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Hansen J, von Melchner H, Wurst W. Mutant non-coding RNA resource in mouse embryonic stem cells. Dis Model Mech 2021; 14:14/2/dmm047803. [PMID: 33729986 PMCID: PMC7875499 DOI: 10.1242/dmm.047803] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 12/14/2020] [Indexed: 01/23/2023] Open
Abstract
Gene trapping is a high-throughput approach that has been used to introduce insertional mutations into the genome of mouse embryonic stem (ES) cells. It is performed with generic gene trap vectors that simultaneously mutate and report the expression of the endogenous gene at the site of insertion and provide a DNA sequence tag for the rapid identification of the disrupted gene. Large-scale international efforts assembled a gene trap library of 566,554 ES cell lines with single gene trap integrations distributed throughout the genome. Here, we re-investigated this unique library and identified mutations in 2202 non-coding RNA (ncRNA) genes, in addition to mutations in 12,078 distinct protein-coding genes. Moreover, we found certain types of gene trap vectors preferentially integrating into genes expressing specific long non-coding RNA (lncRNA) biotypes. Together with all other gene-trapped ES cell lines, lncRNA gene-trapped ES cell lines are readily available for functional in vitro and in vivo studies.
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Affiliation(s)
- Jens Hansen
- Institute of Developmental Genetics, Helmholtz Zentrum München GmbH, German Research Center for Environmental Health, Ingolstädter Landstr. 1, D-85764 Neuherberg, Germany
| | - Harald von Melchner
- Department of Molecular Hematology, University Hospital Frankfurt, Goethe University, D-60590 Frankfurt am Main, Germany
| | - Wolfgang Wurst
- Institute of Developmental Genetics, Helmholtz Zentrum München GmbH, German Research Center for Environmental Health, Ingolstädter Landstr. 1, D-85764 Neuherberg, Germany .,Technische Universität München-Weihenstephan, c/o Helmholtz Zentrum München, Ingolstädter Landstr. 1, D-85764 Neuherberg, Germany.,German Center for Neurodegenerative Diseases (DZNE), Site Munich, Feodor-Lynen-Str. 17, D-81377 Munich, Germany.,Munich Cluster for Systems Neurology (SyNergy), Adolf-Butenandt-Institut, Ludwig-Maximilians-Universität München, Feodor-Lynen-Str. 17, D-81377 München, Germany
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2
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García-García MJ. A History of Mouse Genetics: From Fancy Mice to Mutations in Every Gene. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1236:1-38. [PMID: 32304067 DOI: 10.1007/978-981-15-2389-2_1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The laboratory mouse has become the model organism of choice in numerous areas of biological and biomedical research, including the study of congenital birth defects. The appeal of mice for these experimental studies stems from the similarities between the physiology, anatomy, and reproduction of these small mammals with our own, but it is also based on a number of practical reasons: mice are easy to maintain in a laboratory environment, are incredibly prolific, and have a relatively short reproductive cycle. Another compelling reason for choosing mice as research subjects is the number of tools and resources that have been developed after more than a century of working with these small rodents in laboratory environments. As will become obvious from the reading of the different chapters in this book, research in mice has already helped uncover many of the genes and processes responsible for congenital birth malformations and human diseases. In this chapter, we will provide an overview of the methods, scientific advances, and serendipitous circumstances that have made these discoveries possible, with a special emphasis on how the use of genetics has propelled scientific progress in mouse research and paved the way for future discoveries.
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3
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Zhao Y, Song G, Ren J, Li Q, Zhong S, Cui Z. Sleeping beauty transposon-mediated poly(A)-trapping and insertion mutagenesis in mouse embryonic stem cells. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2018; 59:687-697. [PMID: 30280432 DOI: 10.1002/em.22234] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Revised: 07/03/2018] [Accepted: 07/12/2018] [Indexed: 06/08/2023]
Abstract
Saturation mutagenesis of all endogenous genes within the mouse genome remains a challenging task, although a plenty of gene-editing approaches are available for this purpose. Here, a poly(A)-trap vector was generated for insertion mutagenesis in mouse embryonic stem (mES) cells. This vector contains an expression cassette of neomycin (Neo)-resistant gene lacking a poly(A) signal and flanked by two inverted terminal repeats of the Sleeping Beauty (SB) transposon. The whole poly(A)-trap cassette can transpose into target TA dinucleotides, properly splice with endogenous genes and effectively interrupt the transcription of trapped genes in mES cells after transient induction of SB expression by doxycycline (DOX)-treatment at 1 μg/ml, leading to the formation of multiple geneticin (G418)-resistant cell clones. In the first round of mutation screening, we identified six transposition events from 23 cell clones, including four inserted into an endogenous gene and two landed between endogenous genes. The abilities of self-renewal, totipotency, genetic stability and differentiation of syngap1+/- cells were not affected by DOX-treatment and G418-selection. These findings suggest that this SB transposon-mediated poly(A)-trap vector can be used as an alternative tool for a large-scale screening of mES cells with a gene mutation and for further generation of mutant mouse strains. Environ. Mol. Mutagen. 59:687-697, 2018. © 2018 Wiley Periodicals, Inc.
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Affiliation(s)
- Yi Zhao
- Department of Genetics, School of Basic Medical Sciences, Wuhan University, Wuhan, Hubei, China
| | - Guili Song
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Jing Ren
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Qing Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Shan Zhong
- Department of Genetics, School of Basic Medical Sciences, Wuhan University, Wuhan, Hubei, China
- Hubei Provincial Key Laboratory of Developmentally Originated Disease, Wuhan, Hubei, China
- Hubei Province Key Laboratory of Allergy and Immunology, Wuhan, Hubei, China
| | - Zongbin Cui
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
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4
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Kaloff C, Anastassiadis K, Ayadi A, Baldock R, Beig J, Birling MC, Bradley A, Brown S, Bürger A, Bushell W, Chiani F, Collins F, Doe B, Eppig J, Finnell R, Fletcher C, Flicek P, Fray M, Friedel R, Gambadoro A, Gates H, Hansen J, Herault Y, Hicks G, Hörlein A, Hrabé de Angelis M, Iyer V, de Jong P, Koscielny G, Kühn R, Liu P, Lloyd K, Lopez R, Marschall S, Martínez S, McKerlie C, Meehan T, von Melchner H, Moore M, Murray S, Nagy A, Nutter L, Pavlovic G, Pombero A, Prosser H, Ramirez-Solis R, Ringwald M, Rosen B, Rosenthal N, Rossant J, Ruiz Noppinger P, Ryder E, Skarnes W, Schick J, Schnütgen F, Schofield P, Seisenberger C, Selloum M, Smedley D, Simpson E, Stewart A, Teboul L, Tocchini Valentini G, Valenzuela D, West A, Wurst W. Genome wide conditional mouse knockout resources. ACTA ACUST UNITED AC 2016. [DOI: 10.1016/j.ddmod.2017.08.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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5
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Rosen B, Schick J, Wurst W. Beyond knockouts: the International Knockout Mouse Consortium delivers modular and evolving tools for investigating mammalian genes. Mamm Genome 2015; 26:456-66. [PMID: 26340938 DOI: 10.1007/s00335-015-9598-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Accepted: 08/13/2015] [Indexed: 11/29/2022]
Abstract
The International Knockout Mouse Consortium (IKMC; http://www.mousephenotype.org ) has generated mutations in almost every protein-coding mouse gene and is completing the companion Cre driver resource to expand tissue-specific conditional mutagenesis. Accordingly, the IKMC has carried out high-throughput gene trapping and targeting producing conditional mutations in murine embryonic stem cells in more than 18,500 genes, from which at least 4900 mutant mouse lines have been established to date. This resource is currently being upgraded with more powerful tools, such as visualization and manipulation cassettes that can be easily introduced into IKMC alleles for multifaceted functional studies. In addition, we discuss how existing IKMC products can be used in combination with CRISPR technology to accelerate genome engineering projects. All information and materials from this extraordinary biological resource together with coordinated phenotyping efforts can be retrieved at www.mousephenotype.org . The comprehensive IKMC knockout resource in combination with an extensive set of modular gene cassettes will continue to enhance functional gene annotation in the future and solidify its impact on biomedical research.
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Affiliation(s)
- B Rosen
- Stem Cell Engineering, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - J Schick
- German Research Center for Environmental Health, Institute of Developmental Genetics, Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - W Wurst
- German Research Center for Environmental Health, Institute of Developmental Genetics, Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany. .,Technische Universität München-Weihenstephan, Lehrstuhl für Entwicklungsgenetik, c/o Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany. .,Deutsches Zentrum für Neurodegenerative Erkrankungen e. V. (DZNE), Standort München Feodor-Lynen Strasse 17, 81377, Munich, Germany. .,Munich Cluster for Systems Neurology (SyNergy), Adolf-Butenandt-Institut, Ludwig-Maximilians-Universität München, Feodor-Lynen Strasse 17, 81377, Munich, Germany.
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6
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Dokas J, Chadt A, Nolden T, Himmelbauer H, Zierath JR, Joost HG, Al-Hasani H. Conventional knockout of Tbc1d1 in mice impairs insulin- and AICAR-stimulated glucose uptake in skeletal muscle. Endocrinology 2013; 154:3502-14. [PMID: 23892475 DOI: 10.1210/en.2012-2147] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
In the obesity-resistant SJL mouse strain, we previously identified a naturally occurring loss-of-function mutation in the gene for Tbc1d1. Characterization of recombinant inbred mice that carried the Tbc1d1(SJL) allele on a C57BL/6J background indicated that loss of TBC1D1 protects from obesity, presumably by increasing the use of fat as energy source. To provide direct functional evidence for an involvement of TBC1D1 in energy substrate metabolism, we generated and characterized conventional Tbc1d1 knockout mice. TBC1D1-deficient mice showed moderately reduced body weight, decreased respiratory quotient, and an elevated resting metabolic rate. Ex vivo analysis of intact isolated skeletal muscle revealed a severe impairment in insulin- and AICAR-stimulated glucose uptake in glycolytic extensor digitorum longus muscle and a substantially increased rate of fatty acid oxidation in oxidative soleus muscle. Our results provide direct evidence that TBC1D1 plays a major role in glucose and lipid utilization, and energy substrate preference in skeletal muscle.
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Affiliation(s)
- Janine Dokas
- Institute for Clinical Biochemistry and Pathobiochemistry, German Diabetes Center, Leibniz Center for Diabetes Research at the Heinrich-Heine-University Düsseldorf, Auf'm Hennekamp 65, 40225 Düsseldorf, Germany.
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7
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Vertebrate intersectin1 is repurposed to facilitate cortical midline connectivity and higher order cognition. J Neurosci 2013; 33:4055-65. [PMID: 23447614 DOI: 10.1523/jneurosci.4428-12.2013] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Invertebrate studies have highlighted a role for EH and SH3 domain Intersectin (Itsn) proteins in synaptic vesicle recycling and morphology. Mammals have two Itsn genes (Itsn1 and Itsn2), both of which can undergo alternative splicing to include DBL/PH and C2 domains not present in invertebrate Itsn proteins. To probe for specific and redundant functions of vertebrate Itsn genes, we generated Itsn1, Itsn2, and double mutant mice. While invertebrate mutants showed severe synaptic abnormalities, basal synaptic transmission and plasticity were unaffected at Schaffer CA1 synapses in mutant mice. Surprisingly, intercortical tracts-corpus callosum, ventral hippocampal, and anterior commissures-failed to cross the midline in mice lacking Itsn1, but not Itsn2. In contrast, tracts extending within hemispheres and those that decussate to more caudal brain segments appeared normal. Itsn1 mutant mice showed severe deficits in Morris water maze and contextual fear memory tasks, whereas mice lacking Itsn2 showed normal learning and memory. Thus, coincident with the acquisition of additional signaling domains, vertebrate Itsn1 has been functionally repurposed to also facilitate interhemispheric connectivity essential for high order cognitive functions.
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8
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Guerra E, Lattanzio R, La Sorda R, Dini F, Tiboni GM, Piantelli M, Alberti S. mTrop1/Epcam knockout mice develop congenital tufting enteropathy through dysregulation of intestinal E-cadherin/β-catenin. PLoS One 2012; 7:e49302. [PMID: 23209569 PMCID: PMC3509129 DOI: 10.1371/journal.pone.0049302] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2012] [Accepted: 10/08/2012] [Indexed: 01/27/2023] Open
Abstract
Congenital tufting enteropathy (CTE) is a life-threatening hereditary disease that is characterized by enteric mucosa tufting degeneration and early onset, severe diarrhea. Loss-of-function mutations of the human EPCAM gene (TROP1, TACSTD1) have been indicated as the cause of CTE. However, loss of mTrop1/Epcam in mice appeared to lead to death in utero, due to placental malformation. This and indications of residual Trop-1/EpCAM expression in cases of CTE cast doubt on the role of mTrop1/Epcam in this disease. The aim of this study was to determine the role of TROP1/EPCAM in CTE and to generate an animal model of this disease for molecular investigation and therapy development. Using a rigorous gene-trapping approach, we obtained mTrop1/Epcam -null (knockout) mice. These were born alive, but failed to thrive, and died soon after birth because of hemorrhagic diarrhea. The intestine from the mTrop1/Epcam knockout mice showed intestinal tufts, villous atrophy and colon crypt hyperplasia, as in human CTE. No structural defects were detected in other organs. These results are consistent with TROP1/EPCAM loss being the cause of CTE, thus providing a viable animal model for this disease, and a benchmark for its pathogenetic course. In the affected enteric mucosa, E-cadherin and β-catenin were shown to be dysregulated, leading to disorganized transition from crypts to villi, with progressive loss of membrane localization and increasing intracellular accumulation, thus unraveling an essential role for Trop-1/EpCAM in the maintenance of intestinal architecture and functionality. Supporting information is available for this article.
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Affiliation(s)
- Emanuela Guerra
- Unit of Cancer Pathology, CeSI, University G. d'Annunzio Foundation, Chieti, Italy.
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9
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Smith CL, Eppig JT. The Mammalian Phenotype Ontology as a unifying standard for experimental and high-throughput phenotyping data. Mamm Genome 2012; 23:653-68. [PMID: 22961259 PMCID: PMC3463787 DOI: 10.1007/s00335-012-9421-3] [Citation(s) in RCA: 126] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2012] [Accepted: 07/24/2012] [Indexed: 01/16/2023]
Abstract
The Mammalian Phenotype Ontology (MP) is a structured vocabulary for describing mammalian phenotypes and serves as a critical tool for efficient annotation and comprehensive retrieval of phenotype data. Importantly, the ontology contains broad and specific terms, facilitating annotation of data from initial observations or screens and detailed data from subsequent experimental research. Using the ontology structure, data are retrieved inclusively, i.e., data annotated to chosen terms and to terms subordinate in the hierarchy. Thus, searching for "abnormal craniofacial morphology" also returns annotations to "megacephaly" and "microcephaly," more specific terms in the hierarchy path. The development and refinement of the MP is ongoing, with new terms and modifications to its organization undergoing continuous assessment as users and expert reviewers propose expansions and revisions. A wealth of phenotype data on mouse mutations and variants annotated to the MP already exists in the Mouse Genome Informatics database. These data, along with data curated to the MP by many mouse mutagenesis programs and mouse repositories, provide a platform for comparative analyses and correlative discoveries. The MP provides a standard underpinning to mouse phenotype descriptions for existing and future experimental and large-scale phenotyping projects. In this review we describe the MP as it presently exists, its application to phenotype annotations, the relationship of the MP to other ontologies, and the integration of the MP within large-scale phenotyping projects. Finally we discuss future application of the MP in providing standard descriptors of the phenotype pipeline test results from the International Mouse Phenotype Consortium projects.
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Suraneni P, Rubinstein B, Unruh JR, Durnin M, Hanein D, Li R. The Arp2/3 complex is required for lamellipodia extension and directional fibroblast cell migration. ACTA ACUST UNITED AC 2012; 197:239-51. [PMID: 22492726 PMCID: PMC3328382 DOI: 10.1083/jcb.201112113] [Citation(s) in RCA: 258] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Embryonic stem cell–derived fibroblasts with genetic disruption of the Arp2/3 complex are unable to form lamellipodia or undergo sustained directional migration. The Arp2/3 complex nucleates the formation of the dendritic actin network at the leading edge of motile cells, but it is still unclear if the Arp2/3 complex plays a critical role in lamellipodia protrusion and cell motility. Here, we differentiated motile fibroblast cells from isogenic mouse embryonic stem cells with or without disruption of the ARPC3 gene, which encodes the p21 subunit of the Arp2/3 complex. ARPC3−/− fibroblasts were unable to extend lamellipodia but generated dynamic leading edges composed primarily of filopodia-like protrusions, with formin proteins (mDia1 and mDia2) concentrated near their tips. The speed of cell migration, as well as the rates of leading edge protrusion and retraction, were comparable between genotypes; however, ARPC3−/− cells exhibited a strong defect in persistent directional migration. This deficiency correlated with a lack of coordination of the protrusive activities at the leading edge of ARPC3−/− fibroblasts. These results provide insights into the Arp2/3 complex’s critical role in lamellipodia extension and directional fibroblast migration.
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Affiliation(s)
- Praveen Suraneni
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
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11
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Hübener J, Vauti F, Funke C, Wolburg H, Ye Y, Schmidt T, Wolburg-Buchholz K, Schmitt I, Gardyan A, Driessen S, Arnold HH, Nguyen HP, Riess O. N-terminal ataxin-3 causes neurological symptoms with inclusions, endoplasmic reticulum stress and ribosomal dislocation. ACTA ACUST UNITED AC 2011; 134:1925-42. [PMID: 21653538 DOI: 10.1093/brain/awr118] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Mutant ataxin-3 is aberrantly folded and proteolytically cleaved in spinocerebellar ataxia type 3. The C-terminal region of the protein includes a polyglutamine stretch that is expanded in spinocerebellar ataxia type 3. Here, we report on the analysis of an ataxin-3 mutant mouse that has been obtained by gene trap integration. The ataxin-3 fusion protein encompasses 259 N-terminal amino acids including the Josephin domain and an ubiquitin-interacting motif but lacks the C-terminus with the polyglutamine stretch, the valosin-containing protein binding region and part of the ubiquitin-interacting motif 2. Homozygous ataxin-3 mutant mice were viable and showed no apparent anatomical defects at birth. However, at the age of 9 months, homozygous and heterozygous mutant mice revealed significantly altered behaviour and progressing deficits of motor coordination followed by premature death at ∼12 months. At this time, prominent extranuclear protein aggregates and neuronal cell death was found in mutant mice. This was associated with disturbances of the endoplasmic reticulum-mediated unfolded protein response, consistent with the normal role of ataxin-3 in endoplasmic reticulum homeostasis. Thus, the ataxin-3 gene trap model provides evidence for a contribution of the non-polyglutamine containing ataxin-3 N-terminus, which mimics a calpain fragment that has been observed in spinocerebellar ataxia type 3. Consistent with the disease in humans, gene trap mice develop cytoplasmic inclusion bodies and implicate impaired unfolded protein response in the pathogenesis of spinocerebellar ataxia type 3.
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Affiliation(s)
- Jeannette Hübener
- Department of Medical Genetics, University of Tübingen, 72076 Tübingen, Germany
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12
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High throughput gene trapping and postinsertional modifications of gene trap alleles. Methods 2011; 53:347-55. [DOI: 10.1016/j.ymeth.2010.12.037] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2010] [Revised: 12/27/2010] [Accepted: 12/31/2010] [Indexed: 11/17/2022] Open
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Amsterdam A, Varshney GK, Burgess SM. Retroviral-mediated Insertional Mutagenesis in Zebrafish. Methods Cell Biol 2011; 104:59-82. [PMID: 21924157 DOI: 10.1016/b978-0-12-374814-0.00004-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Since the initial publication of this chapter in 2004, additional methodologies have been developed which could improve and/or complement the original retroviral-mediated insertional mutagenesis. Retroviral vectors have also been shown to be useful for goals other than mutagenesis. In addition, retroviral-mediated insertional mutagenesis has been applied to zebrafish for use in reverse genetics as well as forward screening. Finally, the insertional mutant collection described herein has been screened by a number of labs to find a host of mutants (with genes already identified) with developmental and/or growth defects affecting the eye, liver, skin, craniofacial skeleton, kidney, myeloid cells, hematopoietic stem cells, and axon pathfinding, as well as mutants with defects in the cell cycle or DNA damage response, altered aging properties, and modulated cardiac repolarization. The major complementary approaches and new uses of this technique include:
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Affiliation(s)
- Adam Amsterdam
- Koch Institute for Integrative Cancer Research, Massachusetts Institute for Technology, Cambridge, Massachusetts, USA
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14
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Soehn AS, Pham TT, Schaeferhoff K, Floss T, Weisenhorn DMV, Wurst W, Bonin M, Riess O. Periphilin is strongly expressed in the murine nervous system and is indispensable for murine development. Genesis 2010; 47:697-707. [PMID: 19621438 DOI: 10.1002/dvg.20553] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Periphilin is involved in multiple processes in vivo. To explore its physiological role from an organismic perspective, we generated mice with a gene trap insertion in the periphilin-1 gene. Based on beta-gal reporter activity, a widespread periphilin expression was evident, especially in the developing somites and limbs, the embryonic nervous system, and the adult brain. In accordance with this broad expression, homozygous deficiency of periphilin was lethal in early embryogenesis. Mice with a heterozygous deficiency did not show any abnormalities of brain morphology and function, neither histologically nor regarding the transcriptome. Interestingly, the reduction of the periphilin-1 gene dosage was compensated by an increased expression of the remaining wild-type allele in the brain. These results point to an indispensable function of periphilin during murine development and an important role in the nervous system, reflected by a strong and tightly regulated expression in the murine brain.
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Affiliation(s)
- Anne S Soehn
- Department of Medical Genetics, University of Tuebingen, Tuebingen, Germany.
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15
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Wempe F, De-Zolt S, Koli K, Bangsow T, Parajuli N, Dumitrascu R, Sterner-Kock A, Weissmann N, Keski-Oja J, von Melchner H. Inactivation of sestrin 2 induces TGF-beta signaling and partially rescues pulmonary emphysema in a mouse model of COPD. Dis Model Mech 2010; 3:246-53. [PMID: 20106877 DOI: 10.1242/dmm.004234] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Chronic obstructive pulmonary disease (COPD) is a leading cause of morbidity and mortality worldwide. Cigarette smoking has been identified as one of the major risk factors and several predisposing genetic factors have been implicated in the pathogenesis of COPD, including a single nucleotide polymorphism (SNP) in the latent transforming growth factor (TGF)-beta binding protein 4 (Ltbp4)-encoding gene. Consistent with this finding, mice with a null mutation of the short splice variant of Ltbp4 (Ltbp4S) develop pulmonary emphysema that is reminiscent of COPD. Here, we report that the mutational inactivation of the antioxidant protein sestrin 2 (sesn2) partially rescues the emphysema phenotype of Ltbp4S mice and is associated with activation of the TGF-beta and mammalian target of rapamycin (mTOR) signal transduction pathways. The results suggest that sesn2 could be clinically relevant to patients with COPD who might benefit from antagonists of sestrin function.
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Affiliation(s)
- Frank Wempe
- Department of Molecular Hematology, University of Frankfurt Medical School, 60590 Frankfurt am Main, Germany
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16
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Liao WP, Uetzmann L, Burtscher I, Lickert H. Generation of a mouse line expressing Sox17-driven Cre recombinase with specific activity in arteries. Genesis 2009; 47:476-83. [PMID: 19415628 DOI: 10.1002/dvg.20520] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The HMG-box transcription factor Sox17 has been shown to play important roles in both endoderm formation and cardiovascular development. To conditionally inactivate genes in these domains, we have targeted a codon improved Cre Recombinase (iCre) into exon 1 of the Sox17 gene. Surprisingly, Cre-mediated recombination in the Rosa26 reporter mouse line revealed largely specific activity within the vasculature rather than in endoderm-derived tissues. Here we report a new Cre knock-in mouse line, Sox17(iCre) with activity in the vascular endothelial cells of arteries in the cardiovascular system but not in veins. Cre-mediated recombination was also strongly detected in the liver and spleen, the two organs associated with hematopoiesis. Thus, these results indicate that the Sox17(iCre) would be an appropriate tool for conditional mutagenesis of genes in the vasculature and could be used in studies of blood vessel development and angiogenesis. Additionally, we provide evidence that two different promoters drive Sox17 expression in the endodermal and vascular system.
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Affiliation(s)
- W Perry Liao
- Helmholtz Zentrum München, Institute of Stem Cell Research, Neuherberg, Germany
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17
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Feng C, Xu W, Zuo Z. Knockout of the regulatory factor X1 gene leads to early embryonic lethality. Biochem Biophys Res Commun 2009; 386:715-7. [PMID: 19559676 DOI: 10.1016/j.bbrc.2009.06.111] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2009] [Accepted: 06/21/2009] [Indexed: 11/30/2022]
Abstract
The biological function of regulatory factor X1 (RFX1), the prototype member of the transcription factor RFX family, is not clear. We have used gene trap technique to disrupt the expression of RFX1 in mice. Although, heterozygous RFX1(+/-) mice appear normal and fertile, homozygous RFX1(-/-) embryos died at an early stage (most likely before embryonic day 2.5). Our results indicate that RFX1 regulates expression of genes that are essential for early embryonic development/survival and that RFX1 function can not be compensated by other RFX1 family members.
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Affiliation(s)
- Chenzhuo Feng
- Department of Anesthesiology, School of Medicine, University of Virginia, Charlottesville, VA, USA
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18
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De-Zolt S, Altschmied J, Ruiz P, von Melchner H, Schnütgen F. Gene-trap vectors and mutagenesis. Methods Mol Biol 2009; 530:29-47. [PMID: 19266330 DOI: 10.1007/978-1-59745-471-1_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
Gene trapping can be used to introduce insertional mutations into the genome of mouse embryonic stem cells (ESCs). The method has been adapted for high-throughput use, in an effort to inactivate all genes in the mouse genome. Gene trapping is performed with vectors that simultaneously inactivate and report the expression of the trapped gene and provide a molecular tag for its rapid identification. Gene-trap approaches have been used successfully in the past by both academic and commercial organizations to create libraries of ESC lines harboring mutations in single genes that can be used for making mice. Presently, approximately 70% of the protein-coding genes in the mouse genome have been disrupted by gene-trap insertions. Here we describe the basic methodology used to induce and characterize gene-trap mutations in ESCs.
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Affiliation(s)
- Silke De-Zolt
- Department of Molecular Hematology, University of Frankfurt, Frankfurt am Main, Germany
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19
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Trune DR, Zheng QY. Mouse models for human otitis media. Brain Res 2009; 1277:90-103. [PMID: 19272362 DOI: 10.1016/j.brainres.2009.02.047] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2009] [Revised: 02/11/2009] [Accepted: 02/23/2009] [Indexed: 12/20/2022]
Abstract
Otitis media (OM) remains the most common childhood disease and its annual costs exceed $5 billion. Its potential for permanent hearing impairment also emphasizes the need to better understand and manage this disease. The pathogenesis of OM is multifactorial and includes infectious pathogens, anatomy, immunologic status, genetic predisposition, and environment. Recent progress in mouse model development is helping to elucidate the respective roles of these factors and to significantly contribute toward efforts of OM prevention and control. Genetic predisposition is recognized as an important factor in OM and increasing numbers of mouse models are helping to uncover the potential genetic bases for human OM. Furthermore, the completion of the mouse genome sequence has offered a powerful set of tools for investigating gene function and is generating a rich resource of mouse mutants for studying the genetic factors underlying OM.
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Affiliation(s)
- Dennis R Trune
- Oregon Hearing Research Center, Mail Code NRC04, Oregon Health & Science University, 3181 S.W. Sam Jackson Park Road, Portland, OR 97239-3098, USA
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20
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Komori K, Takagi Y, Sanada M, Lim TH, Nakatsu Y, Tsuzuki T, Sekiguchi M, Hidaka M. A novel protein, MAPO1, that functions in apoptosis triggered by O6-methylguanine mispair in DNA. Oncogene 2009; 28:1142-50. [PMID: 19137017 DOI: 10.1038/onc.2008.462] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
O(6)-Methylguanine produced in DNA induces mutation due to its ambiguous base-pairing properties during DNA replication. To suppress such an outcome, organisms possess a mechanism to eliminate cells carrying O(6)-methylguanine by inducing apoptosis that requires the function of mismatch repair proteins. To identify other factors involved in this apoptotic process, we performed retrovirus-mediated gene-trap mutagenesis and isolated a mutant that acquired resistance to a simple alkylating agent, N-methyl-N-nitrosourea (MNU). However, it was still sensitive to methyl methanesulfonate, 1-(4-amino-2-methyl-5-pyrimidinyl)methyl-3-(2-chloroethyl)-3-nitrosourea, etoposide and ultraviolet irradiation. Moreover, the mutant exhibited an increased mutant frequency after exposure to MNU. The gene responsible was identified and designated Mapo1 (O(6)-methylguanine-induced apoptosis 1). When the expression of the gene was inhibited by small interfering RNA, MNU-induced apoptosis was significantly suppressed. In the Mapo1-defective mutant cells treated with MNU, the mitochondrial membrane depolarization and caspase-3 activation were severely suppressed, although phosphorylation of p53, CHK1 and histone H2AX was observed. The orthologs of the Mapo1 gene are present in various organisms from nematode to humans. Both mouse and human MAPO1 proteins expressed in cells localize in the cytoplasm. We therefore propose that MAPO1 may play a role in the signal-transduction pathway of apoptosis induced by O(6)-methylguanine-mispaired lesions.
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Affiliation(s)
- K Komori
- Department of Molecular Biology, Biomolecular Engineering Research Institute, Suita, Japan
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21
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Söker T, Dalke C, Puk O, Floss T, Becker L, Bolle I, Favor J, Hans W, Hölter SM, Horsch M, Kallnik M, Kling E, Moerth C, Schrewe A, Stigloher C, Topp S, Gailus-Durner V, Naton B, Beckers J, Fuchs H, Ivandic B, Klopstock T, Schulz H, Wolf E, Wurst W, Bally-Cuif L, de Angelis MH, Graw J. Pleiotropic effects in Eya3 knockout mice. BMC DEVELOPMENTAL BIOLOGY 2008; 8:118. [PMID: 19102749 PMCID: PMC2653502 DOI: 10.1186/1471-213x-8-118] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/06/2008] [Accepted: 12/22/2008] [Indexed: 01/29/2023]
Abstract
BACKGROUND In Drosophila, mutations in the gene eyes absent (eya) lead to severe defects in eye development. The functions of its mammalian orthologs Eya1-4 are only partially understood and no mouse model exists for Eya3. Therefore, we characterized the phenotype of a new Eya3 knockout mouse mutant. RESULTS Expression analysis of Eya3 by in-situ hybridizations and beta-Gal-staining of Eya3 mutant mice revealed abundant expression of the gene throughout development, e.g. in brain, eyes, heart, somites and limbs suggesting pleiotropic effects of the mutated gene. A similar complex expression pattern was observed also in zebrafish embryos. The phenotype of young adult Eya3 mouse mutants was systematically analyzed within the German Mouse Clinic. There was no obvious defect in the eyes, ears and kidneys of Eya3 mutant mice. Homozygous mutants displayed decreased bone mineral content and shorter body length. In the lung, the tidal volume at rest was decreased, and electrocardiography showed increased JT- and PQ intervals as well as decreased QRS amplitude. Behavioral analysis of the mutants demonstrated a mild increase in exploratory behavior, but decreased locomotor activity and reduced muscle strength. Analysis of differential gene expression revealed 110 regulated genes in heart and brain. Using real-time PCR, we confirmed Nup155 being down regulated in both organs. CONCLUSION The loss of Eya3 in the mouse has no apparent effect on eye development. The wide-spread expression of Eya3 in mouse and zebrafish embryos is in contrast to the restricted expression pattern in Xenopus embryos. The loss of Eya3 in mice leads to a broad spectrum of minor physiological changes. Among them, the mutant mice move less than the wild-type mice and, together with the effects on respiratory, muscle and heart function, the mutation might lead to more severe effects when the mice become older. Therefore, future investigations of Eya3 function should focus on aging mice.
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Affiliation(s)
- Torben Söker
- Helmholtz Center Munich, German Research Center for Environmental Health, Institute of Developmental Genetics, Neuherberg, Germany.
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Uez N, Lickert H, Kohlhase J, de Angelis MH, Kühn R, Wurst W, Floss T. Sall4 isoforms act during proximal-distal and anterior-posterior axis formation in the mouse embryo. Genesis 2008; 46:463-77. [PMID: 18781635 DOI: 10.1002/dvg.20421] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Reciprocal signals from embryonic and extra-embryonic tissues pattern the embryo in proximal-distal (PD) and anterior-posterior (AP) fashion. Here we have analyzed three gene trap mutations of Sall4, of which one (Sall4-1a) led to a hypomorphic and recessive phenotype, demonstrating that Sall4-1a has yet undescribed extra-embryonic and embryonic functions in regulating PD and AP axis formation. In Sall4-1a mutants the self-maintaining autoregulatory interaction between Bmp4, Nodal and Wnt, which determines the PD axis was disrupted because of defects in the extra-embryonic visceral endoderm. More severely, two distinct Sall4 gene-trap mutants (Sall4-1a,b), resembling null mutants, failed to initiate Bmp4 expression in the extra-embryonic ectoderm and Nodal in the epiblast and were therefore unable to initiate PD axis formation. Tetraploid rescue underlined the extra-embryonic nature of the Sall4-1a phenotype and revealed a further embryonic function in Wnt/beta-catenin signaling to elongate the AP axis during gastrulation. This observation was supported through genetic interaction with beta-catenin mutants, since compound heterozygous mutants recapitulated the defects of Wnt3a mutants in posterior development.
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Affiliation(s)
- Nikolas Uez
- Helmholtz Center Munich, Institute of Developmental Genetics, Ingolstaedter Landstrasse 1, Munich, Neuherberg, Germany
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Tang H, Ariki K, Ohkido M, Murakami Y, Matsufuji S, Li Z, Yamamura KI. Role of ornithine decarboxylase antizyme inhibitor in vivo. Genes Cells 2008; 14:79-87. [PMID: 19077035 DOI: 10.1111/j.1365-2443.2008.01249.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Ornithine decarboxylase (ODC) antizyme inhibitor (AZI) has been shown to regulate ODC activity in cell cultures. However, its biological functions in an organism remain unknown. An embryonic stem (ES) cell clone was established, in which the Azin1 gene was disrupted by the gene trap technique. To identify the function of Azin1 gene in vivo, a mutant mouse line was generated using these trapped ES cells. Homozygous mutant mice died at P0 with abnormal liver morphology. Further analysis indicated that the deletion of Azin1 in homozygous mice resulted in the degradation of ODC, and reduced the biosynthesis of putrescine and spermidine. Our results thus show that AZI plays an important role in regulating the levels of ODC, putrescine and spermidine in mice, and is essential for the survival of mice.
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Affiliation(s)
- Hua Tang
- Key Laboratory of Molecular Infectious Diseases, Ministry of Education, Chongqing Medical University, Chongqing 400016, China
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24
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Ahting U, Floss T, Uez N, Schneider-Lohmar I, Becker L, Kling E, Iuso A, Bender A, de Angelis MH, Gailus-Durner V, Fuchs H, Meitinger T, Wurst W, Prokisch H, Klopstock T. Neurological phenotype and reduced lifespan in heterozygous Tim23 knockout mice, the first mouse model of defective mitochondrial import. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2008; 1787:371-6. [PMID: 19111522 DOI: 10.1016/j.bbabio.2008.12.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Received: 07/30/2008] [Revised: 12/01/2008] [Accepted: 12/02/2008] [Indexed: 11/17/2022]
Abstract
The Tim23 protein is the key component of the mitochondrial import machinery. It locates to the inner mitochondrial membrane and its own import is dependent on the DDP1/TIM13 complex. Mutations in human DDP1 cause the Mohr-Tranebjaerg syndrome (MTS/DFN-1; OMIM #304700), which is one of the two known human diseases of the mitochondrial protein import machinery. We created a Tim23 knockout mouse from a gene trap embryonic stem cell clone. Homozygous Tim23 mice were not viable. Heterozygous F1 mutants showed a 50% reduction of Tim23 protein in Western blot, a neurological phenotype and a markedly reduced life span. Haploinsufficiency of the Tim23 mutation underlines the critical role of the mitochondrial import machinery for maintaining mitochondrial function.
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Affiliation(s)
- Uwe Ahting
- Institute of Human Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany
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25
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Uetzmann L, Burtscher I, Lickert H. A mouse line expressing Foxa2-driven Cre recombinase in node, notochord, floorplate, and endoderm. Genesis 2008; 46:515-22. [DOI: 10.1002/dvg.20410] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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26
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Böhm J, Buck A, Borozdin W, Mannan AU, Matysiak-Scholze U, Adham I, Schulz-Schaeffer W, Floss T, Wurst W, Kohlhase J, Barrionuevo F. Sall1, sall2, and sall4 are required for neural tube closure in mice. THE AMERICAN JOURNAL OF PATHOLOGY 2008; 173:1455-63. [PMID: 18818376 DOI: 10.2353/ajpath.2008.071039] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Four homologs to the Drosophila homeotic gene spalt (sal) exist in both humans and mice (SALL1 to SALL4/Sall1 to Sall4, respectively). Mutations in both SALL1 and SALL4 result in the autosomal-dominant developmental disorders Townes-Brocks and Okihiro syndrome, respectively. In contrast, no human diseases have been associated with SALL2 to date, and Sall2-deficient mice have shown no apparent abnormal phenotype. We generated mice deficient in Sall2 and, contrary to previous reports, 11% of our Sall2-deficient mice showed background-specific neural tube defects, suggesting that Sall2 has a role in neurogenesis. To investigate whether Sall4 may compensate for the absence of Sall2, we generated compound Sall2 knockout/Sall4 genetrap mutant mice. In these mutants, the incidence of neural tube defects was significantly increased. Furthermore, we found a similar phenotype in compound Sall1/4 mutant mice, and in vitro studies showed that SALL1, SALL2, and SALL4 all co-localized in the nucleus. We therefore suggest a fundamental and redundant function of the Sall proteins in murine neurulation, with the heterozygous loss of a particular SALL protein also possibly compensated in humans during development.
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Affiliation(s)
- Johann Böhm
- Institut für Humangenetik und Anthropologie, Universität Freiburg, Freiburg, Germany
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Transcriptional regulator BPTF/FAC1 is essential for trophoblast differentiation during early mouse development. Mol Cell Biol 2008; 28:6819-27. [PMID: 18794365 DOI: 10.1128/mcb.01058-08] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The putative transcriptional regulator BPTF/FAC1 is expressed in embryonic and extraembryonic tissues of the early mouse conceptus. The extraembryonic trophoblast lineage in mammals is essential to form the fetal part of the placenta and hence for the growth and viability of the embryo in utero. Here, we describe a loss-of-function allele of the BPTF/FAC1 gene that causes embryonic lethality in the mouse. BPTF/FAC1-deficient embryos form apparently normal blastocysts that implant and develop epiblast, visceral endoderm, and extraembryonic ectoderm including trophoblast stem cells. Subsequent development of mutants, however, is arrested at the early gastrula stage (embryonic day 6.5), and virtually all null embryos die before midgestation. Most notably, the ectoplacental cone is drastically reduced or absent in mutants, which may cause the embryonic lethality. Development of the mutant epiblast is also affected, as the anterior visceral endoderm and the primitive streak do not form correctly, while brachyury-expressing mesodermal cells arise but are delayed. The mutant phenotype suggests that gastrulation is initiated, but no complete anteroposterior axis of the epiblast appears. We conclude that BPTF/FAC1 is essential in the extraembryonic lineage for correct development of the ectoplacental cone and fetomaternal interactions. In addition, BPTF/FAC1 may also play a role either directly or indirectly in anterior-posterior patterning of the epiblast.
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Deb KD, Jayaprakash AD, Sharma V, Totey S. Embryonic stem cells: from markers to market. Rejuvenation Res 2008; 11:19-37. [PMID: 17973601 DOI: 10.1089/rej.2007.0558] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
ABSTRACT Embryonic stem cells are considered the mother of all kinds of tissues and cells and it is envisioned as the holy grail of regenerative medicine. However, their use in cell replacement therapies (CRT) has so far been limited and their potentials are yet to be fully realized. The use of human embryonic stem cells (hESC) involves many safety issues pertaining to culture conditions and epigenetic changes. The role and importance of an epigenomic signature in derivation and maintenance of hESC are discussed. We provide a list of important epigenetic markers, which should be studied for evaluation of safety in hESC-based cell replacement therapies. These genes also need to be screened to determine an epigenetic signature for pluripotency in the hESCs. Finally a comprehensive list of all known stemness signature genes and the marker genes for different germ line lineages are presented. This review aims at summing up most of the intriguing molecules that can play a role in the maintenance of pluripotency and can help in determining hESC differentiation to various lineages. Extensive understanding of these markers will eventually help the researchers to transform the hESC research from bench to the bedside. The use of hESCs in CRTs is still in its infancy; much effort is warranted to turn them into the much dreamed about magic wand of regenerative medicine.
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Affiliation(s)
- Kaushik Dilip Deb
- Embryonic Stem Cells Program, Manipal Institute of Regenerative Medicine, Manipal University Branch Campus, Bangalore, India
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29
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Abstract
The knowledge about the complete genome sequences of mouse, human, and other organisms is only the first step toward the functional annotation of all genes. It facilitates the recognition of sequence conservation, which helps to distinguish between important and not important and also coding from noncoding sequence. Nevertheless, approximately only 50% of all mouse genes have been entirely annotated to date. In the postgenomic era, large-scale projects have been initiated to describe also the expression (Emap, Eurexpress) and the function (International Gene Trap Consortium, Eucomm, Norcomm, Komp) of all mouse genes. By building up on these resources, the average amount of time starting from a gene-coding sequence to finally studying its function in a living organism or embryo, has shortened significantly within the last decade. Several recent developments, namely, in bioinformatics and gene synthesis but also in targeted and random mutagenesis have contributed to the current status. This chapter will highlight the milestones that have been undertaken in order to saturate the mouse genome with gene trap mutations. We have no intention to cover the entire field but will instead focus on most recent vectors and protocols, which have turned out to be most useful in order to promote the technology. Therefore, we apologize upfront to the many studies that could not be mentioned here solely owing to space limitations but which nevertheless made significant contributions to our current understanding. This chapter will finally provide guidance on possible uses of conditional gene trap alleles as well as detailed protocols for the application of this recent technology.
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Affiliation(s)
- Thomas Floss
- Institute of Developmental Genetics, GSF-National Research Center for Environment and Health, Neuherberg, Germany
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30
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Mao L, Zabel C, Herrmann M, Nolden T, Mertes F, Magnol L, Chabert C, Hartl D, Herault Y, Delabar JM, Manke T, Himmelbauer H, Klose J. Proteomic shifts in embryonic stem cells with gene dose modifications suggest the presence of balancer proteins in protein regulatory networks. PLoS One 2007; 2:e1218. [PMID: 18043732 PMCID: PMC2077926 DOI: 10.1371/journal.pone.0001218] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2007] [Accepted: 11/01/2007] [Indexed: 11/25/2022] Open
Abstract
Large numbers of protein expression changes are usually observed in mouse models for neurodegenerative diseases, even when only a single gene was mutated in each case. To study the effect of gene dose alterations on the cellular proteome, we carried out a proteomic investigation on murine embryonic stem cells that either overexpressed individual genes or displayed aneuploidy over a genomic region encompassing 14 genes. The number of variant proteins detected per cell line ranged between 70 and 110, and did not correlate with the number of modified genes. In cell lines with single gene mutations, up and down-regulated proteins were always in balance in comparison to parental cell lines regarding number as well as concentration of differentially expressed proteins. In contrast, dose alteration of 14 genes resulted in an unequal number of up and down-regulated proteins, though the balance was kept at the level of protein concentration. We propose that the observed protein changes might partially be explained by a proteomic network response. Hence, we hypothesize the existence of a class of “balancer” proteins within the proteomic network, defined as proteins that buffer or cushion a system, and thus oppose multiple system disturbances. Through database queries and resilience analysis of the protein interaction network, we found that potential balancer proteins are of high cellular abundance, possess a low number of direct interaction partners, and show great allelic variation. Moreover, balancer proteins contribute more heavily to the network entropy, and thus are of high importance in terms of system resilience. We propose that the “elasticity” of the proteomic regulatory network mediated by balancer proteins may compensate for changes that occur under diseased conditions.
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Affiliation(s)
- Lei Mao
- Institute for Human Genetics, Charité-University Medicine Berlin, Germany.
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Arp3 is required during preimplantation development of the mouse embryo. FEBS Lett 2007; 581:5691-7. [PMID: 18035060 DOI: 10.1016/j.febslet.2007.11.031] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2007] [Revised: 11/09/2007] [Accepted: 11/12/2007] [Indexed: 12/11/2022]
Abstract
The role of Arp3 in mouse development was investigated utilizing a gene trap mutation in the Arp3 gene. Heterozygous Arp3(WT/GT) mice are normal, however, homozygous Arp3(GT/GT) embryos die at blastocyst stage. Earlier embryonic stages appear unaffected by the mutation, probably due to maternal Arp3 protein. Mutant blastocysts isolated at E3.5 fail to continue development in vitro, lack outgrowth of trophoblast-like cells in culture and express reduced levels of the trophoblast marker Cdx2, while markers for inner cell mass continue to be present. The recessive embryonic lethal phenotype indicates that Arp3 plays a vital role for early mouse development, possibly when trophoblast cells become critical for implantation.
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32
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Roma G, Sardiello M, Cobellis G, Cruz P, Lago G, Sanges R, Stupka E. The UniTrap resource: tools for the biologist enabling optimized use of gene trap clones. Nucleic Acids Res 2007; 36:D741-6. [PMID: 17942430 PMCID: PMC2238955 DOI: 10.1093/nar/gkm825] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
We have developed a comprehensive resource devoted to biologists wanting to optimize the use of gene trap clones in their experiments. We have processed 300 602 such clones from both public and private projects to generate 28 199 ‘UniTraps’, i.e. distinct collections of unambiguous insertions at the same subgenic region of annotated genes. The UniTrap resource contains data relative to 9583 trapped genes, which represent 42.3% of the mouse gene content. Among the trapped genes, 7 728 have a counterpart in humans, and 677 are known to be involved in the pathogenesis of human diseases. The aim of this analysis is to provide the wet lab researchers with a comprehensive database and curated tools for (i) identifying and comparing the clones carrying a trap into the genes of interest, (ii) evaluating the severity of the mutation to the protein function in each independent trapping event and (iii) supplying complete information to perform PCR, RT-PCR and restriction experiments to verify the clone and identify the exact point of vector insertion. To share this unique resource with the scientific community, we have designed and implemented a web interface that is freely accessible at http://unitrap.cbm.fvg.it/.
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Affiliation(s)
- Guglielmo Roma
- Telethon Institute of Genetics and Medicine (TIGEM), Via P. Castellino, 111, 80131, Napoli, Italy
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33
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Lee T, Shah C, Xu EY. Gene trap mutagenesis: a functional genomics approach towards reproductive research. ACTA ACUST UNITED AC 2007; 13:771-9. [PMID: 17890780 DOI: 10.1093/molehr/gam069] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
We have entered a new era of genomics in biomedical research with the availability of genome-wide sequences and expression data, resulting in the identification of a huge number of novel reproductive genes. The challenge we are facing today is how to determine the function of those novel and known genes and their roles in normal reproductive physiology, such as gamete production, pregnancy and fertilization, and the disease physiology such as infertility, spontaneous abortion and gynecological cancers. Mouse genetics has contributed tremendously to our understanding of the genetic causes of human diseases in the past decades. The establishment of mouse mutations is an effective way to understand the function of many reproductive proteins. One of the fast-growing mouse mutagenesis technologies-gene trap mutagenesis-represents a cost-effective way to generate mutations because of the public availability of mouse embryonic stem (ES) cell lines carrying insertional mutations and the continuing expansion of those ES gene trap cell lines. We review here the gene trapping technology and in particular examine its efficacy in generating mouse mutations for reproductive research. Even with the existing gene trap cell lines, many of the genes important for reproductive function through traditional knockout and chemical mutagenesis have been trapped, demonstrating gene trapping's efficacy in mutating genes involved in reproductive development. Comparing genes expressed in specific reproductive sub-cellular organelles and in the entire testis and ovary with gene trap lines in the International Gene Trap Consortium (IGTC) database, we could identify a significant portion of those genes as having been trapped, representing a great resource for establishing mouse models for reproductive research. Establishment and analysis of these mouse models, for example, could help with identifying genetic abnormalities underlying male infertility and other reproductive diseases.
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Affiliation(s)
- Terrance Lee
- Division of Reproductive Biology Research, Department of Obstetrics and Gynecology, Center for Genetic Medicine, Feinberg School of Medicine, Northwestern University, Lurie 7-117, 303 E Superior Street, Chicago, IL 60611, USA
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34
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Roma G, Cobellis G, Claudiani P, Maione F, Cruz P, Tripoli G, Sardiello M, Peluso I, Stupka E. A novel view of the transcriptome revealed from gene trapping in mouse embryonic stem cells. Genome Res 2007; 17:1051-60. [PMID: 17540781 PMCID: PMC1899116 DOI: 10.1101/gr.5720807] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Embryonic stem (ES) cells are pluripotent cell lines with the capacity of self-renewal and the ability to differentiate into specific cell types. We performed the first genome-wide analysis of the mouse ES cell transcriptome using approximately 250,000 gene trap sequence tags deposited in public databases. We unveiled >8000 novel transcripts, mostly non-coding, and >1000 novel alternative and often tissue-specific exons of known genes. Experimental verification of the expression of these genes and exons by RT-PCR yielded a 70% validation rate. A novel non-coding transcript within the set studied showed a highly specific pattern of expression by in situ hybridization. Our analysis also shows that the genome presents gene trapping hotspots, which correspond to 383 known and 87 novel genes. These "hypertrapped" genes show minimal overlap with previously published expression profiles of ES cells; however, we prove by real-time PCR that they are highly expressed in this cell type, thus potentially contributing to the phenotype of ES cells. Although gene trapping was initially devised as an insertional mutagenesis technique, our study demonstrates its impact on the discovery of a substantial and unprecedented portion of the transcriptome.
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Affiliation(s)
- Guglielmo Roma
- Telethon Institute of Genetics and Medicine (TIGEM), 80131 Napoli, Italy
| | - Gilda Cobellis
- Telethon Institute of Genetics and Medicine (TIGEM), 80131 Napoli, Italy
- Dipartimento di Patologia Generale, Seconda Universita’ di Napoli, 80100 Napoli, Italy
| | - Pamela Claudiani
- Telethon Institute of Genetics and Medicine (TIGEM), 80131 Napoli, Italy
| | - Francesco Maione
- Telethon Institute of Genetics and Medicine (TIGEM), 80131 Napoli, Italy
| | - Pedro Cruz
- Telethon Institute of Genetics and Medicine (TIGEM), 80131 Napoli, Italy
| | - Gaetano Tripoli
- Telethon Institute of Genetics and Medicine (TIGEM), 80131 Napoli, Italy
| | - Marco Sardiello
- Telethon Institute of Genetics and Medicine (TIGEM), 80131 Napoli, Italy
| | - Ivana Peluso
- Telethon Institute of Genetics and Medicine (TIGEM), 80131 Napoli, Italy
| | - Elia Stupka
- Telethon Institute of Genetics and Medicine (TIGEM), 80131 Napoli, Italy
- CBM S.c.r.l., Area Science Park, Basovizza- SS14, Km 163,5 Trieste, 34012 Italy
- Corresponding author.E-mail ; fax 39-040-3757710
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Schnütgen F, Ghyselinck NB. Adopting the good reFLEXes when generating conditional alterations in the mouse genome. Transgenic Res 2007; 16:405-13. [PMID: 17415672 DOI: 10.1007/s11248-007-9089-8] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2007] [Accepted: 02/28/2007] [Indexed: 12/24/2022]
Abstract
Major advances have been made in the use of the Cre/loxP system for conditional gene targeting in the mouse. By combining the ability of Cre recombinase to invert or excise a DNA fragment, depending upon the orientation of the flanking loxP sites, and the use of wild-type loxP and variant lox511 sites, we devised an efficient and reliable Cre-mediated genetic switch, called FLEX, through which expression of a given gene can be turned off, while expression of another one can be simultaneously turned on. We discuss how this innovative, flexible and powerful approach, which virtually adapts to any kind of site-specific recombinase (e.g., Cre and Flp recombinases), can be used to easily generate, even at high throughput and genome wide scale, many genetic modifications in a conditional manner, including those which were considered as difficult or impossible to achieve.
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Affiliation(s)
- Frank Schnütgen
- Department of Molecular Haematology, University of Frankfurt Medical School, Theodor Stern Kai 7, Frankfurt am Main, Germany
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Zhang FP, Domanskyi A, Palvimo JJ, Sariola H, Partanen J, Jänne OA. An adenosine triphosphatase of the sucrose nonfermenting 2 family, androgen receptor-interacting protein 4, is essential for mouse embryonic development and cell proliferation. Mol Endocrinol 2007; 21:1430-42. [PMID: 17374848 DOI: 10.1210/me.2007-0052] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
An adenosine triphosphatase of the sucrose nonfermenting 2 protein family, androgen receptor-interacting protein 4 (ARIP4), modulates androgen receptor activity. To elucidate receptor-dependent and -independent functions of ARIP4, we have analyzed Arip4 gene-targeted mice. Heterozygous Arip4 mutants were normal. Arip4 is expressed mainly in the neural tube and limb buds during early embryonic development. Arip4-/- embryos were abnormal already at embryonic d 9.5 (E9.5) and died by E11.5. At E9.5 and E10.5, almost all major tissues of Arip4-null embryos were proportionally smaller than those of wild-type embryos, and the neural tube was shrunk in some Arip4-/- embryos. Dramatically reduced cell proliferation and increased apoptosis were observed in E9.5 and E10.5 Arip4-null embryos. Mouse embryonic fibroblasts (MEFs) isolated from Arip4-/- embryos ceased to grow after two to three passages and exhibited increased apoptosis and decreased DNA synthesis compared with wild-type MEFs. Comparison of gene expression profiles of Arip4-/- and wild-type MEFs at E9.5 revealed that putative ARIP4 target genes are involved in cell growth and proliferation, apoptosis, cell death, DNA replication and repair, and development. Collectively, ARIP4 plays an essential role in mouse embryonic development and cell proliferation, and it appears to coordinate multiple essential biological processes, possibly through a complex chromatin remodeling system.
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Affiliation(s)
- Fu-Ping Zhang
- Biomedicum Helsinki, Institute of Biomedicine, University of Helsinki, Haartmaninkatu 8, FI-00014, Helsinki, Finland
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37
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Qu S, Rinehart C, Wu HH, Wang SE, Carter B, Xin H, Kotlikoff M, Arteaga CL. Gene targeting of ErbB3 using a Cre-mediated unidirectional DNA inversion strategy. Genesis 2007; 44:477-86. [PMID: 16991114 DOI: 10.1002/dvg.20243] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Recombinase-mediated unidirectional DNA inversion and transcriptional arrest is a promising strategy for high throughput conditional mutagenesis in the mouse. Banks of mouse embryonic stem cells with defined, transcriptionally silent insertions that can be activated by Cre recombinase would take advantage of existing transgenic Cre lines to rapidly produce hundreds of lineage specific and temporally controlled knockout mice for each gene, thereby introducing significant parallelism to functional gene annotation. However, the extent to which this strategy results in effective gene knockout has not been established. To test the feasibility of this strategy we targeted ErbB3, a member of the ErbB family of tyrosine kinase receptors, using this strategy. Insertion of a reversed "flipflox" vector consisting of a gene inactivation cassette (GI) and an internal ribosome entry site (IRES)-GFP reporter into intron 1 of ErbB3 was transcriptionally silent and did not affect ErbB3 expression. Crosses with ubiquitous and lineage specific Cre recombinase expressing lines permanently inverted the inserted GI cassette and blocked ErbB3 expression. Unidirectional DNA inversion by in vivo recombination is an effective strategy for targeted or ubiquitous gene knockout.
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Affiliation(s)
- Shimian Qu
- Department of Cancer Biology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-6838, USA.
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38
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Abstract
Our ability to genetically manipulate the mouse has had a great impact on medical research over the last few decades. Mouse genetics has developed into a powerful tool for dissecting the genetic causes of human disease and identifying potential targets for pharmaceutical intervention. With the recent sequencing of the human and mouse genomes, a large number of novel genes have been identified whose function in normal and disease physiology remains largely unknown. Government-sponsored multinational efforts are underway to analyze the function of all mouse genes through mutagenesis and phenotyping, making the mouse the interpreter of the human genome. A number of technologies are available for the generation of mutant mice, including gene targeting, gene trapping and transposon, chemical or radiation-induced mutagenesis. In this chapter, we review the current status of gene trapping technology, including its applicability to conditional mutagenesis.
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Affiliation(s)
- A Abuin
- Lexicon Genetics, 8800 Technology Forest Place, The Woodlands, TX 77381, USA.
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Vauti F, Goller T, Beine R, Becker L, Klopstock T, Hölter SM, Wurst W, Fuchs H, Gailus-Durner V, de Angelis MH, Arnold HH. The mouse Trm1-like gene is expressed in neural tissues and plays a role in motor coordination and exploratory behaviour. Gene 2006; 389:174-85. [PMID: 17198746 DOI: 10.1016/j.gene.2006.11.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2006] [Revised: 10/13/2006] [Accepted: 11/06/2006] [Indexed: 10/23/2022]
Abstract
Using a gene trap approach in ES cells, the novel mouse gene Trm1-like with substantial sequence homology to human C1orf25 mRNA (GenBank accession no. ) was identified. Murine Trm1-like encodes a putative protein with limited similarity to N2,N2-dimethylguanosine tRNA methyltransferase (Trm1) from other organisms, however its function is not known. The potential role of Trm1-like was investigated in a mouse mutant lacking intact Trm1-like transcripts due to integration of the gene trap vector in the first intron. Trm1-like deficient mice are viable and show no apparent anatomical defects. Behavioural tests, however, revealed significantly altered motor coordination and aberrant exploratory behaviour. LacZ activity of the trapped mouse Trm1-like gene reflects expression in various neuronal structures during embryonic development, including spinal ganglia, trigeminal nerve and ganglion, olfactory and nasopharyngeal epithelium, and nuclei of the metencephalon, thalamus and medulla oblongata. The gene is also expressed in lung, oesophagus, epiglottis, ependyma, vertebral column, spinal cord, and brown adipose tissue. Trm1-like expression persists in the adult brain with dynamically changing patterns in cortex and cerebellum. Although Trm1-like is not essential for embryonic mouse development, it may have a role in modulating postnatal neuronal functions.
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Affiliation(s)
- Franz Vauti
- Department of Cell and Molecular Biology, Institute of Biochemistry and Biotechnology, Technical University of Braunschweig, Spielmannstrasse 7, 38106 Braunschweig, Germany.
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40
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Beekman C, Nichane M, De Clercq S, Maetens M, Floss T, Wurst W, Bellefroid E, Marine JC. Evolutionarily conserved role of nucleostemin: controlling proliferation of stem/progenitor cells during early vertebrate development. Mol Cell Biol 2006; 26:9291-301. [PMID: 17000755 PMCID: PMC1698517 DOI: 10.1128/mcb.01183-06] [Citation(s) in RCA: 87] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Nucleostemin (NS) is a putative GTPase expressed preferentially in the nucleoli of neuronal and embryonic stem cells and several cancer cell lines. Transfection and knockdown studies indicated that NS controls the proliferation of these cells by interacting with the p53 tumor suppressor protein and regulating its activity. To assess the physiological role of NS in vivo, we generated a mutant mouse line with a specific gene trap event that inactivates the NS allele. The corresponding NS(-/-) embryos died around embryonic day 4. Analyses of NS mutant blastocysts indicated that NS is not required to maintain pluripotency, nucleolar integrity, or survival of the embryonic stem cells. However, the homozygous mutant blastocysts failed to enter S phase even in the absence of functional p53. Haploid insufficiency of NS in mouse embryonic fibroblasts leads to decreased cell proliferation. NS also functions in early amphibian development to control cell proliferation of neural progenitor cells. Our results show that NS has a unique ability, derived from an ancestral function, to control the proliferation rate of stem/progenitor cells in vivo independently of p53.
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Affiliation(s)
- Chantal Beekman
- Laboratory for Molecular Cancer Biology, Flanders Interuniversity Institute for Biotechnology (VIB), Technologiepark, 927, B-9052 Ghent, Belgium
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41
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Harper CA, Huang CC, Stryke D, Kawamoto M, Ferrin TE, Babbitt PC. Comparison of methods for genomic localization of gene trap sequences. BMC Genomics 2006; 7:236. [PMID: 16982004 PMCID: PMC1617135 DOI: 10.1186/1471-2164-7-236] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2006] [Accepted: 09/18/2006] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Gene knockouts in a model organism such as mouse provide a valuable resource for the study of basic biology and human disease. Determining which gene has been inactivated by an untargeted gene trapping event poses a challenging annotation problem because gene trap sequence tags, which represent sequence near the vector insertion site of a trapped gene, are typically short and often contain unresolved residues. To understand better the localization of these sequences on the mouse genome, we compared stand-alone versions of the alignment programs BLAT, SSAHA, and MegaBLAST. A set of 3,369 sequence tags was aligned to build 34 of the mouse genome using default parameters for each algorithm. Known genome coordinates for the cognate set of full-length genes (1,659 sequences) were used to evaluate localization results. RESULTS In general, all three programs performed well in terms of localizing sequences to a general region of the genome, with only relatively subtle errors identified for a small proportion of the sequence tags. However, large differences in performance were noted with regard to correctly identifying exon boundaries. BLAT correctly identified the vast majority of exon boundaries, while SSAHA and MegaBLAST missed the majority of exon boundaries. SSAHA consistently reported the fewest false positives and is the fastest algorithm. MegaBLAST was comparable to BLAT in speed, but was the most susceptible to localizing sequence tags incorrectly to pseudogenes. CONCLUSION The differences in performance for sequence tags and full-length reference sequences were surprisingly small. Characteristic variations in localization results for each program were noted that affect the localization of sequence at exon boundaries, in particular.
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Affiliation(s)
- Courtney A Harper
- Department of Biopharmaceutical Sciences, University of California San Francisco, 1700 4th Street, San Francisco, CA 94143-2250, USA
| | - Conrad C Huang
- Department of Pharmaceutical Chemistry, University of California San Francisco, 1700 4th Street, San Francisco, CA 94143-2250, USA
| | - Doug Stryke
- Department of Pharmaceutical Chemistry, University of California San Francisco, 1700 4th Street, San Francisco, CA 94143-2250, USA
| | - Michiko Kawamoto
- Department of Pharmaceutical Chemistry, University of California San Francisco, 1700 4th Street, San Francisco, CA 94143-2250, USA
| | - Thomas E Ferrin
- Department of Biopharmaceutical Sciences, University of California San Francisco, 1700 4th Street, San Francisco, CA 94143-2250, USA
- Department of Pharmaceutical Chemistry, University of California San Francisco, 1700 4th Street, San Francisco, CA 94143-2250, USA
| | - Patricia C Babbitt
- Department of Biopharmaceutical Sciences, University of California San Francisco, 1700 4th Street, San Francisco, CA 94143-2250, USA
- Department of Pharmaceutical Chemistry, University of California San Francisco, 1700 4th Street, San Francisco, CA 94143-2250, USA
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42
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Zheng QY, Hardisty-Hughes R, Brown SDM. Mouse models as a tool to unravel the genetic basis for human otitis media. Brain Res 2006; 1091:9-15. [PMID: 16917982 PMCID: PMC2855297 DOI: 10.1016/j.brainres.2006.01.046] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The pathogenesis of otitis media (OM) is multifactorial and includes infection, anatomical factors, immunologic status, genetic predisposition, and environmental factors. OM remains the most common cause of hearing impairment in childhood. Genetic predisposition is increasingly recognized as an important factor. The completion of the mouse genome sequence has offered a powerful basket of tools for investigating gene function and can expect to generate a rich resource of mouse mutants for the elucidation of genetic factors underlying OM. We review the literature and discuss recent progresses in developing mouse models and using mouse models to uncover the genetic basis for human OM.
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Affiliation(s)
- Qing Yin Zheng
- Department of Otolaryngology, Case Western Reserve Universuty, Cleveland, OH 44106, USA.
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Nord AS, Chang PJ, Conklin BR, Cox AV, Harper CA, Hicks GG, Huang CC, Johns SJ, Kawamoto M, Liu S, Meng EC, Morris JH, Rossant J, Ruiz P, Skarnes WC, Soriano P, Stanford WL, Stryke D, von Melchner H, Wurst W, Yamamura KI, Young SG, Babbitt PC, Ferrin TE. The International Gene Trap Consortium Website: a portal to all publicly available gene trap cell lines in mouse. Nucleic Acids Res 2006; 34:D642-8. [PMID: 16381950 PMCID: PMC1347459 DOI: 10.1093/nar/gkj097] [Citation(s) in RCA: 109] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Gene trapping is a method of generating murine embryonic stem (ES) cell lines containing insertional mutations in known and novel genes. A number of international groups have used this approach to create sizeable public cell line repositories available to the scientific community for the generation of mutant mouse strains. The major gene trapping groups worldwide have recently joined together to centralize access to all publicly available gene trap lines by developing a user-oriented Website for the International Gene Trap Consortium (IGTC). This collaboration provides an impressive public informatics resource comprising ∼45 000 well-characterized ES cell lines which currently represent ∼40% of known mouse genes, all freely available for the creation of knockout mice on a non-collaborative basis. To standardize annotation and provide high confidence data for gene trap lines, a rigorous identification and annotation pipeline has been developed combining genomic localization and transcript alignment of gene trap sequence tags to identify trapped loci. This information is stored in a new bioinformatics database accessible through the IGTC Website interface. The IGTC Website () allows users to browse and search the database for trapped genes, BLAST sequences against gene trap sequence tags, and view trapped genes within biological pathways. In addition, IGTC data have been integrated into major genome browsers and bioinformatics sites to provide users with outside portals for viewing this data. The development of the IGTC Website marks a major advance by providing the research community with the data and tools necessary to effectively use public gene trap resources for the large-scale characterization of mammalian gene function.
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Affiliation(s)
- Alex S. Nord
- University of CaliforniaSan Francisco, 600 16th Street, San Francisco, CA 94143-2240, USA
- Wellcome Trust Sanger InstituteHinxton, Cambridge CB10 1SA, UK
| | - Patricia J. Chang
- University of CaliforniaSan Francisco, 600 16th Street, San Francisco, CA 94143-2240, USA
| | - Bruce R. Conklin
- Gladstone Institute of Cardiovascular Disease, University of California San Francisco Department of Medicine and Pharmacology1650 Owens Street, San Francisco, CA 94158, USA
| | - Antony V. Cox
- Wellcome Trust Sanger InstituteHinxton, Cambridge CB10 1SA, UK
| | - Courtney A. Harper
- University of CaliforniaSan Francisco, 600 16th Street, San Francisco, CA 94143-2240, USA
| | - Geoffrey G. Hicks
- Manitoba Institute of Cell Biology, University of Manitoba675 McDermot Avenue, Winnipeg, Manitoba, Canada R3E 0V9
| | - Conrad C. Huang
- University of CaliforniaSan Francisco, 600 16th Street, San Francisco, CA 94143-2240, USA
| | - Susan J. Johns
- University of CaliforniaSan Francisco, 600 16th Street, San Francisco, CA 94143-2240, USA
| | - Michiko Kawamoto
- University of CaliforniaSan Francisco, 600 16th Street, San Francisco, CA 94143-2240, USA
| | - Songyan Liu
- Manitoba Institute of Cell Biology, University of Manitoba675 McDermot Avenue, Winnipeg, Manitoba, Canada R3E 0V9
| | - Elaine C. Meng
- University of CaliforniaSan Francisco, 600 16th Street, San Francisco, CA 94143-2240, USA
| | - John H. Morris
- University of CaliforniaSan Francisco, 600 16th Street, San Francisco, CA 94143-2240, USA
| | - Janet Rossant
- The Hospital for Sick ChildrenToronto, Ontario, Canada M5G 1X8
| | - Patricia Ruiz
- Center for Cardiovascular Research, Charité Universitätsmedizin and Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics14195 Berlin, Germany
| | | | - Philippe Soriano
- Fred Hutchinson Cancer Research Center1100 Fairview Avenue North, Seattle, WA 98109-1024, USA
| | | | - Doug Stryke
- University of CaliforniaSan Francisco, 600 16th Street, San Francisco, CA 94143-2240, USA
| | - Harald von Melchner
- Department of Molecular Hematology, University of Frankfurt Medical School60590 Frankfurt am Main, Germany
| | - Wolfgang Wurst
- GSF Research Center for Environment and Health, Institute for Developmental GeneticsIngolstaedter Landstrasse 1, D-85764 Neuherberg, Germany
| | - Ken-ichi Yamamura
- Institute of Molecular Embryology and Genetics, Kumamoto University2-2-1 Honjo, Kumamoto 860-0811, Japan
| | - Stephen G. Young
- University of CaliforniaLos Angeles, 650 Charles E. Young Dr So., Los Angeles, CA 90095, USA
| | - Patricia C. Babbitt
- University of CaliforniaSan Francisco, 600 16th Street, San Francisco, CA 94143-2240, USA
| | - Thomas E. Ferrin
- University of CaliforniaSan Francisco, 600 16th Street, San Francisco, CA 94143-2240, USA
- To whom correspondence should be addressed.
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44
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De-Zolt S, Schnütgen F, Seisenberger C, Hansen J, Hollatz M, Floss T, Ruiz P, Wurst W, von Melchner H. High-throughput trapping of secretory pathway genes in mouse embryonic stem cells. Nucleic Acids Res 2006; 34:e25. [PMID: 16478711 PMCID: PMC1369290 DOI: 10.1093/nar/gnj026] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
High-throughput gene trapping is a random approach for inducing insertional mutations across the mouse genome. This approach uses gene trap vectors that simultaneously inactivate and report the expression of the trapped gene at the insertion site, and provide a DNA tag for the rapid identification of the disrupted gene. Gene trapping has been used by both public and private institutions to produce libraries of embryonic stem (ES) cells harboring mutations in single genes. Presently, ∼66% of the protein coding genes in the mouse genome have been disrupted by gene trap insertions. Among these, however, genes encoding signal peptides or transmembrane domains (secretory genes) are underrepresented because they are not susceptible to conventional trapping methods. Here, we describe a high-throughput gene trapping strategy that effectively targets secretory genes. We used this strategy to assemble a library of ES cells harboring mutations in 716 unique secretory genes, of which 61% were not trapped by conventional trapping, indicating that the two strategies are complementary. The trapped ES cell lines, which can be ordered from the International Gene Trap Consortium (), are freely available to the scientific community.
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Affiliation(s)
| | | | - Claudia Seisenberger
- Institute of Developmental Genetics, GSF-National Research Center for Environment and HealthNeuherberg, Germany
| | - Jens Hansen
- Institute of Developmental Genetics, GSF-National Research Center for Environment and HealthNeuherberg, Germany
| | - Melanie Hollatz
- Institute of Developmental Genetics, GSF-National Research Center for Environment and HealthNeuherberg, Germany
| | - Thomas Floss
- Institute of Developmental Genetics, GSF-National Research Center for Environment and HealthNeuherberg, Germany
| | - Patricia Ruiz
- Center for Cardiovascular Research, Charité UniversitätsmedizinBerlin, Germany
- Department of Vertebrate Genomics, Max-Planck Institute for Molecular GeneticsBerlin, Germany
| | - Wolfgang Wurst
- Institute of Developmental Genetics, GSF-National Research Center for Environment and HealthNeuherberg, Germany
- Department for Molecular Neurogenetics, Max-Planck Institute of PsychiatryMunich, Germany
| | - Harald von Melchner
- To whom correspondence should be addressed. Tel: +49 69 63016696; Fax: +49 69 63016390;
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45
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Zohn IE, Anderson KV, Niswander L. Using genomewide mutagenesis screens to identify the genes required for neural tube closure in the mouse. ACTA ACUST UNITED AC 2006; 73:583-90. [PMID: 15971254 DOI: 10.1002/bdra.20164] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
BACKGROUND Neural tube closure is a critical embryological process that requires the coordination of many molecular and cellular events. Only recently has the molecular basis of the cell movements that drive neural tube closure begun to be elucidated. This has been accomplished in part due to the analysis of a growing number of genetically targeted and naturally occurring mouse mutant strains that have neural tube defects (NTDs). Currently there are more than 100 genes that when mutated result in NTDs in the mouse. Yet only approximately 10% of genes in the mouse genome have been mutated and their gross phenotype analyzed, suggesting that only a small percentage of the genes that can cause NTDs have been identified. METHODS In order to more systematically and fully understand the genetic basis of neural tube closure and to begin to define the molecular pathways that direct this key embryonic event, our laboratories have undertaken a forward genetic screen in mice. From this we hope to gain a better understanding of the regulation of this complex morphogenic processes. CONCLUSIONS The mouse provides a good model for human neural tube closure, and therefore the information gained from generating novel mouse models of NTDs will help to predict the genes responsible for human NTDs and provide experimental evidence for how they function.
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Affiliation(s)
- Irene E Zohn
- Developmental Biology Program, Sloan-Kettering Institute, New York, NY, USA.
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46
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Brown SDM, Chambon P, de Angelis MH. EMPReSS: standardized phenotype screens for functional annotation of the mouse genome. Nat Genet 2006; 37:1155. [PMID: 16254554 DOI: 10.1038/ng1105-1155] [Citation(s) in RCA: 136] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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47
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Augustin M, Sedlmeier R, Peters T, Huffstadt U, Kochmann E, Simon D, Schöniger M, Garke-Mayerthaler S, Laufs J, Mayhaus M, Franke S, Klose M, Graupner A, Kurzmann M, Zinser C, Wolf A, Voelkel M, Kellner M, Kilian M, Seelig S, Koppius A, Teubner A, Korthaus D, Nehls M, Wattler S. Efficient and fast targeted production of murine models based on ENU mutagenesis. Mamm Genome 2005; 16:405-13. [PMID: 16075367 DOI: 10.1007/s00335-004-3028-2] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2004] [Accepted: 03/03/2005] [Indexed: 11/30/2022]
Abstract
Mice with targeted genetic alterations are the most effective tools for deciphering organismal gene function. We generated an ENU-based parallel C3HeB/FeJ sperm and DNA archive characterized by a high probability to identify allelic variants of target genes as well as high efficiencies in allele retrieval and model revitalization. Our archive size of over 17,000 samples contains approximately 340,000 independent alleles (20 functional mutations per individual sample). Based on an estimated number of approximately 30,000 mouse genes, the parallel sperm/DNA archive should permit the identification and recovery of ten or more alleles per average target gene which translates to a calculated 99% success rate in the discovery of five allelic variants for any given average gene. The low rate of unrelated ENU-induced passenger mutations has no practical impact on the analysis of the allele-specific phenotype at the G3 generation because of dilution and free segregation of such unrelated passenger mutations. To date 39 mouse models representing 33 different genes have been recovered from our archive using in vitro fertilization techniques. The generation time for a murine model heterozygous for a mutation in a gene of interest is less than 2 months, i.e., three to four times faster compared with current embryonic stem-cell-based technologies. We conclude that ENU-based targeted mutagenesis is a powerful tool for the fast and high-throughput production of murine gene-specific models for biomedical research.
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Affiliation(s)
- M Augustin
- Ingenium Pharmaceuticals AG, Fraunhoferstr.13, 82152 Martinsried, Germany.
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48
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Kist R, Watson M, Wang X, Cairns P, Miles C, Reid DJ, Peters H. Reduction of Pax9 gene dosage in an allelic series of mouse mutants causes hypodontia and oligodontia. Hum Mol Genet 2005; 14:3605-17. [PMID: 16236760 DOI: 10.1093/hmg/ddi388] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Missing teeth (hypodontia and oligodontia) are a common developmental abnormality in humans and heterozygous mutations of PAX9 have recently been shown to underlie a number of familial, non-syndromic cases. Whereas PAX9 haploinsufficiency has been suggested as the underlying genetic mechanism, it is not known how this affects tooth development. Here we describe a novel, hypomorphic Pax9 mutant allele (Pax9neo) producing decreased levels of Pax9 wild-type mRNA and show that this causes oligodontia in mice. Homozygous Pax9neo mutants (Pax9neo/neo) exhibit hypoplastic or missing lower incisors and third molars, and when combined with the null allele Pax9lacZ, the compound mutants (Pax9neo/lacZ) develop severe forms of oligodontia. The missing molars are arrested at different developmental stages and posterior molars are consistently arrested at an earlier stage, suggesting that a reduction of Pax9 gene dosage affects the dental field as a whole. In addition, hypomorphic Pax9 mutants show defects in enamel formation of the continuously growing incisors, whereas molars exhibit increased attrition and reparative dentin formation. Together, we conclude that changes of Pax9 expression levels have a direct consequence for mammalian dental patterning and that a minimal Pax9 gene dosage is required for normal morphogenesis and differentiation throughout tooth development.
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Affiliation(s)
- Ralf Kist
- Institute of Human Genetics, University of Newcastle upon Tyne, International Centre for Life, UK
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Forrai A, Robb L. The gene trap resource: a treasure trove for hemopoiesis research. Exp Hematol 2005; 33:845-56. [PMID: 16038776 DOI: 10.1016/j.exphem.2005.03.016] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2005] [Accepted: 03/23/2005] [Indexed: 11/16/2022]
Abstract
The laboratory mouse is an invaluable tool for functional gene discovery because of its genetic malleability and a biological similarity to human systems that facilitates identification of human models of disease. A number of mutagenic technologies are being used to elucidate gene function in the mouse. Gene trapping is an insertional mutagenesis strategy that is being undertaken by multiple research groups, both academic and private, in an effort to introduce mutations across the mouse genome. Large-scale, publicly funded gene trap programs have been initiated in several countries with the International Gene Trap Consortium coordinating certain efforts and resources. We outline the methodology of mammalian gene trapping and how it can be used to identify genes expressed in both primitive and definitive blood cells and to discover hemopoietic regulator genes. Mouse mutants with hematopoietic phenotypes derived using gene trapping are described. The efforts of the large-scale gene trapping consortia have now led to the availability of libraries of mutagenized ES cell clones. The identity of the trapped locus in each of these clones can be identified by sequence-based searching via the world wide web. This resource provides an extraordinary tool for all researchers wishing to use mouse genetics to understand gene function.
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Affiliation(s)
- Ariel Forrai
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
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Tagalakis AD, Owen JS, Simons JP. Lack of RNA-DNA oligonucleotide (chimeraplast) mutagenic activity in mouse embryos. Mol Reprod Dev 2005; 71:140-4. [PMID: 15791601 DOI: 10.1002/mrd.20250] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
There are numerous reports of the use of RNA-DNA oligonucleotides (chimeraplasts) to correct point mutations in vitro and in vivo, including the human apolipoprotein E gene (ApoE). Despite the absence of selection for targeting, high efficiency conversion has been reported. Although mainly used to revert deleterious mutations for gene therapy applications, successful use of this approach would have the potential to greatly facilitate the production of defined mutations in mice and other species. We have attempted to create a point mutation in the mouse ApoE gene by microinjection of chimeraplast into the pronuclei of 1-cell mouse eggs. Following transfer of microinjected eggs we analysed 139 E12.5 embryos, but obtained no evidence for successful conversion.
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Affiliation(s)
- Aristides D Tagalakis
- Department of Anatomy and Developmental Biology, Hampstead Campus, University College London, London, United Kingdom
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