1
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Yan Y, Wang Q. BMP Signaling: Lighting up the Way for Embryonic Dorsoventral Patterning. Front Cell Dev Biol 2022; 9:799772. [PMID: 35036406 PMCID: PMC8753366 DOI: 10.3389/fcell.2021.799772] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 12/06/2021] [Indexed: 11/13/2022] Open
Abstract
One of the most significant events during early embryonic development is the establishment of a basic embryonic body plan, which is defined by anteroposterior, dorsoventral (DV), and left-right axes. It is well-known that the morphogen gradient created by BMP signaling activity is crucial for DV axis patterning across a diverse set of vertebrates. The regulation of BMP signaling during DV patterning has been strongly conserved across evolution. This is a remarkable regulatory and evolutionary feat, as the BMP gradient has been maintained despite the tremendous variation in embryonic size and shape across species. Interestingly, the embryonic DV axis exhibits robust stability, even in face of variations in BMP signaling. Multiple lines of genetic, molecular, and embryological evidence have suggested that numerous BMP signaling components and their attendant regulators act in concert to shape the developing DV axis. In this review, we summarize the current knowledge of the function and regulation of BMP signaling in DV patterning. Throughout, we focus specifically on popular model animals, such as Xenopus and zebrafish, highlighting the similarities and differences of the regulatory networks between species. We also review recent advances regarding the molecular nature of DV patterning, including the initiation of the DV axis, the formation of the BMP gradient, and the regulatory molecular mechanisms behind BMP signaling during the establishment of the DV axis. Collectively, this review will help clarify our current understanding of the molecular nature of DV axis formation.
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Affiliation(s)
- Yifang Yan
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China.,National Clinical Research Center for Obstetrics and Gynecology (Peking University Third Hospital), Beijing, China.,Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing, China.,Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, China
| | - Qiang Wang
- State Key Laboratory of Membrane Biology, CAS Center for Excellence in Molecular Cell Science, Institute of Zoology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China.,Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
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2
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Itoh K, Ossipova O, Sokol SY. Pinhead antagonizes Admp to promote notochord formation. iScience 2021; 24:102520. [PMID: 34142034 PMCID: PMC8188501 DOI: 10.1016/j.isci.2021.102520] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 03/18/2021] [Accepted: 05/05/2021] [Indexed: 12/05/2022] Open
Abstract
Dorsoventral patterning of a vertebrate embryo critically depends on the activity of Smad1 that mediates signaling by BMP proteins, anti-dorsalizing morphogenetic protein (Admp), and their antagonists. Pinhead (Pnhd), a cystine-knot-containing secreted protein, is expressed in the ventrolateral mesoderm during Xenopus gastrulation; however, its molecular targets and signaling mechanisms have not been fully elucidated. Our mass spectrometry-based screen of the gastrula secretome identified Admp as Pnhd-associated protein. We show that Pnhd binds Admp and inhibits its ventralizing activity by reducing Smad1 phosphorylation and its transcriptional targets. Importantly, Pnhd depletion further increased phospho-Smad1 levels in the presence of Admp. Furthermore, Pnhd synergized with Chordin and a truncated BMP4 receptor in the induction of notochord markers in ectoderm cells, and Pnhd-depleted embryos displayed notochord defects. Our findings suggest that Pnhd binds and inactivates Admp to promote notochord development. We propose that the interaction between Admp and Pnhd refines Smad1 activity gradients during vertebrate gastrulation.
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Affiliation(s)
- Keiji Itoh
- Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Olga Ossipova
- Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Sergei Y. Sokol
- Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, USA
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3
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Ossipova O, Itoh K, Radu A, Ezan J, Sokol SY. Pinhead signaling regulates mesoderm heterogeneity via the FGF receptor-dependent pathway. Development 2020; 147:dev.188094. [PMID: 32859582 DOI: 10.1242/dev.188094] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 08/04/2020] [Indexed: 12/29/2022]
Abstract
Among the three embryonic germ layers, the mesoderm plays a central role in the establishment of the vertebrate body plan. The mesoderm is specified by secreted signaling proteins from the FGF, Nodal, BMP and Wnt families. No new classes of extracellular mesoderm-inducing factors have been identified in more than two decades. Here, we show that the pinhead (pnhd) gene encodes a secreted protein that is essential for the activation of a subset of mesodermal markers in the Xenopus embryo. RNA sequencing revealed that many transcriptional targets of Pnhd are shared with those of the FGF pathway. Pnhd activity was accompanied by Erk phosphorylation and required FGF and Nodal but not Wnt signaling. We propose that during gastrulation Pnhd acts in the marginal zone to contribute to mesoderm heterogeneity via an FGF receptor-dependent positive feedback mechanism.
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Affiliation(s)
- Olga Ossipova
- Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Keiji Itoh
- Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Aurelian Radu
- Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jerome Ezan
- Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Sergei Y Sokol
- Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
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4
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Sepe RM, Ghiron JHL, Zucchetti I, Caputi L, Tarallo R, Crocetta F, De Santis R, D'Aniello S, Sordino P. The EJC component Magoh in non-vertebrate chordates. Dev Genes Evol 2020; 230:295-304. [PMID: 32632492 DOI: 10.1007/s00427-020-00664-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 07/01/2020] [Indexed: 11/26/2022]
Abstract
Earliest craniates possess a newly enlarged, elaborated forebrain with new cell types and neuronal networks. A key question in vertebrate evolution is when and how this cerebral expansion took place. The exon-junction complex (EJC) plays an essential role in mRNA processing of all Eukarya. Recently, it has been proposed that the EJC represses recursive RNA splicing in Deuterostomes, with implication in human brain diseases like microcephaly and depression. However, the EJC or EJC subunit contribution to brain development in non-vertebrate Deuterostomes remained unknown. Being interested in the evolution of chordate characters, we focused on the model species, Branchiostoma lanceolatum (Cephalochordata) and Ciona robusta (Tunicata), with the aim to investigate the ancestral and the derived expression state of Magoh orthologous genes. This study identifies that Magoh is part of a conserved syntenic group exclusively in vertebrates and suggests that Magoh has experienced duplication and loss events in mammals. During early development in amphioxus and ascidian, maternal contribution and zygotic expression of Magoh genes in various types of progenitor cells and tissues are consistent with the condition observed in other Bilateria. Later in development, we also show expression of Magoh in the brain of cephalochordate and ascidian larvae. Collectively, these results provide a basis to further define what functional role(s) Magoh exerted during nervous system development and evolution.
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Affiliation(s)
- Rosa Maria Sepe
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn Napoli, 80121, Naples, Italy
| | - Jung Hee Levialdi Ghiron
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn Napoli, 80121, Naples, Italy
| | - Ivana Zucchetti
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn Napoli, 80121, Naples, Italy
| | - Luigi Caputi
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn Napoli, 80121, Naples, Italy
| | - Raffaella Tarallo
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn Napoli, 80121, Naples, Italy
| | - Fabio Crocetta
- Department of Integrated Marine Ecology, Stazione Zoologica Anton Dohrn Napoli, 80121, Naples, Italy
| | - Rosaria De Santis
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn Napoli, 80121, Naples, Italy
| | - Salvatore D'Aniello
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn Napoli, 80121, Naples, Italy.
| | - Paolo Sordino
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn Napoli, 80121, Naples, Italy.
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5
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Yan Y, Ning G, Li L, Liu J, Yang S, Cao Y, Wang Q. The BMP ligand Pinhead together with Admp supports the robustness of embryonic patterning. SCIENCE ADVANCES 2019; 5:eaau6455. [PMID: 32064309 PMCID: PMC6989304 DOI: 10.1126/sciadv.aau6455] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 04/30/2019] [Accepted: 10/29/2019] [Indexed: 06/10/2023]
Abstract
Vertebrate embryonic dorsoventral axis is robustly stable in the face of variations in bone morphogenetic protein (BMP) signaling. However, the molecular mechanism behind this robustness remains uncharacterized. In this study, we show that zebrafish Pinhead, together with Admp, plays an important compensatory role in ensuring the robustness of axial patterning through fine-tuning of BMP signaling. pinhead encodes a BMP-like ligand expressed in the ventrolateral margin of the early gastrula. Transcription of pinhead and admp is under opposing regulation, where pinhead depletion results in a compensatory increase in admp transcription and vice versa, leading to normal axis formation in pinhead or admp mutants. Expression of pinhead and admp is directly repressed by the BMP/Smad pathway. When BMP signals were inhibited or excessively activated, pinhead/admp expression changed accordingly, allowing for self-regulation. Thus, this study reveals a negative feedback loop between BMP signaling and pinhead/admp that effectively stabilizes embryonic patterning by buffering against fluctuations in BMP signaling.
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Affiliation(s)
- Yifang Yan
- State Key Laboratory of Membrane Biology, Institute of Zoology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100101, China
| | - Guozhu Ning
- State Key Laboratory of Membrane Biology, Institute of Zoology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100101, China
| | - Linwei Li
- State Key Laboratory of Membrane Biology, Institute of Zoology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100101, China
| | - Jie Liu
- State Key Laboratory of Membrane Biology, Institute of Zoology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100101, China
| | - Shuyan Yang
- State Key Laboratory of Membrane Biology, Institute of Zoology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100101, China
| | - Yu Cao
- State Key Laboratory of Membrane Biology, Institute of Zoology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100101, China
| | - Qiang Wang
- State Key Laboratory of Membrane Biology, Institute of Zoology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100101, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
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6
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Muha V, Williamson R, Hills R, McNeilly AD, McWilliams TG, Alonso J, Schimpl M, Leney AC, Heck AJR, Sutherland C, Read KD, McCrimmon RJ, Brooks SP, van Aalten DMF. Loss of CRMP2 O-GlcNAcylation leads to reduced novel object recognition performance in mice. Open Biol 2019; 9:190192. [PMID: 31771416 PMCID: PMC6893399 DOI: 10.1098/rsob.190192] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 11/05/2019] [Indexed: 12/14/2022] Open
Abstract
O-GlcNAcylation is an abundant post-translational modification in the nervous system, linked to both neurodevelopmental and neurodegenerative disease. However, the mechanistic links between these phenotypes and site-specific O-GlcNAcylation remain largely unexplored. Here, we show that Ser517 O-GlcNAcylation of the microtubule-binding protein Collapsin Response Mediator Protein-2 (CRMP2) increases with age. By generating and characterizing a Crmp2S517A knock-in mouse model, we demonstrate that loss of O-GlcNAcylation leads to a small decrease in body weight and mild memory impairment, suggesting that Ser517 O-GlcNAcylation has a small but detectable impact on mouse physiology and cognitive function.
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Affiliation(s)
- Villo Muha
- Gene Regulation and Expression, University of Dundee, Dundee DD1 5EH, UK
| | - Ritchie Williamson
- Gene Regulation and Expression, University of Dundee, Dundee DD1 5EH, UK
- School of Pharmacy and Medical Sciences, Faculty of Life Sciences, University of Bradford, Bradford BD7 1DP, UK
| | - Rachel Hills
- Division of Neuroscience, School of Bioscience, Cardiff University, Cardiff CF10 3AX, UK
| | | | - Thomas G. McWilliams
- Stem Cells and Metabolism, Research Programs Unit, Faculty of Medicine, University of Helsinki, PL 63 Haartmaninkatu 8, Helsinki 00014, Finland
| | - Jana Alonso
- Gene Regulation and Expression, University of Dundee, Dundee DD1 5EH, UK
| | - Marianne Schimpl
- Gene Regulation and Expression, University of Dundee, Dundee DD1 5EH, UK
| | - Aneika C. Leney
- School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, 3584 CH Utrecht, The Netherlands
- Netherlands Proteomics Centre, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Albert J. R. Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, 3584 CH Utrecht, The Netherlands
- Netherlands Proteomics Centre, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Calum Sutherland
- Cellular Medicine, School of Medicine, University of Dundee, Dundee DD1 9SY, UK
| | - Kevin D. Read
- Wellcome Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | | | - Simon P. Brooks
- Division of Neuroscience, School of Bioscience, Cardiff University, Cardiff CF10 3AX, UK
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7
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Catalytic deficiency of O-GlcNAc transferase leads to X-linked intellectual disability. Proc Natl Acad Sci U S A 2019; 116:14961-14970. [PMID: 31296563 PMCID: PMC6660750 DOI: 10.1073/pnas.1900065116] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
O-GlcNAc transferase (OGT) is an X-linked gene product that is essential for normal development of the vertebrate embryo. It catalyses the O-GlcNAc posttranslational modification of nucleocytoplasmic proteins and proteolytic maturation of the transcriptional coregulator Host cell factor 1 (HCF1). Recent studies have suggested that conservative missense mutations distal to the OGT catalytic domain lead to X-linked intellectual disability in boys, but it is not clear if this is through changes in the O-GlcNAc proteome, loss of protein-protein interactions, or misprocessing of HCF1. Here, we report an OGT catalytic domain missense mutation in monozygotic female twins (c. X:70779215 T > A, p. N567K) with intellectual disability that allows dissection of these effects. The patients show limited IQ with developmental delay and skewed X-inactivation. Molecular analyses revealed decreased OGT stability and disruption of the substrate binding site, resulting in loss of catalytic activity. Editing this mutation into the Drosophila genome results in global changes in the O-GlcNAc proteome, while in mouse embryonic stem cells it leads to loss of O-GlcNAcase and delayed differentiation down the neuronal lineage. These data imply that catalytic deficiency of OGT could contribute to X-linked intellectual disability.
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8
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Selvan N, George S, Serajee FJ, Shaw M, Hobson L, Kalscheuer V, Prasad N, Levy SE, Taylor J, Aftimos S, Schwartz CE, Huq AM, Gecz J, Wells L. O-GlcNAc transferase missense mutations linked to X-linked intellectual disability deregulate genes involved in cell fate determination and signaling. J Biol Chem 2018; 293:10810-10824. [PMID: 29769320 DOI: 10.1074/jbc.ra118.002583] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Revised: 04/27/2018] [Indexed: 01/17/2023] Open
Abstract
It is estimated that ∼1% of the world's population has intellectual disability, with males affected more often than females. OGT is an X-linked gene encoding for the enzyme O-GlcNAc transferase (OGT), which carries out the reversible addition of N-acetylglucosamine (GlcNAc) to Ser/Thr residues of its intracellular substrates. Three missense mutations in the tetratricopeptide (TPR) repeats of OGT have recently been reported to cause X-linked intellectual disability (XLID). Here, we report the discovery of two additional novel missense mutations (c.775 G>A, p.A259T, and c.1016 A>G, p.E339G) in the TPR domain of OGT that segregate with XLID in affected families. Characterization of all five of these XLID missense variants of OGT demonstrates modest declines in thermodynamic stability and/or activities of the variants. We engineered each of the mutations into a male human embryonic stem cell line using CRISPR/Cas9. Investigation of the global O-GlcNAc profile as well as OGT and O-GlcNAc hydrolase levels by Western blotting showed no gross changes in steady-state levels in the engineered lines. However, analyses of the differential transcriptomes of the OGT variant-expressing stem cells revealed shared deregulation of genes involved in cell fate determination and liver X receptor/retinoid X receptor signaling, which has been implicated in neuronal development. Thus, here we reveal two additional mutations encoding residues in the TPR regions of OGT that appear causal for XLID and provide evidence that the relatively stable and active TPR variants may share a common, unelucidated mechanism of altering gene expression profiles in human embryonic stem cells.
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Affiliation(s)
- Nithya Selvan
- From the Department of Biochemistry and Molecular Biology, Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602
| | - Stephan George
- From the Department of Biochemistry and Molecular Biology, Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602
| | - Fatema J Serajee
- the Departments of Pediatrics and of Neurology, Wayne State University, Detroit, Michigan 48201
| | - Marie Shaw
- the Adelaide Medical School, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide South Australia 5006, Australia
| | - Lynne Hobson
- the Women's and Children's Hospital, North Adelaide, South Australia 5006, Australia
| | - Vera Kalscheuer
- the Research Group Development and Disease, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Nripesh Prasad
- the Genomic Services Laboratory, HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806
| | - Shawn E Levy
- the Genomic Services Laboratory, HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806
| | - Juliet Taylor
- the Genetic Health Services New Zealand-Northern Hub, Auckland City Hospital, Auckland 1142, New Zealand
| | - Salim Aftimos
- the Genetic Health Services New Zealand-Northern Hub, Auckland City Hospital, Auckland 1142, New Zealand
| | | | - Ahm M Huq
- the Departments of Pediatrics and of Neurology, Wayne State University, Detroit, Michigan 48201
| | - Jozef Gecz
- the Adelaide Medical School, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide South Australia 5006, Australia.,the South Australian Health and Medical Research Institute, Adelaide, South Australia 5006, Australia
| | - Lance Wells
- From the Department of Biochemistry and Molecular Biology, Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602,
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9
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Mariappa D, Ferenbach AT, van Aalten DMF. Effects of hypo- O-GlcNAcylation on Drosophila development. J Biol Chem 2018; 293:7209-7221. [PMID: 29588363 PMCID: PMC5950000 DOI: 10.1074/jbc.ra118.002580] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 03/21/2018] [Indexed: 01/12/2023] Open
Abstract
Post-translational modification of serine/threonine residues in nucleocytoplasmic proteins with GlcNAc (O-GlcNAcylation) is an essential regulatory mechanism in many cellular processes. In Drosophila, null mutants of the Polycomb gene O-GlcNAc transferase (OGT; also known as super sex combs (sxc)) display homeotic phenotypes. To dissect the requirement for O-GlcNAc signaling in Drosophila development, we used CRISPR/Cas9 gene editing to generate rationally designed sxc catalytically hypomorphic or null point mutants. Of the fertile males derived from embryos injected with the CRISPR/Cas9 reagents, 25% produced progeny carrying precise point mutations with no detectable off-target effects. One of these mutants, the catalytically inactive sxcK872M, was recessive lethal, whereas a second mutant, the hypomorphic sxcH537A, was homozygous viable. We observed that reduced total protein O-GlcNAcylation in the sxcH537A mutant is associated with a wing vein phenotype and temperature-dependent lethality. Genetic interaction between sxcH537A and a null allele of Drosophila host cell factor (dHcf), encoding an extensively O-GlcNAcylated transcriptional coactivator, resulted in abnormal scutellar bristle numbers. A similar phenotype was also observed in sxcH537A flies lacking a copy of skuld (skd), a Mediator complex gene known to affect scutellar bristle formation. Interestingly, this phenotype was independent of OGT Polycomb function or dHcf downstream targets. In conclusion, the generation of the endogenous OGT hypomorphic mutant sxcH537A enabled us to identify pleiotropic effects of globally reduced protein O-GlcNAc during Drosophila development. The mutants generated and phenotypes observed in this study provide a platform for discovery of OGT substrates that are critical for Drosophila development.
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Affiliation(s)
- Daniel Mariappa
- Division of Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, United Kingdom.
| | - Andrew T Ferenbach
- Division of Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, United Kingdom
| | - Daan M F van Aalten
- Division of Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, United Kingdom.
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10
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Selvan N, Williamson R, Mariappa D, Campbell DG, Gourlay R, Ferenbach AT, Aristotelous T, Hopkins-Navratilova I, Trost M, van Aalten DMF. A mutant O-GlcNAcase enriches Drosophila developmental regulators. Nat Chem Biol 2017; 13:882-887. [PMID: 28604694 DOI: 10.1038/nchembio.2404] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Accepted: 03/14/2017] [Indexed: 01/09/2023]
Abstract
Protein O-GlcNAcylation is a reversible post-translational modification of serines and threonines on nucleocytoplasmic proteins. It is cycled by the enzymes O-GlcNAc transferase (OGT) and O-GlcNAc hydrolase (O-GlcNAcase or OGA). Genetic approaches in model organisms have revealed that protein O-GlcNAcylation is essential for early embryogenesis. The Drosophila melanogaster gene supersex combs (sxc), which encodes OGT, is a polycomb gene, whose null mutants display homeotic transformations and die at the pharate adult stage. However, the identities of the O-GlcNAcylated proteins involved and the underlying mechanisms linking these phenotypes to embryonic development are poorly understood. Identification of O-GlcNAcylated proteins from biological samples is hampered by the low stoichiometry of this modification and by limited enrichment tools. Using a catalytically inactive bacterial O-GlcNAcase mutant as a substrate trap, we have enriched the O-GlcNAc proteome of the developing Drosophila embryo, identifying, among others, known regulators of Hox genes as candidate conveyors of OGT function during embryonic development.
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Affiliation(s)
- Nithya Selvan
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
| | - Ritchie Williamson
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
| | - Daniel Mariappa
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK.,Division of Gene Regulation and Expression, University of Dundee, Dundee, UK
| | - David G Campbell
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
| | - Robert Gourlay
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
| | - Andrew T Ferenbach
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK.,Division of Gene Regulation and Expression, University of Dundee, Dundee, UK
| | - Tonia Aristotelous
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee, UK
| | - Iva Hopkins-Navratilova
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee, UK
| | - Matthias Trost
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK.,Institute for Cell and Molecular Biosciences (ICaMB), Newcastle University, Newcastle-upon-Tyne, UK
| | - Daan M F van Aalten
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK.,Division of Gene Regulation and Expression, University of Dundee, Dundee, UK
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11
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Suzuki A, Yoshida H, van Heeringen SJ, Takebayashi-Suzuki K, Veenstra GJC, Taira M. Genomic organization and modulation of gene expression of the TGF-β and FGF pathways in the allotetraploid frog Xenopus laevis. Dev Biol 2017; 426:336-359. [DOI: 10.1016/j.ydbio.2016.09.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Revised: 06/10/2016] [Accepted: 09/19/2016] [Indexed: 12/13/2022]
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12
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Mariappa D, Zheng X, Schimpl M, Raimi O, Ferenbach AT, Müller HAJ, van Aalten DMF. Dual functionality of O-GlcNAc transferase is required for Drosophila development. Open Biol 2016; 5:150234. [PMID: 26674417 PMCID: PMC4703063 DOI: 10.1098/rsob.150234] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Post-translational modification of intracellular proteins with O-linked N-acetylglucosamine (O-GlcNAc) catalysed by O-GlcNAc transferase (OGT) has been linked to regulation of diverse cellular functions. OGT possesses a C-terminal glycosyltransferase catalytic domain and N-terminal tetratricopeptide repeats that are implicated in protein-protein interactions. Drosophila OGT (DmOGT) is encoded by super sex combs (sxc), mutants of which are pupal lethal. However, it is not clear if this phenotype is caused by reduction of O-GlcNAcylation. Here we use a genetic approach to demonstrate that post-pupal Drosophila development can proceed with negligible OGT catalysis, while early embryonic development is OGT activity-dependent. Structural and enzymatic comparison between human OGT (hOGT) and DmOGT informed the rational design of DmOGT point mutants with a range of reduced catalytic activities. Strikingly, a severely hypomorphic OGT mutant complements sxc pupal lethality. However, the hypomorphic OGT mutant-rescued progeny do not produce F2 adults, because a set of Hox genes is de-repressed in F2 embryos, resulting in homeotic phenotypes. Thus, OGT catalytic activity is required up to late pupal stages, while further development proceeds with severely reduced OGT activity.
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Affiliation(s)
- Daniel Mariappa
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
| | - Xiaowei Zheng
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
| | - Marianne Schimpl
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
| | - Olawale Raimi
- Division of Molecular Microbiology, University of Dundee, Dundee, UK
| | - Andrew T Ferenbach
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
| | - H-Arno J Müller
- Division of Cell and Developmental Biology, College of Life Sciences, University of Dundee, Dundee, UK
| | - Daan M F van Aalten
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK Division of Molecular Microbiology, University of Dundee, Dundee, UK
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13
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Marlétaz F, Maeso I, Faas L, Isaacs HV, Holland PWH. Cdx ParaHox genes acquired distinct developmental roles after gene duplication in vertebrate evolution. BMC Biol 2015; 13:56. [PMID: 26231746 PMCID: PMC4522105 DOI: 10.1186/s12915-015-0165-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Accepted: 07/08/2015] [Indexed: 01/03/2023] Open
Abstract
Background The functional consequences of whole genome duplications in vertebrate evolution are not fully understood. It remains unclear, for instance, why paralogues were retained in some gene families but extensively lost in others. Cdx homeobox genes encode conserved transcription factors controlling posterior development across diverse bilaterians. These genes are part of the ParaHox gene cluster. Multiple Cdx copies were retained after genome duplication, raising questions about how functional divergence, overlap, and redundancy respectively contributed to their retention and evolutionary fate. Results We examined the degree of regulatory and functional overlap between the three vertebrate Cdx genes using single and triple morpholino knock-down in Xenopus tropicalis followed by RNA-seq. We found that one paralogue, Cdx4, has a much stronger effect on gene expression than the others, including a strong regulatory effect on FGF and Wnt genes. Functional annotation revealed distinct and overlapping roles and subtly different temporal windows of action for each gene. The data also reveal a colinear-like effect of Cdx genes on Hox genes, with repression of Hox paralogy groups 1 and 2, and activation increasing from Hox group 5 to 11. We also highlight cases in which duplicated genes regulate distinct paralogous targets revealing pathway elaboration after whole genome duplication. Conclusions Despite shared core pathways, Cdx paralogues have acquired distinct regulatory roles during development. This implies that the degree of functional overlap between paralogues is relatively low and that gene expression pattern alone should be used with caution when investigating the functional evolution of duplicated genes. We therefore suggest that developmental programmes were extensively rewired after whole genome duplication in the early evolution of vertebrates. Electronic supplementary material The online version of this article (doi:10.1186/s12915-015-0165-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ferdinand Marlétaz
- Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK.
| | - Ignacio Maeso
- Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK. .,Present address: Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide, Sevilla, Spain.
| | - Laura Faas
- Department of Biology, University of York, Heslington, York, YO10 5DD, UK.
| | - Harry V Isaacs
- Department of Biology, University of York, Heslington, York, YO10 5DD, UK.
| | - Peter W H Holland
- Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK.
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Peterson RT. Discovery of therapeutic targets by phenotype-based zebrafish screens. DRUG DISCOVERY TODAY. TECHNOLOGIES 2014; 1:49-54. [PMID: 24981267 DOI: 10.1016/j.ddtec.2004.07.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
The easy identification of phenotypes in the transparent zebrafish embryo has enabled numerous genetic, antisense morpholino oligonucleotide, and small molecule screens. Can zebrafish screens also be used for unbiased discovery of novel drug targets?:
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Affiliation(s)
- Randall T Peterson
- Developmental Biology Laboratory, Cardiovascular Research Center, Massachusetts General Hospital, Harvard Medical School, 149 13th Street, Charlestown, MA 02129, USA.
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15
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Bae CJ, Park BY, Lee YH, Tobias JW, Hong CS, Saint-Jeannet JP. Identification of Pax3 and Zic1 targets in the developing neural crest. Dev Biol 2013; 386:473-83. [PMID: 24360908 DOI: 10.1016/j.ydbio.2013.12.011] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2013] [Revised: 10/07/2013] [Accepted: 12/10/2013] [Indexed: 11/28/2022]
Abstract
The neural crest (NC) is a multipotent population of migratory cells unique to the vertebrate embryo, contributing to the development of multiple organ systems. Transcription factors pax3 and zic1 are among the earliest genes activated in NC progenitors, and they are both necessary and sufficient to promote NC fate. In order to further characterize the function of these transcription factors during NC development we have used hormone inducible fusion proteins in a Xenopus animal cap assay, and DNA microarray to identify downstream targets of Pax3 and Zic1. Here we present the results of this screen and the initial validation of these targets using quantitative RT-PCR, in situ hybridization and morpholinos-mediated knockdown. Among the targets identified we found several well-characterized NC-specific genes, including snail2, foxd3, gbx2, twist, sox8 and sox9, which validate our approach. We also obtained several factors with no known function in Xenopus NC, which represent novel regulators of NC fate. The comprehensive characterization of Pax3 and Zic1 targets function in the NC gene regulatory network, are essential to understanding the mechanisms regulating the emergence of this important cell population.
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Affiliation(s)
- Chang-Joon Bae
- Department of Basic Science & Craniofacial Biology, College of Dentistry, New York University, New York, USA
| | - Byung-Yong Park
- Department of Anatomy, College of Veterinary Medicine, Chonbuk National University, Jeonju, Republic of Korea
| | - Young-Hoon Lee
- Department of Oral Anatomy, School of Dentistry & Institute of Oral Biosciences, Chonbuk National University, Jeonju, Republic of Korea
| | - John W Tobias
- Bioinformatics Group, Molecular Profiling Facility, University of Pennsylvania, Philadelphia, PA, USA
| | - Chang-Soo Hong
- Department of Basic Science & Craniofacial Biology, College of Dentistry, New York University, New York, USA; Department of Biological Sciences, College of Natural Sciences, Daegu University, Gyeongsan, Republic of Korea.
| | - Jean-Pierre Saint-Jeannet
- Department of Basic Science & Craniofacial Biology, College of Dentistry, New York University, New York, USA; Department of Animal Biology, University of Pennsylvania School of Veterinary Medicine, Philadelphia, PA, USA.
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16
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Imai KS, Daido Y, Kusakabe TG, Satou Y. Cis-acting transcriptional repression establishes a sharp boundary in chordate embryos. Science 2012; 337:964-7. [PMID: 22923581 DOI: 10.1126/science.1222488] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
The function of bone morphogenetic protein (BMP) signaling in dorsoventral (DV) patterning of animal embryos is conserved among Bilateria. In vertebrates, the BMP ligand antidorsalizing morphogenetic protein (Admp) is expressed dorsally and moves to the opposite side to specify the ventral fate. Here, we show that Pinhead is an antagonist specific for Admp with a role in establishing the DV axis of the trunk epidermis in embryos of the ascidian Ciona intestinalis. Pinhead and Admp exist in tandem in the genomes of various animals from arthropods to vertebrates. This genomic configuration is important for mutually exclusive expression of these genes, because Pinhead transcription directly disturbs the action of the Admp enhancer. Our data suggest that this dual negative regulatory mechanism is widely conserved in animals.
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Affiliation(s)
- Kaoru S Imai
- Department of Biodiversity, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
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17
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Eif4a3 is required for accurate splicing of the Xenopus laevis ryanodine receptor pre-mRNA. Dev Biol 2012; 372:103-10. [PMID: 22944195 DOI: 10.1016/j.ydbio.2012.08.013] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2012] [Revised: 07/17/2012] [Accepted: 08/19/2012] [Indexed: 11/22/2022]
Abstract
The Exon Junction Complex (EJC) plays a critical role in multiple posttranscriptional events, including RNA subcellular localization, nonsense-mediated decay (NMD), and translation. We previously reported that knockdown of the EJC core component Eukaryotic initiation factor 4a3 (Eif4a3) results in full-body paralysis of embryos of the frog, Xenopus laevis. Here, we explore the cellular and molecular mechanisms underlying this phenotype. We find that cultured muscle cells derived from Eif4a3 morphants do not contract, and fail to undergo calcium-dependent calcium release in response to electrical stimulation or treatment with caffeine. We show that ryr (ryanodine receptor) transcripts are incorrectly spliced in Eif4a3 morphants, and demonstrate that inhibition of Xenopus Ryr function similarly results in embryonic paralysis. These results suggest that the EJC mediates muscle cell function via regulation of pre-mRNA splicing during early vertebrate embryogenesis.
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18
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Clulow J, Clulow S, Guo J, French AJ, Mahony MJ, Archer M. Optimisation of an oviposition protocol employing human chorionic and pregnant mare serum gonadotropins in the barred frog Mixophyes fasciolatus (Myobatrachidae). Reprod Biol Endocrinol 2012; 10:60. [PMID: 22909256 PMCID: PMC3488330 DOI: 10.1186/1477-7827-10-60] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/04/2012] [Accepted: 08/03/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Protocols for the hormonal induction of ovulation and oviposition are essential tools for managing threatened amphibians with assisted reproduction, but responses vary greatly between species and even broad taxon groups. Consequently, it is necessary to assess effectiveness of such protocols in representative species when new taxa become targets for induction. The threatened genus Mixophyes (family Myobatrachidae) has amongst the highest proportion of endangered species of all the Australian amphibians. This study developed and optimised the induction of oviposition in a non-threatened member of this taxon, the great barred frog (Mixophyes fasciolatus). METHODS Gravid female M. fasciolatus were induced to oviposit on one or more occasions by administration of human chorionic gonadotropin (hCG) with or without priming with pregnant mare serum gonadotropin (PMSG). Treatments involved variations in hormone doses and combinations (administered via injection into the dorsal lymph sacs), and timing of administration. Pituitary homogenates from an unrelated bufonid species (Rhinella marina) were also examined with hCG. RESULTS When injected alone, hCG (900 to 1400 IU) induced oviposition. However, priming with two time dependent doses of PMSG (50 IU, 25 IU) increased responses, with lower doses of hCG (200 IU). Priming increased response rates in females from around 30% (hCG alone) to more than 50% (p = 0.035), and up to 67%. Increasing the interval between the first PMSG dose and first hCG dose from 3 to 6 days also produced significant improvement (p<0.001). Heterologous pituitary extracts administered with hCG were no more effective than hCG alone (p = 0.628). CONCLUSIONS This study found that M. fasciolatus is amongst the few amphibian species (including Xenopus (Silurana) and some bufonids) that respond well to the induction of ovulation utilising mammalian gonadotropins (hCG). The optimal protocol for M. fasciolatus involved two priming doses of PMSG (50 IU and 25 IU) administered at 6 and 4 days respectively, prior to two doses of hCG (100 IU), 24 hours apart. This study is also the first to demonstrate in an amphibian species that responds to mammalian gonadotropins that an increase in the ovulation rate occurs after priming with a gonadotropin (PMSG) with FSH activity.
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Affiliation(s)
- John Clulow
- School of Environmental and Life Sciences, University of Newcastle, Callaghan Drive, Callaghan, NSW, 2308, Australia
| | - Simon Clulow
- School of Environmental and Life Sciences, University of Newcastle, Callaghan Drive, Callaghan, NSW, 2308, Australia
| | - Jitong Guo
- Inner Mongolia Saikexing Reproductive Biotechnology Co., Ltd. 6 F, Mengniu Dairy R&D Center, Shengle Economic Zone of Helingeer County, Hohhot, 011517, Inner Mongolia, People's Republic of China
| | - Andrew J French
- Centre for Animal Biotechnology, Faculty of Veterinary Science, The University of Melbourne, Parkville, 3010, VIC, Australia
| | - Michael J Mahony
- School of Environmental and Life Sciences, University of Newcastle, Callaghan Drive, Callaghan, NSW, 2308, Australia
| | - Michael Archer
- School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, 2052, Australia
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19
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Gilchrist MJ. From expression cloning to gene modeling: the development of Xenopus gene sequence resources. Genesis 2012; 50:143-54. [PMID: 22344767 PMCID: PMC3488295 DOI: 10.1002/dvg.22008] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2011] [Revised: 12/09/2011] [Accepted: 12/21/2011] [Indexed: 11/08/2022]
Abstract
The Xenopus community has made concerted efforts over the last 10–12 years systematically to improve the available sequence information for this amphibian model organism ideally suited to the study of early development in vertebrates. Here I review progress in the collection of both sequence data and physical clone reagents for protein coding genes. I conclude that we have cDNA sequences for around 50% and full-length clones for about 35% of the genes in Xenopus tropicalis, and similar numbers but a smaller proportion for Xenopus laevis. In addition, I demonstrate that the gaps in the current genome assembly create problems for the computational elucidation of gene sequences, and suggest some ways to ameliorate the effects of this. genesis 50:143–154, 2012. © 2012 Wiley Periodicals, Inc.
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Affiliation(s)
- Michael J Gilchrist
- Division of Systems Biology, MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London, United Kingdom.
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20
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Méreau A, Le Sommer C, Lerivray H, Lesimple M, Hardy S. Xenopus as a model to study alternative splicing in vivo. Biol Cell 2012; 99:55-65. [PMID: 17155935 DOI: 10.1042/bc20060073] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
An increasing number of genes are being identified for which the corresponding mRNAs contain different combinations of the encoded exons. This highly regulated exon choice, or alternative splicing, is often tissue-specific and potentially could differentially affect cellular functions. Alternative splicing is therefore not only a means to increase the coding capacity of the genome, but also to regulate gene expression during differentiation or development. To both evaluate the importance for cellular functions and define the regulatory pathways of alternative splicing, it is necessary to progress from the in vitro or ex vivo experimental models actually used towards in vivo whole-animal studies. We present here the amphibian, Xenopus, as an experimental model highly amenable for such studies. The various experimental approaches that can be used with Xenopus oocytes and embryos to characterize regulatory sequence elements and factors are presented and the advantages and drawbacks of these approaches are discussed. Finally, the real possibilities for large-scale identification of mRNAs containing alternatively spliced exons, the tissue-specific patterns of exon usage and the way in which these patterns are modified by perturbing the relative amount of splicing factors are discussed.
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Affiliation(s)
- Agnes Méreau
- UMR 6061 CNRS-Université de Rennes 1, IFR 140 Génétique Fonctionnelle, Agronomie et Santé, Faculté de Médecine, 2 avenue de Pr. Léon Bernard, 35043 Rennes cedex, France
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21
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Abstract
Xenopus tropicalis combine the advantages of X. laevis, for example using explants and targeted gain of function, with the ability to take classical genetics approaches to answering cell and developmental biology questions making it arguably the most versatile of the model organisms. Against this background, husbandry of X. tropicalis is less well developed than for its larger, more robust relative. Here we describe the methods used to keep and breed these frogs successfully.
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Affiliation(s)
- Alan Jafkins
- European Xenopus Resource Centre, School of Biological Sciences, University of Portsmouth, Portsmouth, England, UK
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22
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Haremaki T, Sridharan J, Dvora S, Weinstein DC. Regulation of vertebrate embryogenesis by the exon junction complex core component Eif4a3. Dev Dyn 2010; 239:1977-87. [PMID: 20549732 DOI: 10.1002/dvdy.22330] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
The establishment and maintenance of cellular identity are ultimately dependent upon the accurate regulation of gene expression, the process by which genetic information is used to synthesize functional gene products. The post-transcriptional, pre-translational regulation of RNA constitutes RNA processing, which plays a prominent role in the modulation of gene expression in differentiated animal cells. The multi-protein Exon Junction Complex (EJC) serves as a critical signaling hub within the network that underlies many RNA processing events. Here, we identify a requirement for the EJC during early vertebrate embryogenesis. Knockdown of the EJC component Eukaryotic initiation factor 4a3 (Eif4a3) in embryos of the frog Xenopus laevis results in full-body paralysis, with defects in sensory neuron, pigment cell, and cardiac development; similar phenotypes are seen following knockdown of other "core" EJC protein constituents. Our studies point to an essential role for the EJC in the development of neural plate border derivatives.
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Affiliation(s)
- Tomomi Haremaki
- Biology Department, Queens College of the City University of New York, 65-30 Kissena Boulevard, Flushing, NY 11367, USA
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23
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Love DC, Krause MW, Hanover JA. O-GlcNAc cycling: emerging roles in development and epigenetics. Semin Cell Dev Biol 2010; 21:646-54. [PMID: 20488252 DOI: 10.1016/j.semcdb.2010.05.001] [Citation(s) in RCA: 89] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2010] [Revised: 04/30/2010] [Accepted: 05/10/2010] [Indexed: 10/19/2022]
Abstract
The nutrient-sensing hexosamine signaling pathway modulates the levels of O-linked N-acetylglucosamine (O-GlcNAc) on key targets impacting cellular signaling, protein turnover and gene expression. O-GlcNAc cycling may be deregulated in neurodegenerative disease, cancer, and diabetes. Studies in model organisms demonstrate that the O-GlcNAc transferase (OGT/Sxc) is essential for Polycomb group (PcG) repression of the homeotic genes, clusters of genes responsible for the adult body plan. Surprisingly, from flies to man, the O-GlcNAcase (OGA, MGEA5) gene is embedded within the NK cluster, the most evolutionarily ancient of three homeobox gene clusters regulated by PcG repression. PcG repression also plays a key role in maintaining stem cell identity, recruiting the DNA methyltransferase machinery for imprinting, and in X-chromosome inactivation. Intriguingly, the Ogt gene resides near the Xist locus in vertebrates and is subject to regulation by PcG-dependent X-inactivation. OGT is also an enzymatic component of the human dosage compensation complex. These 'evo-devo' relationships linking O-GlcNAc cycling to higher order chromatin structure provide insights into how nutrient availability may influence the epigenetic regulation of gene expression. O-GlcNAc cycling at promoters and PcG repression represent concrete mechanisms by which nutritional information may be transmitted across generations in the intra-uterine environment. Thus, the nutrient-sensing hexosamine signaling pathway may be a key contributor to the metabolic deregulation resulting from prenatal exposure to famine, or the 'vicious cycle' observed in children of mothers with type-2 diabetes and metabolic disease.
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Affiliation(s)
- Dona C Love
- Laboratory of Cell Biochemistry and Biology, NIDDK, National Institutes of Health, NIH, Bethesda, MD 20892-0850, USA
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Chen CM, Chiu SL, Shen W, Cline HT. Co-expression of Argonaute2 Enhances Short Hairpin RNA-induced RNA Interference in Xenopus CNS Neurons In Vivo. Front Neurosci 2009; 3:63. [PMID: 20582287 PMCID: PMC2858607 DOI: 10.3389/neuro.17.001.2009] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2009] [Accepted: 06/16/2009] [Indexed: 11/25/2022] Open
Abstract
RNA interference (RNAi) is an evolutionarily conserved mechanism for sequence-specific gene silencing. Recent advances in our understanding of RNAi machinery make it possible to reduce protein expression by introducing short hairpin RNA (shRNA) into cells of many systems, however, the efficacy of RNAi-mediated protein knockdown can be quite variable, especially in intact animals, and this limits its application. We built adaptable molecular tools, pSilencer (pSi) and pReporter (pRe) constructs, to evaluate the impact of different promoters, shRNA structures and overexpression of Ago2, the key enzyme in the RNA-induced silencing complex, on the efficiency of RNAi. The magnitude of RNAi knockdown was evaluated in cultured cells and intact animals by comparing fluorescence intensity levels of GFP, the RNAi target, relative to mCherry, which was not targeted. Co-expression of human Ago2 with shRNA significantly enhanced efficiency of GFP knockdown in cell lines and in neurons of intact Xenopus tadpoles. Human H1- and U6-promotors alone or the U6-promotor with an enhancer element were equally effective at driving GFP knockdown. shRNA derived from the microRNA-30 design (shRNAmir30) enhanced the efficiency of GFP knockdown. Expressing pSi containing Ago2 with shRNA increased knockdown efficiency of an endogenous neuronal protein, the GluR2 subunit of the AMPA receptor, functionally accessed by recording AMPA receptor-mediated spontaneous synaptic currents in Xenopus CNS neurons. Our data suggest that co-expression of Ago2 and shRNA is a simple method to enhance RNAi in intact animals. While morpholino antisense knockdown is effective in Xenopus and Zebrafish, a principle advantage of the RNAi method is the possibility of spatial and temporal control of protein knockdown by use of cell type specific and regulatable pol II promoters to drive shRNA and Ago2. This should extend the application of RNAi to study gene function of intact brain circuits.
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Affiliation(s)
- Chih-Ming Chen
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory Cold Spring Harbor, NY, USA
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25
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Ogino H, Ochi H. Resources and transgenesis techniques for functional genomics in Xenopus. Dev Growth Differ 2009; 51:387-401. [PMID: 19382936 DOI: 10.1111/j.1440-169x.2009.01098.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Recent developments in genomic resources and high-throughput transgenesis techniques have allowed Xenopus to 'metamorphose' from a classic model for embryology to a leading-edge experimental system for functional genomics. This process has incorporated the fast-breeding diploid frog, Xenopus tropicalis, as a new model-system for vertebrate genomics and genetics. Sequencing of the X. tropicalis genome is nearly complete, and its comparison with mammalian sequences offers a reliable guide for the genome-wide prediction of cis-regulatory elements. Unique cDNA sets have been generated for both X. tropicalis and X. laevis, which have facilitated non-redundant, systematic gene expression screening and comprehensive gene expression analysis. A variety of transgenesis techniques are available for both X. laevis and X. tropicalis, and the appropriate procedure may be chosen depending on the purpose for which it is required. Effective use of these resources and techniques will help to reveal the overall picture of the complex wiring of gene regulatory networks that control vertebrate development.
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Affiliation(s)
- Hajime Ogino
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara, Japan.
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26
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Wheeler GN, Brändli AW. Simple vertebrate models for chemical genetics and drug discovery screens: Lessons from zebrafish andXenopus. Dev Dyn 2009; 238:1287-308. [DOI: 10.1002/dvdy.21967] [Citation(s) in RCA: 135] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
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Abstract
Xenopus is an established and powerful model system for the study of Wnt signaling in vertebrates. Above all, the relatively large size of the embryos enables microinjection experiments, which have led to key discoveries not only about the functional role of Wnt signaling in vertebrate embryos, but also about the molecular mechanisms of Wnt signaling in vertebrate cells. A major advantage of the Xenopus model is the ability to obtain large numbers of embryos, which develop relatively rapidly and which can be studied in natural separation from sentient adult parental animals. In order to obtain Xenopus embryos, ovulation in females is induced with a simple hormone injection, the eggs collected and fertilized with sperm from males. The Xenopus model system has been further strengthened by recent advances such as morpholino technology and efficient transgenic methods, as well as the development of Xenopus tropicalis as a diploid genetic model system with a shorter generation time and a genome similar to higher vertebrates.
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Affiliation(s)
- Stefan Hoppler
- School of Medical Sciences, University of Aberdeen, Aberdeen, Scotland, UK
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28
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Abstract
Xenopus tropicalis is rapidly being adopted as a model organism for developmental biology research and has enormous potential for increasing our understanding of how embryonic development is controlled. In recent years there has been a well-organized initiative within the Xenopus community, funded largely through the support of the National Institutes of Health in the US, to develop X. tropicalis as a new genetic model system with the potential to impact diverse fields of research. Concerted efforts have been made both to adapt established methodologies for use in X. tropicalis and to develop new techniques. A key resource to come out of these efforts is the genome sequence, produced by the US Department of Energy's Joint Genome Institute and made freely available to the community in draft form for the past three years. In this review, we focus on how advances in X. tropicalis genetics coupled with the sequencing of its genome are likely to form a foundation from which we can build a better understanding of the genetic control of vertebrate development and why, when we already have other vertebrate genetic models, we should want to develop genetic analysis in the frog.
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Affiliation(s)
- Chris Showell
- Carolina Cardiovascular Biology Center and Department of Genetics, University of North Carolina, Chapel Hill, North Carolina
| | - Frank L. Conlon
- Carolina Cardiovascular Biology Center and Department of Genetics, University of North Carolina, Chapel Hill, North Carolina
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina
- Correspondence to: Frank L. Conlon, 220 Fordham Hall, Medical Drive, Chapel Hill, NC 27599-3280., E-mail:
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Hilton EN, Manson FDC, Urquhart JE, Johnston JJ, Slavotinek AM, Hedera P, Stattin EL, Nordgren A, Biesecker LG, Black GCM. Left-sided embryonic expression of the BCL-6 corepressor, BCOR, is required for vertebrate laterality determination. Hum Mol Genet 2007; 16:1773-82. [PMID: 17517692 DOI: 10.1093/hmg/ddm125] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Oculofaciocardiodental (OFCD) syndrome is an X-linked male lethal condition encompassing cardiac septal defects, as well as ocular and dental anomalies. The gene mutated in OFCD syndrome, the BCL-6 corepressor (BCOR), is part of a transcriptional repression complex whose transcriptional targets remain largely unknown. We reviewed cases of OFCD syndrome and identified patients exhibiting defective lateralization including dextrocardia, asplenia and intestinal malrotation, suggesting that BCOR is required in normal laterality determination. To study the function of BCOR, we used morpholino oligonucleotides (MOs) to knockdown expression of xtBcor in Xenopus tropicalis, thus creating an animal model for OFCD syndrome. The resulting tadpoles had cardiac and ocular features characteristic of OFCD syndrome. Reversed cardiac orientation and disorganized gut patterning were seen when MOs were injected into the left side of embryos, demonstrating a left-sided requirement for xtBcor in lateral determination in Xenopus. Ocular defects displayed no left-right bias and included anterior and posterior segment disorders such as microphthalmia and coloboma. Expression of xtPitx2c was shown to be downregulated when xtBcor was depleted. This identifies a pathway in which xtBcor is required for lateral specification, a process intrinsically linked to correct cardiac septal development.
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Affiliation(s)
- Emma N Hilton
- Academic Unit of Medical Genetics and Regional Genetic Service, St Mary's Hospital, Manchester, UK
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Pickart MA, Klee EW, Nielsen AL, Sivasubbu S, Mendenhall EM, Bill BR, Chen E, Eckfeldt CE, Knowlton M, Robu ME, Larson JD, Deng Y, Schimmenti LA, Ellis LB, Verfaillie CM, Hammerschmidt M, Farber SA, Ekker SC. Genome-wide reverse genetics framework to identify novel functions of the vertebrate secretome. PLoS One 2006; 1:e104. [PMID: 17218990 PMCID: PMC1766371 DOI: 10.1371/journal.pone.0000104] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2006] [Accepted: 11/12/2006] [Indexed: 11/18/2022] Open
Abstract
Background Understanding the functional role(s) of the more than 20,000 proteins of the vertebrate genome is a major next step in the post-genome era. The approximately 4,000 co-translationally translocated (CTT) proteins – representing the vertebrate secretome – are important for such vertebrate-critical processes as organogenesis. However, the role(s) for most of these genes is currently unknown. Results We identified 585 putative full-length zebrafish CTT proteins using cross-species genomic and EST-based comparative sequence analyses. We further investigated 150 of these genes (Figure 1) for unique function using morpholino-based analysis in zebrafish embryos. 12% of the CTT protein-deficient embryos resulted in specific developmental defects, a notably higher rate of gene function annotation than the 2%–3% estimate from random gene mutagenesis studies. Conclusion(s) This initial collection includes novel genes required for the development of vascular, hematopoietic, pigmentation, and craniofacial tissues, as well as lipid metabolism, and organogenesis. This study provides a framework utilizing zebrafish for the systematic assignment of biological function in a vertebrate genome.
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Affiliation(s)
- Michael A. Pickart
- Department of Oral Sciences and Minnesota Craniofacial Research Training Program MinnCResT, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Eric W. Klee
- Laboratory Medicine and Pathology and Computer Science and Engineering, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Aubrey L. Nielsen
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, Minnesota, United States of America
- Arnold and Mabel Beckman Center for Transposon Research, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Sridhar Sivasubbu
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, Minnesota, United States of America
- Arnold and Mabel Beckman Center for Transposon Research, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Eric M. Mendenhall
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, Minnesota, United States of America
- Arnold and Mabel Beckman Center for Transposon Research, University of Minnesota, Minneapolis, Minnesota, United States of America
- Department of Medicine, Division of Hematology, Oncology, and Transplantation, and Stem Cell Institute, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Brent R. Bill
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, Minnesota, United States of America
- Arnold and Mabel Beckman Center for Transposon Research, University of Minnesota, Minneapolis, Minnesota, United States of America
- Department of Pediatrics, Genetics and Metabolism and Department of Ophthalmology, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Eleanor Chen
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, Minnesota, United States of America
- Arnold and Mabel Beckman Center for Transposon Research, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Craig E. Eckfeldt
- Department of Medicine, Division of Hematology, Oncology, and Transplantation, and Stem Cell Institute, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Michelle Knowlton
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, Minnesota, United States of America
- Arnold and Mabel Beckman Center for Transposon Research, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Mara E. Robu
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, Minnesota, United States of America
- Arnold and Mabel Beckman Center for Transposon Research, University of Minnesota, Minneapolis, Minnesota, United States of America
- Department of Oral Sciences and Minnesota Craniofacial Research Training Program MinnCResT, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Jon D. Larson
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, Minnesota, United States of America
- Arnold and Mabel Beckman Center for Transposon Research, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Yun Deng
- Carnegie Institute of Washington, Baltimore, Maryland, United States of America
| | - Lisa A. Schimmenti
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, Minnesota, United States of America
- Department of Pediatrics, Genetics and Metabolism and Department of Ophthalmology, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Lynda B.M. Ellis
- Laboratory Medicine and Pathology and Computer Science and Engineering, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Catherine M. Verfaillie
- Department of Medicine, Division of Hematology, Oncology, and Transplantation, and Stem Cell Institute, University of Minnesota, Minneapolis, Minnesota, United States of America
| | | | - Steven A. Farber
- Carnegie Institute of Washington, Baltimore, Maryland, United States of America
| | - Stephen C. Ekker
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, Minnesota, United States of America
- Arnold and Mabel Beckman Center for Transposon Research, University of Minnesota, Minneapolis, Minnesota, United States of America
- * To whom correspondence should be addressed. E-mail:
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Rana AA, Collart C, Gilchrist MJ, Smith JC. Defining synphenotype groups in Xenopus tropicalis by use of antisense morpholino oligonucleotides. PLoS Genet 2006; 2:e193. [PMID: 17112317 PMCID: PMC1636699 DOI: 10.1371/journal.pgen.0020193] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2006] [Accepted: 10/03/2006] [Indexed: 12/03/2022] Open
Abstract
To identify novel genes involved in early development, and as proof-of-principle of a large-scale reverse genetics approach in a vertebrate embryo, we have carried out an antisense morpholino oligonucleotide (MO) screen in Xenopus tropicalis, in the course of which we have targeted 202 genes expressed during gastrula stages. MOs were designed to complement sequence between −80 and +25 bases of the initiating AUG codons of the target mRNAs, and the specificities of many were tested by (i) designing different non-overlapping MOs directed against the same mRNA, (ii) injecting MOs differing in five bases, and (iii) performing “rescue” experiments. About 65% of the MOs caused X. tropicalis embryos to develop abnormally (59% of those targeted against novel genes), and we have divided the genes into “synphenotype groups,” members of which cause similar loss-of-function phenotypes and that may function in the same developmental pathways. Analysis of the expression patterns of the 202 genes indicates that members of a synphenotype group are not necessarily members of the same synexpression group. This screen provides new insights into early vertebrate development and paves the way for a more comprehensive MO-based analysis of gene function in X. tropicalis. Genome sequencing projects have provided remarkable insights into the expression and regulation of many genes. For some species, such as the invertebrates Caenorhabditis elegans and Drosophila melanogaster, it has been possible to assign functions to these genes on a genome-wide scale. For the vertebrates, similar efforts are being made in mouse and zebrafish, but work in the former species is expensive and slow, and the zebrafish experienced a whole genome duplication event, so that some genes may have retained redundant functions. Here, this study uses antisense morpholino oligonucleotides (MOs) to show that the diploid amphibian Xenopus tropicalis provides a powerful alternative species. The authors have designed MOs to target sequences around the initiating AUG codons of 202 genes expressed during early development and confirmed that these function in a specific manner. About 65% of the MOs caused embryos to develop abnormally, and the authors have divided the genes into “synphenotype groups,” members of which cause similar loss-of-function phenotypes. Expression pattern analysis indicates that members of a synphenotype group are not necessarily members of the same synexpression group. This screen provides new insights into vertebrate development and paves the way for a comprehensive MO-based analysis of gene function in X. tropicalis.
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Affiliation(s)
- Amer Ahmed Rana
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, United Kingdom
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom
| | - Clara Collart
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, United Kingdom
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom
| | - Michael J Gilchrist
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, United Kingdom
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom
| | - J. C Smith
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, United Kingdom
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom
- * To whom correspondence should be addressed. E-mail:
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Ogino H, McConnell WB, Grainger RM. Highly efficient transgenesis in Xenopus tropicalis using I-SceI meganuclease. Mech Dev 2006; 123:103-13. [PMID: 16413175 DOI: 10.1016/j.mod.2005.11.006] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2005] [Revised: 11/23/2005] [Accepted: 11/23/2005] [Indexed: 02/07/2023]
Abstract
In this study, we report a highly efficient transgenesis technique for Xenopus tropicalis based on a method described first for Medaka. This simple procedure entails co-injection of meganuclease I-SceI and a transgene construct flanked by two I-SceI sites into fertilized eggs. Approximately 30% of injected embryos express transgenes in a promoter-dependent manner. About 1/3 of such embryos show incorporation of the transgene at the one-cell stage and the remainder are 'half-transgenics' suggesting incorporation at the two-cell stage. Transgenes from both classes of embryos are shown to be transmitted and expressed in offspring. The procedure also works efficiently in Xenopus laevis. Because the needle injection procedure does not significantly damage embryos, a high fraction develop normally and can, as well, be injected with a second reagent, for example an mRNA or antisense morpholino oligonucleotide, thus allowing one to perform several genetic manipulations on embryos at one time. This simple and efficient technique will be a powerful tool for high-throughput transgenesis assays in founder animals, and for facilitating genetic studies in the fast-breeding diploid frog, X. tropicalis.
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Affiliation(s)
- Hajime Ogino
- Department of Biology, University of Virginia, Charlottesville, VA 22904, USA
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33
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Vonica A, Brivanlou AH. An obligatory caravanserai stop on the silk road to neural induction: Inhibition of BMP/GDF signaling. Semin Cell Dev Biol 2006; 17:117-32. [PMID: 16516504 DOI: 10.1016/j.semcdb.2005.11.013] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Work in Xenopus laevis produced the first molecular explanation for neural specification, the default model, where inactivation of the BMP pathway in ectodermal cells changes fates from epidermal to neural. This review covers the present status of our understanding of neural specification, with emphasis on Xenopus, but including relevant facts in other model systems. While recent experiments have increased the complexity of the molecular picture, they have also provided additional support for the default model and the central position of the BMP pathway. We conclude that synergy between accumulated knowledge and technical progress will maintain Xenopus at the forefront of research in neural development.
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Affiliation(s)
- Alin Vonica
- Laboratory of Molecular Embryology, The Rockefeller University, 1230 York Avenue, New York, NY 10021, USA
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Abstract
Xenopus genomics, or Xenomics for short, is coming of age. Indeed, biological insight into processes such as growth factor signaling and patterning of the early embryo is now being gained by combining the value of Xenopus as a model organism for cell and developmental biology with genomic approaches. In this review I address these recent advances and explore future possibilities gained from combining this powerful experimental system with genomic approaches, as well as how our quest to understand basic biological principles will be greatly facilitated though the marriage of Xenopus and genomics.
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Affiliation(s)
- Enrique Amaya
- The Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, CB2 1QN, United Kingdom.
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35
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Gonzales B, Yang H, Henning D, Valdez BC. Cloning and functional characterization of the Xenopus orthologue of the Treacher Collins syndrome (TCOF1) gene product. Gene 2005; 359:73-80. [PMID: 16125876 DOI: 10.1016/j.gene.2005.04.042] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2005] [Revised: 04/21/2005] [Accepted: 04/28/2005] [Indexed: 12/01/2022]
Abstract
Treacher Collins syndrome (TCS) is an autosomal dominant disorder of craniofacial development caused by mutations in the TCOF1 gene, which encodes the nucleolar phosphoprotein treacle. We previously reported a function for mammalian treacle in ribosomal DNA gene transcription by its interaction with upstream binding factor. As an initial step in the development of a TCS model for frog the cDNA that encodes the Xenopus laevis treacle was cloned. Although the derived amino acid sequence shows a poor homology with its mammalian orthologues, Xenopus treacle has 11 highly homologous direct repeats near the center of the protein molecule similar to those present in its human, dog and mouse orthologues. Comparison of their amino acid compositions indicates conservation of predominant specific amino acid residues. Antisense-mediated down-regulation of treacle expression in X. laevis oocytes resulted in inhibition of rDNA gene transcription. The results suggest evolutionary conservation of the function of treacle in ribosomal RNA biogenesis in higher eukaryotes.
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MESH Headings
- Amino Acid Sequence
- Animals
- Cell Line
- Cloning, Molecular
- DNA, Complementary/chemistry
- DNA, Complementary/genetics
- DNA, Ribosomal/genetics
- Down-Regulation/drug effects
- Down-Regulation/genetics
- Female
- Fluorescent Antibody Technique, Indirect
- HeLa Cells
- Humans
- Mandibulofacial Dysostosis/genetics
- Microinjections
- Molecular Sequence Data
- Molecular Weight
- Nuclear Proteins/chemistry
- Nuclear Proteins/genetics
- Nuclear Proteins/metabolism
- Oligonucleotides, Antisense/genetics
- Oligonucleotides, Antisense/pharmacology
- Oocytes/drug effects
- Oocytes/metabolism
- Phosphoproteins/chemistry
- Phosphoproteins/genetics
- Phosphoproteins/metabolism
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Reverse Transcriptase Polymerase Chain Reaction
- Sequence Alignment
- Sequence Analysis, DNA
- Sequence Homology, Amino Acid
- Transcription, Genetic/drug effects
- Xenopus Proteins/chemistry
- Xenopus Proteins/genetics
- Xenopus Proteins/metabolism
- Xenopus laevis/genetics
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Affiliation(s)
- Bianca Gonzales
- Department of Pharmacology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030 USA
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36
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Klee EW, Shim KJ, Pickart MA, Ekker SC, Ellis LBM. AMOD: a morpholino oligonucleotide selection tool. Nucleic Acids Res 2005; 33:W506-11. [PMID: 15980523 PMCID: PMC1160214 DOI: 10.1093/nar/gki453] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
AMOD is a web-based program that aids in the functional evaluation of nucleotide sequences through sequence characterization and antisense morpholino oligonucleotide (target site) selection. Submitted sequences are analyzed by translation initiation site prediction algorithms and sequence-to-sequence comparisons; results are used to characterize sequence features required for morpholino design. Within a defined subsequence, base composition and homodimerization values are computed for all putative morpholino oligonucleotides. Using these properties, morpholino candidates are selected and compared with genomic and transcriptome databases with the goal to identify target-specific enriched morpholinos. AMOD has been used at the University of Minnesota to design approximately 200 morpholinos for a functional genomics screen in zebrafish. The AMOD web server and a tutorial are freely available to both academic and commercial users at http://www.secretomes.umn.edu/AMOD/.
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Affiliation(s)
- Eric W. Klee
- Department of Laboratory Medicine and Pathology, University of MinnesotaMinneapolis, MN, USA
- Arnold and Mabel Beckman Center for Transposon Research, University of MinnesotaMinneapolis, MN, USA
| | - Kyong Jin Shim
- Department of Computer Science and Engineering, University of MinnesotaMinneapolis, MN, USA
- Arnold and Mabel Beckman Center for Transposon Research, University of MinnesotaMinneapolis, MN, USA
| | - Michael A. Pickart
- Department of Genetics, Cell Biology and Development, University of MinnesotaMinneapolis, MN, USA
- Arnold and Mabel Beckman Center for Transposon Research, University of MinnesotaMinneapolis, MN, USA
| | - Stephen C. Ekker
- Department of Genetics, Cell Biology and Development, University of MinnesotaMinneapolis, MN, USA
- Arnold and Mabel Beckman Center for Transposon Research, University of MinnesotaMinneapolis, MN, USA
| | - Lynda B. M. Ellis
- Department of Laboratory Medicine and Pathology, University of MinnesotaMinneapolis, MN, USA
- Arnold and Mabel Beckman Center for Transposon Research, University of MinnesotaMinneapolis, MN, USA
- To whom correspondence should be addressed at Mayo Mail Code 609, 420 SE Delaware Street, Minneapolis, MN 55455, USA. Tel: +1 612 625 9122; Fax: +1 612 624 6404;
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37
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Affiliation(s)
- J C Smith
- Wellcome Trust/Cancer Research UK Gurdon Institute, The Henry Wellcome Building of Cancer and Developmental Biology, Tennis Court Road, Cambridge CB2 1QN, UK.
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38
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Sivak JM, Petersen LF, Amaya E. FGF Signal Interpretation Is Directed by Sprouty and Spred Proteins during Mesoderm Formation. Dev Cell 2005; 8:689-701. [PMID: 15866160 DOI: 10.1016/j.devcel.2005.02.011] [Citation(s) in RCA: 124] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2004] [Revised: 01/05/2005] [Accepted: 02/28/2005] [Indexed: 11/16/2022]
Abstract
Vertebrate gastrulation requires coordination of mesoderm specification with morphogenetic movements. While both of these processes require FGF signaling, it is not known how mesoderm specification and cell movements are coordinated during gastrulation. The related Sprouty and Spred protein families are recently discovered regulators of receptor tyrosine kinase signaling. We identified two genes for each family in Xenopus tropicalis: Xtsprouty1, Xtsprouty2, Xtspred1, and Xtspred2. In gain- and loss-of-function experiments we show that XtSprouty and XtSpred proteins modulate different signaling pathways downstream of the FGF receptor (FGFR), and consequently different developmental processes. Notably, XtSproutys inhibit morphogenesis and Ca(2+) and PKCdelta signaling, leaving MAPK activation and mesoderm specification intact. In contrast, XtSpreds inhibit MAPK activation and mesoderm specification, with little effect on Ca(2+) or PKCdelta signaling. These differences, combined with the timing of their developmental expression, suggest a mechanism to switch FGFR signal interpretation to coordinate mesoderm formation and cell movements during gastrulation.
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Affiliation(s)
- Jeremy M Sivak
- The Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge
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39
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Voigt J, Chen JA, Gilchrist M, Amaya E, Papalopulu N. Expression cloning screening of a unique and full-length set of cDNA clones is an efficient method for identifying genes involved in Xenopus neurogenesis. Mech Dev 2005; 122:289-306. [PMID: 15763209 DOI: 10.1016/j.mod.2004.11.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2004] [Accepted: 11/04/2004] [Indexed: 01/07/2023]
Abstract
Functional screens, where a large numbers of cDNA clones are assayed for certain biological activity, are a useful tool in elucidating gene function. In Xenopus, gain of function screens are performed by pool screening, whereby RNA transcribed in vitro from groups of cDNA clones, ranging from thousands to a hundred, are injected into early embryos. Once an activity is detected in a pool, the active clone is identified by sib-selection. Such screens are intrinsically biased towards potent genes, whose RNA is active at low quantities. To improve the sensitivity and efficiency of a gain of function screen we have bioinformatically processed an arrayed and EST sequenced set of 100,000 gastrula and neurula cDNA clones, to create a unique and full-length set of approximately 2500 clones. Reducing the redundancy and excluding truncated clones from the starting clone set reduced the total number of clones to be screened, in turn allowing us to reduce the pool size to just eight clones per pool. We report that the efficiency of screening this clone set is five-fold higher compared to a redundant set derived from the same libraries. We have screened 960 cDNA clones from this set, for genes that are involved in neurogenesis. We describe the overexpression phenotypes of 18 single clones, the majority of which show a previously uncharacterised phenotype and some of which are completely novel. In situ hybridisation analysis shows that a large number of these genes are specifically expressed in neural tissue. These results demonstrate the effectiveness of a unique full-length set of cDNA clones for uncovering players in a developmental pathway.
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Affiliation(s)
- Jana Voigt
- Department of Anatomy, University of Cambridge, Downing Site, Cambridge CB2 3DY, UK
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40
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Taverner NV, Kofron M, Shin Y, Kabitschke C, Gilchrist MJ, Wylie C, Cho KWY, Heasman J, Smith JC. Microarray-based identification of VegT targets in Xenopus. Mech Dev 2005; 122:333-54. [PMID: 15763211 DOI: 10.1016/j.mod.2004.10.010] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2004] [Revised: 10/14/2004] [Accepted: 10/21/2004] [Indexed: 11/20/2022]
Abstract
The Xenopus T box family member VegT is expressed maternally in the vegetal hemisphere of the embryo. Mis-expression of VegT in prospective ectodermal tissue causes ectopic activation of mesodermal and endodermal markers, and ablation of VegT transcripts prevents proper formation of the mesendoderm, with the entire embryo developing as epidermis. These observations define VegT as a key initiator of mesendodermal development in the Xenopus embryo, and in an effort to understand how it exerts its effects we have used microarray analysis to compare gene expression in control animal caps with that in ectodermal tissue expressing an activated form of VegT. This procedure allowed the identification of 99 potential VegT targets, and we went on to study the expression patterns of these genes and then to ask, for those that are expressed in mesoderm or endoderm, which are direct targets of VegT. The putative regulatory regions of the resulting 14 genes were examined for T domain binding sites, and we also asked whether their expression is down-regulated in embryos in which VegT RNA is ablated. Finally, the functions of these genes were assayed by both over-expression and by use of antisense morpholino oligonucleotides. Our results provide new insights into the function of VegT during early Xenopus development.
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Affiliation(s)
- Nicola V Taverner
- Department of Zoology, Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Henry Wellcome Building of Cancer and Developmental Biology, Tennis Court Road, Cambridge CB2 1QN, UK
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41
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Chen JA, Voigt J, Gilchrist M, Papalopulu N, Amaya E. Identification of novel genes affecting mesoderm formation and morphogenesis through an enhanced large scale functional screen in Xenopus. Mech Dev 2005; 122:307-31. [PMID: 15763210 DOI: 10.1016/j.mod.2004.11.008] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2004] [Revised: 10/22/2004] [Accepted: 11/13/2004] [Indexed: 10/25/2022]
Abstract
The formation of mesoderm is an important developmental process of vertebrate embryos, which can be broken down into several steps; mesoderm induction, patterning, morphogenesis and differentiation. Although mesoderm formation in Xenopus has been intensively studied, much remains to be learned about the molecular events responsible for each of these steps. Furthermore, the interplay between mesoderm induction, patterning and morphogenesis remains obscure. Here, we describe an enhanced functional screen in Xenopus designed for large-scale identification of genes controlling mesoderm formation. In order to improve the efficiency of the screen, we used a Xenopus tropicalis unique set of cDNAs, highly enriched in full-length clones. The screening strategy incorporates two mesodermal markers, Xbra and Xmyf-5, to assay for cell fate specification and patterning, respectively. In addition we looked for phenotypes that would suggest effects in morphogenesis, such as gastrulation defects and shortened anterior-posterior axis. Out of 1728 full-length clones we isolated 82 for their ability to alter the phenotype of tadpoles and/or the expression of Xbra and Xmyf-5. Many of the clones gave rise to similar misexpression phenotypes (synphenotypes) and many of the genes within each synphenotype group appeared to be involved in similar pathways. We determined the expression pattern of the 82 genes and found that most of the genes were regionalized and expressed in mesoderm. We expect that many of the genes identified in this screen will be important in mesoderm formation.
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Affiliation(s)
- Jun-An Chen
- Wellcome Trust/Cancer Research UK Gurdon Institute, Tennis Court Road, Cambridge CB2 1QN, UK
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42
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Abstract
The zebrafish has become a widely used model organism because of its fecundity, its morphological and physiological similarity to mammals, the existence of many genomic tools and the ease with which large, phenotype-based screens can be performed. Because of these attributes, the zebrafish might also provide opportunities to accelerate the process of drug discovery. By combining the scale and throughput of in vitro screens with the physiological complexity of animal studies, the zebrafish promises to contribute to several aspects of the drug development process, including target identification, disease modelling, lead discovery and toxicology.
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Affiliation(s)
- Leonard I Zon
- Howard Hughes Medical Institute, Division of Hematology/Oncology, Children's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA
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43
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Tomlinson ML, Field RA, Wheeler GN. Xenopus as a model organism in developmental chemical genetic screens. MOLECULAR BIOSYSTEMS 2005; 1:223-8. [PMID: 16880986 DOI: 10.1039/b506103b] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Chemical genetics is a potentially powerful tool for studying developmental processes in vertebrate systems. We present data showing Xenopus laevis as a model organism in which systematic chemical genetic screens can be carried out. Previous forward chemical genetic screens, including those with developing zebrafish embryos, have demonstrated the nature and value of biological information gained with this approach. We show how amenable Xenopus is to chemical genetics by investigating a series of compounds either with known biochemical effects, or previously identified to give developmental phenotypes, on a range of biological functions, including the development of pigmentation, the heart and the central nervous system in zebrafish. We have found that the compounds give comparable phenotypes when applied to developing Xenopus embryos. We have also studied the penetrance and expressivity of these chemical genetic phenotypes in relation to genetic variation and the developmental window during which the compound is present. Finally, we assess the feasibility and the potential throughput of a screen in this vertebrate species.
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Gilchrist MJ, Zorn AM, Voigt J, Smith JC, Papalopulu N, Amaya E. Defining a large set of full-length clones from a Xenopus tropicalis EST project. Dev Biol 2004; 271:498-516. [PMID: 15223350 DOI: 10.1016/j.ydbio.2004.04.023] [Citation(s) in RCA: 85] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2004] [Revised: 04/07/2004] [Accepted: 04/07/2004] [Indexed: 02/06/2023]
Abstract
Amphibian embryos from the genus Xenopus are among the best species for understanding early vertebrate development and for studying basic cell biological processes. Xenopus, and in particular the diploid Xenopus tropicalis, is also ideal for functional genomics. Understanding the behavior of genes in this accessible model system will have a significant and beneficial impact on the understanding of similar genes in other vertebrate systems. Here we describe the analysis of 219,270 X. tropicalis expressed sequence tags (ESTs) from four early developmental stages. From these, we have deduced a set of unique expressed sequences comprising approximately 20,000 clusters and 16,000 singletons. Furthermore, we developed a computational method to identify clones that contain the complete coding sequence and describe the creation for the first time of a set of approximately 7000 such clones, the full-length (FL) clone set. The entire EST set is cloned in a eukaryotic expression vector and is flanked by bacteriophage promoters for in vitro transcription, allowing functional experiments to be carried out without further subcloning. We have created a publicly available database containing the FL clone set and related clustering data (http://www.gurdon.cam.ac.uk/informatics/Xenopus.html) and we make the FL clone set publicly available as a resource to accelerate the process of gene discovery and function in this model organism. The creation of the unique set of expressed sequences and the FL clone set pave the way toward a large-scale systematic analysis of gene sequence, gene expression, and gene function in this vertebrate species.
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