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Kinoshita A, Shqirat M, Kageyama R, Ohtsuka T. Modification of gene expression and soluble factor secretion in the lateral ventricle choroid plexus: Analysis of the impacts on the neocortical development. Neurosci Res 2021; 177:38-51. [PMID: 34968558 DOI: 10.1016/j.neures.2021.12.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Revised: 12/15/2021] [Accepted: 12/23/2021] [Indexed: 01/03/2023]
Abstract
The choroid plexus (ChP) is the center of soluble factor secretion into the cerebrospinal fluid in the central nervous system. It is known that various signaling factors secreted from the ChP are involved in the regulation of brain development and homeostasis. Intriguingly, the size of the ChP was prominently expanded in the brains of primates, including humans, suggesting that the expansion of the ChP contributed to mammalian brain evolution, leading to the acquisition of higher intelligence and cognitive functions. To address this hypothesis, we established transgenic (Tg) systems using regulatory elements that direct expression of candidate genes in the ChP. Overexpression of sonic hedgehog (Shh) in the developing ChP led to the expansion of the ChP with greater arborization. Shh produced in the ChP caused an increase in neural stem cells (NSCs) in the neocortical region, leading to the expansion of ventricles, ventricular zone, neocortical surface area, and neocortical surface folding. These findings suggest that the activation of Shh signaling via its enhanced secretion from the developing ChP contributed to the evolution of the neocortex. Furthermore, we found that Shh produced in the ChP enhanced NSC proliferation in the postnatal Tg brain, demonstrating that our Tg system can be used to estimate the effects of candidate factors secreted from the ChP on various aspects of brain morphogenesis and functions.
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Affiliation(s)
- Akira Kinoshita
- Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, 606-8507, Japan; Graduate School of Biostudies, Kyoto University, Kyoto, 606-8501, Japan
| | - Mohammed Shqirat
- Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, 606-8507, Japan; Graduate School of Medicine, Kyoto University, Kyoto, 606-8501, Japan
| | - Ryoichiro Kageyama
- Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, 606-8507, Japan; Graduate School of Biostudies, Kyoto University, Kyoto, 606-8501, Japan; Graduate School of Medicine, Kyoto University, Kyoto, 606-8501, Japan; Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University, Kyoto, 606-8501, Japan
| | - Toshiyuki Ohtsuka
- Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, 606-8507, Japan; Graduate School of Biostudies, Kyoto University, Kyoto, 606-8501, Japan; Graduate School of Medicine, Kyoto University, Kyoto, 606-8501, Japan.
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2
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Sendell-Price AT, Ruegg KC, Robertson BC, Clegg SM. An island-hopping bird reveals how founder events shape genome-wide divergence. Mol Ecol 2021; 30:2495-2510. [PMID: 33826187 DOI: 10.1111/mec.15898] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 03/09/2021] [Accepted: 03/18/2021] [Indexed: 12/16/2022]
Abstract
When populations colonize new areas, both strong selection and strong drift can be experienced due to novel environments and small founding populations, respectively. Empirical studies have predominantly focused on the phenotype when assessing the role of selection, and limited neutral-loci when assessing founder-induced loss of diversity. Consequently, the extent to which processes interact to influence evolutionary trajectories is difficult to assess. Genomic-level approaches provide the opportunity to simultaneously consider these processes. Here, we examine the roles of selection and drift in shaping genomic diversity and divergence in historically documented sequential island colonizations by the silvereye (Zosterops lateralis). We provide the first empirical demonstration of the rapid appearance of highly diverged genomic regions following population founding, the position of which are highly idiosyncratic. As these regions rarely contained loci putatively under selection, it is most likely that these differences arise via the stochastic nature of the founding process. However, selection is required to explain rapid evolution of larger body size in insular silvereyes. Reconciling our genomic data with these phenotypic patterns suggests there may be many genomic routes to the island phenotype, which vary across populations. Finally, we show that accelerated divergence associated with multiple founding steps is the product of genome-wide rather than localized differences, and that diversity erodes due to loss of rare alleles. However, even multiple founder events do not result in divergence and diversity levels seen in evolutionary older subspecies, and therefore do not provide a shortcut to speciation as proposed by founder-effect speciation models.
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Affiliation(s)
- Ashley T Sendell-Price
- Edward Grey Institute of Field Ornithology, Department of Zoology, University of Oxford, Oxford, UK
| | - Kristen C Ruegg
- Edward Grey Institute of Field Ornithology, Department of Zoology, University of Oxford, Oxford, UK.,Department of Biology, Colorado State University, Fort Collins, CO, USA
| | | | - Sonya M Clegg
- Edward Grey Institute of Field Ornithology, Department of Zoology, University of Oxford, Oxford, UK.,Environmental Futures Research Institute, Griffith University, Nathan, Qld, Australia
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3
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Han X, Chen H, Huang D, Chen H, Fei L, Cheng C, Huang H, Yuan GC, Guo G. Mapping human pluripotent stem cell differentiation pathways using high throughput single-cell RNA-sequencing. Genome Biol 2018; 19:47. [PMID: 29622030 PMCID: PMC5887227 DOI: 10.1186/s13059-018-1426-0] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Accepted: 03/21/2018] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Human pluripotent stem cells (hPSCs) provide powerful models for studying cellular differentiations and unlimited sources of cells for regenerative medicine. However, a comprehensive single-cell level differentiation roadmap for hPSCs has not been achieved. RESULTS We use high throughput single-cell RNA-sequencing (scRNA-seq), based on optimized microfluidic circuits, to profile early differentiation lineages in the human embryoid body system. We present a cellular-state landscape for hPSC early differentiation that covers multiple cellular lineages, including neural, muscle, endothelial, stromal, liver, and epithelial cells. Through pseudotime analysis, we construct the developmental trajectories of these progenitor cells and reveal the gene expression dynamics in the process of cell differentiation. We further reprogram primed H9 cells into naïve-like H9 cells to study the cellular-state transition process. We find that genes related to hemogenic endothelium development are enriched in naïve-like H9. Functionally, naïve-like H9 show higher potency for differentiation into hematopoietic lineages than primed cells. CONCLUSIONS Our single-cell analysis reveals the cellular-state landscape of hPSC early differentiation, offering new insights that can be harnessed for optimization of differentiation protocols.
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Affiliation(s)
- Xiaoping Han
- Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, 310058, China.,Institute of Hematology, The 1st Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China.,Stem Cell Institute, Zhejiang University, Hangzhou, 310058, China
| | - Haide Chen
- Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, 310058, China. .,Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regenerative Medicine, Zhejiang Provincial Key Lab for Tissue Engineering and Regenerative Medicine, Hangzhou, 310058, China. .,College of Animal Science, Zhejiang University, Hangzhou, 310058, China.
| | - Daosheng Huang
- Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, 310058, China.,Stem Cell Institute, Zhejiang University, Hangzhou, 310058, China
| | - Huidong Chen
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Harvard Chan School of Public Health, Boston, MA, 02115, USA.,Department of Computer Science and Technology, Tongji University, Shanghai, 201804, China
| | - Lijiang Fei
- Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, 310058, China.,Stem Cell Institute, Zhejiang University, Hangzhou, 310058, China
| | - Chen Cheng
- College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - He Huang
- Institute of Hematology, The 1st Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China.,Stem Cell Institute, Zhejiang University, Hangzhou, 310058, China
| | - Guo-Cheng Yuan
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Harvard Chan School of Public Health, Boston, MA, 02115, USA.
| | - Guoji Guo
- Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, 310058, China. .,Institute of Hematology, The 1st Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China. .,Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regenerative Medicine, Zhejiang Provincial Key Lab for Tissue Engineering and Regenerative Medicine, Hangzhou, 310058, China. .,Stem Cell Institute, Zhejiang University, Hangzhou, 310058, China.
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4
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Armstrong C, Richardson DS, Hipperson H, Horsburgh GJ, Küpper C, Percival‐Alwyn L, Clark M, Burke T, Spurgin LG. Genomic associations with bill length and disease reveal drift and selection across island bird populations. Evol Lett 2018; 2:22-36. [PMID: 30283662 PMCID: PMC6121843 DOI: 10.1002/evl3.38] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Revised: 12/19/2017] [Accepted: 12/21/2017] [Indexed: 12/15/2022] Open
Abstract
Island species provide excellent models for investigating how selection and drift operate in wild populations, and for determining how these processes act to influence local adaptation and speciation. Here, we examine the role of selection and drift in shaping genomic and phenotypic variation across recently separated populations of Berthelot's pipit (Anthus berthelotii), a passerine bird endemic to three archipelagos in the Atlantic. We first characterized genetic diversity and population structuring that supported previous inferences of a history of recent colonizations and bottlenecks. We then tested for regions of the genome associated with the ecologically important traits of bill length and malaria infection, both of which vary substantially across populations in this species. We identified a SNP associated with variation in bill length among individuals, islands, and archipelagos; patterns of variation at this SNP suggest that both phenotypic and genotypic variation in bill length is largely shaped by founder effects. Malaria was associated with SNPs near/within genes involved in the immune response, but this relationship was not consistent among archipelagos, supporting the view that disease resistance is complex and rapidly evolving. Although we found little evidence for divergent selection at candidate loci for bill length and malaria resistance, genome scan analyses pointed to several genes related to immunity and metabolism as having important roles in divergence and adaptation. Our findings highlight the utility and challenges involved with combining association mapping and population genetic analysis in nonequilibrium populations, to disentangle the effects of drift and selection on shaping genotypes and phenotypes.
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Affiliation(s)
- Claire Armstrong
- School of Biological Sciences, University of East AngliaNorwich Research ParkNorwich NR4 7TJUnited Kingdom
| | - David S. Richardson
- School of Biological Sciences, University of East AngliaNorwich Research ParkNorwich NR4 7TJUnited Kingdom
| | - Helen Hipperson
- NERC Biomolecular Analysis Facility, Department of Animal and Plant SciencesUniversity of SheffieldSheffield S10 2TNUnited Kingdom
| | - Gavin J. Horsburgh
- NERC Biomolecular Analysis Facility, Department of Animal and Plant SciencesUniversity of SheffieldSheffield S10 2TNUnited Kingdom
| | - Clemens Küpper
- Max Planck Institute for Ornithology82319 SeewiesenGermany
| | | | - Matt Clark
- Earlham InstituteNorwich Research ParkNorwich NR4 7UZUnited Kingdom
| | - Terry Burke
- NERC Biomolecular Analysis Facility, Department of Animal and Plant SciencesUniversity of SheffieldSheffield S10 2TNUnited Kingdom
| | - Lewis G. Spurgin
- School of Biological Sciences, University of East AngliaNorwich Research ParkNorwich NR4 7TJUnited Kingdom
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5
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Münst S, Koch P, Kesavan J, Alexander-Mays M, Münst B, Blaess S, Brüstle O. In vitro segregation and isolation of human pluripotent stem cell-derived neural crest cells. Methods 2017; 133:65-80. [PMID: 29037816 DOI: 10.1016/j.ymeth.2017.09.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Revised: 09/24/2017] [Accepted: 09/27/2017] [Indexed: 01/17/2023] Open
Abstract
The neural crest (NC) is a transient embryonic cell population with remarkable characteristics. After delaminating from the neural tube, NC cells (NCCs) migrate extensively, populate nearly every tissue of the body and differentiate into highly diverse cell types such as peripheral neurons and glia, but also mesenchymal cells including chondrocytes, osteocytes, and adipocytes. While the NC has been extensively studied in several animal models, little is known about human NC development. A number of methods have been established to derive NCCs in vitro from human pluripotent stem cells (hPSC). Typically, these protocols comprise several cell culture steps to enrich for NCCs in the neural derivatives of the differentiating hPSCs. Here we report on a remarkable and hitherto unnoticed in vitro segregation phenomenon that enables direct extraction of virtually pure NCCs during the earliest stages of hPSC differentiation. Upon aggregation to embryoid bodies (EB) and replating, differentiating hPSCs give rise to a population of NCCs, which spontaneously segregate from the EB outgrowth to form conspicuous, macroscopically visible atoll-shaped clusters in the periphery of the EB outgrowth. Isolation of these NC clusters yields p75NTR(+)/SOXE(+) NCCs, which differentiate to peripheral neurons and glia as well as mesenchymal derivatives. Our data indicate that differentiating hPSC cultures recapitulate, in a simplified manner, the physical segregation of central nervous system (CNS) tissue and NCCs. This phenomenon may be exploited for NCC purification and for studying segregation and differentiation processes observed during early human NC development in vitro.
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Affiliation(s)
- Sabine Münst
- Institute of Reconstructive Neurobiology, Life & Brain Center, University of Bonn Medical Faculty, 53127 Bonn, Germany
| | - Philipp Koch
- Institute of Reconstructive Neurobiology, Life & Brain Center, University of Bonn Medical Faculty, 53127 Bonn, Germany
| | - Jaideep Kesavan
- Institute of Reconstructive Neurobiology, Life & Brain Center, University of Bonn Medical Faculty, 53127 Bonn, Germany
| | - Michael Alexander-Mays
- Institute of Human Genetics, Life & Brain Center, University of Bonn Medical Faculty, 53127 Bonn, Germany
| | - Bernhard Münst
- Institute of Reconstructive Neurobiology, Life & Brain Center, University of Bonn Medical Faculty, 53127 Bonn, Germany
| | - Sandra Blaess
- Institute of Reconstructive Neurobiology, Life & Brain Center, University of Bonn Medical Faculty, 53127 Bonn, Germany
| | - Oliver Brüstle
- Institute of Reconstructive Neurobiology, Life & Brain Center, University of Bonn Medical Faculty, 53127 Bonn, Germany.
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6
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Lumb R, Buckberry S, Secker G, Lawrence D, Schwarz Q. Transcriptome profiling reveals expression signatures of cranial neural crest cells arising from different axial levels. BMC DEVELOPMENTAL BIOLOGY 2017; 17:5. [PMID: 28407732 PMCID: PMC5390458 DOI: 10.1186/s12861-017-0147-z] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Accepted: 04/03/2017] [Indexed: 01/13/2023]
Abstract
Background Cranial neural crest cells (NCCs) are a unique embryonic cell type which give rise to a diverse array of derivatives extending from neurons and glia through to bone and cartilage. Depending on their point of origin along the antero-posterior axis cranial NCCs are rapidly sorted into distinct migratory streams that give rise to axial specific structures. These migratory streams mirror the underlying segmentation of the brain with NCCs exiting the diencephalon and midbrain following distinct paths compared to those exiting the hindbrain rhombomeres (r). The genetic landscape of cranial NCCs arising at different axial levels remains unknown. Results Here we have used RNA sequencing to uncover the transcriptional profiles of mouse cranial NCCs arising at different axial levels. Whole transcriptome analysis identified over 120 transcripts differentially expressed between NCCs arising anterior to r3 (referred to as r1-r2 migratory stream for simplicity) and the r4 migratory stream. Eight of the genes differentially expressed between these populations were validated by RT-PCR with 2 being further validated by in situ hybridisation. We also explored the expression of the Neuropilins (Nrp1 and Nrp2) and their co-receptors and show that the A-type Plexins are differentially expressed in different cranial NCC streams. Conclusions Our analyses identify a large number of genes differentially regulated between cranial NCCs arising at different axial levels. This data provides a comprehensive description of the genetic landscape driving diversity of distinct cranial NCC streams and provides novel insight into the regulatory networks controlling the formation of specific skeletal elements and the mechanisms promoting migration along different paths. Electronic supplementary material The online version of this article (doi:10.1186/s12861-017-0147-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Rachael Lumb
- Centre for Cancer Biology, University of South Australia and SA Pathology, Frome Road, Adelaide, SA, 5000, Australia.,University of Adelaide, Frome Road, Adelaide, SA, 5000, Australia
| | - Sam Buckberry
- Harry Perkins Institute of Medical Research, Perth, WA, 6008, Australia.,Australian Research Council Centre of Excellence in Plant Energy Biology, University of Western Australia, Perth, 6009, WA, Australia
| | - Genevieve Secker
- Centre for Cancer Biology, University of South Australia and SA Pathology, Frome Road, Adelaide, SA, 5000, Australia
| | - David Lawrence
- ACRF Cancer Genomics Facility, Centre for Cancer Biology, SA Pathology, Adelaide, Australia.,School of Molecular and Biomedical Science, University of Adelaide, Adelaide, Australia
| | - Quenten Schwarz
- Centre for Cancer Biology, University of South Australia and SA Pathology, Frome Road, Adelaide, SA, 5000, Australia.
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7
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Hoshino H, Shioi G, Aizawa S. AVE protein expression and visceral endoderm cell behavior during anterior-posterior axis formation in mouse embryos: Asymmetry in OTX2 and DKK1 expression. Dev Biol 2015; 402:175-91. [PMID: 25910836 DOI: 10.1016/j.ydbio.2015.03.023] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2014] [Revised: 03/20/2015] [Accepted: 03/21/2015] [Indexed: 11/27/2022]
Abstract
The initial landmark of anterior-posterior (A-P) axis formation in mouse embryos is the distal visceral endoderm, DVE, which expresses a series of anterior genes at embryonic day 5.5 (E5.5). Subsequently, DVE cells move to the future anterior region, generating anterior visceral endoderm (AVE). Questions remain regarding how the DVE is formed and how the direction of the movement is determined. This study compares the detailed expression patterns of OTX2, HHEX, CER1, LEFTY1 and DKK1 by immunohistology and live imaging at E4.5-E6.5. At E6.5, the AVE is subdivided into four domains: most anterior (OTX2, HHEX, CER1-low/DKK1-high), anterior (OTX2, HHEX, CER1-high/DKK1-low), main (OTX2, HHEX, CER1, LEFTY1-high) and antero-lateral and posterior (OTX2, HHEX-low). The study demonstrates how this pattern is established. AVE protein expression in the DVE occurs de novo at E5.25-E5.5. Neither HHEX, LEFTY1 nor CER1 expression is asymmetric. In contrast, OTX2 expression is tilted on the future posterior side with the DKK1 expression at its proximal domain; the DVE cells move in the opposite direction of the tilt.
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Affiliation(s)
- Hideharu Hoshino
- Laboratory for Vertebrate Body Plan, Center for Developmental Biology (CDB), RIKEN Kobe, 2-2-3 Minatojima Minami-machi, Chuo-ku, Kobe 650-0046, Japan.
| | - Go Shioi
- Laboratory for Animal Resources and Genetic Engineering, Center for Developmental Biology (CDB), RIKEN Kobe, 2-2-3 Minatojima Minami-machi, Chuo-ku, Kobe 650-0046, Japan.
| | - Shinichi Aizawa
- Laboratory for Vertebrate Body Plan, Center for Developmental Biology (CDB), RIKEN Kobe, 2-2-3 Minatojima Minami-machi, Chuo-ku, Kobe 650-0046, Japan; Laboratory for Animal Resources and Genetic Engineering, Center for Developmental Biology (CDB), RIKEN Kobe, 2-2-3 Minatojima Minami-machi, Chuo-ku, Kobe 650-0046, Japan.
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8
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Kimura-Yoshida C, Mochida K, Ellwanger K, Niehrs C, Matsuo I. Fate Specification of Neural Plate Border by Canonical Wnt Signaling and Grhl3 is Crucial for Neural Tube Closure. EBioMedicine 2015; 2:513-27. [PMID: 26288816 PMCID: PMC4535158 DOI: 10.1016/j.ebiom.2015.04.012] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Revised: 04/17/2015] [Accepted: 04/17/2015] [Indexed: 12/05/2022] Open
Abstract
During primary neurulation, the separation of a single-layered ectodermal sheet into the surface ectoderm (SE) and neural tube specifies SE and neural ectoderm (NE) cell fates. The mechanisms underlying fate specification in conjunction with neural tube closure are poorly understood. Here, by comparing expression profiles between SE and NE lineages, we observed that uncommitted progenitor cells, expressing stem cell markers, are present in the neural plate border/neural fold prior to neural tube closure. Our results also demonstrated that canonical Wnt and its antagonists, DKK1/KREMEN1, progressively specify these progenitors into SE or NE fates in accord with the progress of neural tube closure. Additionally, SE specification of the neural plate border via canonical Wnt signaling is directed by the grainyhead-like 3 (Grhl3) transcription factor. Thus, we propose that the fate specification of uncommitted progenitors in the neural plate border by canonical Wnt signaling and its downstream effector Grhl3 is crucial for neural tube closure. This study implicates that failure in critical genetic factors controlling fate specification of progenitor cells in the neural plate border/neural fold coordinated with neural tube closure may be potential causes of human neural tube defects. Neural plate border/neural fold possesses stem cell-like characters during primary neurulation. Canonical Wnt and its antagonists progressively specify progenitors into surface or neural fates upon neural tube closure. Fate specification into surface ectoderm in the neural fold is directed by the Grhl3 transcription factor. Fate specification of uncommitted progenitors in the neural plate border is intimately coupled to neural tube closure.
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Affiliation(s)
- Chiharu Kimura-Yoshida
- Department of Molecular Embryology, Osaka Medical Center, Research Institute for Maternal and Child Health, Osaka Prefectural Hospital Organization, 840 Murodo-cho, Izumi, Osaka 594-1101, Japan
| | - Kyoko Mochida
- Department of Molecular Embryology, Osaka Medical Center, Research Institute for Maternal and Child Health, Osaka Prefectural Hospital Organization, 840 Murodo-cho, Izumi, Osaka 594-1101, Japan
| | - Kristina Ellwanger
- Division of Molecular Embryology, DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany
| | - Christof Niehrs
- Division of Molecular Embryology, DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany ; Institute of Molecular Biology, 55128 Mainz, Germany
| | - Isao Matsuo
- Department of Molecular Embryology, Osaka Medical Center, Research Institute for Maternal and Child Health, Osaka Prefectural Hospital Organization, 840 Murodo-cho, Izumi, Osaka 594-1101, Japan
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9
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Differentiation of human epidermal neural crest stem cells (hEPI-NCSC) into virtually homogenous populations of dopaminergic neurons. Stem Cell Rev Rep 2014; 10:316-26. [PMID: 24399192 PMCID: PMC3969515 DOI: 10.1007/s12015-013-9493-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Here we provide a protocol for the directed differentiation of hEPI-NCSC into midbrain dopaminergic neurons, which degenerate in Parkinson's disease. hEPI-NCSC are neural crest-derived multipotent stem cells that persist into adulthood in the bulge of hair follicles. The experimental design is distinctly different from conventional protocols for embryonic stem cells and induced pluripotent stem (iPS) cells. It includes pre-differentiation of the multipotent hEPI-NCSC into neural stem cell-like cells, followed by ventralizing, patterning, continued exposure to the TGFβ receptor inhibitor, SB431542, and at later stages of differentiation the presence of the WNT inhibitor, IWP-4. All cells expressed A9 midbrain dopaminergic neuron progenitor markers with gene expression levels comparable to those in normal human substantia nigra. The current study shows for the first time that virtually homogeneous populations of dopaminergic neurons can be derived ex vivo from somatic stem cells without the need for purification, with useful timeliness and high efficacy. This novel development is an important first step towards the establishment of fully functional dopaminergic neurons from an ontologically relevant stem cell type, hEPI-NCSC.
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10
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Fukuta M, Nakai Y, Kirino K, Nakagawa M, Sekiguchi K, Nagata S, Matsumoto Y, Yamamoto T, Umeda K, Heike T, Okumura N, Koizumi N, Sato T, Nakahata T, Saito M, Otsuka T, Kinoshita S, Ueno M, Ikeya M, Toguchida J. Derivation of mesenchymal stromal cells from pluripotent stem cells through a neural crest lineage using small molecule compounds with defined media. PLoS One 2014; 9:e112291. [PMID: 25464501 PMCID: PMC4251837 DOI: 10.1371/journal.pone.0112291] [Citation(s) in RCA: 122] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Accepted: 10/06/2014] [Indexed: 12/27/2022] Open
Abstract
Neural crest cells (NCCs) are an embryonic migratory cell population with the ability to differentiate into a wide variety of cell types that contribute to the craniofacial skeleton, cornea, peripheral nervous system, and skin pigmentation. This ability suggests the promising role of NCCs as a source for cell-based therapy. Although several methods have been used to induce human NCCs (hNCCs) from human pluripotent stem cells (hPSCs), such as embryonic stem cells (ESCs) and induced pluripotent stem cells (iPSCs), further modifications are required to improve the robustness, efficacy, and simplicity of these methods. Chemically defined medium (CDM) was used as the basal medium in the induction and maintenance steps. By optimizing the culture conditions, the combination of the GSK3β inhibitor and TGFβ inhibitor with a minimum growth factor (insulin) very efficiently induced hNCCs (70-80%) from hPSCs. The induced hNCCs expressed cranial NCC-related genes and stably proliferated in CDM supplemented with EGF and FGF2 up to at least 10 passages without changes being observed in the major gene expression profiles. Differentiation properties were confirmed for peripheral neurons, glia, melanocytes, and corneal endothelial cells. In addition, cells with differentiation characteristics similar to multipotent mesenchymal stromal cells (MSCs) were induced from hNCCs using CDM specific for human MSCs. Our simple and robust induction protocol using small molecule compounds with defined media enabled the generation of hNCCs as an intermediate material producing terminally differentiated cells for cell-based innovative medicine.
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Affiliation(s)
- Makoto Fukuta
- Department of Tissue Regeneration, Institute for Frontier Medical Sciences, Kyoto University, Kyoto, Japan
- Department of Cell Growth and Differentiation, Center for iPS Cell Research and Application, Kyoto University, Kyoto, Japan
- Department of Orthopaedic Surgery, Graduate School of Medical Sciences, Nagoya City University, Nagoya, Japan
| | - Yoshinori Nakai
- Department of Ophthalmology, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Kosuke Kirino
- Department of Clinical Application, Center for iPS Cell Research and Application, Kyoto University, Kyoto, Japan
| | - Masato Nakagawa
- Department of Reprogramming Science, Center for iPS Cell Research and Application, Kyoto University, Kyoto, Japan
| | - Kazuya Sekiguchi
- Department of Tissue Regeneration, Institute for Frontier Medical Sciences, Kyoto University, Kyoto, Japan
- Department of Cell Growth and Differentiation, Center for iPS Cell Research and Application, Kyoto University, Kyoto, Japan
- Department of Orthopaedic Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Sanae Nagata
- Department of Cell Growth and Differentiation, Center for iPS Cell Research and Application, Kyoto University, Kyoto, Japan
| | - Yoshihisa Matsumoto
- Department of Tissue Regeneration, Institute for Frontier Medical Sciences, Kyoto University, Kyoto, Japan
- Department of Cell Growth and Differentiation, Center for iPS Cell Research and Application, Kyoto University, Kyoto, Japan
- Department of Orthopaedic Surgery, Graduate School of Medical Sciences, Nagoya City University, Nagoya, Japan
| | - Takuya Yamamoto
- Department of Reprogramming Science, Center for iPS Cell Research and Application, Kyoto University, Kyoto, Japan
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Kyoto, Japan
| | - Katsutsugu Umeda
- Department of Pediatrics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Toshio Heike
- Department of Pediatrics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Naoki Okumura
- Department of Biomedical Engineering, Faculty of Life and Medical Sciences, Doshisha University, Kyotanabe, Japan
| | - Noriko Koizumi
- Department of Biomedical Engineering, Faculty of Life and Medical Sciences, Doshisha University, Kyotanabe, Japan
| | - Takahiko Sato
- Department of Ophthalmology, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Tatsutoshi Nakahata
- Department of Clinical Application, Center for iPS Cell Research and Application, Kyoto University, Kyoto, Japan
| | - Megumu Saito
- Department of Clinical Application, Center for iPS Cell Research and Application, Kyoto University, Kyoto, Japan
| | - Takanobu Otsuka
- Department of Orthopaedic Surgery, Graduate School of Medical Sciences, Nagoya City University, Nagoya, Japan
| | - Shigeru Kinoshita
- Department of Ophthalmology, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Morio Ueno
- Department of Ophthalmology, Kyoto Prefectural University of Medicine, Kyoto, Japan
- * E-mail: (MU); (MI); (JT)
| | - Makoto Ikeya
- Department of Cell Growth and Differentiation, Center for iPS Cell Research and Application, Kyoto University, Kyoto, Japan
- * E-mail: (MU); (MI); (JT)
| | - Junya Toguchida
- Department of Tissue Regeneration, Institute for Frontier Medical Sciences, Kyoto University, Kyoto, Japan
- Department of Cell Growth and Differentiation, Center for iPS Cell Research and Application, Kyoto University, Kyoto, Japan
- Department of Orthopaedic Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- * E-mail: (MU); (MI); (JT)
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11
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Gupta R, Wills A, Ucar D, Baker J. Developmental enhancers are marked independently of zygotic Nodal signals in Xenopus. Dev Biol 2014; 395:38-49. [PMID: 25205067 DOI: 10.1016/j.ydbio.2014.08.034] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2014] [Revised: 08/06/2014] [Accepted: 08/31/2014] [Indexed: 02/08/2023]
Abstract
To determine the hierarchy of transcriptional regulation within the in vivo vertebrate embryo, we examined whether developmental enhancers were influenced by Nodal signaling during early embryogenesis in Xenopus tropicalis. We find that developmental enhancers, defined by the active enhancer chromatin marks H3K4me1 and H3K27ac, are established as early as blastula stage and that Smad2/3 only strongly associates with these regions at gastrula stages. Significantly, when we perturb Nodal signaling using the drug SB431542, most enhancers remain marked, including at genes known to be sensitive to Nodal signaling. Overall, as enhancers are in an active conformation prior to Nodal signaling and are established independently of Nodal signaling, we suggest that many developmental enhancers are marked maternally, prior to exposure to extrinsic signals.
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Affiliation(s)
- Rakhi Gupta
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Andrea Wills
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Duygu Ucar
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Julie Baker
- Department of Genetics, Stanford University, Stanford, CA 94305, USA.,Department of Obstetrics and Gynecology, Stanford University, Stanford, CA 94305, USA
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12
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Kurokawa D, Ohmura T, Sakurai Y, Inoue K, Suda Y, Aizawa S. Otx2 expression in anterior neuroectoderm and forebrain/midbrain is directed by more than six enhancers. Dev Biol 2014; 387:203-13. [PMID: 24457099 DOI: 10.1016/j.ydbio.2014.01.011] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2013] [Revised: 01/12/2014] [Accepted: 01/14/2014] [Indexed: 11/25/2022]
Abstract
Otx2 plays essential roles in each site at each step of head development. We previously identified the AN1 enhancer at 91kb 5' upstream for the Otx2 expressions in anterior neuroectoderm (AN) at neural plate stage before E8.5, and the FM1 enhancer at 75kb 5' upstream and the FM2 enhancer at 122kb 3' downstream for the expression in forebrain/midbrain (FM) at brain vesicle stage after E8.5. The present study identified a second AN enhancer (AN2) at 88kb 5' upstream; the AN2 enhancer also recapitulates the endogenous Otx2 expression in choroid plexus, cortical hem and choroidal roof. However, the enhancer mutants indicated the presence of another AN enhancer. The study also identified a third FM enhancer (FM3) at 153kb 5' upstream. Thus, the Otx2 expressions in anterior neuroectoderm and forebrain/midbrain are regulated by more than six enhancers located far from the coding region. The enhancers identified are differentially conserved among vertebrates; none of the AN enhancers has activities in caudal forebrain and midbrain at brain vesicle stage after E8.5, nor do any of the FM enhancers in anterior neuroectoderm at neural plate stage before E8.5.
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Affiliation(s)
- Daisuke Kurokawa
- Laboratory for Vertebrate Body Plan, Center for Developmental Biology (CDB), RIKEN Kobe, 2-2-3 Minatojima Minami-machi, Chuo-Ku, Kobe, Hyogo 650-0047, Japan; Misaki Marine Biological Station, Graduate School of Science, The University of Tokyo, 1024 Koajiro, Misaki, Miura, Kanagawa 238-0225, Japan
| | - Tomomi Ohmura
- Laboratory for Vertebrate Body Plan, Center for Developmental Biology (CDB), RIKEN Kobe, 2-2-3 Minatojima Minami-machi, Chuo-Ku, Kobe, Hyogo 650-0047, Japan
| | - Yusuke Sakurai
- Laboratory for Vertebrate Body Plan, Center for Developmental Biology (CDB), RIKEN Kobe, 2-2-3 Minatojima Minami-machi, Chuo-Ku, Kobe, Hyogo 650-0047, Japan
| | - Kenichi Inoue
- Laboratory for Animal Resources and Genetic Engineering, Center for Developmental Biology (CDB), RIKEN Kobe, 2-2-3 Minatojima Minami-machi, Chuo-Ku, Kobe, Hyogo 650-0047, Japan
| | - Yoko Suda
- Laboratory for Vertebrate Body Plan, Center for Developmental Biology (CDB), RIKEN Kobe, 2-2-3 Minatojima Minami-machi, Chuo-Ku, Kobe, Hyogo 650-0047, Japan
| | - Shinichi Aizawa
- Laboratory for Vertebrate Body Plan, Center for Developmental Biology (CDB), RIKEN Kobe, 2-2-3 Minatojima Minami-machi, Chuo-Ku, Kobe, Hyogo 650-0047, Japan; Laboratory for Animal Resources and Genetic Engineering, Center for Developmental Biology (CDB), RIKEN Kobe, 2-2-3 Minatojima Minami-machi, Chuo-Ku, Kobe, Hyogo 650-0047, Japan.
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13
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Billingsley CN, Allen JR, Baumann DD, Deitz SL, Blazek JD, Newbauer A, Darrah A, Long BC, Young B, Clement M, Doerge RW, Roper RJ. Non-trisomic homeobox gene expression during craniofacial development in the Ts65Dn mouse model of Down syndrome. Am J Med Genet A 2013; 161A:1866-74. [PMID: 23843306 DOI: 10.1002/ajmg.a.36006] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2012] [Accepted: 04/08/2013] [Indexed: 01/25/2023]
Abstract
Trisomy 21 in humans causes cognitive impairment, craniofacial dysmorphology, and heart defects collectively referred to as Down syndrome. Yet, the pathophysiology of these phenotypes is not well understood. Craniofacial alterations may lead to complications in breathing, eating, and communication. Ts65Dn mice exhibit craniofacial alterations that model Down syndrome including a small mandible. We show that Ts65Dn embryos at 13.5 days gestation (E13.5) have a smaller mandibular precursor but a normal sized tongue as compared to euploid embryos, suggesting a relative instead of actual macroglossia originates during development. Neurological tissues were also altered in E13.5 trisomic embryos. Our array analysis found 155 differentially expressed non-trisomic genes in the trisomic E13.5 mandible, including 20 genes containing a homeobox DNA binding domain. Additionally, Sox9, important in skeletal formation and cell proliferation, was upregulated in Ts65Dn mandible precursors. Our results suggest trisomy causes altered expression of non-trisomic genes in development leading to structural changes associated with DS. Identification of genetic pathways disrupted by trisomy is an important step in proposing rational therapies at relevant time points to ameliorate craniofacial abnormalities in DS and other congenital disorders.
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Affiliation(s)
- Cherie N Billingsley
- Department of Biology and Indiana University Center for Regenerative Biology and Medicine, Indiana University-Purdue University Indianapolis, Indianapolis, IN, USA
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14
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Bohnsack BL, Kahana A. Thyroid hormone and retinoic acid interact to regulate zebrafish craniofacial neural crest development. Dev Biol 2013; 373:300-9. [PMID: 23165295 PMCID: PMC3534885 DOI: 10.1016/j.ydbio.2012.11.005] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2012] [Revised: 11/07/2012] [Accepted: 11/08/2012] [Indexed: 01/17/2023]
Abstract
Craniofacial and ocular morphogenesis require proper regulation of cranial neural crest migration, proliferation, survival and differentiation. Although alterations in maternal thyroid hormone (TH) are associated with congenital craniofacial anomalies, the role of TH on the neural crest has not been previously described. Using zebrafish, we demonstrate that pharmacologic and genetic alterations in TH signaling disrupt cranial neural crest migration, proliferation, and survival, leading to craniofacial, extraocular muscle, and ocular developmental abnormalities. In the rostral cranial neural crest that gives rise to the periocular mesenchyme and the frontonasal process, retinoic acid (RA) rescued migratory defects induced by decreased TH signaling. In the caudal cranial neural crest, TH and RA had reciprocal effects on anterior and posterior pharyngeal arch development. The interactions between TH and RA signaling were partially mediated by the retinoid X receptor. We conclude that TH regulates both rostral and caudal cranial neural crest. Further, coordinated interactions of TH and RA are required for proper craniofacial and ocular development.
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Affiliation(s)
- Brenda L. Bohnsack
- Department of Ophthalmology and Visual Sciences, Kellogg Eye Center, University of Michigan, Ann Arbor MI
| | - Alon Kahana
- Department of Ophthalmology and Visual Sciences, Kellogg Eye Center, University of Michigan, Ann Arbor MI
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15
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Ohmura T, Shioi G, Hirano M, Aizawa S. Neural tube defects by NUAK1 and NUAK2 double mutation. Dev Dyn 2012; 241:1350-64. [PMID: 22689267 DOI: 10.1002/dvdy.23816] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/03/2012] [Indexed: 11/09/2022] Open
Abstract
BACKGROUND NUAK1 and NUAK2, members of the AMP-activated protein kinase family of serine/threonine kinases, are prominently expressed in neuroectoderm, but their functions in neurulation have not been elucidated. RESULTS NUAK1 and NUAK2 double mutants exhibited exencephaly, facial clefting, and spina bifida. Median hinge point was formed, but dorsolateral hinge point formation was not apparent in cranial neural plate; neither apical constriction nor apico-basal elongation took place efficiently in the double mutants during the 5-10-somite stages. Concomitantly, the apical concentration of phosphorylated myosin light chain 2, F-actin, and cortactin was insignificant, and development of acetylated α-tubulin-positive microtubules was poor. However, the distribution of F-actin, cortactin, Shroom3, Rho, myosin heavy chain IIB, phosphorylated myosin light chain 2, α-tubulin, γ-tubulin, or acetylated α-tubulin was apparently normal in the double mutant neuroepithelia at the 5-somite stage. CONCLUSIONS NUAK1 and NUAK2 complementarily function in the apical constriction and apico-basal elongation that associate with the dorsolateral hinge point formation in cephalic neural plate during the 5- to 10-somite stages. In the double mutant neural plate, phosphorylated myosin light chain 2, F-actin, and cortactin did not concentrate efficiently in apical surfaces, and acetylated α-tubulin-positive microtubules did not develop significantly.
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Affiliation(s)
- Tomomi Ohmura
- Laboratory for Vertebrate Body Plan, Center for Developmental Biology, RIKEN Kobe, Kobe, Japan
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16
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Sato S, Ikeda K, Shioi G, Nakao K, Yajima H, Kawakami K. Regulation of Six1 expression by evolutionarily conserved enhancers in tetrapods. Dev Biol 2012; 368:95-108. [PMID: 22659139 DOI: 10.1016/j.ydbio.2012.05.023] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2012] [Revised: 05/16/2012] [Accepted: 05/21/2012] [Indexed: 11/16/2022]
Abstract
The Six1 homeobox gene plays critical roles in vertebrate organogenesis. Mice deficient for Six1 show severe defects in organs such as skeletal muscle, kidney, thymus, sensory organs and ganglia derived from cranial placodes, and mutations in human SIX1 cause branchio-oto-renal syndrome, an autosomal dominant developmental disorder characterized by hearing loss and branchial defects. The present study was designed to identify enhancers responsible for the dynamic expression pattern of Six1 during mouse embryogenesis. The results showed distinct enhancer activities of seven conserved non-coding sequences (CNSs) retained in tetrapod Six1 loci. The activities were detected in all cranial placodes (excluding the lens placode), dorsal root ganglia, somites, nephrogenic cord, notochord and cranial mesoderm. The major Six1-expression domains during development were covered by the sum of activities of these enhancers, together with the previously identified enhancer for the pre-placodal region and foregut endoderm. Thus, the eight CNSs identified in a series of our study represent major evolutionarily conserved enhancers responsible for the expression of Six1 in tetrapods. The results also confirmed that chick electroporation is a robust means to decipher regulatory information stored in vertebrate genomes. Mutational analysis of the most conserved placode-specific enhancer, Six1-21, indicated that the enhancer integrates a variety of inputs from Sox, Pax, Fox, Six, Wnt/Lef1 and basic helix-loop-helix proteins. Positive autoregulation of Six1 is achieved through the regulation of Six protein-binding sites. The identified Six1 enhancers provide valuable tools to understand the mechanism of Six1 regulation and to manipulate gene expression in the developing embryo, particularly in the sensory organs.
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Affiliation(s)
- Shigeru Sato
- Division of Biology, Center for Molecular Medicine, Jichi Medical University, Yakushiji, Shimotsuke, Tochigi 329-0498, Japan
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17
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Gbx2 directly restricts Otx2 expression to forebrain and midbrain, competing with class III POU factors. Mol Cell Biol 2012; 32:2618-27. [PMID: 22566684 DOI: 10.1128/mcb.00083-12] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Otx2 plays essential roles in rostral brain development, and its counteraction with Gbx2 has been suggested to determine the midbrain-hindbrain boundary (MHB) in vertebrates. We previously identified the FM enhancer that is conserved among vertebrates and drives Otx2 transcription in forebrain/midbrain from the early somite stage. In this study, we found that the POU homeodomain of class III POU factors (Brn1, Brn2, Brn4, and Oct6) associates with noncanonical target sequence TAATTA in the FM enhancer. MicroRNA-mediated knockdown of Brn2 and Oct6 diminished the FM enhancer activity in anterior neural progenitor cells (NPCs) differentiated from P19 cells. The class III POU factors associate with the FM enhancer in forebrain and midbrain but not in hindbrain. We also demonstrated that the Gbx2 homeodomain recognizes the same target TAATTA in the FM enhancer, and Gbx2 associates with the FM enhancer in hindbrain. Gbx2 misexpression in the anterior NPCs repressed the FM enhancer activity and inhibited Brn2 association with the enhancer, whereas Gbx2 knockdown caused ectopic Brn2 association in the posterior NPCs. These results suggest that class III POU factors and Gbx2 share the same target site, TAATTA, in the FM enhancer and that their region-specific binding restricts Otx2 expression at the MHB.
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18
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López SL, Aiassa D, Benítez-Leite S, Lajmanovich R, Mañas F, Poletta G, Sánchez N, Simoniello MF, Carrasco AE. Pesticides Used in South American GMO-Based Agriculture. ADVANCES IN MOLECULAR TOXICOLOGY VOLUME 6 2012. [DOI: 10.1016/b978-0-444-59389-4.00002-1] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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19
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Herman S, Delio M, Morrow B, Samanich J. Agnathia-otocephaly complex: a case report and examination of the OTX2 and PRRX1 genes. Gene 2011; 494:124-9. [PMID: 22198066 DOI: 10.1016/j.gene.2011.11.033] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2011] [Accepted: 11/15/2011] [Indexed: 10/14/2022]
Abstract
Agnathia-otocephaly is a rare, often lethal malformation characterized by absence or hypoplasia of the mandible, microstomia, hypoglossia/aglossia, and variable anterior midline fusion of the ears (melotia, synotia). Etiologies have been linked to both genetic and teratogenic factors and to date, a definitive, commonly identifiable cause has not been recognized. Mouse and human genetic studies have implicated OTX2 and PRRX1 as potential candidate genes for agnathia-otocephaly. In this study we report a sporadic case of agnathia-otocephaly complex with associated features of maldevelopment and examine the roles of OTX2 and PRRX1. The proband, a male born at 31 weeks, displayed severe micrognathia, microstomia, posteriorly-rotated and low set ears, and downward slanting palpebral fissures. Mutation analysis was performed after sequencing the entire coding regions of OTX2 and PRRX1 genes isolated from the proband and his parents. After thorough analysis, no DNA variations were detected. This suggests that mutations in different genes or environmental causes are responsible.
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Affiliation(s)
- Sean Herman
- Albert Einstein College of Medicine, Bronx, NY, USA
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20
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Kurokawa D, Ohmura T, Akasaka K, Aizawa S. A lineage specific enhancer drives Otx2 expression in teleost organizer tissues. Mech Dev 2011; 128:653-61. [PMID: 22108260 DOI: 10.1016/j.mod.2011.11.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2011] [Revised: 10/01/2011] [Accepted: 11/07/2011] [Indexed: 10/15/2022]
Abstract
In mouse Otx2 plays essential roles in anterior-posterior axis formation and head development in anterior visceral endoderm and anterior mesendoderm. The Otx2 expression in these sites is regulated by VE and CM enhancers at the 5' proximal to the translation start site, and we proposed that these enhancers would have been established in ancestral sarcoptergians after divergence from actinopterigians for the use of Otx2 as the head organizer gene (Kurokawa et al., 2010). This would make doubtful an earlier proposal of ours that a 1.1 kb fragment located at +14.4 to +15.5 kb 3' (3'En) of fugu Otx2a gene harbors enhancers phylogenetically and functionally homologous to mouse VE and CM enhancers (Kimura-Yoshida et al., 2007). In the present study, we demonstrate that fugu Otx2a is not expressed in the dorsal margin of blastoderm, shield and early anterior mesendoderm, and that the fugu Otx2a 3'En do not exhibit activities at these sites of fugu embryos. We conclude that the fugu Otx2a 3'En does not harbor an organizer enhancer, but encodes an enhancer for the expression in later anterior mesendodermal tissues. Instead, in fugu embryos Otx2b is expressed in the dorsal margin of blastoderm at blastula stage and shield at 50% epiboly, and this expression is directed by an enhancer, 5'En, located at -1000 to -800 bp, which is uniquely conserved among teleost Otx2b orthologues.
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Affiliation(s)
- Daisuke Kurokawa
- Laboratory for Vertebrate Body Plan, Center for Developmental Biology, RIKEN Kobe, 2-2-1 Minatojima Minami-machi, Chuo-ku, Kobe 650-0047, Japan
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21
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Emerson MM, Cepko CL. Identification of a retina-specific Otx2 enhancer element active in immature developing photoreceptors. Dev Biol 2011; 360:241-55. [PMID: 21963459 DOI: 10.1016/j.ydbio.2011.09.012] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2011] [Revised: 09/09/2011] [Accepted: 09/13/2011] [Indexed: 01/20/2023]
Abstract
The homeodomain protein, Otx2, is a critical regulator of vertebrate photoreceptor genesis. However, the genetic elements that define the expression of Otx2 during photoreceptor development are unknown. Therefore, we sought to identify an Otx2 enhancer element that functions in photoreceptor development in order to better understand this specification event. Using the technique of electroporation, we tested a number of evolutionarily conserved elements (ECRs) for expression in the developing retina, and identified ECR2 as having robust activity in the retina. We have characterized this element using a number of assays, including Cre-fate mapping experiments. We found that ECR2 recapitulates expression/function of Otx2 primarily in newly postmitotic photoreceptor cells (PRs), as well as in a subset of retinal progenitor cells (RPCs). ECR2 was also found to be expressed in a subset of horizontal cells (HCs), in keeping with the role of Otx2 in HC development. Furthermore, we determined that the ECR2 element is not active in other Otx2-positive cells such as retinal bipolar cells (BPs), retinal pigmented epithelium (RPE), or the tectum, suggesting that the transcriptional networks controlling Otx2 expression in these cells are unique from those of developing PRs and HCs. These results reveal a distinct molecular state in dividing retinal cells and their newly postmitotic progeny, and provide genetic access to an early and critical transcriptional node involved in the genesis of vertebrate PRs.
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Affiliation(s)
- Mark M Emerson
- Department of Genetics, Department of Ophthamology, Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA.
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22
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Paganelli A, Gnazzo V, Acosta H, López SL, Carrasco AE. Glyphosate-based herbicides produce teratogenic effects on vertebrates by impairing retinoic acid signaling. Chem Res Toxicol 2010; 23:1586-95. [PMID: 20695457 DOI: 10.1021/tx1001749] [Citation(s) in RCA: 161] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
The broad spectrum herbicide glyphosate is widely used in agriculture worldwide. There has been ongoing controversy regarding the possible adverse effects of glyphosate on the environment and on human health. Reports of neural defects and craniofacial malformations from regions where glyphosate-based herbicides (GBH) are used led us to undertake an embryological approach to explore the effects of low doses of glyphosate in development. Xenopus laevis embryos were incubated with 1/5000 dilutions of a commercial GBH. The treated embryos were highly abnormal with marked alterations in cephalic and neural crest development and shortening of the anterior-posterior (A-P) axis. Alterations on neural crest markers were later correlated with deformities in the cranial cartilages at tadpole stages. Embryos injected with pure glyphosate showed very similar phenotypes. Moreover, GBH produced similar effects in chicken embryos, showing a gradual loss of rhombomere domains, reduction of the optic vesicles, and microcephaly. This suggests that glyphosate itself was responsible for the phenotypes observed, rather than a surfactant or other component of the commercial formulation. A reporter gene assay revealed that GBH treatment increased endogenous retinoic acid (RA) activity in Xenopus embryos and cotreatment with a RA antagonist rescued the teratogenic effects of the GBH. Therefore, we conclude that the phenotypes produced by GBH are mainly a consequence of the increase of endogenous retinoid activity. This is consistent with the decrease of Sonic hedgehog (Shh) signaling from the embryonic dorsal midline, with the inhibition of otx2 expression and with the disruption of cephalic neural crest development. The direct effect of glyphosate on early mechanisms of morphogenesis in vertebrate embryos opens concerns about the clinical findings from human offspring in populations exposed to GBH in agricultural fields.
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Affiliation(s)
- Alejandra Paganelli
- Laboratorio de Embriología Molecular, CONICET-UBA, Facultad de Medicina, Universidad de Buenos Aires, Paraguay 2155, 3° Piso 1121, Ciudad Autónoma de Buenos Aires, Argentina
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23
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Sakurai Y, Kurokawa D, Kiyonari H, Kajikawa E, Suda Y, Aizawa S. Otx2 and Otx1 protect diencephalon and mesencephalon from caudalization into metencephalon during early brain regionalization. Dev Biol 2010; 347:392-403. [PMID: 20816794 DOI: 10.1016/j.ydbio.2010.08.028] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2010] [Revised: 08/24/2010] [Accepted: 08/25/2010] [Indexed: 10/19/2022]
Abstract
Otx2 is expressed in each step and site of head development. To dissect each Otx2 function we have identified a series of Otx2 enhancers. The Otx2 expression in the anterior neuroectoderm is regulated by the AN enhancer and the subsequent expression in forebrain and midbrain later than E8.5 by FM1 and FM2 enhancers; the Otx1 expression takes place at E8.0. In telencephalon later than E9.5 Otx1 continues to be expressed in the entire pallium, while the Otx2 expression is confined to the most medial pallium. To determine the Otx functions in forebrain and midbrain development we have generated mouse mutants that lack both FM1 and FM2 enhancers (DKO: Otx2(ΔFM1ΔFM2/ΔFM1ΔFM2)) and examined the TKO (Otx1(-/-)Otx2(ΔFM1ΔFM2/ΔFM1ΔFM2)) phenotype. The mutants develop normally until E8.0, but subsequently by E9.5 the diencephalon, including thalamic eminence and prethalamus, and the mesencephalon are caudalized into metencephalon consisting of isthmus and rhombomere 1; the caudalization does not extend to rhombomere 2 and more caudal rhombomeres. In rostral forebrain, neopallium, ganglionic eminences and hypothalamus in front of prethalamus develop; we propose that they become insensitive to the caudalization with the switch from the Otx2 expression under the AN enhancer to that under FM1 and FM2 enhancers. In contrast, the medial pallium requires Otx1 and Otx2 for its development later than E9.5, and the Otx2 expression in diencepalon and mesencephalon later than E9.5 is also directed by an enhancer other than FM1 and FM2 enhancers.
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Affiliation(s)
- Yusuke Sakurai
- Laboratory for Vertebrate Body Plan, Center for Developmental Biology, RIKEN Kobe, 2-2-3 Minatojima Minamimachi, Chuo-ku, Kobe 650-0047, Japan
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24
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Minoux M, Rijli FM. Molecular mechanisms of cranial neural crest cell migration and patterning in craniofacial development. Development 2010; 137:2605-21. [DOI: 10.1242/dev.040048] [Citation(s) in RCA: 329] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
During vertebrate craniofacial development, neural crest cells (NCCs) contribute much of the cartilage, bone and connective tissue that make up the developing head. Although the initial patterns of NCC segmentation and migration are conserved between species, the variety of vertebrate facial morphologies that exist indicates that a complex interplay occurs between intrinsic genetic NCC programs and extrinsic environmental signals during morphogenesis. Here, we review recent work that has begun to shed light on the molecular mechanisms that govern the spatiotemporal patterning of NCC-derived skeletal structures – advances that are central to understanding craniofacial development and its evolution.
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Affiliation(s)
- Maryline Minoux
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
- Faculté de Chirurgie Dentaire, 1, Place de l'Hôpital, 67000 Strasbourg, France
| | - Filippo M. Rijli
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
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25
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Sato S, Ikeda K, Shioi G, Ochi H, Ogino H, Yajima H, Kawakami K. Conserved expression of mouse Six1 in the pre-placodal region (PPR) and identification of an enhancer for the rostral PPR. Dev Biol 2010; 344:158-71. [PMID: 20471971 DOI: 10.1016/j.ydbio.2010.04.029] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2010] [Revised: 04/24/2010] [Accepted: 04/26/2010] [Indexed: 10/19/2022]
Abstract
All cranial sensory organs and sensory neurons of vertebrates develop from cranial placodes. In chick, amphibians and zebrafish, all placodes originate from a common precursor domain, the pre-placodal region (PPR), marked by the expression of Six1/4 and Eya1/2. However, the PPR has never been described in mammals and the mechanism involved in the formation of PPR is poorly defined. Here, we report the expression of Six1 in the horseshoe-shaped mouse ectoderm surrounding the anterior neural plate in a pattern broadly similar to that of non-mammalian vertebrates. To elucidate the identity of Six1-positive mouse ectoderm, we searched for enhancers responsible for Six1 expression by in vivo enhancer assays. One conserved non-coding sequence, Six1-14, showed specific enhancer activity in the rostral PPR of chick and Xenopus and in the mouse ectoderm. These results strongly suggest the presence of PPR in mouse and that it is conserved in vertebrates. Moreover, we show the importance of the homeodomain protein-binding sites of Six1-14, the Six1 rostral PPR enhancer, for enhancer activity, and that Dlx5, Msx1 and Pax7 are candidate binding factors that regulate the level and area of Six1 expression, and thereby the location of the PPR. Our findings provide critical information and tools to elucidate the molecular mechanism of early sensory development and have implications for the development of sensory precursor/stem cells.
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Affiliation(s)
- Shigeru Sato
- Division of Biology, Center for Molecular Medicine, Jichi Medical University, 3311-1 Yakushiji, Shimotsuke, Tochigi 329-0498, Japan.
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Kurokawa D, Ohmura T, Ogino H, Takeuchi M, Inoue A, Inoue F, Suda Y, Aizawa S. Evolutionary origin of the Otx2 enhancer for its expression in visceral endoderm. Dev Biol 2010; 342:110-20. [PMID: 20353765 DOI: 10.1016/j.ydbio.2010.03.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2009] [Revised: 03/15/2010] [Accepted: 03/16/2010] [Indexed: 11/27/2022]
Abstract
In the mouse, the Otx2 gene has been shown to play essential roles in the visceral endoderm during anterior-posterior axis formation and head induction. While these are primary processes in vertebrate embryogenesis, the visceral endoderm is a tissue unique to mammals. Two enhancers (VE and CM) have been previously found to direct Otx2 expression during early embryogenesis. This study demonstrates that in anterior visceral endoderm the CM enhancer does not have an activity by itself, but enhances the activity of the VE enhancer. These two enhancers also cooperate for the activities in anterior mesendoderm and cephalic mesenchyme. Comparative studies suggest that VE enhancer function was most likely established before the divergence of sarcopterygians into Actinistia, Dipnoi and tetrapods, while the nucleotide sequence corresponding to the VE enhancer was already present in the last common ancestor of bony fishes. The CM enhancer sequence and function would have been also established in ancestral sarcopterygians. The VE/CM enhancers and their gene cascades in the ancestral sarcopterygian head organizer would then have been co-opted by amphibian deep endoderm cells and mammalian visceral endoderm cells for the head development.
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Affiliation(s)
- Daisuke Kurokawa
- Laboratory for Vertebrate Body Plan, Center for Developmental Biology, RIKEN Kobe, 2-2-3 Minatojima Minamimachi, Chuou-ku, Kobe 650-0047, Japan
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Non-homeodomain regions of Hox proteins mediate activation versus repression of Six2 via a single enhancer site in vivo. Dev Biol 2009; 335:156-65. [PMID: 19716816 DOI: 10.1016/j.ydbio.2009.08.020] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2009] [Revised: 08/19/2009] [Accepted: 08/21/2009] [Indexed: 10/20/2022]
Abstract
Hox genes control many developmental events along the AP axis, but few target genes have been identified. Whether target genes are activated or repressed, what enhancer elements are required for regulation, and how different domains of the Hox proteins contribute to regulatory specificity are poorly understood. Six2 is genetically downstream of both the Hox11 paralogous genes in the developing mammalian kidney and Hoxa2 in branchial arch and facial mesenchyme. Loss-of-function of Hox11 leads to loss of Six2 expression and loss-of-function of Hoxa2 leads to expanded Six2 expression. Herein we demonstrate that a single enhancer site upstream of the Six2 coding sequence is responsible for both activation by Hox11 proteins in the kidney and repression by Hoxa2 in the branchial arch and facial mesenchyme in vivo. DNA-binding activity is required for both activation and repression, but differential activity is not controlled by differences in the homeodomains. Rather, protein domains N- and C-terminal to the homeodomain confer activation versus repression activity. These data support a model in which the DNA-binding specificity of Hox proteins in vivo may be similar, consistent with accumulated in vitro data, and that unique functions result mainly from differential interactions mediated by non-homeodomain regions of Hox proteins.
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Hall BK. Evolutionary Origins of the Neural Crest and Neural Crest Cells. Evol Biol 2008. [DOI: 10.1007/s11692-008-9033-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Suda Y, Kurokawa D, Takeuchi M, Kajikawa E, Kuratani S, Amemiya C, Aizawa S. Evolution of Otx paralogue usages in early patterning of the vertebrate head. Dev Biol 2008; 325:282-95. [PMID: 18848537 DOI: 10.1016/j.ydbio.2008.09.018] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2008] [Revised: 09/10/2008] [Accepted: 09/12/2008] [Indexed: 11/17/2022]
Abstract
To assess evolutional changes in the expression pattern of Otx paralogues, expression analyses were undertaken in fugu, bichir, skate and lamprey. Together with those in model vertebrates, the comparison suggested that a gnathostome ancestor would have utilized all of Otx1, Otx2 and Otx5 paralogues in organizer and anterior mesendoderm for head development. In this animal, Otx1 and Otx2 would have also functioned in specification of the anterior neuroectoderm at presomite stage and subsequent development of forebrain/midbrain at somite stage, while Otx5 expression would have already been specialized in epiphysis and eyes. Otx1 and Otx2 functions in anterior neuroectoderm and brain of the gnathostome ancestor would have been differentially maintained by Otx1 in a basal actinopterygian and by Otx2 in a basal sarcopterygian. Otx5 expression in head organizer and anterior mesendoderm seems to have been lost in the teleost lineage after divergence of bichir, and also from the amniotes after divergence of amphibians as independent events. Otx1 expression was lost from the organizer in the tetrapod lineage. In contrast, in a teleost ancestor prior to whole genome duplication, Otx1 and Otx2 would have both been expressed in the dorsal margin of blastoderm, embryonic shield, anterior mesendoderm, anterior neuroectoderm and forebrain/midbrain, at respective stages of head development. Subsequent whole genome duplication and the following genome changes would have caused different Otx paralogue usages in each teleost lineage. Lampreys also have three Otx paralogues; their sequences are highly diverged from gnathostome cognates, but their expression pattern is well related to those of skate Otx cognates.
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Affiliation(s)
- Yoko Suda
- Laboratory for Vertebrate Body Plan, Center for Developmental Biology, RIKEN Kobe, Chuo-ku, Kobe 650-0047, Japan
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Abstract
The transcription factor Yin Yang 1 (YY1) is a multifunctional protein that can activate or repress gene expression depending on the cellular context. YY1 is ubiquitously expressed and highly conserved between species. However, its role varies in diverse cell types and includes proliferation, differentiation, and apoptosis. This review will focus on the function of YY1 in the nervous system including its role in neural development, neuronal function, developmental myelination, and neurological disease. The multiple functions of YY1 in distinct cell types are reviewed and the possible mechanisms underlying the cell specificity for these functions are discussed.
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Affiliation(s)
- Ye He
- Department of Neuroscience and Cell Biology, Robert Wood Johnson Medical School, University of Medicine and Dentistry of New Jersey, Piscataway, New Jersey, USA.
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31
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Beaster-Jones L, Schubert M, Holland LZ. Cis-regulation of the amphioxus engrailed gene: Insights into evolution of a muscle-specific enhancer. Mech Dev 2007; 124:532-42. [PMID: 17624741 DOI: 10.1016/j.mod.2007.06.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2006] [Revised: 06/04/2007] [Accepted: 06/05/2007] [Indexed: 11/24/2022]
Abstract
To gain insights into the relation between evolution of cis-regulatory DNA and evolution of gene function, we identified tissue-specific enhancers of the engrailed gene of the basal chordate amphioxus (Branchiostoma floridae) and compared their ability to direct expression in both amphioxus and its nearest chordate relative, the tunicate Ciona intestinalis. In amphioxus embryos, the native engrailed gene is expressed in three domains - the eight most anterior somites, a few cells in the central nervous system (CNS) and a few ectodermal cells. In contrast, in C. intestinalis, in which muscle development is highly divergent, engrailed expression is limited to the CNS. To characterize the tissue-specific enhancers of amphioxus engrailed, we first showed that 7.8kb of upstream DNA of amphioxus engrailed directs expression to all three domains in amphioxus that express the native gene. We then identified the amphioxus engrailed muscle-specific enhancer as the 1.2kb region of upstream DNA with the highest sequence identity to the mouse en-2 jaw muscle enhancer. This amphioxus enhancer directed expression to both the somites in amphioxus and to the larval muscles in C. intestinalis. These results show that even though expression of the native engrailed has apparently been lost in developing C. intestinalis muscles, they express the transcription factors necessary to activate transcription from the amphioxus engrailed enhancer, suggesting that gene networks may not be completely disrupted if an individual component is lost.
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Affiliation(s)
- Laura Beaster-Jones
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA 92093-0202, USA
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Furushima K, Yamamoto A, Nagano T, Shibata M, Miyachi H, Abe T, Ohshima N, Kiyonari H, Aizawa S. Mouse homologues of Shisa antagonistic to Wnt and Fgf signalings. Dev Biol 2007; 306:480-92. [PMID: 17481602 DOI: 10.1016/j.ydbio.2007.03.028] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2006] [Revised: 03/12/2007] [Accepted: 03/19/2007] [Indexed: 12/28/2022]
Abstract
In an effort to identify Otx2 targets in mouse anterior neuroectoderm we identified a gene, mShisa, which is homologous to xShisa1 that we previously reported as a head inducer in Xenopus. mShisa encodes an antagonist against both Wnt and Fgf signalings; it inhibits these signalings cell-autonomously as xShisa1 does. The mShisa expression is lost or greatly reduced in Otx2 mutant visceral endoderm, anterior mesendoderm and anterior neuroectoderm. However, mShisa mutants exhibited no defects in head development. Shisa is composed of five subfamilies, but normal head development in mShisa mutants is unlikely to be explained in terms of the compensation of mShisa deficiency by its paralogues or by known Wnt antagonists in anterior visceral endoderm and/or anterior mesendoderm.
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Affiliation(s)
- Kenryo Furushima
- Laboratory for Animal Resources and Genetic Engineering, Center for Developmental Biology (CDB), RIKEN Kobe, 2-2-3 Minatojima Minami, Chuo-ku, Kobe 650-0047, Japan
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A new method to transfect the hypoblast of the chick embryo reveals conservation of the regulation of an Otx2 enhancer between mouse and chick extraembryonic endoderm. BMC DEVELOPMENTAL BIOLOGY 2007; 7:25. [PMID: 17407554 PMCID: PMC1852305 DOI: 10.1186/1471-213x-7-25] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2006] [Accepted: 04/02/2007] [Indexed: 11/26/2022]
Abstract
Background The mouse anterior visceral endoderm (AVE) and the chick hypoblast are thought to have homologous roles in the early stages of neural induction and primitive streak formation. In mouse, many regulatory elements directing gene expression to the AVE have been identified. However, there is no technique to introduce DNA into the chick hypoblast that would enable a comparison of their activity and this has hampered a direct comparison of the regulation of gene expression in the mouse and chick extraembryonic endoderm. Results Here we describe a new method to introduce DNA into the chick hypoblast, using lipofectamine-mediated transfection. We show that the hypoblast can be easily transfected and that it starts to express a luciferase reporter within 2 hours of transfection. The validity of technique is tested by following the movement and fate of hypoblast cells, which reveals their translocation to the anterior germinal crescent. We then introduce a vector containing GFP driven by the mouse VEcis-Otx2 enhancer (which directs gene expression to the mouse AVE) and we detect activity in the hypoblast. Conclusion The new technique for delivering expression constructs to the chick hypoblast will enable studies on gene activity and regulation to be performed in this tissue, which has proved difficult to transfect by electroporation. Our findings also reveal that regulatory elements that direct gene expression to the mouse AVE are active in chick hypoblast, supporting the idea that these two tissues have homologous functions.
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Takasaki N, Kurokawa D, Nakayama R, Nakayama JI, Aizawa S. Acetylated YY1 regulates Otx2 expression in anterior neuroectoderm at two cis-sites 90 kb apart. EMBO J 2007; 26:1649-59. [PMID: 17332747 PMCID: PMC1829384 DOI: 10.1038/sj.emboj.7601619] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2006] [Accepted: 01/23/2007] [Indexed: 11/09/2022] Open
Abstract
The mouse homeobox gene Otx2 plays essential roles at each step and in every tissue during head development. We have previously identified a series of enhancers that are responsible for driving the Otx2 expression in these contexts. Among them the AN enhancer, existing 92 kb 5' upstream, directs Otx2 expression in anterior neuroectoderm (AN) at the headfold stage. Analysis of the enhancer mutant Otx2(DeltaAN/-) indicated that Otx2 expression under the control of this enhancer is essential to the development of AN. This study demonstrates that the AN enhancer is promoter-dependent and regulated by acetylated YY1. YY1 binds to both the AN enhancer and promoter region. YY1 is acetylated in the anterior head, and only acetylated YY1 can bind to the sequence in the enhancer. Moreover, YY1 binding to both of these two sites is essential to Otx2 expression in AN. These YY1 binding sites are highly conserved in AN enhancers in tetrapods, coelacanth and skate, suggesting that establishment of the YY1 regulation coincides with that of OTX2 function in AN development in an ancestral gnathostome.
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Affiliation(s)
- Nobuyoshi Takasaki
- Laboratory for Vertebrate Body Plan, Center for Developmental Biology (CDB), RIKEN Kobe, Chuo-ku, Kobe, Japan
| | - Daisuke Kurokawa
- Laboratory for Vertebrate Body Plan, Center for Developmental Biology (CDB), RIKEN Kobe, Chuo-ku, Kobe, Japan
| | - Rika Nakayama
- Laboratory for Animal Resources and Genetic Engineering, Center for Developmental Biology (CDB), RIKEN Kobe, Chuo-ku, Kobe, Japan
| | - Jun-ichi Nakayama
- Laboratory for Chromatin Dynamics, Center for Developmental Biology (CDB), RIKEN Kobe, Chuo-ku, Kobe, Japan
| | - Shinichi Aizawa
- Laboratory for Vertebrate Body Plan, Center for Developmental Biology (CDB), RIKEN Kobe, Chuo-ku, Kobe, Japan
- Laboratory for Animal Resources and Genetic Engineering, Center for Developmental Biology (CDB), RIKEN Kobe, Chuo-ku, Kobe, Japan
- Laboratory for Vertebrate Body Plan, RIKEN Kobe, 2-2-3, Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Japan. Tel.: +81783063149; Fax: +81783063148; E-mail:
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Shim S, Kim Y, Shin J, Kim J, Park S. Regulation of EphA8 gene expression by TALE homeobox transcription factors during development of the mesencephalon. Mol Cell Biol 2006; 27:1614-30. [PMID: 17178831 PMCID: PMC1820445 DOI: 10.1128/mcb.01429-06] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
The mouse ephA8 gene is expressed in a rostral-to-caudal gradient in the developing superior colliculus, and these EphA gradients may contribute to the proper development of the retinocollicular projection. Thus, it is of considerable interest to elucidate how the ephA8 gene expression is controlled by upstream regulators during the development of the mesencephalon. In this study, we employed in vivo expression analysis in transgenic mouse embryos to dissect the cis-acting DNA regulatory region, leading to the identification of a CGGTCA sequence critical for the ephA8 enhancer activity. Using this element as the target in a yeast one-hybrid system, we identified a Meis homeobox transcription factor. Significantly, DNA binding sites for Pbx, another TALE homeobox transcription factor, were also identified in the ephA8 enhancer region. Meis2 and Pbx1/2 are specifically expressed in the entire region of the dorsal mesencephalon, where specific colocalization of EphA8 and Meis is restricted to a subset of cells. Meis2 and Pbx2 synergistically bind the ephA8 regulatory sequence in vitro, and this interaction is critical for the transcriptional activation of a reporter construct bearing the ephA8 regulatory region in the presence of histone deacetylase inhibitor. More importantly, when expressed in the embryonic midbrain, the dominant-negative form of Meis down-regulates endogenous ephA8. Interestingly, we found that both Meis2 and Pbx2 are constitutively bound in the ephA8 regulatory region in the dorsal mesencephalon. These studies strongly suggest that Meis and Pbx homeobox transcription factors tightly associate with the ephA8 regulatory sequence and require an additional unidentified regulator to ensure the specific activation of ephA8.
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Affiliation(s)
- Sungbo Shim
- Department of Biological Science, Sookmyung Women's University, Chungpa-Dong 2-Ka, Yongsan-Ku, Seoul 140-742, South Korea
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36
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Kurokawa D, Sakurai Y, Inoue A, Nakayama R, Takasaki N, Suda Y, Miyake T, Amemiya CT, Aizawa S. Evolutionary constraint on Otx2 neuroectoderm enhancers-deep conservation from skate to mouse and unique divergence in teleost. Proc Natl Acad Sci U S A 2006; 103:19350-5. [PMID: 17159156 PMCID: PMC1748229 DOI: 10.1073/pnas.0604686103] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Otx2 is a paired type homeobox gene that plays essential roles in each step and site of head development in vertebrates. In the mouse, Otx2 expression in the anterior neuroectoderm is regulated primarily by two distinct enhancers: anterior neuroectoderm (AN) and forebrain/midbrain (FM) enhancers at 92 kb and 75 kb 5'of the Otx2 locus, respectively. The AN enhancer has activity in the entire anterior neuroectoderm at headfold and early somite stages, whereas the FM enhancer is subsequently active in the future caudal forebrain and midbrain ectoderm. In tetrapods, both AN and FM enhancers are conserved, whereas the AN region is missing in teleosts, despite overt Otx2 expression in the anterior neuroectoderm. Here, we show that zebrafish and fugu FM regions drive expression not only in the forebrain and midbrain but also in the anterior neuroectoderm at headfold stage. The analysis of coelacanth and skate genomic Otx2 orthologues suggests that the utilization of the two enhancers, AN and FM, is an ancestral condition. In contrast, the AN enhancer has been specifically lost in the teleost lineage with a compensatory establishment of AN activity within the FM enhancer. Furthermore, the AN activity in the fish FM enhancer was established by recruiting upstream factors different from those that direct the tetrapod AN enhancer, yet zebrafish FM enhancer is active in both mouse and zebrafish anterior neuroectoderm at the headfold stage.
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Affiliation(s)
| | | | - Ai Inoue
- *Laboratory for Vertebrate Body Plan and
| | - Rika Nakayama
- Animal Resource and Genetic Engineering, RIKEN Center for Developmental Biology, 2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Japan; and
| | | | - Yoko Suda
- *Laboratory for Vertebrate Body Plan and
| | - Tsutomu Miyake
- Molecular Genetics Program, Benaroya Research Institute at Virginia Mason, 1201 Ninth Avenue, Seattle, WA 98101
| | - Chris T. Amemiya
- Molecular Genetics Program, Benaroya Research Institute at Virginia Mason, 1201 Ninth Avenue, Seattle, WA 98101
| | - Shinichi Aizawa
- *Laboratory for Vertebrate Body Plan and
- Animal Resource and Genetic Engineering, RIKEN Center for Developmental Biology, 2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Japan; and
- To whom correspondence should be sent at the * address. E-mail:
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Abstract
Cichlids have undergone extensive evolutionary modifications of their feeding apparatus, making them an ideal model to study the factors that underlie craniofacial diversity. Recent studies have provided critical insights into the molecular mechanisms that have contributed to the origin and maintenance of cichlid trophic diversity. We review this body of work, which shows that the cichlid jaw is regulated by a few genes of major additive effect, and is composed of modules that have evolved under strong divergent selection. Adaptive variation in cichlid jaw shape is evident early in development and is associated with allelic variation in and expression of bmp4. Modulating this growth factor in the experimentally tractable zebrafish model reproduces natural variation in cichlid jaw shape, supporting a role for bmp4 in craniofacial evolution. These data demonstrate the utility of the cichlid jaw as a model for studying the genetic and developmental basis of evolutionary changes in craniofacial morphology.
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Affiliation(s)
- R C Albertson
- Department of Cytokine Biology, The Forsyth Institute, Boston, MA 02115, USA.
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38
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Gómez-Skarmeta JL, Lenhard B, Becker TS. New technologies, new findings, and new concepts in the study of vertebrate cis-regulatory sequences. Dev Dyn 2006; 235:870-85. [PMID: 16395688 DOI: 10.1002/dvdy.20659] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
All vertebrates share a similar early embryonic body plan and use the same regulatory genes for their development. The availability of numerous sequenced vertebrate genomes and significant advances in bioinformatics have resulted in the finding that the genomic regions of many of these developmental regulatory genes also contain highly conserved noncoding sequence. In silico discovery of conserved noncoding regions and of transcription factor binding sites as well as the development of methods for high throughput transgenesis in Xenopus and zebrafish are dramatically increasing the speed with which regulatory elements can be discovered, characterized, and tested in the context of whole live embryos. We review here some of the recent technological developments that will likely lead to a surge in research on how vertebrate genomes encode regulation of transcriptional activity, how regulatory sequences constrain genomic architecture, and ultimately how vertebrate form has evolved.
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Bagheri-Fam S, Barrionuevo F, Dohrmann U, Günther T, Schüle R, Kemler R, Mallo M, Kanzler B, Scherer G. Long-range upstream and downstream enhancers control distinct subsets of the complex spatiotemporal Sox9 expression pattern. Dev Biol 2006; 291:382-97. [PMID: 16458883 DOI: 10.1016/j.ydbio.2005.11.013] [Citation(s) in RCA: 125] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2005] [Revised: 11/09/2005] [Accepted: 08/29/2005] [Indexed: 11/20/2022]
Abstract
SOX9 is an evolutionary conserved transcription factor that is expressed in a variety of tissues, with essential functions in cartilage, testis, heart, glial cell, inner ear and neural crest development. By comparing human and pufferfish genomic sequences, we previously identified eight highly conserved sequence elements between 290 kb 5' and 450 kb 3' to human SOX9. In this study, we assayed the regulatory potential of elements E1 to E7 in transgenic mice using a lacZ reporter gene driven by a 529 bp minimal mouse Sox9 promoter. We found that three of these elements and the Sox9 promoter control distinct subsets of the tissue-specific expression pattern of Sox9. E3, located 251 kb 5' to SOX9, directs lacZ expression to cranial neural crest cells and to the inner ear. E1 is located 28 kb 5' to SOX9 and controls expression in the node, notochord, gut, bronchial epithelium and pancreas. Transgene expression in the neuroectoderm is mediated by E7, located 95 kb 3' to SOX9, which regulates expression in the telencephalon and midbrain, and by the Sox9 minimal promoter which controls expression in the ventral spinal cord and hindbrain. We show that E3-directed reporter gene expression in neural crest cells of the first but not of the second and third pharyngeal arch is dependent on beta-catenin, revealing a complex regulation of Sox9 in cranial neural crest cells. Moreover, we identify and discuss highly conserved transcription factor binding sites within enhancer E3 that are in good agreement with current models for neural crest and inner ear development. Finally, we identify enhancer E1 as a cis-regulatory element conserved between vertebrates and invertebrates, indicating that some cis-regulatory sequences that control developmental genes in vertebrates might be phylogenetically ancient.
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Affiliation(s)
- Stefan Bagheri-Fam
- Institute of Human Genetics and Anthropology, University of Freiburg, Breisacherstr. 33, D-79106 Freiburg, Germany
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Tsend-Ayush E, O'Sullivan LA, Grützner FS, Onnebo SMN, Lewis RS, Delbridge ML, Marshall Graves JA, Ward AC. RBMX gene is essential for brain development in zebrafish. Dev Dyn 2006; 234:682-8. [PMID: 15895365 DOI: 10.1002/dvdy.20432] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
The human RBMX gene was discovered recently through its homology to the spermatogenesis candidate gene RBMY. Its position on the human X chromosome suggests that it may be involved in X-linked mental retardation syndromes. However, to date there is scant information on the in vivo role of RBMX. To address this issue, we have isolated a zebrafish rbmx orthologue and characterized its embryonic expression pattern. Zebrafish rbmx is maternally expressed and then widely expressed in the embryo up to 24 hr postfertilization. In later stages of embryonic development, rbmx transcripts are localized predominantly in the brain, branchial arches, and liver primordium. The function of rbmx during embryonic development was examined by the use of an antisense morpholino targeting rbmx. The rbmx-morphants displayed an underdeveloped head and eyes, reduced body size, defective somite patterning, and absence of jaws. Furthermore, in the absence of functional rbmx, expression of specific markers for the fore- and hindbrain (otx2, krox20) was severely reduced. These studies demonstrate for the first time that rbmx is required for normal embryonic development, in particular of the brain, consistent with a role in X-linked mental retardation.
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Affiliation(s)
- Enkhjargal Tsend-Ayush
- Research School of Biological Sciences, Australian National University, Canberra, Australian Capital Territory, Australia.
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41
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Uemura O, Okada Y, Ando H, Guedj M, Higashijima SI, Shimazaki T, Chino N, Okano H, Okamoto H. Comparative functional genomics revealed conservation and diversification of three enhancers of the isl1 gene for motor and sensory neuron-specific expression. Dev Biol 2005; 278:587-606. [PMID: 15680372 DOI: 10.1016/j.ydbio.2004.11.031] [Citation(s) in RCA: 118] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2004] [Revised: 11/22/2004] [Accepted: 11/23/2004] [Indexed: 12/30/2022]
Abstract
Islet-1 (Isl1) is a member of the Isl1 family of LIM-homeodomain transcription factors (LIM-HD) that is expressed in a defined subset of motor and sensory neurons during vertebrate embryogenesis. To investigate how this specific expression of isl1 is regulated, we searched for enhancers of the isl1 gene that are conserved in vertebrate evolution. Initially, two enhancer elements, CREST1 and CREST2, were identified downstream of the isl1 locus in the genomes of fugu, chick, mouse, and human by BLAST searching for highly similar elements to those originally identified as motor and sensory neuron-specific enhancers in the zebrafish genome. The combined action of these elements is sufficient for completely recapitulating the subtype-specific expression of the isl1 gene in motor neurons of the mouse spinal cord. Furthermore, by direct comparison of the upstream flanking regions of the zebrafish and human isl1 genes, we identified another highly conserved noncoding element, CREST3, and subsequently C3R, a similar element to CREST3 with two CDP CR1 recognition motifs, in the upstream regions of all other isl1 family members. In mouse and human, CRESTs are located as far as more than 300 kb away from the isl1 locus, while they are much closer to the isl1 locus in zebrafish. Although all of zebrafish CREST2, CREST3, and C3R activate gene expression in the sensory neurons of zebrafish, CREST2 of mouse and human does not have the sequence necessary for sensory neuron-specific expression. Our results revealed both a remarkable conservation of the regulatory elements regulating subtype-specific gene expression in motor and sensory neurons and the dynamic process of reorganization of these elements whereby each element increases the level of cell-type specificity by losing redundant functions with the other elements during vertebrate evolution.
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Affiliation(s)
- Osamu Uemura
- Laboratory for Developmental Gene Regulation, Brain Science Institute, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
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Venkatesh B, Yap WH. Comparative genomics using fugu: a tool for the identification of conserved vertebrate cis-regulatory elements. Bioessays 2005; 27:100-7. [PMID: 15612032 DOI: 10.1002/bies.20134] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
With the imminent completion of the whole genome sequence of humans, increasing attention is being focused on the annotation of cis-regulatory elements in the human genome. Comparative genomics approaches based on evolutionary conservation have proved useful in the detection of conserved cis-regulatory elements. The pufferfish, Fugu rubripes, is an attractive vertebrate model for comparative genomics, by virtue of its compact genome and maximal phylogenetic distance from mammals. Fugu has lost a large proportion of nonessential DNA, and retained single orthologs for many duplicate genes that arose in the fish lineage. Non-coding sequences conserved between fugu and mammals have been shown to be functional cis-regulatory elements. Thus, fugu is a model fish genome of choice for discovering evolutionarily conserved regulatory elements in the human genome. Such evolutionarily conserved elements are likely to be shared by all vertebrates, and related to regulatory interactions fundamental to all vertebrates. The functions of these conserved vertebrate elements can be rapidly assayed in mammalian cell lines or in transgenic systems such as zebrafish/medaka and Xenopus, followed by validation of crucial elements in transgenic rodents.
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Affiliation(s)
- Byrappa Venkatesh
- Institute of Molecular and Cell Biology, 61 Biopolis Drive, Singapore 138673.
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Stapleton T, Luchman A, Johnston J, Browder L, Brenner S, Venkatesh B, Jirik FR. Compact intergenic regions of the pufferfish genome facilitate isolation of gene promoters: characterization ofFugu3′-phosphoadenosine 5′-phosphosulfate synthase 2 (fPapss2) gene promoter function in transgenicXenopus. FEBS Lett 2003; 556:59-63. [PMID: 14706826 DOI: 10.1016/s0014-5793(03)01353-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
The highly compact nature of the pufferfish (Fugu rubripes) genome renders it a useful tool not only for annotating coding regions within vertebrate genomes, but also for the identification of sequences important to gene regulation. Indeed, owing to this compaction it will be feasible in many instances to initiate analyses using entire intergenic regions when mapping gene promoters; a strategy that is very rarely feasible with the expanded genomes of other species. Stemming from our interest in studying promoters expressed in chondrocytes, we selected for study the intergenic region upstream of Fugu 3'-phosphoadenosine 5'-phosphosulfate synthase 2, fPapss2, a gene required for the normal development of cartilage extracellular matrix. Functional characterization of the entire fPapss2 5' intergenic region was carried out by monitoring expression of the enhanced green fluorescent protein (EGFP) gene reporter in the developing cartilage of transgenic Xenopus laevis. By evaluating a series of 5' intergenic region deletions we defined a minimal fPapss2 sequence of approximately 300 bp that was essential for EGFP expression in tadpole cartilage. This functional analysis of an entire Fugu intergenic region, combined with the efficiency of Xenopus transgenesis, serves as a model for the rapid characterization of evolutionarily-conserved regulatory regions of other pufferfish genes.
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Affiliation(s)
- Tara Stapleton
- Department of Biochemistry and Molecular Biology, University of Calgary, 3330 Hospital Drive N.W., T2N 4N1, Calgary, AB, Canada
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Montpetit A, Wilson MD, Chevrette M, Koop BF, Sinnett D. Analysis of the conservation of synteny between Fugu and human chromosome 12. BMC Genomics 2003; 4:30. [PMID: 12877756 PMCID: PMC179898 DOI: 10.1186/1471-2164-4-30] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2003] [Accepted: 07/23/2003] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The pufferfish Fugu rubripes (Fugu) with its compact genome is increasingly recognized as an important vertebrate model for comparative genomic studies. In particular, large regions of conserved synteny between human and Fugu genomes indicate its utility to identify disease-causing genes. The human chromosome 12p12 is frequently deleted in various hematological malignancies and solid tumors, but the actual tumor suppressor gene remains unidentified. RESULTS We investigated approximately 200 kb of the genomic region surrounding the ETV6 locus in Fugu (fETV6) in order to find conserved functional features, such as genes or regulatory regions, that could give insight into the nature of the genes targeted by deletions in human cancer cells. Seven genes were identified near the fETV6 locus. We found that the synteny with human chromosome 12 was conserved, but extensive genomic rearrangements occurred between the Fugu and human ETV6 loci. CONCLUSION This comparative analysis led to the identification of previously uncharacterized genes in the human genome and some potentially important regulatory sequences as well. This is a good indication that the analysis of the compact Fugu genome will be valuable to identify functional features that have been conserved throughout the evolution of vertebrates.
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Affiliation(s)
- Alexandre Montpetit
- Division of Hematology-Oncology, Charles-Bruneau Cancer Center, Research Center, Sainte-Justine Hospital, 3175 Côte Ste-Catherine, Montreal, QC, H3T 1C5, Canada
- Department of Biochemistry, University of Montreal, Montreal, QC, Canada
| | - Michael D Wilson
- Centre for Biomedical Research, University of Victoria, Victoria, BC, V8W 2Y2, Canada
| | - Mario Chevrette
- The Research Institute of the McGill University Health Centre and Department of Surgery, McGill University, Montreal, QC, H3G 1A4, Canada
| | - Ben F Koop
- Centre for Biomedical Research, University of Victoria, Victoria, BC, V8W 2Y2, Canada
| | - Daniel Sinnett
- Division of Hematology-Oncology, Charles-Bruneau Cancer Center, Research Center, Sainte-Justine Hospital, 3175 Côte Ste-Catherine, Montreal, QC, H3T 1C5, Canada
- Department of Biochemistry, University of Montreal, Montreal, QC, Canada
- Department of Pediatrics, University of Montreal, Montreal, QC, Canada
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Oda-Ishii I, Saiga H. Genomic organization and promoter and transcription regulatory regions for the expression in the anterior brain (sensory vesicle) of Hroth, the otx homologue of the ascidian, Halocynthia roretzi. Dev Dyn 2003; 227:104-13. [PMID: 12701103 DOI: 10.1002/dvdy.10295] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Otx (otd in Drosophila) is a well-conserved homeobox gene throughout animal phylogeny and commonly expressed in the anterior part of the embryo. In embryos of the ascidian Halocynthia roretzi, Hroth, the otx homologue in this species, is expressed in the endoderm and the sensory vesicle, the anterior part of the larval ascidian central nervous system (CNS), which has been thought to be homologous to vertebrate forebrain and midbrain. The developmental expression pattern of Hroth is very similar to that of vertebrate counterparts, which leads to a possibility that a similar mechanism may exist in the patterning of the CNS between ascidians and vertebrates. To better understand the mechanism, we decided to undertake analysis of the transcriptional regulatory regions of Hroth. We isolated and determined the nucleotide sequence of the 11.4-kbp region upstream of the translation start site of Hroth. We found that Hroth transcripts are modified likely with spliced leader RNA; therefore, we could not determine the transcription start site. However, first, we identified three introns that are unknown with vertebrate otx genes. Second, we found two regions that are capable of functioning as a promoter through deletion analysis, one of which appeared to be an endogenous promoter of Hroth. We analyzed the 5' upstream region 5402-1473bp, the region between 1473 and 5402 base pairs upstream from the translation start site of Hroth, including the putative endogenous promoter. This region was capable of driving Hroth expression in the sensory vesicle lineage cells as well as some other lineages at the early tail bud stage. Deletion analysis of this region suggested that three regions, 1659-1650bp, 1628-1613bp, and 1542-1473bp are responsible for regulating Hroth expression in the sensory vesicle cells at the tail bud stage. Among these regions, no apparent sequence conservation was observed. The present study has revealed a complex organization of transcription regulatory regions for the ascidian otx.
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Affiliation(s)
- Izumi Oda-Ishii
- Department of Biological Sciences, Graduate School of Science, Tokyo Metropolitan University, Hachiohji, Tokyo, Japan
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Courtois V, Chatelain G, Han ZY, Le Novère N, Brun G, Lamonerie T. New Otx2 mRNA isoforms expressed in the mouse brain. J Neurochem 2003; 84:840-53. [PMID: 12562527 DOI: 10.1046/j.1471-4159.2003.01583.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The mouse Otx2 gene is essential throughout head and brain development, from anterior-posterior polarity determination and neuroectoderm induction to post-natal sensory organ maturation. These numerous activities must rely on a very finely tuned regulation of expression. In order to understand the molecular control of the Otx2 gene, we set out to isolate its promoter. During this quest, we identified three remote transcription start sites, two defining two new upstream exons and one mapping within the previously reported first exon. The three transcripts differed in their 5' non-coding region but encoded the same protein. The transcription start nucleotides of each mRNA species have been mapped by RNase protection assays and by an RNA circularization technique. We have demonstrated that they are all used and linked to functional promoters. In addition to leader versatility, we also detected alternative splicing within the coding sequence that gives rise to a new protein endowed with an 8 amino-acid insertion upstream of the homeodomain. Combined analysis of the relative abundance of Otx2 mRNA isoforms in representative tissues and in situ hybridization studies revealed distinct spatial and temporal, although partially overlapping, expression patterns of the mRNA isoforms. These findings provide new clues to a better understanding of the relationships between Otx2 gene architecture and its complex regulatory requirements.
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Gilligan P, Brenner S, Venkatesh B. Fugu and human sequence comparison identifies novel human genes and conserved non-coding sequences. Gene 2002; 294:35-44. [PMID: 12234665 DOI: 10.1016/s0378-1119(02)00793-x] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The compact genome of the pufferfish, Fugu rubripes, has been proposed as a 'reference' genome to aid in annotating and analysing the human genome. We have annotated and compared 85 kb of Fugu sequence containing 17 genes with its homologous loci in the human draft genome and identified three 'novel' human genes that were missed or incompletely predicted by the previous gene prediction methods. Two of the novel genes contain zinc finger domains and are designated ZNF366 and ZNF367. They map to human chromosomes 5q13.2 and 9q22.32, respectively. The third novel gene, designated C9orf21, maps to chromosome 9q22.32. This gene is unique to vertebrates, and the protein encoded by it does not contain any known domains. We could not find human homologs for two Fugu genes, a novel chemokine gene and a kinase gene. These genes are either specific to teleosts or lost in the human lineage. The Fugu-human comparison identified several conserved non-coding sequences in the promoter and intronic regions. These sequences, conserved during 450 million years of vertebrate evolution, are likely to be involved in gene regulation. The 85 kb Fugu locus is dispersed over four human loci, occupying about 1.5 Mb. Contiguity is conserved in the human genome between six out of 16 Fugu gene pairs. These contiguous chromosomal segments should share a common evolutionary history dating back to the common ancestor of mammals and teleosts. We propose contiguity as strong evidence to identify orthologous genes in distant organisms. This study confirms the utility of the Fugu as a supplementary tool to uncover and confirm novel genes and putative gene regulatory regions in the human genome.
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Affiliation(s)
- Patrick Gilligan
- Institute of Molecular and Cell Biology, 30 Medical Drive, 117609, Singapore
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Müller F, Blader P, Strähle U. Search for enhancers: teleost models in comparative genomic and transgenic analysis of cis regulatory elements. Bioessays 2002; 24:564-72. [PMID: 12111739 DOI: 10.1002/bies.10096] [Citation(s) in RCA: 73] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Homology searches between DNA sequences of evolutionary distant species (phylogenetic footprinting) offer a fast detection method for regulatory sequences. Because of the small size of their genomes, tetraodontid species such as the Japanese pufferfish and green spotted pufferfish have become attractive models for comparative genomics. A disadvantage of the tetraodontid species is, however, that they cannot be bred and manipulated routinely under laboratory conditions, so these species are less attractive for developmental and genetic analysis. In contrast, an increasing arsenal of transgene techniques with the developmental model species zebrafish and medaka are being used for functional analysis of cis regulatory sequences. The main disadvantage is the much larger genome. While comparison between many loci proved the suitability of phylogenetic footprinting using fish and mammalian sequences, fast rate of change in enhancer structure and gene duplication within teleosts may obscure detection of homologies. Here we discuss the contribution and potentials provided by different teleost models for the detection and functional analysis of conserved cis-regulatory elements.
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Affiliation(s)
- Ferenc Müller
- Institute of Toxicology and Genetics, Research Center Karlsruhe, Germany.
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Brenner S, Venkatesh B, Yap WH, Chou CF, Tay A, Ponniah S, Wang Y, Tan YH. Conserved regulation of the lymphocyte-specific expression of lck in the Fugu and mammals. Proc Natl Acad Sci U S A 2002; 99:2936-41. [PMID: 11867707 PMCID: PMC122451 DOI: 10.1073/pnas.032680599] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The lck gene encodes a lymphocyte-specific protein-tyrosine kinase that is implicated in T cell maturation and signaling. In mammals, the transcription of the lck gene is regulated by two independent promoters, the proximal promoter, which is active in thymocytes, and the distal promoter, which dominates in mature T cells. In the human and mouse lck gene loci, the two promoter elements are separated by at least 40 kb and 10 kb, respectively. In this study, we have cloned and sequenced 60 kb from the pufferfish (Fugu rubripes) lck locus. The promoter region of the Fugu lck spans only 4.2 kb and contains a proximal and a distal promoter in the 2.3-kb region adjacent to the coding sequence. By generating transgenic mice, we have demonstrated that the compact promoter of the Fugu lck contains regulatory elements that direct expression to lymphoid organs of mice. We were able to localize the regulatory elements to a short region of 830 bp without losing specificity to cultured human T cell line. These results show that the basic mechanisms that mediate lymphocyte-specific expression are conserved between teleosts and mammals. The short promoter of the Fugu lck isolated by us offers a powerful tool for labeling T cells, targeting expression, and manipulating T cell activity in fishes as well as in mammals.
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Affiliation(s)
- Sydney Brenner
- Institute of Molecular and Cell Biology, 30 Medical Drive, Singapore 117609, USA
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Degenhardt K, Rentschler S, Fishman G, Sassoon DA. Cellular and cis-regulation of En-2 expression in the mandibular arch. Mech Dev 2002; 111:125-36. [PMID: 11804784 DOI: 10.1016/s0925-4773(01)00618-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Investigations into early muscle development have focused primarily on somite derived cells. Cranial mesoderm does not undergo somitogenesis, and muscle formation in this region is less well understood. In the present study, we have focused upon the expression of engrailed in mandibular arch myoblasts. We demonstrate that En-2 is expressed in mandibular arch myoblasts of the mouse. The activity of the En-2 enhancer is maintained in several functionally related muscles that arise from the first arch. Through the use of reporter transgenics, we demonstrate that local cell-cell interactions are important in maintaining En-2 expression in the mandibular arch cells. En-2 enhancer activity in the first arch requires a combination of cis-acting sequences that includes a motif which is identical to one found in the Otx2 enhancer and which is sufficient to direct expression in the first arch. These data support the notion that cranial muscle development is regulated by local cell-cell interactions which distinguish distinct anatomical and functional muscle groups.
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Affiliation(s)
- Karl Degenhardt
- Department of Biochemistry and Molecular Biology, Mount Sinai School of Medicine, 1 G. Levy Place, New York, NY 10029, USA
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