-stranded DNA templates into Xenopus oocyte nuclei. In both forms the genes are faithfully transcribed after injection. Some single-stranded DNA is converted into double-stranded DNA in the oocyte nucleus. This conversion is necessary for the expression of the injected tRNA gene: no tRNA transcription is observed when DNA synthesis is inhibited. We conclude that single-stranded DNA does not serve as a template for faithful transcription of this gene in injected oocytes.
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Research Interests: Developmental Biology, Biology, Membrane Proteins, Cell Biology, Medicine, and 15 moreBiological Sciences, Mice, Animals, Endoplasmic Reticulum, Osteoblast, Research Articles, Cells, Experimental Medicine, The cell, Osteogenesis, Bone Formation, Cell Proliferation, Osteoblasts, Cultured, and Medical and Health Sciences
Research Interests: Genetics, Biology, Medicine, Signal Transduction, Biological Sciences, and 15 moreHumans, Nomenclature, Mice, Animals, Cell, Gene, GenBank, Base Sequence, Calcium Binding Proteins, Cell Cycle Proteins, Gene Family, DNA binding proteins, Smad proteins, Molecular Sequence Data, and Medical and Health Sciences
Research Interests: Algorithms, Developmental Biology, Biology, Medicine, Databases, and 15 moreBiological Sciences, Humans, Microdissection, Animals, Gastrulation, Gene ontology, Cluster Analysis, Gene Regulatory Networks, Developmental, Internet, Gene Expression Regulation, Gene expression profiling, Genetic, Medical and Health Sciences, and ectoderm
Synthetic capped RNA transcripts injected into fertilized eggs of Xenopus laevis have a half-life of 3 –4 h. Addition of a long (∼200 nucleotide) poly(A) tail increases the half-life to 6 –8 h which approaches the half-life of natural... more
Synthetic capped RNA transcripts injected into fertilized eggs of Xenopus laevis have a half-life of 3 –4 h. Addition of a long (∼200 nucleotide) poly(A) tail increases the half-life to 6 –8 h which approaches the half-life of natural polyadenylated globin RNA injected into embryos. Since exonucleolytic action alone could account for the degradation of RNA, we tested whether circular RNA is stable after injection and find that circles are exceptionally stable (half-life greater than 40 h). After the midblastula transition, polyadenylated chloramphenicol transferase (CAT) mRNAs transcribed from injected plasmids have a half-life of 2 ·5 h. Insertion of a 1000 nucleotide 3′ untranslated region from the Xhox-36 gene into the transcripts does not affect the half-life. In contrast to the finding that internal sequences do not affect stability, we find that sequences from the TFIIIA message reduce the half-life of CAT mRNA from 2 ·5 h to less than 30 min. We conclude that most RNAs are de...
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We have isolated and characterized cDNAs corresponding to the Xenopus En-2 gene. Comparison of amino acid sequences between the entire Xenopus En-2 and the Drosophila engrailed proteins confirms conservation of sequences inside as well as... more
We have isolated and characterized cDNAs corresponding to the Xenopus En-2 gene. Comparison of amino acid sequences between the entire Xenopus En-2 and the Drosophila engrailed proteins confirms conservation of sequences inside as well as proximal to the homeobox and reveals a region of similarity towards the N terminus. Two transcripts encode the Xenopus En-2 protein. Both transcripts are regulated temporally in an identical fashion and are likely to be transcribed from two copies of the En-2 gene. We have also analyzed the distribution of the protein in the head tissue and in the dissected brain of tailbud stage embryos. In addition to the main band of expression at the midbrain–hindbrain boundary, we show that the protein is expressed in three novel areas: the mandibular arch, the optic tectum and the region of anterior pituitary.
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DYRK1A (dual specificity tyrosine-(Y)-phosphorylation-regulated kinase 1 A) is a high confidence autism risk gene that encodes a conserved kinase. In addition to autism, patients with putative loss of function variants in DYRK1A exhibit... more
DYRK1A (dual specificity tyrosine-(Y)-phosphorylation-regulated kinase 1 A) is a high confidence autism risk gene that encodes a conserved kinase. In addition to autism, patients with putative loss of function variants in DYRK1A exhibit microcephaly, intellectual disability, developmental delay, and/or congenital anomalies of the kidney and urinary tract. DYRK1A is also located within the critical region for Down syndrome; therefore, understanding the role of DYRK1A in brain development is crucial for understanding the pathobiology of multiple developmental disorders. To characterize the function of this gene, we used the diploid frog, Xenopus tropicalis. We discover that Dyrk1a is expressed in ciliated tissues, localizes to ciliary axonemes and basal bodies, and is required for ciliogenesis. We also demonstrate that Dyrk1a localizes to mitotic spindles and that its inhibition leads to decreased forebrain size, abnormal cell cycle progression, and cell death during brain development...
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Research Interests: Genetics, Developmental Biology, Genome assembly, Biotechnology, Comparative Genomics, and 15 moreBiology, Medicine, Biological Sciences, Humans, Animals, Genome, Gene, Human Genome, De Novo Genome Assembly, Genetic Mapping, Gene Expression Analysis, Chromosomes, Genome Project, Gene expression profiling, and Medical and Health Sciences
Multiple Xhox 36 transcripts accumulate in Xenopus embryos from gastrula to early tadpole stages. The transcripts were characterized by sequencing cDNA clones and by S1 protection and Northern (RNA) blotting of embryonic RNA with probes... more
Multiple Xhox 36 transcripts accumulate in Xenopus embryos from gastrula to early tadpole stages. The transcripts were characterized by sequencing cDNA clones and by S1 protection and Northern (RNA) blotting of embryonic RNA with probes derived from the cDNAs. The Xhox 36 RNAs included unspliced precursor transcripts that accumulated in the embryonic nuclei, spliced transcripts that contained multiple stop codons in frame with the homeobox, and less abundant coding mRNAs. These transcripts were generated either by alternative splicing or multiple initiations from a single Xhox 36 gene. The sequence of a cDNA clone of the unspliced transcript showed that the intron contained a noncanonical 3' splice site. However, the intron was spliced efficiently when expressed from a plasmid injected into Xenopus embryos, suggesting that the inefficient splicing of the endogenous RNA is not due to the unusual 3' splice site. The accumulation of noncoding and unspliced transcripts suggests ...
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Upon cell cycle exit, centriole-to-basal body transition facilitates cilia formation. The centriolar protein Cp110 is a regulator of this process and cilia inhibitor, but its positive roles in ciliogenesis remain poorly understood. Using... more
Upon cell cycle exit, centriole-to-basal body transition facilitates cilia formation. The centriolar protein Cp110 is a regulator of this process and cilia inhibitor, but its positive roles in ciliogenesis remain poorly understood. Using Xenopus we show that Cp110 inhibits cilia formation at high levels, while optimal levels promote ciliogenesis. Cp110 localizes to cilia-forming basal bodies and rootlets, and is required for ciliary adhesion complexes that facilitate Actin interactions. The opposing roles of Cp110 in ciliation are generated in part by coiled-coil domains that mediate preferential binding to centrioles over rootlets. Because of its dual role in ciliogenesis, Cp110 levels must be precisely controlled. In multiciliated cells, this is achieved by both transcriptional and post-transcriptional regulation through ciliary transcription factors and microRNAs, which activate and repress cp110 to produce optimal Cp110 levels during ciliogenesis. Our data provide novel insights...
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To explore the origins and consequences of tetraploidy in the African clawed frog, we sequenced the Xenopus laevis genome and compared it to the related diploid X. tropicalis genome. We characterize the allotetraploid origin of X. laevis... more
To explore the origins and consequences of tetraploidy in the African clawed frog, we sequenced the Xenopus laevis genome and compared it to the related diploid X. tropicalis genome. We characterize the allotetraploid origin of X. laevis by partitioning its genome into two homoeologous subgenomes, marked by distinct families of 'fossil' transposable elements. On the basis of the activity of these elements and the age of hundreds of unitary pseudogenes, we estimate that the two diploid progenitor species diverged around 34 million years ago (Ma) and combined to form an allotetraploid around 17-18 Ma. More than 56% of all genes were retained in two homoeologous copies. Protein function, gene expression, and the amount of conserved flanking sequence all correlate with retention rates. The subgenomes have evolved asymmetrically, with one chromosome set more often preserving the ancestral state and the other experiencing more gene loss, deletion, rearrangement, and reduced gene e...
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Wnt signaling is a critical pathway for tissue morphogenesis participating in cellular behavior changes, notably during the convergent-extension process. Interactions between Wnt secreting and receiving cells during convergence-extension... more
Wnt signaling is a critical pathway for tissue morphogenesis participating in cellular behavior changes, notably during the convergent-extension process. Interactions between Wnt secreting and receiving cells during convergence-extension remain elusive. We investigated the role and genetic interactions of Wnt ligands and their trafficking factors, Wls, Gpc4 and Frzb in the context of palate morphogenesis. We described that the chaperon Wls and its ligands Wnt9a and Wnt5b are expressed in the ectoderm, whereas juxtaposed chondrocytes express Frzb and Gpc4. Using wls, gpc4, frzb, wnt9a and wnt5b mutants, we genetically dissected Wnt signal operating between secreting ectoderm and receiving chondrocytes. Our analysis delineates that non-canonical Wnt signaling is required for cell intercalation, and that wnt5b and wnt9a are required for palate extension, in the antero-posterior and transverse axes, respectively.
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The articular cartilage, which lines the joints of the limb skeleton, is distinct from the adjoining transient cartilage, and yet, it differentiates as a unique population within a contiguous cartilage element. Current literature suggests... more
The articular cartilage, which lines the joints of the limb skeleton, is distinct from the adjoining transient cartilage, and yet, it differentiates as a unique population within a contiguous cartilage element. Current literature suggests that articular cartilage and transient cartilage originate from different cell populations. Using a combination of lineage tracing and pulse-chase of actively proliferating chondrocytes, we here demonstrate that, similar to transient cartilage, embryonic articular cartilage cells also originate from the proliferating chondrocytes situated near the distal ends of skeletal anlagen. We show that nascent cartilage cells are capable of differentiating as articular or transient cartilage, depending on exposure to Wnt or BMP signaling, respectively. The spatial organization of the articular cartilage results from a band of Nog-expressing cells, which insulates these proliferating chondrocytes from BMP signaling and allows them to differentiate as articula...
Research Interests: Developmental Biology, Biology, Immunohistochemistry, Cell Biology, Development, and 15 moreMedicine, In Situ Hybridization, Bone Morphogenetic Proteins, Biological Sciences, Anatomy, Cell Differentiation, Cartilage, Mice, Animals, Articular Cartilage Wear, Chondrocytes, Cell Proliferation, Alcian blue, Chick embryo, and Medical and Health Sciences
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The pluripotency factor POU5F1 (OCT4) is well known as a key regulator of stem cell fate. Homologues of POU5F1 exist throughout vertebrates, but the evolutionary and functional relationships between the various family members have been... more
The pluripotency factor POU5F1 (OCT4) is well known as a key regulator of stem cell fate. Homologues of POU5F1 exist throughout vertebrates, but the evolutionary and functional relationships between the various family members have been unclear. The level to which function has been conserved within this family provides insight into the evolution of early embryonic potency. Here, we seek to clarify the relationship between POU5F1 homologues in the vertebrate lineage, both phylogenetically and functionally. We resolve the confusion over the identity of the zebrafish gene, which was originally named pou2, then changed to pou5f1 and again, more recently, to pou5f3. We argue that the use of correct nomenclature is crucial when discussing the degree to which the networks regulating early embryonic differentiation are conserved.
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The bacteriophage SP6 promoter and RNA polymerase were used to synthesize sense and antisense RNAs coding for the enzymes thymidine kinase (TK) and chloramphenicol acetyl transferase (CAT). Injection of antisense CAT RNA into frog oocytes... more
The bacteriophage SP6 promoter and RNA polymerase were used to synthesize sense and antisense RNAs coding for the enzymes thymidine kinase (TK) and chloramphenicol acetyl transferase (CAT). Injection of antisense CAT RNA into frog oocytes inhibited expression of sense CAT mRNA. Similarly, antisense TK RNA inhibited expression of sense TK mRNA. Antisense RNAs were stable in oocytes and had no detectable effect on either the expression of endogenous proteins or on the expression of nonhomologous RNA transcripts. CAT activity expressed from a plasmid transcribed in the oocyte nucleus was also inhibited by antisense RNA injected into the oocyte cytoplasm. The data suggest that antisense RNA will be useful in identifying the function of specific mRNA sequences during early development of the frog.
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The African clawed frog Xenopus laevis has been instrumental to investigations of both development and cell biology, but the utility of this model organism for genetic and proteomic studies is limited by its long generation time and... more
The African clawed frog Xenopus laevis has been instrumental to investigations of both development and cell biology, but the utility of this model organism for genetic and proteomic studies is limited by its long generation time and unsequenced pseudotetraploid genome. Xenopus tropicalis, which is a small, faster-breeding relative of X. laevis, has recently been adopted for research in developmental genetics and functional genomics, and has been chosen for genome sequencing. We show that X. tropicalis egg extracts reconstitute the fundamental cell cycle events of nuclear formation and bipolar spindle assembly around exogenously added sperm nuclei. Interestingly, X. tropicalis spindles were ∼30% shorter than X. laevis spindles, and mixing experiments revealed a dynamic, dose-dependent regulation of spindle size by cytoplasmic factors. Measurements of microtubule dynamics revealed that microtubules polymerized slower in X. tropicalis extracts compared to X. laevis, but that this diffe...
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Plasmid DNA methylated at Hpa II sites was injected into eggs of Xenopus laevis. The methylated DNA replicates extrachromosomally, and the methylated state of the H pa II sites is inherited through replication. Unmethylated sites remain... more
Plasmid DNA methylated at Hpa II sites was injected into eggs of Xenopus laevis. The methylated DNA replicates extrachromosomally, and the methylated state of the H pa II sites is inherited through replication. Unmethylated sites remain unmethylated in progeny molecules. To test whether replication is necessary for new methylation to occur, DNA methylated on one strand only was injected and unreplicated DNA was selected for analysis. Methylation was copied onto a previously unmethylated strand in the absence of replication but less efficiently than in its presence. These experiments show that the individual methylated site contains enough information for inheritance of the methylated state and that inheritance of methylation does not require integration of the DNA into the chromosome.
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Research Interests: Genetics, Biology, Medicine, Bone Morphogenetic Proteins, Signal Transduction, and 15 moreBiological Sciences, Mutation, Mice, Female, Animals, Male, Proteins, Fibroblast Growth Factor, Body Patterning, Limb Development, Knockout Mice, Bone and Bones, Noggin, Medical and Health Sciences, and Fibroblast growth factors
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Research Interests: Chemistry, Biology, Cell Biology, Biological Chemistry, Medicine, and 15 moreBone Regeneration, Bone Morphogenetic Proteins, Biological Sciences, In Vitro, Mice, Animals, Biological, CHEMICAL SCIENCES, In Vivo, Bone Formation, Osteoblasts, Gene expression profiling, Noggin, Medical and Health Sciences, and Fractures Bone
Previously, a small region of the 3'-untranslated region (3' UTR) of Xlhbox2B mRNA was shown to be sufficient for sequence-specific endonucleolytic cleavage after injection into Xenopus oocytes. Here, we report an in vitro RNA... more
Previously, a small region of the 3'-untranslated region (3' UTR) of Xlhbox2B mRNA was shown to be sufficient for sequence-specific endonucleolytic cleavage after injection into Xenopus oocytes. Here, we report an in vitro RNA degradation reaction that mimics the in vivo result accurately. The reaction also reveals that oocytes contain a sequence-specific RNA-binding factor that inhibits the endoribonuclease. These opposing activities may be regulated during Xenopus oogenesis. Partial purification shows that the endonuclease does not require translation or ribosomes and does not resemble previously described RNA processing complexes. We have isolated another Xenopus cDNA, Xoo1, that contains a long, repetitive destabilizing element similar to the one in Xlhbox2B. Based on a comparison of these natural destabilizing sequences and in vitro mutagenesis experiments, we find that a single destabilizing site is, at most, 19 bases in length and that the endonuclease and protective ...
Research Interests: RNA, Biology, Drosophila melanogaster, Cell Biology, Medicine, and 14 moreBiological Sciences, Xenopus, Animals, Substrate Specificity, Xenopus laevis, Base Sequence, Oocytes, Site-directed Mutagenesis, Molecular Sequence Data, Restriction Mapping, binding sites, Psychology and Cognitive Sciences, conserved sequence , and Medical and Health Sciences
We have identified a messenger RNA (mRNA) sequence from a Xenopus homeo box-containing gene that is the target for a sequence-specific endoribonuclease in vivo. Synthetic RNA transcribed from an allele of the maternal gene Xlhbox2B is... more
We have identified a messenger RNA (mRNA) sequence from a Xenopus homeo box-containing gene that is the target for a sequence-specific endoribonuclease in vivo. Synthetic RNA transcribed from an allele of the maternal gene Xlhbox2B is efficiently cleaved when injected into Xenopus oocytes. The cleavage sequence lies between the protein-coding region and a 600-base 3'-untranslated region. Intermediates in degradation are readily observed: Both the 5' and 3' products of cleavage are recovered, thus showing that the cleavage activity is an endonuclease. When a 90-base region of the Xlhbox2B sequence is inserted into a second homeo box RNA that is normally stable, it is sufficient to confer an identical cleavage reaction on the hybrid RNA. The cleaved region contains a repeated sequence motif and is cut at multiple sites. Inhibition of translation does not affect the rate or extent of cleavage, while the coinjection of antisense RNA complementary to the 90-base region comple...
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Research Interests: Developmental Biology, Computational Biology, Biology, Evolution, Medicine, and 15 moreIn Situ Hybridization, Bone Morphogenetic Proteins, Biological Sciences, Molecular, Mice, Animals, Molecular Phylogenetics and Evolution, Glycoproteins, Developmental, Polydactyly, Microarray Analysis, Gene Expression Regulation, Extremities, Medical and Health Sciences, and ectoderm
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Properly positioned synovial joints are crucial to coordinated skeletal movement. Despite their importance for skeletal development and function, the molecular mechanisms that underlie joint positioning are not well understood. We show... more
Properly positioned synovial joints are crucial to coordinated skeletal movement. Despite their importance for skeletal development and function, the molecular mechanisms that underlie joint positioning are not well understood. We show that mice carrying an insertional mutation in a previously uncharacterized gene, which we have named Jaws (joints abnormal with splitting), die perinatally with striking skeletal defects, including ectopic interphalangeal joints. These ectopic joints develop along the longitudinal axis and persist at birth, suggesting that JAWS is uniquely required for the orientation and consequent positioning of interphalangeal joints within the endochondral skeleton. Jaws mutant mice also exhibit severe chondrodysplasia characterized by delayed and disorganized maturation of growth plate chondrocytes, together with impaired chondroitin sulfation and abnormal metabolism of the chondroitin sulfate proteoglycan aggrecan. Our findings identify JAWS as a key regulator o...
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Background Ancient whole genome duplications have been implicated in the vertebrate and teleost radiations, and in the emergence of diverse angiosperm lineages, but the evolutionary response to such a perturbation is still poorly... more
Background Ancient whole genome duplications have been implicated in the vertebrate and teleost radiations, and in the emergence of diverse angiosperm lineages, but the evolutionary response to such a perturbation is still poorly understood. The African clawed frog Xenopus laevis experienced a relatively recent tetraploidization ~40 million years ago. Analysis of the considerable amount of EST sequence available for this species together with the genome sequence of the related diploid Xenopus tropicalis provides a unique opportunity to study the genomic response to whole genome duplication. Results We identified 2218 gene triplets in which a single gene in X. tropicalis corresponds to precisely two co-orthologous genes in X. laevis – the largest such collection published from any duplication event in animals. Analysis of these triplets reveals accelerated evolution or relaxation of constraint in the peptides of the X. laevis pairs compared with the orthologous sequences in X. tropic...
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Research Interests: Bioinformatics, Computer Science, Information Retrieval, Data Management, Medicine, and 15 moreDatabases, Annotation, Biological Sciences, Humans, Mathematical Sciences, Animals, BMC Bioinformatics, Gene Annotation, Information Storage and Retrieval, Base Sequence, Literature Search, Genetic, Data Retrieval, Sequence similarity, and Similarity Geometry
Secreted noggin protein regulates bone morphogenetic protein activity during development. In mice, a complete loss of noggin protein leads to multiple malformations including joint fusion, whereas mice heterozygous for Nog... more
Secreted noggin protein regulates bone morphogenetic protein activity during development. In mice, a complete loss of noggin protein leads to multiple malformations including joint fusion, whereas mice heterozygous for Nog loss-of-function mutations are normal. In humans, heterozygous NOG missense mutations have been found in patients with two autosomal dominant disorders of joint development, multiple synostosis syndrome (SYNS1) and a milder disorder proximal symphalangism (SYM1). This study investigated the effect of one SYNS1 and two SYM1 disease-causing missense mutations on the structure and function of noggin. The SYNS1 mutation abolished, and the SYM1 mutations reduced, the secretion of functional noggin dimers in transiently transfected COS-7 cells. Coexpression of mutant noggin with wild-type noggin, to resemble the heterozygous state, did not interfere with wild-type noggin secretion. These data indicate that the human disease-causing mutations are hypomorphic alleles that...
Research Interests: Biology, Medicine, Multidisciplinary, Bone Morphogenetic Proteins, Protein Structure and Function, and 15 moreCercopithecus aethiops, Humans, Female, Animals, Proteins, Synostosis, Xenopus laevis, Transfection, Human Disease, Oocytes, Recombinant Proteins, Protein Biosynthesis, Dimerization, Noggin, and Autosomal Dominant
Research Interests: Genetics, Developmental Biology, Genomics, Computational Biology, Embryology, and 15 moreBiotechnology, Biology, Genetic Networks, Medicine, Gene expression, Functional Genomics, Genetic Engineering, Biological Sciences, Animals, Gene, Animal models, Chromatin Immunoprecipitation, Larva, Enhancer, and DNA Transcription
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Research Interests: Developmental Biology, MicroRNA, Biology, Cell Biology, Apoptosis, and 15 moreMedicine, Biological Sciences, Cell Differentiation, Animals, Retina, Eye, Caspase, microRNAs, Xenopus laevis, Hydroxyurea, Cell Proliferation, Apoptotic Protease Activating Factor-1, Cysteine Proteinase Inhibitors, Psychology and Cognitive Sciences, and Medical and Health Sciences
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The homeobox containing transcript Xhox-36 is expressed exclusively in the posterior mesoderm and ectoderm of early Xenopus embryos. Therefore, the transcript shows region-specific rather than tissuespecific expression in the gastrula and... more
The homeobox containing transcript Xhox-36 is expressed exclusively in the posterior mesoderm and ectoderm of early Xenopus embryos. Therefore, the transcript shows region-specific rather than tissuespecific expression in the gastrula and neurula, a time when cells are becoming committed to defined fates. Exposure of early embryos to LiCl, which shifts posterior cells to more anterior fates, reduces the abundance of this posterior-specific transcript. In contrast, embryos ventralized by u.v. treatment express normal levels of the transcript, implying that expression of the gene is not absolutely linked to dorsal cell identity. The sequence of a full-length cDNA corresponding to this transcript predicts a homeodomain-containing protein of 209 amino acids.
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We have adapted a non-radioactive technique to detect localized mRNAs in whole-mount Xenopus embryos. Synthetic antisense RNA transcribed in the presence of digoxygenin-UTP is used as a probe and is detected via an anti-digoxygenin... more
We have adapted a non-radioactive technique to detect localized mRNAs in whole-mount Xenopus embryos. Synthetic antisense RNA transcribed in the presence of digoxygenin-UTP is used as a probe and is detected via an anti-digoxygenin antibody. We show that localized mRNAs can be detected from late gastrula to tadpole stages and that high as well as low abundance RNAs can be detected. The method was tested on muscle actin and alpha-globin RNAs, whose localization has previously been characterized. In addition, we used the method to determine the distribution of XA-1 RNA, an anterior ectoderm-specific RNA, which we show is expressed in the periphery of the cement gland as well as in the region of the hatching gland. The sequence of an XA-1 cDNA predicts a protein rich in proline and histidine.
Research Interests: Molecular Biology, RNA, Biology, Development, Medicine, and 15 moreIn Situ Hybridization, Embryo, Biological Sciences, Xenopus, Animals, Nucleic acid hybridization, Gastrulation, Xenopus laevis, Reproducibility of Results, Amino Acid Sequence, Base Sequence, Sensitivity and Specificity, Molecular Sequence Data, Medical and Health Sciences, and ectoderm
We have used a monoclonal antibody directed against the C-terminus of the Drosophila inverted homeodomain to detect a nuclear protein in brain cells of Xenopus laevis embryos. We refer to this antigen as the Xenopus EN protein. The EN... more
We have used a monoclonal antibody directed against the C-terminus of the Drosophila inverted homeodomain to detect a nuclear protein in brain cells of Xenopus laevis embryos. We refer to this antigen as the Xenopus EN protein. The EN protein is localized at midneunda stage to a band of cells in the anterior portion of the neural plate, on each side of the neural groove. Later in development, the expression coincides with the boundary of the midbrain and hindbrain, and persists at least to the swimming tadpole stage. These properties make the EN protein an excellent molecular marker for anterior neural structures. In embryos where inductive interactions between mesodermal and ectodermal tissues have been perturbed, the expression of the EN protein is altered; in embryos that have been anterodorsalized by LiCl treatment, the region that expresses the EN protein is expanded, but still well organized. In ventralized UV-irradiated embryos, the absence of the protein is correlated with t...
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We have cloned a cDNA encoding a Xenopus POU domain protein, XLPOU91, which is expressed at high levels in gastrula embryos. XLPOU91 transcription initiates at the midblastula transition, and declines to low levels by late neurula stages.... more
We have cloned a cDNA encoding a Xenopus POU domain protein, XLPOU91, which is expressed at high levels in gastrula embryos. XLPOU91 transcription initiates at the midblastula transition, and declines to low levels by late neurula stages. In early neurula embryos, XLPOU91 transcripts are enriched 35-fold in the most ventroposterior versus anterior regions. Initial transcriptional activation of the gene is cell autonomous; the gene is activated in dissociated gastrula stage embryos as well as in animal cap explants. Cell-cell communication is needed for proper temporal down-regulation of XLPOU91 expression in late neurula embryos; cell dissociation during blastula stages or removal of explants from the embryo prevents normal transcriptional shunt down. Explants treated with peptide growth factors (PGFs) mimic the normal temporal and spatial shut down in whole embryos. This negative regulatory pathway may be important for determining cell fate or maintaining an inducible state in the ...
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XMyoD is the earliest marker of muscle development in Xenopus embryos and is expressed in presumptive somites in the late gastrula. In the early gastrula, in situ hybridization showed XMyoD transcripts in precursors of both muscle and... more
XMyoD is the earliest marker of muscle development in Xenopus embryos and is expressed in presumptive somites in the late gastrula. In the early gastrula, in situ hybridization showed XMyoD transcripts in precursors of both muscle and non-muscle mesoderm. Embryos ventralized by UV irradiation made no muscle, but expressed XMyoD transiently. Embryo explants that differentiated ventral mesoderm also expressed XMyoD transiently. These results show that the initiation of XMyoD expression is not sufficient to convert cells to muscle and suggest that XMyoD is expressed in response to a general mesodermalizing signal; expression is stabilized and enhanced only in muscle precursors that have received a dorsalizing signal.