1
|
Nakayama T, Kulkarni S. Genomic Complexity of ccdc40 in Xenopus : Implications for CRISPR Targeting and Disease Modeling. MICROPUBLICATION BIOLOGY 2025; 2025:10.17912/micropub.biology.001596. [PMID: 40415903 PMCID: PMC12100157 DOI: 10.17912/micropub.biology.001596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/09/2025] [Revised: 04/25/2025] [Accepted: 05/03/2025] [Indexed: 05/27/2025]
Abstract
Mutations in CCDC40 cause primary ciliary dyskinesia in humans. To evaluate the pathogenicity of variants in CCDC40 , we examined the genomic structure of this gene in Xenopus tropicalis , a diploid frog suitable as a model for genetic studies. We identified inconsistencies in the current ccdc40 gene model and discovered two distinct ccdc40 genes near the previously annotated locus. Surprisingly, Xenopus laevis , an allotetraploid species that typically has two homoeologs, contains only one homoeolog ( ccdc40.S ), making it a more suitable genetic model for studying ccdc40 function and potentially expediting the functional characterization of CCDC40 variants linked to primary ciliary dyskinesia.
Collapse
Affiliation(s)
- Takuya Nakayama
- Department of Biology, University of Virginia, Charlottesville, Virginia, United States
| | - Saurabh Kulkarni
- Department of Biology, University of Virginia, Charlottesville, Virginia, United States
- Department of Cell Biology, University of Virginia, Charlottesville, Virginia, United States
| |
Collapse
|
2
|
Lin XL, Lin JH, Cao Y, Zhang H, He SY, Wu HY, Ye ZB, Zheng L, Qi XF. Cardiomyocyte proliferation and heart regeneration in adult Xenopus tropicalis evidenced by a transgenic reporter line. NPJ Regen Med 2024; 9:40. [PMID: 39702515 DOI: 10.1038/s41536-024-00384-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Accepted: 12/06/2024] [Indexed: 12/21/2024] Open
Abstract
Cardiomyocyte proliferation in adult Xenopus tropicalis during heart regeneration has remained largely contentious due to the absence of genetic evidence. Here, we generated a transgenic reporter line Tg(mlc2:H2C) expressing mCherry specifically in cardiomyocyte nuclei driven by the promoter of myosin light chain 2 (mlc2). Using the reporter line, we found that traditional whole-cell staining is not a rigorous way to identify cardiomyocytes in adult Xenopus tropicalis when using a cryosection with common thickness (5 μm) which leading to a high error, but this deviation could be reduced by increasing section thickness. In addition, the reporter line confirmed that apex resection injury greatly increased the proliferation of mlc2+ cardiomyocytes at 3-30 days post-resection (dpr), thereby regenerating the lost cardiac muscle by 30 dpr in adult Xenopus tropicalis. Our findings from the reporter line have rigorously defined cardiomyocyte proliferation in adult heart upon injury, thereby contributing heart regeneration in adult Xenopus tropicalis.
Collapse
Affiliation(s)
- Xiao-Lin Lin
- Key Laboratory of Regenerative Medicine of Ministry of Education, Institute of Aging and Regenerative Medicine, Department of Developmental & Regenerative Biology, College of Life Science and Technology, Department of Cardiology, The Affiliated Guangdong Second Provincial General Hospital, Jinan University, Guangzhou, 510632, China
| | - Jin-Hua Lin
- Key Laboratory of Regenerative Medicine of Ministry of Education, Institute of Aging and Regenerative Medicine, Department of Developmental & Regenerative Biology, College of Life Science and Technology, Department of Cardiology, The Affiliated Guangdong Second Provincial General Hospital, Jinan University, Guangzhou, 510632, China
| | - Yan Cao
- Key Laboratory of Regenerative Medicine of Ministry of Education, Institute of Aging and Regenerative Medicine, Department of Developmental & Regenerative Biology, College of Life Science and Technology, Department of Cardiology, The Affiliated Guangdong Second Provincial General Hospital, Jinan University, Guangzhou, 510632, China
| | - Han Zhang
- Key Laboratory of Regenerative Medicine of Ministry of Education, Institute of Aging and Regenerative Medicine, Department of Developmental & Regenerative Biology, College of Life Science and Technology, Department of Cardiology, The Affiliated Guangdong Second Provincial General Hospital, Jinan University, Guangzhou, 510632, China
| | - Si-Yi He
- Key Laboratory of Regenerative Medicine of Ministry of Education, Institute of Aging and Regenerative Medicine, Department of Developmental & Regenerative Biology, College of Life Science and Technology, Department of Cardiology, The Affiliated Guangdong Second Provincial General Hospital, Jinan University, Guangzhou, 510632, China
| | - Hai-Yan Wu
- Department of Hematology, The First Affiliated Hospital, Jinan University, Guangzhou, China
| | - Ze-Bing Ye
- Department of Cardiology, The Affiliated Guangdong Second Provincial General Hospital, Jinan University, Guangzhou, China.
| | - Li Zheng
- School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou, China.
| | - Xu-Feng Qi
- Key Laboratory of Regenerative Medicine of Ministry of Education, Institute of Aging and Regenerative Medicine, Department of Developmental & Regenerative Biology, College of Life Science and Technology, Department of Cardiology, The Affiliated Guangdong Second Provincial General Hospital, Jinan University, Guangzhou, 510632, China.
| |
Collapse
|
3
|
Fosl1 is vital to heart regeneration upon apex resection in adult Xenopus tropicalis. NPJ Regen Med 2021; 6:36. [PMID: 34188056 PMCID: PMC8242016 DOI: 10.1038/s41536-021-00146-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 06/11/2021] [Indexed: 02/06/2023] Open
Abstract
Cardiovascular disease is the leading cause of death in the world due to losing regenerative capacity in the adult heart. Frogs possess remarkable capacities to regenerate multiple organs, including spinal cord, tail, and limb, but the response to heart injury and the underlying molecular mechanism remains largely unclear. Here we demonstrated that cardiomyocyte proliferation greatly contributes to heart regeneration in adult X. tropicalis upon apex resection. Using RNA-seq and qPCR, we found that the expression of Fos-like antigen 1 (Fosl1) was dramatically upregulated in early stage of heart injury. To study Fosl1 function in heart regeneration, its expression was modulated in vitro and in vivo. Overexpression of X. tropicalis Fosl1 significantly promoted the proliferation of cardiomyocyte cell line H9c2. Consistently, endogenous Fosl1 knockdown suppressed the proliferation of H9c2 cells and primary cardiomyocytes isolated from neonatal mice. Taking use of a cardiomyocyte-specific dominant-negative approach, we show that blocking Fosl1 function leads to defects in cardiomyocyte proliferation during X. tropicalis heart regeneration. We further show that knockdown of Fosl1 can suppress the capacity of heart regeneration in neonatal mice, but overexpression of Fosl1 can improve the cardiac function in adult mouse upon myocardium infarction. Co-immunoprecipitation, luciferase reporter, and ChIP analysis reveal that Fosl1 interacts with JunB and promotes the expression of Cyclin-T1 (Ccnt1) during heart regeneration. In conclusion, we demonstrated that Fosl1 plays an essential role in cardiomyocyte proliferation and heart regeneration in vertebrates, at least in part, through interaction with JunB, thereby promoting expression of cell cycle regulators including Ccnt1.
Collapse
|
4
|
Lane M, Slocum M, Khokha MK. Raising and Maintaining Xenopus tropicalis from Tadpole to Adult. Cold Spring Harb Protoc 2021; 2022:Pdb.prot106369. [PMID: 34031210 DOI: 10.1101/pdb.prot106369] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Xenopus tropicalis is a powerful model organism for cell and developmental biology research. Recently, precise gene-editing methods such as CRISPR-Cas9 have allowed facile creation of mutants. The ability to raise and maintain lines of wild-type and mutant animals through all life stages is thus critical for researchers using this model organism. The long fertile life (>8-10 yr) and relatively hardy nature of X. tropicalis makes this a straightforward process. Environmental parameters such as water temperature, pH, and conductivity often vary slightly among husbandry protocols. However, the stability of these variables is essential for rearing success. This protocol describes conditions to optimally raise and maintain X. tropicalis from embryos to adulthood.
Collapse
Affiliation(s)
- Maura Lane
- Pediatric Genomics Discovery Program, Department of Pediatrics and Genetics, Yale University School of Medicine, New Haven, Connecticut 06510, USA
| | - Michael Slocum
- Pediatric Genomics Discovery Program, Department of Pediatrics and Genetics, Yale University School of Medicine, New Haven, Connecticut 06510, USA
| | - Mustafa K Khokha
- Pediatric Genomics Discovery Program, Department of Pediatrics and Genetics, Yale University School of Medicine, New Haven, Connecticut 06510, USA
| |
Collapse
|
5
|
Mitros T, Lyons JB, Session AM, Jenkins J, Shu S, Kwon T, Lane M, Ng C, Grammer TC, Khokha MK, Grimwood J, Schmutz J, Harland RM, Rokhsar DS. A chromosome-scale genome assembly and dense genetic map for Xenopus tropicalis. Dev Biol 2019; 452:8-20. [PMID: 30980799 DOI: 10.1016/j.ydbio.2019.03.015] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Revised: 03/12/2019] [Accepted: 03/22/2019] [Indexed: 12/19/2022]
Abstract
The Western clawed frog Xenopus tropicalis is a diploid model system for both frog genetics and developmental biology, complementary to the paleotetraploid X. laevis. Here we report a chromosome-scale assembly of the X. tropicalis genome, improving the previously published draft genome assembly through the use of new assembly algorithms, additional sequence data, and the addition of a dense genetic map. The improved genome enables the mapping of specific traits (e.g., the sex locus or Mendelian mutants) and the characterization of chromosome-scale synteny with other tetrapods. We also report an improved annotation of the genome that integrates deep transcriptome sequence from diverse tissues and stages. The exon-intron structures of these genes are highly conserved relative to both X. laevis and human, as are chromosomal linkages ("synteny") and local gene order. A network analysis of developmental gene expression will aid future studies.
Collapse
Affiliation(s)
- Therese Mitros
- University of California, Berkeley, Department of Molecular and Cell Biology, Life Sciences Addition, Berkeley, CA 94720-3200, USA.
| | - Jessica B Lyons
- University of California, Berkeley, Department of Molecular and Cell Biology, Life Sciences Addition, Berkeley, CA 94720-3200, USA.
| | - Adam M Session
- Joint Genome Institute, 2800 Mitchell Dr # 100, Walnut Creek, CA 94598, USA.
| | - Jerry Jenkins
- Joint Genome Institute, 2800 Mitchell Dr # 100, Walnut Creek, CA 94598, USA; HudsonAlpha Institute of Biotechnology, 601 Genome Way, Huntsville, AL 35806, USA.
| | - Shengquiang Shu
- Joint Genome Institute, 2800 Mitchell Dr # 100, Walnut Creek, CA 94598, USA.
| | - Taejoon Kwon
- Department of Biomedical Engineering, School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea.
| | - Maura Lane
- Pediatric Genomics Discovery Program, Department of Pediatrics and Genetics, Yale University School of Medicine, FMP 410, 333 Cedar St./LCI 305, New Haven, CT 06520, USA.
| | - Connie Ng
- University of California, Berkeley, Department of Molecular and Cell Biology, Life Sciences Addition, Berkeley, CA 94720-3200, USA.
| | - Timothy C Grammer
- University of California, Berkeley, Department of Molecular and Cell Biology, Life Sciences Addition, Berkeley, CA 94720-3200, USA.
| | - Mustafa K Khokha
- Pediatric Genomics Discovery Program, Department of Pediatrics and Genetics, Yale University School of Medicine, FMP 410, 333 Cedar St./LCI 305, New Haven, CT 06520, USA.
| | - Jane Grimwood
- Joint Genome Institute, 2800 Mitchell Dr # 100, Walnut Creek, CA 94598, USA; HudsonAlpha Institute of Biotechnology, 601 Genome Way, Huntsville, AL 35806, USA.
| | - Jeremy Schmutz
- Joint Genome Institute, 2800 Mitchell Dr # 100, Walnut Creek, CA 94598, USA; HudsonAlpha Institute of Biotechnology, 601 Genome Way, Huntsville, AL 35806, USA.
| | - Richard M Harland
- University of California, Berkeley, Department of Molecular and Cell Biology, Life Sciences Addition, Berkeley, CA 94720-3200, USA.
| | - Daniel S Rokhsar
- University of California, Berkeley, Department of Molecular and Cell Biology, Life Sciences Addition, Berkeley, CA 94720-3200, USA; Joint Genome Institute, 2800 Mitchell Dr # 100, Walnut Creek, CA 94598, USA; Molecular Genetics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 9040495, Japan.
| |
Collapse
|
6
|
Rebouças R, Silva HRD, Solé M. Malformations in Insular and Coastal Populations of Toads in Rio de Janeiro, Southeastern Brazil. SOUTH AMERICAN JOURNAL OF HERPETOLOGY 2019. [DOI: 10.2994/sajh-d-17-00031.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Affiliation(s)
- Raoni Rebouças
- Programa de Pós-Graduação em Ciências Biológicas - Biologia Animal, Universidade Federal do Espírito Santo. Avenida Fernando Ferrari, 514, Vitória, ES, Brazil
| | - Hélio Ricardo da Silva
- Departamento de Biologia Animal, Universidade Federal Rural do Rio de Janeiro. Caixa Postal: 74524, 23897-970, Seropédica, RJ, Brazil
| | - Mirco Solé
- Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz. Rodovia Jorge Amado, km 16 - Salobrinho, 45662-900, Ilhéus, BA, Brazil
| |
Collapse
|
7
|
Bessa-Silva AR, Vallinoto M, Sodré D, da Cunha DB, Hadad D, Asp NE, Sampaio I, Schneider H, Sequeira F. Patterns of Genetic Variability in Island Populations of the Cane Toad (Rhinella marina) from the Mouth of the Amazon. PLoS One 2016; 11:e0152492. [PMID: 27073849 PMCID: PMC4830453 DOI: 10.1371/journal.pone.0152492] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Accepted: 03/15/2016] [Indexed: 11/19/2022] Open
Abstract
The Amazonian coast has several unique geological characteristics resulting from the interaction between drainage pattern of the Amazon River and the Atlantic Ocean. It is one of the most extensive and sedimentologically dynamic regions of the world, with a large number of continental islands mostly formed less than 10,000 years ago. The natural distribution of the cane toad (Rhinella marina), one of the world's most successful invasive species, in this complex Amazonian system provides an intriguing model for the investigation of the effects of isolation or the combined effects of isolation and habitat dynamic changes on patterns of genetic variability and population differentiation. We used nine fast-evolving microsatellite loci to contrast patterns of genetic variability in six coastal (three mainlands and three islands) populations of the cane toad near the mouth of the Amazon River. Results from Bayesian multilocus clustering approach and Discriminant Analyses of Principal Component were congruent in showing that each island population was genetically differentiated from the mainland populations. All FST values obtained from all pairwise comparisons were significant, ranging from 0.048 to 0.186. Estimates of both recent and historical gene flow were not significantly different from zero across all population pairs, except the two mainland populations inhabiting continuous habitats. Patterns of population differentiation, with a high level of population substructure and absence/restricted gene flow, suggested that island populations of R. marina are likely isolated since the Holocene sea-level rise. However, considering the similar levels of genetic variability found in both island and mainland populations, it is reliable to assume that they were also isolated for longer periods. Given the genetic uniqueness of each cane toad population, together with the high natural vulnerability of the coastal regions and intense human pressures, we suggest that these populations should be treated as discrete units for conservation management purposes.
Collapse
Affiliation(s)
- Adam Rick Bessa-Silva
- Laboratório de Evolução (LEVO), Instituto de Estudos Costeiros (IECOS), Universidade Federal do Pará, Campus de Bragança, Pará, Brasil
| | - Marcelo Vallinoto
- Laboratório de Evolução (LEVO), Instituto de Estudos Costeiros (IECOS), Universidade Federal do Pará, Campus de Bragança, Pará, Brasil
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Laboratório Associado, Campus Agrário de Vairão, Universidade do Porto, Vairão, Portugal
- * E-mail:
| | - Davidson Sodré
- Laboratório de Evolução (LEVO), Instituto de Estudos Costeiros (IECOS), Universidade Federal do Pará, Campus de Bragança, Pará, Brasil
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Laboratório Associado, Campus Agrário de Vairão, Universidade do Porto, Vairão, Portugal
| | - Divino Bruno da Cunha
- Laboratório de Evolução (LEVO), Instituto de Estudos Costeiros (IECOS), Universidade Federal do Pará, Campus de Bragança, Pará, Brasil
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Laboratório Associado, Campus Agrário de Vairão, Universidade do Porto, Vairão, Portugal
| | - Dante Hadad
- Laboratório de Evolução (LEVO), Instituto de Estudos Costeiros (IECOS), Universidade Federal do Pará, Campus de Bragança, Pará, Brasil
| | - Nils Edvin Asp
- Laboratório de Geologia Costeira (LAGECO), Instituto de Estudos Costeiros (IECOS), Universidade Federal do Pará, Campus de Bragança, Pará, Brasil
| | - Iracilda Sampaio
- Laboratório de Filogenômica e Bioinformática, Instituto de Estudos Costeiros (IECOS), Universidade Federal do Pará, Campus de Bragança, Pará, Brasil
| | - Horacio Schneider
- Laboratório de Filogenômica e Bioinformática, Instituto de Estudos Costeiros (IECOS), Universidade Federal do Pará, Campus de Bragança, Pará, Brasil
| | - Fernando Sequeira
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Laboratório Associado, Campus Agrário de Vairão, Universidade do Porto, Vairão, Portugal
| |
Collapse
|
8
|
Igawa T, Watanabe A, Suzuki A, Kashiwagi A, Kashiwagi K, Noble A, Guille M, Simpson DE, Horb ME, Fujii T, Sumida M. Inbreeding Ratio and Genetic Relationships among Strains of the Western Clawed Frog, Xenopus tropicalis. PLoS One 2015. [PMID: 26222540 PMCID: PMC4519292 DOI: 10.1371/journal.pone.0133963] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The Western clawed frog, Xenopus tropicalis, is a highly promising model amphibian, especially in developmental and physiological research, and as a tool for understanding disease. It was originally found in the West African rainforest belt, and was introduced to the research community in the 1990s. The major strains thus far known include the Nigerian and Ivory Coast strains. However, due to its short history as an experimental animal, the genetic relationship among the various strains has not yet been clarified, and establishment of inbred strains has not yet been achieved. Since 2003 the Institute for Amphibian Biology (IAB), Hiroshima University has maintained stocks of multiple X. tropicalis strains and conducted consecutive breeding as part of the National BioResource Project. In the present study we investigated the inbreeding ratio and genetic relationship of four inbred strains at IAB, as well as stocks from other institutions, using highly polymorphic microsatellite markers and mitochondrial haplotypes. Our results show successive reduction of heterozygosity in the genome of the IAB inbred strains. The Ivory Coast strains clearly differed from the Nigerian strains genetically, and three subgroups were identified within both the Nigerian and Ivory Coast strains. It is noteworthy that the Ivory Coast strains have an evolutionary divergent genetic background. Our results serve as a guide for the most effective use of X. tropicalis strains, and the long-term maintenance of multiple strains will contribute to further research efforts.
Collapse
Affiliation(s)
- Takeshi Igawa
- Institute for Amphibian Biology, Graduate School of Science, Hiroshima University, Higashi-Hiroshima, Hiroshima, Japan
- * E-mail:
| | - Ai Watanabe
- Institute for Amphibian Biology, Graduate School of Science, Hiroshima University, Higashi-Hiroshima, Hiroshima, Japan
| | - Atsushi Suzuki
- Institute for Amphibian Biology, Graduate School of Science, Hiroshima University, Higashi-Hiroshima, Hiroshima, Japan
| | - Akihiko Kashiwagi
- Institute for Amphibian Biology, Graduate School of Science, Hiroshima University, Higashi-Hiroshima, Hiroshima, Japan
| | - Keiko Kashiwagi
- Institute for Amphibian Biology, Graduate School of Science, Hiroshima University, Higashi-Hiroshima, Hiroshima, Japan
| | - Anna Noble
- School of Biological Sciences, Institute of Biomedical and Biomolecular Science, University of Portsmouth, Portsmouth, United Kingdom
| | - Matt Guille
- School of Biological Sciences, Institute of Biomedical and Biomolecular Science, University of Portsmouth, Portsmouth, United Kingdom
| | - David E. Simpson
- The Wellcome Trust/Cancer Research UK Gurdon Institute, The Henry Wellcome Building of Cancer and Developmental Biology, University of Cambridge, Cambridge, United Kingdom
| | - Marko E. Horb
- Bell Center for Regenerative Biology and Tissue Engineering and National Xenopus Resource, Marine Biological Laboratory, Woods Hole, MA, United States of America
| | - Tamotsu Fujii
- Department of Health Sciences, Faculty of Human Culture & Science, Prefectural University of Hiroshima, Hiroshima, Japan
| | - Masayuki Sumida
- Institute for Amphibian Biology, Graduate School of Science, Hiroshima University, Higashi-Hiroshima, Hiroshima, Japan
| |
Collapse
|
9
|
Krylov V, Tlapakova T. Xenopus Cytogenetics and Chromosomal Evolution. Cytogenet Genome Res 2015; 145:192-200. [PMID: 26022679 DOI: 10.1159/000406550] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The genus Xenopus represents important model organisms in the field of developmental biology and chromosomal evolution. Developmental processes are tightly coupled with the analysis of gene function via genetic linkage and mapping. Cytogenetic techniques such as chromosome banding or FISH are essential tools for the determination of gene position and subsequently for the construction of linkage and physical maps. Here, we present a summary of key achievements in X. tropicalis and X. laevis cytogenetics with emphasis on the gene localization to chromosomes. The second part of this review is focused on the chromosomal evolution regarding both above-mentioned species. With respect to methodology, hybridization techniques such as FISH and chromosome-specific painting FISH are highlighted.
Collapse
Affiliation(s)
- Vladimir Krylov
- Department of Cell Biology, Faculty of Science, Charles University in Prague, Prague, Czech Republic
| | | |
Collapse
|
10
|
Edens LJ, Levy DL. cPKC regulates interphase nuclear size during Xenopus development. ACTA ACUST UNITED AC 2014; 206:473-83. [PMID: 25135933 PMCID: PMC4137061 DOI: 10.1083/jcb.201406004] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
During Xenopus development, increased nuclear cPKC activity and decreased nuclear association of lamins mediate nuclear scaling. Dramatic changes in cell and nuclear size occur during development and differentiation, and aberrant nuclear size is associated with many disease states. However, the mechanisms that regulate nuclear size are largely unknown. A robust system for investigating nuclear size is early Xenopus laevis development, during which reductions in nuclear size occur without changes in DNA content. To identify cellular factors that regulate nuclear size during development, we developed a novel nuclear resizing assay wherein nuclei assembled in Xenopus egg extract become smaller in the presence of cytoplasmic interphase extract isolated from post-gastrula Xenopus embryos. We show that nuclear shrinkage depends on conventional protein kinase C (cPKC). Increased nuclear cPKC localization and activity and decreased nuclear association of lamins mediate nuclear size reductions during development, and manipulating cPKC activity in vivo during interphase alters nuclear size in the embryo. We propose a model of steady-state nuclear size regulation whereby nuclear expansion is balanced by an active cPKC-dependent mechanism that reduces nuclear size.
Collapse
Affiliation(s)
- Lisa J Edens
- Department of Molecular Biology, University of Wyoming, Laramie, WY 82071
| | - Daniel L Levy
- Department of Molecular Biology, University of Wyoming, Laramie, WY 82071
| |
Collapse
|
11
|
del Viso F, Bhattacharya D, Kong Y, Gilchrist MJ, Khokha MK. Exon capture and bulk segregant analysis: rapid discovery of causative mutations using high-throughput sequencing. BMC Genomics 2012; 13:649. [PMID: 23171430 PMCID: PMC3526394 DOI: 10.1186/1471-2164-13-649] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2012] [Accepted: 11/15/2012] [Indexed: 11/21/2022] Open
Abstract
Background Exome sequencing has transformed human genetic analysis and may do the same for other vertebrate model systems. However, a major challenge is sifting through the large number of sequence variants to identify the causative mutation for a given phenotype. In models like Xenopus tropicalis, an incomplete and occasionally incorrect genome assembly compounds this problem. To facilitate cloning of X. tropicalis mutants identified in forward genetic screens, we sought to combine bulk segregant analysis and exome sequencing into a single step. Results Here we report the first use of exon capture sequencing to identify mutations in a non-mammalian, vertebrate model. We demonstrate that bulk segregant analysis coupled with exon capture sequencing is not only able to identify causative mutations but can also generate linkage information, facilitate the assembly of scaffolds, identify misassembles, and discover thousands of SNPs for fine mapping. Conclusion Exon capture sequencing and bulk segregant analysis is a rapid, inexpensive method to clone mutants identified in forward genetic screens. With sufficient meioses, this method can be generalized to any model system with a genome assembly, polished or unpolished, and in the latter case, it also provides many critical genomic resources.
Collapse
Affiliation(s)
- Florencia del Viso
- Department of Pediatrics and Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA
| | | | | | | | | |
Collapse
|
12
|
Khokha MK. Xenopuswhite papers and resources: Folding functional genomics and genetics into the frog. Genesis 2012; 50:133-42. [DOI: 10.1002/dvg.22015] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2011] [Revised: 01/13/2012] [Accepted: 01/15/2012] [Indexed: 02/04/2023]
|
13
|
Abu-Daya A, Khokha MK, Zimmerman LB. The hitchhiker's guide to Xenopus genetics. Genesis 2012; 50:164-75. [PMID: 22344745 DOI: 10.1002/dvg.22007] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2011] [Revised: 12/19/2011] [Accepted: 12/23/2011] [Indexed: 01/12/2023]
Abstract
A decade after the human genome sequence, most vertebrate gene functions remain poorly understood, limiting benefits to human health from rapidly advancing genomic technologies. Systematic in vivo functional analysis is ideally suited to the experimentally accessible Xenopus embryo, which combines embryological accessibility with a broad range of transgenic, biochemical, and gain-of-function assays. The diploid X. tropicalis adds loss-of-function genetics and enhanced genomics to this repertoire. In the last decade, diverse phenotypes have been recovered from genetic screens, mutations have been cloned, and reverse genetics in the form of TILLING and targeted gene editing have been established. Simple haploid genetics and gynogenesis and the very large number of embryos produced streamline screening and mapping. Improved genomic resources and the revolution in high-throughput sequencing are transforming mutation cloning and reverse genetic approaches. The combination of loss-of-function mutant backgrounds with the diverse array of conventional Xenopus assays offers a uniquely flexible platform for analysis of gene function in vertebrate development.
Collapse
Affiliation(s)
- Anita Abu-Daya
- Division of Developmental Biology, MRC-National Institute for Medical Research, Mill Hill, London, United Kingdom
| | | | | |
Collapse
|
14
|
Abstract
The pipid frog Xenopus tropicalis has emerged as a powerful new model system for combining genetic and genomic analysis of tetrapod development with robust embryological, molecular, and biochemical assays. Its early development closely resembles that of its well-understood relative X. laevis, from which techniques and reagents can be readily transferred. In contrast to the tetraploid X. laevis, X. tropicalis has a compact diploid genome with strong synteny to those of amniotes. Recently, advances in high-throughput sequencing together with solution-hybridization whole-exome enrichment technology offer powerful strategies for cloning novel mutations as well as reverse genetic identification of sequence lesions in specific genes of interest. Further advantages include the wide range of functional and molecular assays available, the large number of embryos/meioses produced, and the ease of haploid genetics and gynogenesis. The addition of these genetic tools to X. tropicalis provides a uniquely flexible platform for analysis of gene function in vertebrate development.
Collapse
Affiliation(s)
- Timothy J. Geach
- National Institute for Medical Research, The Ridgeway, Mill Hill, London, NW7 1AA United Kingdom
| | | | - Lyle B. Zimmerman
- National Institute for Medical Research, The Ridgeway, Mill Hill, London, NW7 1AA United Kingdom
| |
Collapse
|
15
|
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.
Collapse
Affiliation(s)
- Alan Jafkins
- European Xenopus Resource Centre, School of Biological Sciences, University of Portsmouth, Portsmouth, England, UK
| | | | | | | | | |
Collapse
|
16
|
Abstract
Xenopus tropicalis was introduced as a model system for genetic, and then genomic research, in the early 1990s, complementing work on the widely used model organism Xenopus laevis. Its shorter generation time and diploid genome has facilitated a number of experimental approaches. It has permitted multigenerational experiments (e.g., preparation of transgenic lines and generation of mutant lines) that have added powerful approaches for research by the Xenopus community. As a diploid animal, its simpler genome was sequenced before X. laevis, and has provided a highly valuable resource indispensable for all Xenopus researchers. As more sophisticated transgenic technologies for manipulating gene expression are developed, and mutations, particularly null mutations, are identified in widely studied genes involved in critical cellular and developmental processes, researchers will increasingly turn to X. tropicalis for definitive analysis of complex genetic pathways. This chapter describes the historical and conceptual development of X. tropicalis as a genetic and genomic model system for higher vertebrate development.
Collapse
Affiliation(s)
- Robert M Grainger
- Department of Biology, University of Virginia, Charlottesville, VA, USA.
| |
Collapse
|
17
|
Abstract
Reverse genetics in Xenopus has been limited to knockdown strategies using antisense morpholino oligonucleotides (MOs). Recently, engineered zinc-finger nucleases have been used to induce targeted mutations resulting in null alleles. Zinc-finger nuclease (ZFN) technology has been adapted to induce null mutations in many systems previously refractory to targeted gene inactivation. Here we provide a general protocol for inducing targeted mutations in Xenopus tropicalis using ZFNs, a method to detect resulting mutations, and the steps to generate homozygous mutant embryos.
Collapse
|
18
|
Harland RM, Grainger RM. Xenopus research: metamorphosed by genetics and genomics. Trends Genet 2011; 27:507-15. [PMID: 21963197 PMCID: PMC3601910 DOI: 10.1016/j.tig.2011.08.003] [Citation(s) in RCA: 139] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2011] [Revised: 08/25/2011] [Accepted: 08/25/2011] [Indexed: 01/18/2023]
Abstract
Research using Xenopus takes advantage of large, abundant eggs and readily manipulated embryos in addition to conserved cellular, developmental and genomic organization with mammals. Research on Xenopus has defined key principles of gene regulation and signal transduction, embryonic induction, morphogenesis and patterning as well as cell cycle regulation. Genomic and genetic advances in this system, including the development of Xenopus tropicalis as a genetically tractable complement to the widely used Xenopus laevis, capitalize on the classical strengths and wealth of achievements. These attributes provide the tools to tackle the complex biological problems of the new century, including cellular reprogramming, organogenesis, regeneration, gene regulatory networks and protein interactions controlling growth and development, all of which provide insights into a multitude of human diseases and their potential treatments.
Collapse
Affiliation(s)
- Richard M Harland
- Department of Molecular and Cell Biology, Center for Integrative Genomics, University of California Berkeley, CA 94720, USA
| | | |
Collapse
|
19
|
Showell C, Carruthers S, Hall A, Pardo-Manuel de Villena F, Stemple D, Conlon FL. A comparative survey of the frequency and distribution of polymorphism in the genome of Xenopus tropicalis. PLoS One 2011; 6:e22392. [PMID: 21829622 PMCID: PMC3150332 DOI: 10.1371/journal.pone.0022392] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2011] [Accepted: 06/20/2011] [Indexed: 11/18/2022] Open
Abstract
Naturally occurring DNA sequence variation within a species underlies evolutionary adaptation and can give rise to phenotypic changes that provide novel insight into biological questions. This variation exists in laboratory populations just as in wild populations and, in addition to being a source of useful alleles for genetic studies, can impact efforts to identify induced mutations in sequence-based genetic screens. The Western clawed frog Xenopus tropicalis (X. tropicalis) has been adopted as a model system for studying the genetic control of embryonic development and a variety of other areas of research. Its diploid genome has been extensively sequenced and efforts are underway to isolate mutants by phenotype- and genotype-based approaches. Here, we describe a study of genetic polymorphism in laboratory strains of X. tropicalis. Polymorphism was detected in the coding and non-coding regions of developmental genes distributed widely across the genome. Laboratory strains exhibit unexpectedly high frequencies of genetic polymorphism, with alleles carrying a variety of synonymous and non-synonymous codon substitutions and nucleotide insertions/deletions. Inter-strain comparisons of polymorphism uncover a high proportion of shared alleles between Nigerian and Ivory Coast strains, in spite of their distinct geographical origins. These observations will likely influence the design of future sequence-based mutation screens, particularly those using DNA mismatch-based detection methods which can be disrupted by the presence of naturally occurring sequence variants. The existence of a significant reservoir of alleles also suggests that existing laboratory stocks may be a useful source of novel alleles for mapping and functional studies.
Collapse
Affiliation(s)
- Chris Showell
- UNC McAllister Heart Institute, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- * E-mail:
| | - Samantha Carruthers
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, United Kingdom
| | - Amanda Hall
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, United Kingdom
| | - Fernando Pardo-Manuel de Villena
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Derek Stemple
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, United Kingdom
| | - Frank L. Conlon
- UNC McAllister Heart Institute, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| |
Collapse
|
20
|
Efficient targeted gene disruption in the soma and germ line of the frog Xenopus tropicalis using engineered zinc-finger nucleases. Proc Natl Acad Sci U S A 2011; 108:7052-7. [PMID: 21471457 DOI: 10.1073/pnas.1102030108] [Citation(s) in RCA: 115] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The frog Xenopus, an important research organism in cell and developmental biology, currently lacks tools for targeted mutagenesis. Here, we address this problem by genome editing with zinc-finger nucleases (ZFNs). ZFNs directed against an eGFP transgene in Xenopus tropicalis induced mutations consistent with nonhomologous end joining at the target site, resulting in mosaic loss of the fluorescence phenotype at high frequencies. ZFNs directed against the noggin gene produced tadpoles and adult animals carrying up to 47% disrupted alleles, and founder animals yielded progeny carrying insertions and deletions in the noggin gene with no indication of off-target effects. Furthermore, functional tests demonstrated an allelic series of activity between three germ-line mutant alleles. Because ZFNs can be designed against any locus, our data provide a generally applicable protocol for gene disruption in Xenopus.
Collapse
|
21
|
Wells DE, Gutierrez L, Xu Z, Krylov V, Macha J, Blankenburg KP, Hitchens M, Bellot LJ, Spivey M, Stemple DL, Kowis A, Ye Y, Pasternak S, Owen J, Tran T, Slavikova R, Tumova L, Tlapakova T, Seifertova E, Scherer SE, Sater AK. A genetic map of Xenopus tropicalis. Dev Biol 2011; 354:1-8. [PMID: 21458440 PMCID: PMC3098391 DOI: 10.1016/j.ydbio.2011.03.022] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2010] [Revised: 03/05/2011] [Accepted: 03/11/2011] [Indexed: 01/22/2023]
Abstract
We present a genetic map for Xenopus tropicalis, consisting of 2886 Simple Sequence Length Polymorphism (SSLP) markers. Using a bioinformatics-based strategy, we identified unique SSLPs within the X. tropicalis genome. Scaffolds from X. tropicalis genome assembly 2.0 (JGI) were scanned for Simple Sequence Repeats (SSRs); unique SSRs were then tested for amplification and polymorphisms using DNA from inbred Nigerian and Ivory Coast individuals. Thus identified, the SSLPs were genotyped against a mapping cross panel of DNA samples from 190 F2 individuals. Nearly 4000 SSLPs were genotyped, yielding a 2886-marker genetic map consisting of 10 major linkage groups between 73 and 132cM in length, and 4 smaller linkage groups between 7 and 40cM. The total effective size of the map is 1658cM, and the average intermarker distance for each linkage group ranged from 0.27 to 0.75cM. Fluorescence In Situ Hybridization (FISH) was carried out using probes for genes located on mapped scaffolds to assign linkage groups to chromosomes. Comparisons of this map with the X. tropicalis genome Assembly 4.1 (JGI) indicate that the map provides representation of a minimum of 66% of the X. tropicalis genome, incorporating 758 of the approximately 1300 scaffolds over 100,000bp. The genetic map and SSLP marker database constitute an essential resource for genetic and genomic analyses in X. tropicalis.
Collapse
Affiliation(s)
- Dan E Wells
- Department of Biology and Biochemistry, University of Houston, 4800 Calhoun Rd., Houston TX 77204-5001, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
22
|
Abstract
The diploid pipid frog Xenopus tropicalis has recently emerged as a powerful new model system for combining genetic and genomic analysis of tetrapod development with embryological and biochemical assays. Its early development closely resembles that of its well-understood tetraploid relative Xenopus laevis, from which techniques and reagents can be readily transferred, but its compact genome is highly syntenic with those of amniotes. Genetic approaches are facilitated by the large number of embryos produced and the ease of haploid genetics and gynogenesis.
Collapse
|
23
|
Kashiwagi K, Kashiwagi A, Kurabayashi A, Hanada H, Nakajima K, Okada M, Takase M, Yaoita Y. Xenopus tropicalis: an ideal experimental animal in amphibia. Exp Anim 2010; 59:395-405. [PMID: 20660986 DOI: 10.1538/expanim.59.395] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Studies using amphibians have contributed to the progress of life science including developmental biology and cell biology for more than one hundred years. Since the 1950s Xenopus laevis in particular has been used by scientists in many fields for experiments, resulting in the development of various techniques such as microsurgery on early embryos, biosynthesis of gene-encoded protein in oocytes by mRNA injection, misexpression experiments by mRNA injection into embryos, gene knockdown studies by injection of morpholino anti-sense oligonucleotide into fertilized eggs, transgenesis by the I-SceI meganuclease method, and so on. In this paper we will introduce Xenopus tropicalis as an alternative experimental animal. It has a shorter generation time and smaller diploid genome, together with whole-genome sequence data. The procedures available for Xenopus laevis can work well with Xenopus tropicalis, and embryos of both species develop at similar rates according to the developmental staging system of Nieuwkoop and Faber. Experimental systems of Xenopus tropicalis will pave the way for a new era of vertebrate genomics and genetics.
Collapse
Affiliation(s)
- Keiko Kashiwagi
- Division of Embryology and Genetics, Institute for Amphibian Biology, Graduate School of Science, Hiroshima University, Higashihiroshima, Japan
| | | | | | | | | | | | | | | |
Collapse
|
24
|
Levy DL, Heald R. Nuclear size is regulated by importin α and Ntf2 in Xenopus. Cell 2010; 143:288-98. [PMID: 20946986 PMCID: PMC2966892 DOI: 10.1016/j.cell.2010.09.012] [Citation(s) in RCA: 188] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2010] [Revised: 07/06/2010] [Accepted: 09/07/2010] [Indexed: 01/14/2023]
Abstract
The size of the nucleus varies among different cell types, species, and disease states, but mechanisms of nuclear size regulation are poorly understood. We investigated nuclear scaling in the pseudotetraploid frog Xenopus laevis and its smaller diploid relative Xenopus tropicalis, which contains smaller cells and nuclei. Nuclear scaling was recapitulated in vitro using egg extracts, demonstrating that titratable cytoplasmic factors determine nuclear size to a greater extent than DNA content. Nuclear import rates correlated with nuclear size, and varying the concentrations of two transport factors, importin α and Ntf2, was sufficient to account for nuclear scaling between the two species. Both factors modulated lamin B3 import, with importin α increasing overall import rates and Ntf2 reducing import based on cargo size. Importin α also contributes to nuclear size changes during early X. laevis development. Thus, nuclear transport mechanisms are physiological regulators of both interspecies and developmental nuclear scaling.
Collapse
Affiliation(s)
- Daniel L Levy
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720-3200, USA
| | | |
Collapse
|
25
|
Geach TJ, Zimmerman LB. Paralysis and delayed Z-disc formation in the Xenopus tropicalis unc45b mutant dicky ticker. BMC DEVELOPMENTAL BIOLOGY 2010; 10:75. [PMID: 20637071 PMCID: PMC2919470 DOI: 10.1186/1471-213x-10-75] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/09/2010] [Accepted: 07/16/2010] [Indexed: 11/10/2022]
Abstract
BACKGROUND The protein components of mature skeletal muscle have largely been characterized, but the mechanics and sequence of their assembly during normal development remain an active field of study. Chaperone proteins specific to sarcomeric myosins have been shown to be necessary in zebrafish and invertebrates for proper muscle assembly and function. RESULTS The Xenopus tropicalis mutation dicky ticker results in disrupted skeletal muscle myofibrillogenesis, paralysis, and lack of heartbeat, and maps to a missense mutation in the muscle-specific chaperone unc45b. Unc45b is known to be required for folding the head domains of myosin heavy chains, and mutant embryos fail to incorporate muscle myosin into sarcomeres. Mutants also show delayed polymerization of alpha-actinin-rich Z-bodies into the Z-disks that flank the myosin-containing A-band. CONCLUSIONS The dicky ticker phenotype confirms that a requirement for myosin-specific chaperones is conserved in tetrapod sarcomerogenesis, and also suggests a novel role for myosin chaperone function in Z-body maturation.
Collapse
Affiliation(s)
- Timothy J Geach
- Division of Developmental Biology, MRC-National Institute for Medical Research, The Ridgeway, Mill Hill, London, NW7 1AA, UK
| | - Lyle B Zimmerman
- Division of Developmental Biology, MRC-National Institute for Medical Research, The Ridgeway, Mill Hill, London, NW7 1AA, UK
| |
Collapse
|
26
|
Abu-Daya A, Sater AK, Wells DE, Mohun TJ, Zimmerman LB. Absence of heartbeat in the Xenopus tropicalis mutation muzak is caused by a nonsense mutation in cardiac myosin myh6. Dev Biol 2009; 336:20-9. [PMID: 19769958 PMCID: PMC2786259 DOI: 10.1016/j.ydbio.2009.09.019] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2009] [Revised: 08/17/2009] [Accepted: 09/14/2009] [Indexed: 11/25/2022]
Abstract
Mechanisms coupling heart function and cardiac morphogenesis can be
accessed in lower vertebrate embryos that can survive to swimming tadpole stages
on diffused oxygen. Forward genetic screens in Xenopus
tropicalis have identified more than 80 mutations affecting diverse
developmental processes, including cardiac morphogenesis and function. In the
first positional cloning of a mutation in X. tropicalis, we
show that non-contractile hearts in muzak (muz) embryos are
caused by a premature stop codon in the cardiac myosin heavy chain gene
myh6. The mutation deletes the coiled-coil domain
responsible for polymerization into thick filaments, severely disrupting the
cardiomyocyte cytoskeleton. Despite the lack of contractile activity and absence
of a major structural protein, early stages of cardiac morphogenesis including
looping and chamber formation are grossly normal. Muz hearts
subsequently develop dilated chambers with compressed endocardium and fail to
form identifiable cardiac valves and trabeculae.
Collapse
Affiliation(s)
- Anita Abu-Daya
- MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London, NW7 1AA, UK
| | | | | | | | | |
Collapse
|
27
|
Blum M, Beyer T, Weber T, Vick P, Andre P, Bitzer E, Schweickert A. Xenopus, an ideal model system to study vertebrate left-right asymmetry. Dev Dyn 2009; 238:1215-25. [DOI: 10.1002/dvdy.21855] [Citation(s) in RCA: 88] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
|
28
|
Khokha MK, Krylov V, Reilly MJ, Gall JG, Bhattacharya D, Cheung CYJ, Kaufman S, Lam DK, Macha J, Ngo C, Prakash N, Schmidt P, Tlapakova T, Trivedi T, Tumova L, Abu-Daya A, Geach T, Vendrell E, Ironfield H, Sinzelle L, Sater AK, Wells DE, Harland RM, Zimmerman LB. Rapid gynogenetic mapping of Xenopus tropicalis mutations to chromosomes. Dev Dyn 2009; 238:1398-46. [PMID: 19441086 PMCID: PMC2962985 DOI: 10.1002/dvdy.21965] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
Pilot forward genetic screens in Xenopus tropicalis have isolated over 60 recessive mutations. Here we present a simple method for mapping mutations to chromosomes using gynogenesis and centromeric markers. When coupled with available genomic resources, gross mapping facilitates evaluation of candidate genes as well as higher resolution linkage studies. Using gynogenesis, we have mapped the genetic locations of the 10 X. tropicalis centromeres, and performed fluorescence in situ hybridization to validate these locations cytologically. We demonstrate the use of this very small set of centromeric markers to map mutations efficiently to specific chromosomes. Developmental Dynamics 238:1398-1406, 2009. (c) 2009 Wiley-Liss, Inc.
Collapse
Affiliation(s)
- Mustafa K. Khokha
- Department of Pediatrics and Genetics, Yale University School of Medicine, New Haven CT 06520
| | - Vladimir Krylov
- Department of Cell Biology, Charles University, Prague, Czech Republic
| | - Michael J. Reilly
- Division of Developmental Biology, National Institute for Medical Research, London UK
| | - Joseph G. Gall
- Department of Embryology, Carnegie Institution for Science, Baltimore MD
| | - Dipankan Bhattacharya
- Department of Molecular & Cell Biology and Center for Integrative Genomics, University of California, Berkeley CA
| | - Chung Yan J. Cheung
- Department of Molecular & Cell Biology and Center for Integrative Genomics, University of California, Berkeley CA
| | - Sarah Kaufman
- Department of Molecular & Cell Biology and Center for Integrative Genomics, University of California, Berkeley CA
| | - Dang Khoa Lam
- Department of Molecular & Cell Biology and Center for Integrative Genomics, University of California, Berkeley CA
| | - Jaroslav Macha
- Department of Cell Biology, Charles University, Prague, Czech Republic
| | - Catherine Ngo
- Department of Molecular & Cell Biology and Center for Integrative Genomics, University of California, Berkeley CA
| | - Neha Prakash
- Department of Molecular & Cell Biology and Center for Integrative Genomics, University of California, Berkeley CA
| | - Philip Schmidt
- Department of Molecular & Cell Biology and Center for Integrative Genomics, University of California, Berkeley CA
| | - Tereza Tlapakova
- Department of Cell Biology, Charles University, Prague, Czech Republic
| | - Toral Trivedi
- Department of Molecular & Cell Biology and Center for Integrative Genomics, University of California, Berkeley CA
| | - Lucie Tumova
- Department of Cell Biology, Charles University, Prague, Czech Republic
| | - Anita Abu-Daya
- Division of Developmental Biology, National Institute for Medical Research, London UK
| | - Timothy Geach
- Division of Developmental Biology, National Institute for Medical Research, London UK
| | - Elisenda Vendrell
- Division of Developmental Biology, National Institute for Medical Research, London UK
| | - Holly Ironfield
- Division of Developmental Biology, National Institute for Medical Research, London UK
| | | | - Amy K. Sater
- Department of Biology and Biochemistry, University of Houston, Houston, TX
| | - Dan E. Wells
- Department of Biology and Biochemistry, University of Houston, Houston, TX
| | - Richard M. Harland
- Department of Molecular & Cell Biology and Center for Integrative Genomics, University of California, Berkeley CA
| | - Lyle B. Zimmerman
- Division of Developmental Biology, National Institute for Medical Research, London UK
| |
Collapse
|
29
|
Gyllenhammar I, Holm L, Eklund R, Berg C. Reproductive toxicity in Xenopus tropicalis after developmental exposure to environmental concentrations of ethynylestradiol. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2009; 91:171-178. [PMID: 18692912 DOI: 10.1016/j.aquatox.2008.06.019] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2008] [Revised: 06/26/2008] [Accepted: 06/27/2008] [Indexed: 05/26/2023]
Abstract
Reproductive disorders in wildlife and humans have been linked to developmental exposure to endocrine disrupting chemicals. In frog tadpoles, environmental concentrations of ethynylestradiol (EE(2)) disrupt gonadal differentiation which results in female-biased sex ratios at metamorphosis indicating sex-reversal of genotypic males. It is not known if developmental exposure to estrogens results in reduced reproductive success in amphibians. The objective of this work was to investigate if exposure to environmentally relevant concentrations of EE(2) during sex differentiation impairs reproductive organ development, fertility, and sexual behavior in adult frogs. A specific aim was to evaluate if testicular structure and function was affected in males that were not sex-reversed. Xenopus tropicalis tadpoles were exposed until metamorphosis to 6, 60, and 600 pM EE(2). Eight months after metamorphosis, reproductive organ morphology and fertility were evaluated. Larval EE(2)-exposure caused an increased proportion of phenotypic females indicating that sex-reversal of genotypic males is persistent. Sex-reversal was implied at concentrations as low as 6 pM (1.8 ng/l), which is comparable to levels observed in the environment. EE(2)-exposed males that were not sex-reversed had a significantly reduced fertilization rate compared with control males. Histological evaluation revealed that EE(2)-exposed males had a reduced amount of spermatozoa in the testis. Among frogs with ovaries there was a significantly higher percentage that lacked oviducts in the group exposed to 600 pM EE(2) compared with control females. No effect of EE(2) on sexual behavior was noted. The results indicate that reproduction in wild frogs might be impaired by estrogenic environmental pollutants. Similarities between the present effects and those reported in fish, birds and mammals after developmental exposure to estrogens suggest that X. tropicalis is a promising animal model for research on developmental reproductive toxicity.
Collapse
Affiliation(s)
- Irina Gyllenhammar
- Department of Environmental Toxicology, Uppsala University, Centre for Reproductive Biology in Uppsala (CRU), Norbyvägen 18A, 75236 Uppsala, Sweden.
| | | | | | | |
Collapse
|
30
|
El Jamil A, Kanhoush R, Magre S, Boizet-Bonhoure B, Penrad-Mobayed M. Sex-specific expression of SOX9 during gonadogenesis in the amphibian Xenopus tropicalis. Dev Dyn 2008; 237:2996-3005. [DOI: 10.1002/dvdy.21692] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
|
31
|
El Jamil A, Magre S, Mazabraud A, Penrad-Mobayed M. Early aspects of gonadal sex differentiation in Xenopus tropicalis with reference to an antero-posterior gradient. ACTA ACUST UNITED AC 2008; 309:127-37. [PMID: 18213628 DOI: 10.1002/jez.439] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
In an effort to contribute to the development of Xenopus tropicalis as an amphibian model system, we carried out a detailed histological analysis of the process of gonadal sex differentiation and were able to find evidence that gonadal differentiation in X. tropicalis follows an antero-posterior gradient. Although the main reason for the presence of a gradient of sex differentiation is still unknown, this gradient enabled us to define the early events that signal ovarian and testicular differentiation and to identify the undifferentiated gonad structure. Given the various advantages of this emerging model, our work paves the way for experiments that should contribute to our understanding of the dynamics and mechanisms of gonadal sex differentiation in amphibians.
Collapse
Affiliation(s)
- Anwar El Jamil
- Institut Jacques Monod, CNRS/Universités Paris 6 et Paris 7, Paris, France
| | | | | | | |
Collapse
|
32
|
Abstract
Amphibians have long been utilized in scientific research and in education. Historically, investigators have accumulated a wealth of information on the natural history and biology of amphibians, and this body of information is continually expanding as researchers describe new species and study the behaviors of these animals. Amphibians evolved as models for a variety of developmental and physiological processes, largely due to their unique ability to undergo metamorphosis. Scientists have used amphibian embryos to evaluate the effects of toxins, mutagens, and teratogens. Likewise, the animals are invaluable in research due to the ability of some species to regenerate limbs. Certain species of amphibians have short generation times and genetic constructs that make them desirable for transgenic and knockout technology, and there is a current national focus on developing these species for genetic and genomic research. This group of vertebrates is also critically important in the investigation of the inter-relationship of humans and the environment based on their sensitivity to climatic and habitat changes and environmental contamination.
Collapse
Affiliation(s)
- Dorcas P O'Rourke
- Department of Comparative Medicine, 208 Ed Warren Life Science Bldg., East Carolina University - The Brody School of Medicine, 600 Moye Blvd., Greenville, NC 27834, USA.
| |
Collapse
|
33
|
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.
Collapse
Affiliation(s)
- Stefan Hoppler
- School of Medical Sciences, University of Aberdeen, Aberdeen, Scotland, UK
| |
Collapse
|
34
|
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.
Collapse
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
| |
Collapse
|
35
|
Abstract
The study of amphibian embryogenesis has provided important insight into the mechanisms of vertebrate development. The frog Xenopus laevis has been an important model of vertebrate cell biology and development for many decades. Genetic studies in this organism are not practical because of the tetraploid nature of the genome and the long generation time of this species. Recently, a closely related frog, namely Xenopus tropicalis, has been proposed as an alternative system; it shares all of the physical characteristics that make X. laevis a useful model but has the advantage of a diploid genome and short generation time. The rapid accumulation of genetic resources for this animal and the success of pilot mutagenesis screens have helped propel this model system forward. Transposable elements will provide invaluable tools for manipulating the frog genome. These integration systems are ideally suited to transgenesis and insertional mutagenesis strategies in the frog. The high fecundity of the frog combined with the ability to remobilize transposon transgenes integrated into frog genome will allow large-scale insertional mutagenesis screens to be performed in laboratories with modest husbandry capacities.
Collapse
Affiliation(s)
- Donald A Yergeau
- Department of Pathology, St. Jude Children's Research Hospital, North Lauderdale Street, Memphis, Tennessee 38105, USA
| | - Paul E Mead
- Department of Pathology, St. Jude Children's Research Hospital, North Lauderdale Street, Memphis, Tennessee 38105, USA
| |
Collapse
|
36
|
Pettersson I, Arukwe A, Lundstedt-Enkel K, Mortensen AS, Berg C. Persistent sex-reversal and oviducal agenesis in adult Xenopus (Silurana) tropicalis frogs following larval exposure to the environmental pollutant ethynylestradiol. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2006; 79:356-65. [PMID: 16942807 DOI: 10.1016/j.aquatox.2006.07.004] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2006] [Revised: 05/31/2006] [Accepted: 07/04/2006] [Indexed: 05/11/2023]
Abstract
It is known that estrogen-like environmental pollutants can feminise gonadal differentiation in frogs resulting in female-biased sex-ratios at metamorphosis. The long-term effects on reproductive function in frogs following larval exposure to pollutants are less known. Amphibian test systems which allow life-cycle studies are therefore needed. The aim of the present study was to characterise long-term estrogenic effects on the reproductive system of the emerging model species Xenopus (Silurana) tropicalis following larval exposure to ethynylestradiol (EE(2)). EE(2) is a synthetic estrogen that has been detected in sewage effluents and in surface waters. Newly hatched tadpoles (Niewkoop Faber (NF) stage 48) were exposed to the nominal EE(2) concentrations 0 (control), 1, 10, and 100 nM (with analytical chemistry support) until complete metamorphosis (NF stage 66). Effects on the reproductive organs were determined in juveniles (1 month after metamorphosis) and in 9-month-old frogs. Larval exposure to EE(2) caused female-biased phenotypic sex-ratios in both juvenile and adult frogs, which is in agreement with previous work on other frog species. Nearly all (97%) of the 63 EE(2)-exposed 9-month-old frogs had ovaries. Histological evaluation of the gonads of the 9-month-old frogs showed that they were sexually mature. Among the adult frogs with ovaries there was a dose-dependent increase in the frequency of individuals lacking oviducts. Adult frogs exposed to 100 nM EE(2) that had ovaries but no oviducts had lower levels of estrogen receptor alpha (ERalpha) mRNA in the brain than control animals and those exposed to 100 nM EE(2) that had ovaries as well as oviducts. EE(2) exposure did not cause any significant changes in ERalpha mRNA levels in the ovaries of the adult frogs. The reduced level of ERalpha mRNA in the brain of individuals with ovaries lacking oviducts suggests an organizing effect of EE(2) on the central nervous system. The results show that transient early life-stage exposure to an environmental pollutant can induce effects on the reproductive organs and the central nervous system that persist into adulthood. Overall, our data suggest that X. tropicalis, which has a shorter generation time than the well-established model species Xenopus laevis, is a suitable model organism for research on developmental reproductive toxicity in anuran species.
Collapse
Affiliation(s)
- Irina Pettersson
- Department of Environmental Toxicology, Uppsala University, Centre for Reproductive Biology in Uppsala, CRU, Norbyvägen 18 A, 752 36 Uppsala, Sweden
| | | | | | | | | |
Collapse
|
37
|
Goda T, Abu-Daya A, Carruthers S, Clark MD, Stemple DL, Zimmerman LB. Genetic screens for mutations affecting development of Xenopus tropicalis. PLoS Genet 2006; 2:e91. [PMID: 16789825 PMCID: PMC1475704 DOI: 10.1371/journal.pgen.0020091] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2005] [Accepted: 04/28/2006] [Indexed: 11/18/2022] Open
Abstract
We present here the results of forward and reverse genetic screens for chemically-induced mutations in Xenopus tropicalis. In our forward genetic screen, we have uncovered 77 candidate phenotypes in diverse organogenesis and differentiation processes. Using a gynogenetic screen design, which minimizes time and husbandry space expenditures, we find that if a phenotype is detected in the gynogenetic F2 of a given F1 female twice, it is highly likely to be a heritable abnormality (29/29 cases). We have also demonstrated the feasibility of reverse genetic approaches for obtaining carriers of mutations in specific genes, and have directly determined an induced mutation rate by sequencing specific exons from a mutagenized population. The Xenopus system, with its well-understood embryology, fate map, and gain-of-function approaches, can now be coupled with efficient loss-of-function genetic strategies for vertebrate functional genomics and developmental genetics.
Collapse
Affiliation(s)
- Tadahiro Goda
- Division of Developmental Biology, National Institute for Medical Research, The Ridgeway, Mill Hill, London, United Kingdom
| | - Anita Abu-Daya
- Division of Developmental Biology, National Institute for Medical Research, The Ridgeway, Mill Hill, London, United Kingdom
| | - Samantha Carruthers
- Vertebrate Development and Genetics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Matthew D Clark
- Vertebrate Development and Genetics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Derek L Stemple
- Vertebrate Development and Genetics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Lyle B Zimmerman
- Division of Developmental Biology, National Institute for Medical Research, The Ridgeway, Mill Hill, London, United Kingdom
| |
Collapse
|
38
|
Abstract
Developmental biology teachers use the example of the frog embryo to introduce young scientists to the wonders of vertebrate development, and to pose the crucial question, 'How does a ball of cells become an exquisitely patterned embryo?'. Classical embryologists also recognized the power of the amphibian model and used extirpation and explant studies to explore early embryo polarity and to define signaling centers in blastula and gastrula stage embryos. This review revisits these early stages of Xenopus development and summarizes the recent explosion of information on the intrinsic and extrinsic factors that are responsible for the first phases of embryonic patterning.
Collapse
Affiliation(s)
- Janet Heasman
- Division of Developmental Biology, Cincinnati Children's Hospital Research Foundation, 3333 Burnet Avenue, OH 45229-3039, USA.
| |
Collapse
|
39
|
Furlow JD, Neff ES. A developmental switch induced by thyroid hormone: Xenopus laevis metamorphosis. Trends Endocrinol Metab 2006; 17:40-7. [PMID: 16464605 DOI: 10.1016/j.tem.2006.01.007] [Citation(s) in RCA: 116] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/06/2005] [Revised: 11/17/2005] [Accepted: 01/19/2006] [Indexed: 12/19/2022]
Abstract
Thyroid hormone induces the complete metamorphosis of anuran tadpoles into juvenile frogs. Arguably, anuran metamorphosis is the most dramatic effect of a hormone in any vertebrate. Recent advances in pharmacology and molecular biology have made the study of this remarkable process in the frog Xenopus laevis attractive to developmental biologists and endocrinologists alike. In particular, the availability of a straightforward transgenesis assay and the near completion of the Xenopus tropicalis genome are enabling significant advances to be made in our understanding of the major remaining problems of metamorphosis: the extraordinary tissue specificity of responses, the precise timing of morphological changes, the degree of cell autonomy of hormone responses and developmental competence. We argue that X. laevis metamorphosis presents an exciting opportunity for understanding the role of thyroid hormone in vertebrate development.
Collapse
Affiliation(s)
- J David Furlow
- Section of Neurobiology, Physiology, and Behavior, University of California-Davis, One Shields Avenue, Davis, CA 95616-8519, USA.
| | | |
Collapse
|
40
|
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: 82] [Impact Index Per Article: 4.3] [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.
Collapse
Affiliation(s)
- Hajime Ogino
- Department of Biology, University of Virginia, Charlottesville, VA 22904, USA
| | | | | |
Collapse
|
41
|
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: 22] [Impact Index Per Article: 1.2] [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.
Collapse
Affiliation(s)
- Alin Vonica
- Laboratory of Molecular Embryology, The Rockefeller University, 1230 York Avenue, New York, NY 10021, USA
| | | |
Collapse
|
42
|
Abstract
Research using Xenopus laevis has made enormous contributions to our understanding of vertebrate development, control of the eukaryotic cell cycle and the cytoskeleton. One limitation, however, has been the lack of systematic genetic studies in Xenopus to complement molecular and cell biological investigations. Work with the closely related diploid frog Xenopus tropicalis is beginning to address this limitation. Here, we review the resources that will make genetic studies using X. tropicalis a reality.
Collapse
Affiliation(s)
- Samantha Carruthers
- Vertebrate Development and Genetics, The Morgan Building, Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1HH, UK
| | | |
Collapse
|
43
|
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.
Collapse
Affiliation(s)
- Enrique Amaya
- The Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, CB2 1QN, United Kingdom.
| |
Collapse
|
44
|
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.
| |
Collapse
|