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Woo S, Strasser L. Atypical RhoUV GTPases in development and disease. Biochem Soc Trans 2024; 52:89-97. [PMID: 38314621 PMCID: PMC10903452 DOI: 10.1042/bst20230212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 01/23/2024] [Accepted: 01/24/2024] [Indexed: 02/06/2024]
Abstract
RhoU and RhoV are members of the Rho family of small GTPases that comprise their own subfamily. RhoUV GTPases are classified as atypical due to the kinetics of their GTP/GDP binding cycles. They also possess unique N- and C-termini that regulate their subcellular localization and activity. RhoU and RhoV have been linked to cytoskeletal regulation, cell adhesion, and cell migration. They each exhibit distinct expression patterns during embryonic development and diseases such as cancer metastasis, suggesting they have specialized functions. In this review, we will discuss the known functions of RhoU and RhoV, with a focus on their roles in early development, organogenesis, and disease.
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Affiliation(s)
- Stephanie Woo
- Department of Molecular Cell Biology, University of California, Merced, CA, U.S.A
- Quantitative and Systems Biology Graduate Program, University of California, Merced, CA, U.S.A
| | - Leesa Strasser
- Department of Molecular Cell Biology, University of California, Merced, CA, U.S.A
- Quantitative and Systems Biology Graduate Program, University of California, Merced, CA, U.S.A
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2
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He S, Shao W, Chen SC, Wang T, Gibson MC. Spatial transcriptomics reveals a cnidarian segment polarity program in Nematostella vectensis. Curr Biol 2023:S0960-9822(23)00676-0. [PMID: 37315559 DOI: 10.1016/j.cub.2023.05.044] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 04/16/2023] [Accepted: 05/18/2023] [Indexed: 06/16/2023]
Abstract
During early animal evolution, the emergence of axially polarized segments was central to the diversification of complex bilaterian body plans. Nevertheless, precisely how and when segment polarity pathways arose remains obscure. Here, we demonstrate the molecular basis for segment polarization in developing larvae of the sea anemone Nematostella vectensis. Utilizing spatial transcriptomics, we first constructed a 3D gene expression atlas of developing larval segments. Capitalizing on accurate in silico predictions, we identified Lbx and Uncx, conserved homeodomain-containing genes that occupy opposing subsegmental domains under the control of both bone morphogenetic protein (BMP) signaling and the Hox-Gbx cascade. Functionally, Lbx mutagenesis eliminated all molecular evidence of segment polarization at the larval stage and caused an aberrant mirror-symmetric pattern of retractor muscles (RMs) in primary polyps. These results demonstrate the molecular basis for segment polarity in a non-bilaterian animal, suggesting that polarized metameric structures were present in the Cnidaria-Bilateria common ancestor over 600 million years ago.
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Affiliation(s)
- Shuonan He
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Wanqing Shao
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA; Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | | | - Ting Wang
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA; Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA
| | - Matthew C Gibson
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA; Department of Anatomy and Cell Biology, The University of Kansas School of Medicine, Kansas City, KS 66160, USA.
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3
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He S, Shao W, Chen S(C, Wang T, Gibson MC. Spatial transcriptomics reveals a conserved segment polarity program that governs muscle patterning in Nematostella vectensis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.09.523347. [PMID: 36711919 PMCID: PMC9882047 DOI: 10.1101/2023.01.09.523347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
During early animal evolution, the emergence of axially-polarized segments was central to the diversification of complex bilaterian body plans. Nevertheless, precisely how and when segment polarity pathways arose remains obscure. Here we demonstrate the molecular basis for segment polarization in developing larvae of the pre-bilaterian sea anemone Nematostella vectensis . Utilizing spatial transcriptomics, we first constructed a 3-D gene expression atlas of developing larval segments. Capitalizing on accurate in silico predictions, we identified Lbx and Uncx, conserved homeodomain-containing genes that occupy opposing subsegmental domains under the control of both BMP signaling and the Hox-Gbx cascade. Functionally, Lbx mutagenesis eliminated all molecular evidence of segment polarization at larval stage and caused an aberrant mirror-symmetric pattern of retractor muscles in primary polyps. These results demonstrate the molecular basis for segment polarity in a pre-bilaterian animal, suggesting that polarized metameric structures were present in the Cnidaria-Bilateria common ancestor over 600 million years ago. Highlights Nematostella endomesodermal tissue forms metameric segments and displays a transcriptomic profile similar to that observed in bilaterian mesoderm Construction of a comprehensive 3-D gene expression atlas enables systematic dissection of segmental identity in endomesoderm Lbx and Uncx , two conserved homeobox-containing genes, establish segment polarity in Nematostella The Cnidarian-Bilaterian common ancestor likely possessed the genetic toolkit to generate polarized metameric structures.
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Affiliation(s)
- Shuonan He
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA,Current Address: Howard Hughes Medical Institute, Department of Organismic & Evolutionary Biology, Harvard University, 16 Divinity Avenue, Cambridge, Massachusetts 02138, USA
| | - Wanqing Shao
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri 63110, USA,Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri 63110, USA,Current Address: Research Computing, Boston Children’s Hospital, 300 Longwood Avenue, Boston, Massachusetts 02115, USA
| | | | - Ting Wang
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri 63110, USA,Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri 63110, USA,McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63108, USA
| | - Matthew C. Gibson
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA,Department of Anatomy and Cell Biology, The University of Kansas School of Medicine, Kansas City, Kansas 66160, USA,Correspodence:
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4
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NUCKS1 is a highly modified, chromatin-associated protein involved in a diverse set of biological and pathophysiological processes. Biochem J 2022; 479:1205-1220. [PMID: 35695515 PMCID: PMC10016235 DOI: 10.1042/bcj20220075] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 05/17/2022] [Accepted: 05/26/2022] [Indexed: 11/17/2022]
Abstract
The Nuclear Casein and Cyclin-dependent Kinase Substrate 1 (NUCKS1) protein is highly conserved in vertebrates, predominantly localized to the nucleus and one of the most heavily modified proteins in the human proteome. NUCKS1 expression is high in stem cells and the brain, developmentally regulated in mice and associated with several diverse malignancies in humans, including cancer, metabolic syndrome and Parkinson's disease. NUCKS1 function has been linked to modulating chromatin architecture and transcription, DNA repair and cell cycle regulation. In this review, we summarize and discuss the published information on NUCKS1 and highlight the questions that remain to be addressed to better understand the complex biology of this multifaceted protein.
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5
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Xu Y, Jang J, Gye MC. The Xenopus laevis teratogenesis assay for developmental toxicity of phthalate plasticizers and alternatives. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 300:118985. [PMID: 35167930 DOI: 10.1016/j.envpol.2022.118985] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Revised: 02/08/2022] [Accepted: 02/08/2022] [Indexed: 06/14/2023]
Abstract
Contamination of phthalate ester plasticizers threatens the wildlife as well as human health. To evaluate the developmental toxicity of commonly used phthalate esters and emerging alternatives, the frog embryo teratogenesis assay-Xenopus (FETAX) was conducted for dibutyl-phthalate (DBP), benzyl-butyl-phthalate (BBP), dioctyl-terephthalate (DOTP), di(2-propylheptyl)-phthalate (DPHP), diisononyl-phthalate (DINP), diisodecyl-phthalate (DIDP), diethyl hexyl cyclohexane (DEHCH), and diisononyl-cyclohexane-1,2-dicarboxylate (DINCH). The 96-hrs LC50 for DBP, BBP, DOTP, DIDP, DINCH, DINP, DPHP, and DEHCH were 18.3, 20.1, 588.7, 718.0, 837.5, 859.3, 899.0, and 899.0 mg/L, respectively. The 96-hrs EC50 of developmental abnormality of DBP, BBP, DPHP, DOTP, DINP, DEHCH, DINCH, and DIDP were 7.5, 18.2, 645.1, 653.6, 664.4, 745.6, 813.7, and 944.5 mg/L, respectively. The lowest observed effective concentration for embryonic survival, malformation, and growth was DINP, DBP, BBP, DIDP, DPHP, DINCH, DEHCH, and DOTP in increasing order. In tadpoles, DBP, BBP, DEHCH, DINP, and DIDP caused inositol-requiring enzyme 1 or protein kinase R-like endoplasmic reticulum kinase pathway endoplasmic reticulum stress (ERS) in order, and BBP, DBP, DOTP, DPHP, DINP, and DIDP caused long term ERS-related apoptosis or mitochondrial apoptosis in order. Together, in Xenopus embryos, the developmental toxicity and the cellular stress-inducing potential of tested plasticizers were DEHCH, DINCH, DPHP, DIDP, DINP, DOTP, BBP, and DBP in increasing order. In consideration of public as well as environmental health this information would be helpful for industrial choice of phthalate ester plasticizers and their alternatives.
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Affiliation(s)
- Yang Xu
- Department of Life Science and Institute for Natural Sciences, Hanyang University, Seoul, 04763, South Korea
| | - Jihyun Jang
- Department of Life Science and Institute for Natural Sciences, Hanyang University, Seoul, 04763, South Korea
| | - Myung Chan Gye
- Department of Life Science and Institute for Natural Sciences, Hanyang University, Seoul, 04763, South Korea.
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6
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Alaiz Noya M, Berti F, Dietrich S. Comprehensive expression analysis for the core cell cycle regulators in the chicken embryo reveals novel tissue-specific synexpression groups and similarities and differences with expression in mouse, frog and zebrafish. J Anat 2022; 241:42-66. [PMID: 35146756 PMCID: PMC9178385 DOI: 10.1111/joa.13629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Revised: 12/07/2021] [Accepted: 01/05/2022] [Indexed: 11/29/2022] Open
Abstract
The core cell cycle machinery is conserved from yeast to humans, and hence it is assumed that all vertebrates share the same set of players. Yet during vertebrate evolution, the genome was duplicated twice, followed by a further genome duplication in teleost fish. Thereafter, distinct genes were retained in different vertebrate lineages; some individual gene duplications also occurred. To which extent these diversifying tendencies were compensated by retaining the same expression patterns across homologous genes is not known. This study for the first time undertook a comprehensive expression analysis for the core cell cycle regulators in the chicken, focusing in on early neurula and pharyngula stages of development, with the latter representing the vertebrate phylotypic stage. We also compared our data with published data for the mouse, Xenopus and zebrafish, the other established vertebrate models. Our work shows that, while many genes are expressed widely, some are upregulated or specifically expressed in defined tissues of the chicken embryo, forming novel synexpression groups with markers for distinct developmental pathways. Moreover, we found that in the neural tube and in the somite, mRNAs of some of the genes investigated accumulate in a specific subcellular localisation, pointing at a novel link between the site of mRNA translation, cell cycle control and interkinetic nuclear movements. Finally, we show that expression patterns of orthologous genes may differ in the four vertebrate models. Thus, for any study investigating cell proliferation, cell differentiation, tissue regeneration, stem cell behaviour and cancer/cancer therapy, it has to be carefully examined which of the observed effects are due to the specific model organism used, and which can be generalised.
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Affiliation(s)
- Marta Alaiz Noya
- Institute for Biomedical and Biomolecular Science (IBBS), School of Pharmacy and Biomedical Sciences, University of Portsmouth, Portsmouth, UK.,Instituto de Neurociencias de Alicante, Universidad Miguel Hernández - Consejo Superior de Investigaciones Científicas, Alicante, Spain
| | - Federica Berti
- Institute for Biomedical and Biomolecular Science (IBBS), School of Pharmacy and Biomedical Sciences, University of Portsmouth, Portsmouth, UK.,Life Sciences Solutions, Thermo Fisher Scientific, Monza, Italy
| | - Susanne Dietrich
- Institute for Biomedical and Biomolecular Science (IBBS), School of Pharmacy and Biomedical Sciences, University of Portsmouth, Portsmouth, UK
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Abstract
Some organisms have a remarkable ability to heal wounds without scars and to regenerate complex tissues following injury. By gaining a more complete understanding of the biological mechanisms that promote scar-free healing and tissue regeneration, it is hoped that novel treatments that can enhance the healing and regenerative capacity of human patients can be found. In the present article, we briefly examine the genetic, molecular and cellular mechanisms underlying the regeneration of the Xenopus tadpole tail.
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Schmitt SM, Gull M, Brändli AW. Engineering Xenopus embryos for phenotypic drug discovery screening. Adv Drug Deliv Rev 2014; 69-70:225-46. [PMID: 24576445 DOI: 10.1016/j.addr.2014.02.004] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2014] [Revised: 02/13/2014] [Accepted: 02/14/2014] [Indexed: 02/08/2023]
Abstract
Many rare human inherited diseases remain untreatable despite the fact that the disease causing genes are known and adequate mouse disease models have been developed. In vivo phenotypic drug screening relies on isolating drug candidates by their ability to produce a desired therapeutic phenotype in whole organisms. Embryos of zebrafish and Xenopus frogs are abundant, small and free-living. They can be easily arrayed in multi-well dishes and treated with small organic molecules. With the development of novel genome modification tools, such a zinc-finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and CRISPR/Cas, it is now possible to efficiently engineer non-mammalian models of inherited human diseases. Here, we will review the rapid progress made in adapting these novel genome editing tools to Xenopus. The advantages of Xenopus embryos as in vivo models to study human inherited diseases will be presented and their utility for drug discovery screening will be discussed. Being a tetrapod, Xenopus complements zebrafish as an indispensable non-mammalian animal model for the study of human disease pathologies and the discovery of novel therapeutics for inherited diseases.
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9
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A functional genome-wide in vivo screen identifies new regulators of signalling pathways during early Xenopus embryogenesis. PLoS One 2013; 8:e79469. [PMID: 24244509 PMCID: PMC3828355 DOI: 10.1371/journal.pone.0079469] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2013] [Accepted: 10/01/2013] [Indexed: 01/09/2023] Open
Abstract
Embryonic development requires exquisite regulation of several essential processes, such as patterning of tissues and organs, cell fate decisions, and morphogenesis. Intriguingly, these diverse processes are controlled by only a handful of signalling pathways, and mis-regulation in one or more of these pathways may result in a variety of congenital defects and diseases. Consequently, investigating how these signalling pathways are regulated at the molecular level is essential to understanding the mechanisms underlying vertebrate embryogenesis, as well as developing treatments for human diseases. Here, we designed and performed a large-scale gain-of-function screen in Xenopus embryos aimed at identifying new regulators of MAPK/Erk, PI3K/Akt, BMP, and TGF-β/Nodal signalling pathways. Our gain-of-function screen is based on the identification of gene products that alter the phosphorylation state of key signalling molecules, which report the activation state of the pathways. In total, we have identified 20 new molecules that regulate the activity of one or more signalling pathways during early Xenopus development. This is the first time that such a functional screen has been performed, and the findings pave the way toward a more comprehensive understanding of the molecular mechanisms regulating the activity of important signalling pathways under normal and pathological conditions.
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10
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Chen JA, Wichterle H. Apoptosis of limb innervating motor neurons and erosion of motor pool identity upon lineage specific dicer inactivation. Front Neurosci 2012; 6:69. [PMID: 22629237 PMCID: PMC3354549 DOI: 10.3389/fnins.2012.00069] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2012] [Accepted: 04/25/2012] [Indexed: 11/13/2022] Open
Abstract
Diversification of mammalian spinal motor neurons into hundreds of subtypes is critical for the maintenance of body posture and coordination of complex movements. Motor neuron differentiation is controlled by extrinsic signals that regulate intrinsic genetic programs specifying and consolidating motor neuron subtype identity. While transcription factors have been recognized as principal regulators of the intrinsic program, the role of posttranscriptional regulations has not been systematically tested. MicroRNAs produced by Dicer mediated cleavage of RNA hairpins contribute to gene regulation by posttranscriptional silencing. Here we used Olig2-cre conditional deletion of Dicer gene in motor neuron progenitors to examine effects of miRNA biogenesis disruption on postmitotic spinal motor neurons. We report that despite the initial increase in the number of motor neuron progenitors, disruption of Dicer function results in a loss of many limb- and sympathetic ganglia-innervating spinal motor neurons. Furthermore, it leads to defects in motor pool identity specification. Thus, our results indicate that miRNAs are an integral part of the genetic program controlling motor neuron survival and acquisition of subtype specific properties.
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Affiliation(s)
- Jun-An Chen
- Departments of Pathology and Cell Biology, Neurology, and Neuroscience, Center for Motor Neuron Biology and Disease, Columbia University Medical Center New York, NY, USA
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11
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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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12
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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: 133] [Impact Index Per Article: 10.2] [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.
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Affiliation(s)
- Richard M Harland
- Department of Molecular and Cell Biology, Center for Integrative Genomics, University of California Berkeley, CA 94720, USA
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A functional screen for genes involved in Xenopus pronephros development. Mech Dev 2008; 125:571-86. [PMID: 18472403 DOI: 10.1016/j.mod.2008.03.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2008] [Revised: 03/05/2008] [Accepted: 03/08/2008] [Indexed: 11/23/2022]
Abstract
In Xenopus, the pronephros is the functional larval kidney and consists of two identifiable components; the glomus, the pronephric tubules, which can be divided into four separate segments, based on marker gene expression. The simplicity of this organ, coupled with the fact that it displays the same basic organization and function as more complex mesonephros and metanephros, makes this an attractive model to study vertebrate kidney formation. In this study, we have performed a functional screen specifically to identify genes involved in pronephros development in Xenopus. Gain-of-function screens are performed by injecting mRNA pools made from a non-redundant X. tropicalis full-length plasmid cDNA library into X. laevis eggs, followed by sib-selection to identify the single clone that caused abnormal phenotypes in the pronephros. Out of 768 egg and gastrula stage cDNA clones, 31 genes, approximately 4% of the screened clones, affected pronephric marker expression examined by whole mount in situ hybridization or antibody staining. Most of the positive clones had clear expression patterns in pronephros and predicted/established functions highly likely to be involved in developmental processes. In order to carry out a more detailed study, we selected Sox7, Cpeb3, P53csv, Mecr and Dnajc15, which had highly specific expression patterns in the pronephric region. The over-expression of these five selected clones indicated that they caused pronephric abnormalities with different temporal and spatial effects. These results suggest that our strategy to identify novel genes involved in pronephros development was highly successful, and that this strategy is effective for the identification of novel genes involved in late developmental events.
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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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15
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Hamada M, Wada S, Kobayashi K, Satoh N. Novel genes involved in Ciona intestinalis embryogenesis: characterization of gene knockdown embryos. Dev Dyn 2007; 236:1820-31. [PMID: 17557306 DOI: 10.1002/dvdy.21181] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
The sequenced genome of the urochordate ascidian Ciona intestinalis contains nearly 2,500 genes that have vertebrate homologues, but their functions are as yet unknown. To identify novel genes involved in early chordates embryogenesis, we previously screened 200 Ciona genes by knockdown experiments using specific morpholino oligonucleotides and found that suppression of the translation of 40 genes caused embryonic defects (Yamada et al. [2003] Development 130:6485-6495). We have since examined an additional 304 genes, that is, screening 504 genes overall, and a total of 111 genes showed morphological defects when gene function was suppressed. We further examined the role of these genes in the differentiation of six major tissues of the embryo: endoderm, muscle, epidermis, neural tissue, mesenchyme, and notochord. Based on the similarity of phenotypes of gene knockdown embryos, genes were categorized into several groups, with the suggestion that the genes within a given group are involved in similar developmental processes. For example, five were shown to be novel genes that are likely involved in beta-catenin-mediated endoderm formation. The type of large-scale screening used is, therefore, a powerful approach to identify novel genes with significant developmental functions, the details of which will be determined in future studies.
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Affiliation(s)
- Mayuko Hamada
- CREST, Japan Science Technology Agency, Kawaguchi, Saitama, Japan.
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16
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Chen JA, Chu ST, Amaya E. Maintenance of motor neuron progenitors in Xenopus requires a novel localized cyclin. EMBO Rep 2007; 8:287-92. [PMID: 17304238 PMCID: PMC1808035 DOI: 10.1038/sj.embor.7400903] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2006] [Revised: 11/27/2006] [Accepted: 12/19/2006] [Indexed: 12/22/2022] Open
Abstract
The ventral spinal cord contains a pool of motor neuron progenitors (pMNs), which sequentially generate motor neurons and oligodendrocytes in the embryo. The mechanisms responsible for the maintenance of pMNs are not clearly understood. We have identified a novel cyclin, cyclin Dx (ccndx), which is specifically expressed in pMNs in Xenopus. Here, we show that inhibition of ccndx causes paralysis in embryos. Furthermore, we show that maintenance of pMNs requires ccndx function. In addition, inhibition of ccndx results in the specific loss of differentiated motor neurons. However, the expression of interneuron or sensory neuron markers is unaffected in these embryos, suggesting that the role of ccndx is specifically to maintain pMNs. Thus, we have identified, for the first time, a tissue-specific cell-cycle regulator that is essential for the maintenance of a pool of neural progenitors in the vertebrate spinal cord.
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Affiliation(s)
- Jun-An Chen
- The Wellcome Trust/Cancer Research UK Gurdon Institute and Department of Zoology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK
| | - Sin-Tak Chu
- Institute of Biological Chemistry, Academia Sinica, Post Box 23-106, Taipei, Taiwan
| | - Enrique Amaya
- The Wellcome Trust/Cancer Research UK Gurdon Institute and Department of Zoology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK
- The Healing Foundation Centre, Michael Smith Building, Faculty of Life Sciences, University of Manchester, Oxford Road, Manchester M13 9PT, UK
- Tel: 44 161 275 1716; Fax: 44 161 275 1505; E-mail:
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17
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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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18
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Abstract
Vertebrate mesoderm induction is one of the classical problems in developmental biology. Various developmental biology approaches, particularly in Xenopus and zebrafish, have identified many of the key factors that are involved in this process and have provided major insights into how these factors interact as part of a signalling and transcription-factor network. These data are beginning to be refined by high-throughput approaches such as microarray assays. Future challenges include understanding how the prospective mesodermal cells integrate the various signals they receive and how they resolve this information to regulate their morphogenetic behaviours and cell-fate decisions.
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Affiliation(s)
- David Kimelman
- Department of Biochemistry, Box 357350, University of Washington, Seattle, Washington 98195-7350, USA.
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19
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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.
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Affiliation(s)
- Samantha Carruthers
- Vertebrate Development and Genetics, The Morgan Building, Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1HH, UK
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20
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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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21
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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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22
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Baldessari D, Shin Y, Krebs O, König R, Koide T, Vinayagam A, Fenger U, Mochii M, Terasaka C, Kitayama A, Peiffer D, Ueno N, Eils R, Cho KW, Niehrs C. Global gene expression profiling and cluster analysis in Xenopus laevis. Mech Dev 2005; 122:441-75. [PMID: 15763214 DOI: 10.1016/j.mod.2004.11.007] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2004] [Revised: 10/04/2004] [Accepted: 11/07/2004] [Indexed: 01/12/2023]
Abstract
We have undertaken a large-scale microarray gene expression analysis using cDNAs corresponding to 21,000 Xenopus laevis ESTs. mRNAs from 37 samples, including embryos and adult organs, were profiled. Cluster analysis of embryos of different stages was carried out and revealed expected affinities between gastrulae and neurulae, as well as between advanced neurulae and tadpoles, while egg and feeding larvae were clearly separated. Cluster analysis of adult organs showed some unexpected tissue-relatedness, e.g. kidney is more related to endodermal than to mesodermal tissues and the brain is separated from other neuroectodermal derivatives. Cluster analysis of genes revealed major phases of co-ordinate gene expression between egg and adult stages. During the maternal-early embryonic phase, genes maintaining a rapidly dividing cell state are predominantly expressed (cell cycle regulators, chromatin proteins). Genes involved in protein biosynthesis are progressively induced from mid-embryogenesis onwards. The larval-adult phase is characterised by expression of genes involved in metabolism and terminal differentiation. Thirteen potential synexpression groups were identified, which encompass components of diverse molecular processes or supra-molecular structures, including chromatin, RNA processing and nucleolar function, cell cycle, respiratory chain/Krebs cycle, protein biosynthesis, endoplasmic reticulum, vesicle transport, synaptic vesicle, microtubule, intermediate filament, epithelial proteins and collagen. Data filtering identified genes with potential stage-, region- and organ-specific expression. The dataset was assembled in the iChip microarray database, , which allows user-defined queries. The study provides insights into the higher order of vertebrate gene expression, identifies synexpression groups and marker genes, and makes predictions for the biological role of numerous uncharacterized genes.
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Affiliation(s)
- Danila Baldessari
- Division of Molecular Embryology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
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23
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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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24
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Current Awareness on Comparative and Functional Genomics. Comp Funct Genomics 2005. [PMCID: PMC2447491 DOI: 10.1002/cfg.425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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25
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Pollet N, Muncke N, Verbeek B, Li Y, Fenger U, Delius H, Niehrs C. An atlas of differential gene expression during early Xenopus embryogenesis. Mech Dev 2004; 122:365-439. [PMID: 15763213 DOI: 10.1016/j.mod.2004.11.009] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2004] [Revised: 10/11/2004] [Accepted: 11/07/2004] [Indexed: 01/24/2023]
Abstract
We have carried out a large-scale, semi-automated whole-mount in situ hybridization screen of 8369 cDNA clones in Xenopus laevis embryos. We confirm that differential gene expression is prevalent during embryogenesis since 24% of the clones are expressed non-ubiquitously and 8% are organ or cell type specific marker genes. Sequence analysis and clustering yielded 723 unique genes displaying a differential expression pattern. Of these, 18% were already described in Xenopus, 47% have homologs and 35% are lacking significant sequence similarity in databases. Many of them encode known developmental regulators. We classified 363 of the 723 genes for which a Gene Ontology annotation for molecular function could be attributed and found 'DNA binding' and 'enzyme' the most represented terms. The most common protein domains encoded in these embryonic, differentially expressed genes are the homeobox and RNA Recognition Motif (RRM). Fifty-nine putative orthologs of human disease genes, and 254 organ or cell specific marker genes were identified. Markers were found for nasal placode and archenteron roof, organs for which a specific marker was previously unavailable. Markers were also found for novel subdomains of various other organs. The tissues for which most markers were found are muscle and epidermis. Expression of cell cycle regulators fell in two classes, containing proliferation-promoting and anti-proliferative genes, respectively. We identified 66 new members of the BMP4, chromatin, endoplasmic reticulum, and karyopherin synexpression groups, thus providing a first glimpse of their probable cellular roles. Cluster analysis of tissues to measure tissue relatedness yielded some unorthodox affinities besides expectable lineage relationships. In conclusion, this study represents an atlas of gene expression patterns, which reveals embryonic regionalization, provides novel marker genes, and makes predictions about the functional role of unknown genes.
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Affiliation(s)
- Nicolas Pollet
- Division of Molecular Embryology, Deutsches Krebsforschungszentrum, Im Neuenheimer Feld 280, D-69120 Heidelberg, Germany.
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