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Abstract
Vertebrate eyes begin as a small patch of cells at the most anterior end of the early brain called the eye field. If these cells are removed from an amphibian embryo, the eyes do not form. If the eye field is transplanted to another location on the embryo or cultured in a dish, it forms eyes. These simple cut and paste experiments were performed at the beginning of the last century and helped to define the embryonic origin of the vertebrate eye. The genes necessary for eye field specification and eventual eye formation, by contrast, have only recently been identified. These genes and the molecular mechanisms regulating the initial formation of the Xenopus laevis eye field are the subjects of this review.
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Affiliation(s)
- Michael E Zuber
- Center for Vision Research, SUNY Eye Institute, Departments of Ophthalmology and Biochemistry & Molecular Biology, Upstate Medical University, Syracuse, New York, USA
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Gilchrist MJ, Christensen MB, Bronchain O, Brunet F, Chesneau A, Fenger U, Geach TJ, Ironfield HV, Kaya F, Kricha S, Lea R, Massé K, Néant I, Paillard E, Parain K, Perron M, Sinzelle L, Souopgui J, Thuret R, Ymlahi-Ouazzani Q, Pollet N. Database of queryable gene expression patterns for Xenopus. Dev Dyn 2009; 238:1379-88. [PMID: 19347954 DOI: 10.1002/dvdy.21940] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
The precise localization of gene expression within the developing embryo, and how it changes over time, is one of the most important sources of information for elucidating gene function. As a searchable resource, this information has up until now been largely inaccessible to the Xenopus community. Here, we present a new database of Xenopus gene expression patterns, queryable by specific location or region in the embryo. Pattern matching can be driven either from an existing in situ image, or from a user-defined pattern based on development stage schematic diagrams. The data are derived from the work of a group of 21 Xenopus researchers over a period of 4 days. We used a novel, rapid manual annotation tool, XenMARK, which exploits the ability of the human brain to make the necessary distortions in transferring data from the in situ images to the standard schematic geometry. Developmental Dynamics 238:1379-1388, 2009. (c) 2009 Wiley-Liss, Inc.
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Dullin JP, Locker M, Robach M, Henningfeld KA, Parain K, Afelik S, Pieler T, Perron M. Ptf1a triggers GABAergic neuronal cell fates in the retina. BMC DEVELOPMENTAL BIOLOGY 2007; 7:110. [PMID: 17910758 PMCID: PMC2212653 DOI: 10.1186/1471-213x-7-110] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/19/2007] [Accepted: 10/02/2007] [Indexed: 11/10/2022]
Abstract
Background In recent years, considerable knowledge has been gained on the molecular mechanisms underlying retinal cell fate specification. However, hitherto studies focused primarily on the six major retinal cell classes (five types of neurons of one type of glial cell), and paid little attention to the specification of different neuronal subtypes within the same cell class. In particular, the molecular machinery governing the specification of the two most abundant neurotransmitter phenotypes in the retina, GABAergic and glutamatergic, is largely unknown. In the spinal cord and cerebellum, the transcription factor Ptf1a is essential for GABAergic neuron production. In the mouse retina, Ptf1a has been shown to be involved in horizontal and most amacrine neurons differentiation. Results In this study, we examined the distribution of neurotransmitter subtypes following Ptf1a gain and loss of function in the Xenopus retina. We found cell-autonomous dramatic switches between GABAergic and glutamatergic neuron production, concomitant with profound defects in the genesis of amacrine and horizontal cells, which are mainly GABAergic. Therefore, we investigated whether Ptf1a promotes the fate of these two cell types or acts directly as a GABAergic subtype determination factor. In ectodermal explant assays, Ptf1a was found to be a potent inducer of the GABAergic subtype. Moreover, clonal analysis in the retina revealed that Ptf1a overexpression leads to an increased ratio of GABAergic subtypes among the whole amacrine and horizontal cell population, highlighting its instructive capacity to promote this specific subtype of inhibitory neurons. Finally, we also found that within bipolar cells, which are typically glutamatergic interneurons, Ptf1a is able to trigger a GABAergic fate. Conclusion Altogether, our results reveal for the first time in the retina a major player in the GABAergic versus glutamatergic cell specification genetic pathway.
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Affiliation(s)
| | - Morgane Locker
- UMR CNRS 8080, Université Paris Sud, Bât. 445, 91405 Orsay, France
| | - Mélodie Robach
- UMR CNRS 8080, Université Paris Sud, Bât. 445, 91405 Orsay, France
| | - Kristine A Henningfeld
- DFG-Center of Molecular Physiology of the Brain, Department of Developmental Biochemistry, University of Goettingen, Justus-von-Liebig-Weg 11, 37077 Goettingen, Germany
| | - Karine Parain
- UMR CNRS 8080, Université Paris Sud, Bât. 445, 91405 Orsay, France
| | - Solomon Afelik
- DFG-Center of Molecular Physiology of the Brain, Department of Developmental Biochemistry, University of Goettingen, Justus-von-Liebig-Weg 11, 37077 Goettingen, Germany
| | - Tomas Pieler
- DFG-Center of Molecular Physiology of the Brain, Department of Developmental Biochemistry, University of Goettingen, Justus-von-Liebig-Weg 11, 37077 Goettingen, Germany
| | - Muriel Perron
- UMR CNRS 8080, Université Paris Sud, Bât. 445, 91405 Orsay, France
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Hayes JM, Kim SK, Abitua PB, Park TJ, Herrington ER, Kitayama A, Grow MW, Ueno N, Wallingford JB. Identification of novel ciliogenesis factors using a new in vivo model for mucociliary epithelial development. Dev Biol 2007; 312:115-30. [PMID: 17961536 DOI: 10.1016/j.ydbio.2007.09.031] [Citation(s) in RCA: 92] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2007] [Revised: 08/24/2007] [Accepted: 09/06/2007] [Indexed: 11/18/2022]
Abstract
Mucociliary epithelia are essential for homeostasis of many organs and consist of mucus-secreting goblet cells and ciliated cells. Here, we present the ciliated epidermis of Xenopus embryos as a facile model system for in vivo molecular studies of mucociliary epithelial development. Using an in situ hybridization-based approach, we identified numerous genes expressed differentially in mucus-secreting cells or in ciliated cells. Focusing on genes expressed in ciliated cells, we have identified new candidate ciliogenesis factors, including several not present in the current ciliome. We find that TTC25-GFP is localized to the base of cilia and to ciliary axonemes, and disruption of TTC25 function disrupts ciliogenesis. Mig12-GFP localizes very strongly to the base of cilia and confocal imaging of this construct allows for simple visualization of the planar polarity of basal bodies that underlies polarized ciliary beating. Knockdown of Mig12 disrupts ciliogenesis. Finally, we show that ciliogenesis factors identified in the Xenopus epidermis are required in the midline to facilitate neural tube closure. These results provide further evidence of a requirement for cilia in neural tube morphogenesis and suggest that genes identified in the Xenopus epidermis play broad roles in ciliogenesis. The suites of genes identified here will provide a foundation for future studies, and may also contribute to our understanding of pathological changes in mucociliary epithelia that accompany diseases such as asthma.
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Affiliation(s)
- Julie M Hayes
- Department of Molecular Cell and Developmental Biology, and Institute for Cellular and Molecular Biology, University Station C1000, University of Texas, Austin, TX 78712, USA
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Goda T, Abu-Daya A, Carruthers S, Clark MD, Stemple DL, Zimmerman LB. Genetic screens for mutations affecting development of Xenopus tropicalis. PLoS Genet 2006; 2:e91. [PMID: 16789825 PMCID: PMC1475704 DOI: 10.1371/journal.pgen.0020091] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2005] [Accepted: 04/28/2006] [Indexed: 11/18/2022] Open
Abstract
We present here the results of forward and reverse genetic screens for chemically-induced mutations in Xenopus tropicalis. In our forward genetic screen, we have uncovered 77 candidate phenotypes in diverse organogenesis and differentiation processes. Using a gynogenetic screen design, which minimizes time and husbandry space expenditures, we find that if a phenotype is detected in the gynogenetic F2 of a given F1 female twice, it is highly likely to be a heritable abnormality (29/29 cases). We have also demonstrated the feasibility of reverse genetic approaches for obtaining carriers of mutations in specific genes, and have directly determined an induced mutation rate by sequencing specific exons from a mutagenized population. The Xenopus system, with its well-understood embryology, fate map, and gain-of-function approaches, can now be coupled with efficient loss-of-function genetic strategies for vertebrate functional genomics and developmental genetics.
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Affiliation(s)
- Tadahiro Goda
- Division of Developmental Biology, National Institute for Medical Research, The Ridgeway, Mill Hill, London, United Kingdom
| | - Anita Abu-Daya
- Division of Developmental Biology, National Institute for Medical Research, The Ridgeway, Mill Hill, London, United Kingdom
| | - Samantha Carruthers
- Vertebrate Development and Genetics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Matthew D Clark
- Vertebrate Development and Genetics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Derek L Stemple
- Vertebrate Development and Genetics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
- * To whom correspondence should be addressed. E-mail: (DLS); (LBZ)
| | - Lyle B Zimmerman
- Division of Developmental Biology, National Institute for Medical Research, The Ridgeway, Mill Hill, London, United Kingdom
- * To whom correspondence should be addressed. E-mail: (DLS); (LBZ)
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Chalmers AD, Lachani K, Shin Y, Sherwood V, Cho KWY, Papalopulu N. Grainyhead-like 3, a transcription factor identified in a microarray screen, promotes the specification of the superficial layer of the embryonic epidermis. Mech Dev 2006; 123:702-18. [PMID: 16916602 DOI: 10.1016/j.mod.2006.04.006] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2005] [Revised: 04/28/2006] [Accepted: 04/28/2006] [Indexed: 11/27/2022]
Abstract
The Xenopus ectoderm consists of two populations of cells, superficial polarised epithelial cells and deep, non-epithelial cells. These two cell types differ in their developmental fate. In the neural ectoderm, primary neurons are derived only from the deep cells. In the epidermal ectoderm, superficial cells express high levels of differentiation markers, while most of the deep cells do not differentiate until later when they produce the stratified adult epidermis. However, few molecular differences are known between the deep and superficial cells. Here, we have undertaken a systematic approach to identify genes that show layer-restricted expression by microarray analysis of deep and superficial cells at the gastrula stage, followed by wholemount in situ hybridisation. We have identified 32 differentially expressed genes, of which 26 show higher expression in the superficial layer and 6 in the deep layer and describe their expression at the gastrula and neurula stage. One of the identified genes is the transcription factor Grhl3, which we found to be expressed in the superficial layer of the gastrula ectoderm and the neurula epidermis. By using markers identified in this work, we show that Grlh3 promotes superficial gene expression in the deep layer of the epidermis. Concomitantly, deep layer specific genes are switched off, showing that Grlh3 can promote deep cells to take on a superficial cell identity in the embryonic epidermis.
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Affiliation(s)
- Andrew D Chalmers
- Wellcome Trust/Cancer Research UK Gurdon Institute, Tennis Court Road, Cambridge CB2 1QR, UK.
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Kitazawa S, Kitazawa R. In situ detection of specific gene expression during and immediately after transcription at electron microscopic level. J Struct Biol 2005; 153:64-72. [PMID: 16337810 DOI: 10.1016/j.jsb.2005.09.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2005] [Revised: 08/31/2005] [Accepted: 09/20/2005] [Indexed: 11/23/2022]
Abstract
In situ hybridization (ISH) is a widely applied technique used for visualizing specific nucleic acid sequences at chromosomal, cytologic, and histologic levels. It sometimes fails, however, to demonstrate precise cell identity, early stages of gene expression and variants of alternative splicing because of its limited resolution. To overcome this shortcoming, we have developed an improved ISH technique at the electron microscopic (EM) level by conducting en bloc hybridization before embedding (pre-embedding) and immuno-EM detection after ultra-thin sectioning (post-embedding). We applied this technique to demonstrate both the dynamic expression of interleukin (IL)-6 mRNA immediately after lipopolysaccharide (LPS) treatment, and the static expression of osteonectin mRNA in a differentiating osteoblastic cell linage. Tissue samples were diced into 1mm cubes, fixed with 4% paraformaldehyde, and then successively hybridized en bloc with the digoxigenin (DIG)-labeled single-stranded probe measuring 200-300 bp with the aid of microwave treatment. After washing, for EM observation, the cubes were embedded in epon for ultra-thin sectioning, and a gold-colloid-labeled anti-DIG antibody was used for post-embedding immuno-EM; some of the cubes was directly incubated with anti-DIG antibody and developed en bloc for stereoscopic and light microscopic observation. IL-6 mRNA during and immediately after transcription was demonstrated in the nuclei of the alveolar macrophages and in neutrophils of mouse lung tissue as early as 15 min after LPS treatment, which was of better sensitivity than that by Northern blot or nuclear run-on techniques. Moreover, in mouse calvaria tissue, osteonectin mRNA both in the nucleus and the cytoplasm was observed in a differentiating osteoblastic cell linage in a differentiation-specific manner. This technique is useful in identifying specific cell types during and immediately after transcribing specific mRNA based on ultrastructural morphology.
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Affiliation(s)
- Sohei Kitazawa
- Division of Molecular Pathology, Kobe University Graduate School of Medicine, Chuo-ku, Japan.
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Abstract
In many of the model organisms used to study development, it is becoming relatively routine to carry out global analyses of gene function. These analyses take many forms, from microarray analyses to the construction of physical interaction maps to the systematic analyses of loss-of-function phenotypes. Such large-scale datasets can be integrated to generate complex gene networks, and we explore how these gene networks can contribute to an understanding of developmental pathways. In particular, we examine how combining large-scale expression experiments and gene networks may move us towards a molecular description of the events of development, embodied in a succession of stage-specific subnetworks sampled from an organism's overall gene network.
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Affiliation(s)
- Andrew G Fraser
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.
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Auffray C, Chen Z, Hood L, Soares B, Sugano S. Foreword: from the TRANSCRIPTOME conferences to the SYSTEMOSCOPE international consortium. C R Biol 2004; 326:867-75. [PMID: 14744093 DOI: 10.1016/j.crvi.2003.09.024] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
This thematic issue issue of the Comptes rendus Biologies contains review articles, original papers and conference reports presented at the first two TRANSCRIPTOME conferences From Functional Genomics to Systems Biology and IMAGE Consortium Invitational workshops (Paris, November 2000 and Seattle, March 2002), and discussed during the inaugural meetings of the SYSTEMOSCOPE International Consortium (Paris, June 2003). We describe the founding principles, missions, working plan and policy for partnership and industrial development of SYSTEMOSCOPE to promote the study of the complexity of biological systems by integrating scientific, medical, ethical and economic issues in implementation of interdisciplinary projects for human health.
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Affiliation(s)
- Charles Auffray
- Genexpress, Functional Genomics and Systemic Biology for Health, CNRS FRE 2571, 7, rue Guy-Môquet, BP 8, 94801 Villejuif cedex, France.
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