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An siRNA-based screen in C2C12 myoblasts identifies novel genes involved in myogenic differentiation. Exp Cell Res 2017; 359:145-153. [DOI: 10.1016/j.yexcr.2017.07.037] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2017] [Revised: 07/16/2017] [Accepted: 07/31/2017] [Indexed: 11/19/2022]
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2
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Doran AG, Wong K, Flint J, Adams DJ, Hunter KW, Keane TM. Deep genome sequencing and variation analysis of 13 inbred mouse strains defines candidate phenotypic alleles, private variation and homozygous truncating mutations. Genome Biol 2016; 17:167. [PMID: 27480531 PMCID: PMC4968449 DOI: 10.1186/s13059-016-1024-y] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Accepted: 07/12/2016] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND The Mouse Genomes Project is an ongoing collaborative effort to sequence the genomes of the common laboratory mouse strains. In 2011, the initial analysis of sequence variation across 17 strains found 56.7 M unique single nucleotide polymorphisms (SNPs) and 8.8 M indels. We carry out deep sequencing of 13 additional inbred strains (BUB/BnJ, C57BL/10J, C57BR/cdJ, C58/J, DBA/1J, I/LnJ, KK/HiJ, MOLF/EiJ, NZB/B1NJ, NZW/LacJ, RF/J, SEA/GnJ and ST/bJ), cataloguing molecular variation within and across the strains. These strains include important models for immune response, leukaemia, age-related hearing loss and rheumatoid arthritis. We now have several examples of fully sequenced closely related strains that are divergent for several disease phenotypes. RESULTS Approximately 27.4 M unique SNPs and 5 M indels are identified across these strains compared to the C57BL/6 J reference genome (GRCm38). The amount of variation found in the inbred laboratory mouse genome has increased to 71 M SNPs and 12 M indels. We investigate the genetic basis of highly penetrant cancer susceptibility in RF/J finding private novel missense mutations in DNA damage repair and highly cancer associated genes. We use two highly related strains (DBA/1J and DBA/2J) to investigate the genetic basis of collagen-induced arthritis susceptibility. CONCLUSIONS This paper significantly expands the catalogue of fully sequenced laboratory mouse strains and now contains several examples of highly genetically similar strains with divergent phenotypes. We show how studying private missense mutations can lead to insights into the genetic mechanism for a highly penetrant phenotype.
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Affiliation(s)
- Anthony G Doran
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1HH, UK
| | - Kim Wong
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1HH, UK
| | - Jonathan Flint
- The Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford, OX3 7BN, UK
| | - David J Adams
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1HH, UK
| | - Kent W Hunter
- Laboratory of Cancer Biology and Genetics, NCI, NIH, Bethesda, Maryland, USA.
| | - Thomas M Keane
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1HH, UK.
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A strategy to identify dominant point mutant modifiers of a quantitative trait. G3-GENES GENOMES GENETICS 2014; 4:1113-21. [PMID: 24747760 PMCID: PMC4065254 DOI: 10.1534/g3.114.010595] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
A central goal in the analysis of complex traits is to identify genes that modify a phenotype. Modifiers of a cancer phenotype may act either intrinsically or extrinsically on the salient cell lineage. Germline point mutagenesis by ethylnitrosourea can provide alleles for a gene of interest that include loss-, gain-, or alteration-of-function. Unlike strain polymorphisms, point mutations with heterozygous quantitative phenotypes are detectable in both essential and nonessential genes and are unlinked from other variants that might confound their identification and analysis. This report analyzes strategies seeking quantitative mutational modifiers of ApcMin in the mouse. To identify a quantitative modifier of a phenotype of interest, a cluster of test progeny is needed. The cluster size can be increased as necessary for statistical significance if the founder is a male whose sperm is cryopreserved. A second critical element in this identification is a mapping panel free of polymorphic modifiers of the phenotype, to enable low-resolution mapping followed by targeted resequencing to identify the causative mutation. Here, we describe the development of a panel of six “isogenic mapping partner lines” for C57BL/6J, carrying single-nucleotide markers introduced by mutagenesis. One such derivative, B6.SNVg, shown to be phenotypically neutral in combination with ApcMin, is an appropriate mapping partner to locate induced mutant modifiers of the ApcMin phenotype. The evolved strategy can complement four current major initiatives in the genetic analysis of complex systems: the Genome-wide Association Study; the Collaborative Cross; the Knockout Mouse Project; and The Cancer Genome Atlas.
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Abstract
Identifying genes involved in behavioural disorders in man is a challenge as the cause is often multigenic and the phenotype is modulated by environmental cues. Mouse mutants are a valuable tool for identifying novel pathways underlying specific neurological phenotypes and exploring the influence both genetic and non-genetic factors. Many human variants causing behavioural disorders are not gene deletions but changes in levels of expression or activity of a gene product; consequently, large-scale mouse ENU mutagenesis has the advantage over the study of null mutants in that it generates a range of point mutations that frequently mirror the subtlety and heterogeneity of human genetic lesions. ENU mutants have provided novel and clinically relevant functional information on genes that influence many aspects of mammalian behaviour, from neuropsychiatric endophenotypes to circadian rhythms. This review will highlight some of the most important findings that have been made using this method in several key areas of neurological disease research.
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Affiliation(s)
- Peter L Oliver
- MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Parks Road, Oxford OX1 3PT, UK
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5
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Fenner D, Odili S, Hong HK, Kobayashi Y, Kohsaka A, Siepka SM, Vitaterna MH, Chen P, Zelent B, Grimsby J, Takahashi JS, Matschinsky FM, Bass J. Generation of N-ethyl-N-nitrosourea (ENU) diabetes models in mice demonstrates genotype-specific action of glucokinase activators. J Biol Chem 2011; 286:39560-72. [PMID: 21921030 PMCID: PMC3234779 DOI: 10.1074/jbc.m111.269100] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2011] [Revised: 08/16/2011] [Indexed: 11/06/2022] Open
Abstract
We performed genome-wide mutagenesis in C57BL/6J mice using N-ethyl-N-nitrosourea to identify mutations causing high blood glucose early in life and to produce new animal models of diabetes. Of a total of 13 new lines confirmed by heritability testing, we identified two semi-dominant pedigrees with novel missense mutations (Gck(K140E) and Gck(P417R)) in the gene encoding glucokinase (Gck), the mammalian glucose sensor that is mutated in human maturity onset diabetes of the young type 2 and the target of emerging anti-hyperglycemic agents that function as glucokinase activators (GKAs). Diabetes phenotype corresponded with genotype (mild-to-severe: Gck(+/+) < Gck(P417R/+), Gck(K140E)(/+) < Gck(P417R/P417R), Gck(P417R/K140E), and Gck(K140E/K140E)) and with the level of expression of GCK in liver. Each mutant was produced as the recombinant enzyme in Escherichia coli, and analysis of k(cat) and tryptophan fluorescence (I(320/360)) during thermal shift unfolding revealed a correlation between thermostability and the severity of hyperglycemia in the whole animal. Disruption of the glucokinase regulatory protein-binding site (GCK(K140E)), but not the ATP binding cassette (GCK(P417R)), prevented inhibition of enzyme activity by glucokinase regulatory protein and corresponded with reduced responsiveness to the GKA drug. Surprisingly, extracts from liver of diabetic GCK mutants inhibited activity of the recombinant enzyme, a property that was also observed in liver extracts from mice with streptozotocin-induced diabetes. These results indicate a relationship between genotype, phenotype, and GKA efficacy. The integration of forward genetic screening and biochemical profiling opens a pathway for preclinical development of mechanism-based diabetes therapies.
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Affiliation(s)
- Deborah Fenner
- From the Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611
- the Department of Neurobiology and Physiology and
| | - Stella Odili
- the Department of Biochemistry and Biophysics, Children's Hospital of Pennsylvania and Diabetes Center, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104
| | - Hee-Kyung Hong
- the Department of Neurobiology and Physiology and
- the Center for Sleep and Circadian Biology, Northwestern University, Evanston, Illinois 60208
| | - Yumiko Kobayashi
- From the Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611
- the Department of Neurobiology and Physiology and
| | - Akira Kohsaka
- the Department of Neurobiology and Physiology and
- the Departments of Medicine and Physiology II, Wakayama Medical University, Wakayama City, 640-8265, Japan
| | - Sandra M. Siepka
- the Department of Neurobiology and Physiology and
- the Center for Sleep and Circadian Biology, Northwestern University, Evanston, Illinois 60208
| | - Martha H. Vitaterna
- the Department of Neurobiology and Physiology and
- the Center for Sleep and Circadian Biology, Northwestern University, Evanston, Illinois 60208
| | - Pan Chen
- the Department of Biochemistry and Biophysics, Children's Hospital of Pennsylvania and Diabetes Center, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104
| | - Bogumil Zelent
- the Department of Biochemistry and Biophysics, Children's Hospital of Pennsylvania and Diabetes Center, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104
| | - Joseph Grimsby
- the Department of Metabolic Diseases, Hoffmann-La Roche, Nutley, New Jersey 07110
| | - Joseph S. Takahashi
- the Department of Neurobiology and Physiology and
- the Department of Neuroscience and Howard Hughes Medical Institute, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas 75390, and
| | - Franz M. Matschinsky
- the Department of Biochemistry and Biophysics, Children's Hospital of Pennsylvania and Diabetes Center, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104
| | - Joseph Bass
- From the Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611
- the Department of Neurobiology and Physiology and
- the Center for Sleep and Circadian Biology, Northwestern University, Evanston, Illinois 60208
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6
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Zeiss CJ, Ward JM, Allore HG. Designing phenotyping studies for genetically engineered mice. Vet Pathol 2011; 49:24-31. [PMID: 21930803 DOI: 10.1177/0300985811417247] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
A phenotyping study records physiologic or morphologic changes in an experimental animal resulting from an intervention. In mice, this intervention is most frequently genetic, but it may be any type of experimental manipulation. Accurate representation of the human condition under study is essential if the model is to yield useful conclusions. In this review, general approaches to the design of phenotyping studies are considered. These approaches take into account major sources of reduced model validity, such as unexpected phenotypic variation in mice, evolutionary divergence between mice and humans, unanticipated sources of variation, and common design errors. As poor design is the most common reason why studies fail to yield enduring results, emphasis is placed on reduction of bias, sampling, controlled study design, and appropriate statistical analysis.
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Affiliation(s)
- C J Zeiss
- Section of Comparative Medicine, Yale University School of Medicine, TAC N230, New Haven, CT 06520, USA.
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Ermakova O, Piszczek L, Luciani L, Cavalli FMG, Ferreira T, Farley D, Rizzo S, Paolicelli RC, Al-Banchaabouchi M, Nerlov C, Moriggl R, Luscombe NM, Gross C. Sensitized phenotypic screening identifies gene dosage sensitive region on chromosome 11 that predisposes to disease in mice. EMBO Mol Med 2011; 3:50-66. [PMID: 21204268 PMCID: PMC3402001 DOI: 10.1002/emmm.201000112] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
The identification of susceptibility genes for human disease is a major goal of current biomedical research. Both sequence and structural variation have emerged as major genetic sources of phenotypic variability and growing evidence points to copy number variation as a particularly important source of susceptibility for disease. Here we propose and validate a strategy to identify genes in which changes in dosage alter susceptibility to disease-relevant phenotypes in the mouse. Our approach relies on sensitized phenotypic screening of megabase-sized chromosomal deletion and deficiency lines carrying altered copy numbers of ∼30 linked genes. This approach offers several advantages as a method to systematically identify genes involved in disease susceptibility. To examine the feasibility of such a screen, we performed sensitized phenotyping in five therapeutic areas (metabolic syndrome, immune dysfunction, atherosclerosis, cancer and behaviour) of a 0.8 Mb reciprocal chromosomal duplication and deficiency on chromosome 11 containing 27 genes. Gene dosage in the region significantly affected risk for high-fat diet-induced metabolic syndrome, antigen-induced immune hypersensitivity, ApoE-induced atherosclerosis, and home cage activity. Follow up studies on individual gene knockouts for two candidates in the region showed that copy number variation in Stat5 was responsible for the phenotypic variation in antigen-induced immune hypersensitivity and metabolic syndrome. These data demonstrate the power of sensitized phenotypic screening of segmental aneuploidy lines to identify disease susceptibility genes.
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Affiliation(s)
- Olga Ermakova
- Mouse Biology Unit, European Molecular Biology Laboratory, Monterotondo, Italy
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8
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Gondo Y, Fukumura R, Murata T, Makino S. ENU-based gene-driven mutagenesis in the mouse: a next-generation gene-targeting system. Exp Anim 2011; 59:537-48. [PMID: 21030782 DOI: 10.1538/expanim.59.537] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
As a new mouse mutant resource, the RIKEN ENU-based gene-driven mutagenesis system in the mouse has been available to the research community since 2002. By using random base-substitution mutagenesis with ENU, a new reverse genetics infrastructure has been developed as a next-generation gene-targeting system. The construction of a large-scale mutant mouse library and high-throughput mutation discovery systems were the keys making it practically feasible. The RIKEN mutant mouse library consists of ~ 10,000 G1 mice, within which 100-150 mutant strains have been established based on users' requests every year. Use of the system is very simple: users 1) download an application form from our web site and send to us, and 2) design the PCR primers for the target gene. Then, we screen the RIKEN mutant mouse library and report all the detected mutations to the user. From among the allelic series of discovered mutations, users decide which mutant strain(s) to analyze and request the live mutant strain for functional studies of the target gene. Users have been reporting various functional mutations in the RIKEN mutant mouse library: e.g., missense, knockout-type and even functional non-coding mutations. In the near future, next-generation re-sequencing systems should drastically enhance the utility of the ENU-based gene-driven mutagenesis not only for the mouse but also for other species.
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Affiliation(s)
- Yoichi Gondo
- Mutagenesis and Genomics Team, RIKEN BioResource Center, Ibaraki, Japan
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9
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Abstract
The generation of genetically modified animals using N-ethyl-N-nitrosourea (ENU) mutagenesis is a fast and highly effective method. The technique is based on treating male animals with the supermutagen ENU, which randomly introduces mutations in the spermatogonial stem cells. By breeding these animals with untreated females, an F1 population is generated in which each individual carries unique random ENU-induced mutations, which can be retrieved using either genotype-driven or phenotype-driven approaches. No complicated cell culturing techniques are required and since no foreign DNA is introduced, the mutant animals that are generated are not transgenic. Here, we describe the detailed protocols for ENU mutagenesis and for mutant retrieval.
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10
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Nguyen N, Judd LM, Kalantzis A, Whittle B, Giraud AS, van Driel IR. Random mutagenesis of the mouse genome: a strategy for discovering gene function and the molecular basis of disease. Am J Physiol Gastrointest Liver Physiol 2011; 300:G1-11. [PMID: 20947703 PMCID: PMC3774088 DOI: 10.1152/ajpgi.00343.2010] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Mutagenesis of mice with N-ethyl-N-nitrosourea (ENU) is a phenotype-driven approach to unravel gene function and discover new biological pathways. Phenotype-driven approaches have the advantage of making no assumptions about the function of genes and their products and have been successfully applied to the discovery of novel gene-phenotype relationships in many physiological systems. ENU mutagenesis of mice is used in many large-scale and more focused projects to generate and identify novel mouse models for the study of gene functions and human disease. This review examines the strategies and tools used in ENU mutagenesis screens to efficiently generate and identify functional mutations.
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Affiliation(s)
- Nhung Nguyen
- 1Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne;
| | - Louise M. Judd
- 2Gastrointestinal Research in Inflammation and Pathology Laboratory, Murdoch Children's Research Institute, Melbourne; and
| | - Anastasia Kalantzis
- 2Gastrointestinal Research in Inflammation and Pathology Laboratory, Murdoch Children's Research Institute, Melbourne; and
| | - Belinda Whittle
- 3Australian Phenomics Facility, John Curtin School of Medical Research, Australian National University, Canberra, Australia
| | - Andrew S. Giraud
- 2Gastrointestinal Research in Inflammation and Pathology Laboratory, Murdoch Children's Research Institute, Melbourne; and
| | - Ian R. van Driel
- 1Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne;
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11
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Now and future of mouse mutagenesis for human disease models. J Genet Genomics 2010; 37:559-72. [DOI: 10.1016/s1673-8527(09)60076-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2010] [Revised: 07/30/2010] [Accepted: 07/31/2010] [Indexed: 11/20/2022]
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12
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Kim IY, Shin JH, Seong JK. Mouse phenogenomics, toolbox for functional annotation of human genome. BMB Rep 2010; 43:79-90. [PMID: 20193125 DOI: 10.5483/bmbrep.2010.43.2.079] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Mouse models are crucial for the functional annotation of human genome. Gene modification techniques including gene targeting and gene trap in mouse have provided powerful tools in the form of genetically engineered mice (GEM) for understanding the molecular pathogenesis of human diseases. Several international consortium and programs are under way to deliver mutations in every gene in mouse genome. The information from studying these GEM can be shared through international collaboration. However, there are many limitations in utility because not all human genes are knocked out in mouse and they are not yet phenotypically characterized by standardized ways which is required for sharing and evaluating data from GEM. The recent improvement in mouse genetics has now moved the bottleneck in mouse functional genomics from the production of GEM to the systematic mouse phenotype analysis of GEM. Enhanced, reproducible and comprehensive mouse phenotype analysis has thus emerged as a prerequisite for effectively engaging the phenotyping bottleneck. In this review, current information on systematic mouse phenotype analysis and an issue-oriented perspective will be provided.
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Affiliation(s)
- Il Yong Kim
- Laboratory of Developmental Biology and Genomics, BK21 Program for Veterinary Science, Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul 151-742, Korea
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13
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Beckers J, Wurst W, de Angelis MH. Towards better mouse models: enhanced genotypes, systemic phenotyping and envirotype modelling. Nat Rev Genet 2010; 10:371-80. [PMID: 19434078 DOI: 10.1038/nrg2578] [Citation(s) in RCA: 89] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The mouse is the leading mammalian model organism for basic genetic research and for studying human diseases. Coordinated international projects are currently in progress to generate a comprehensive map of mouse gene functions - the first for any mammalian genome. There are still many challenges ahead to maximize the value of the mouse as a model, particularly for human disease. These involve generating mice that are better models of human diseases at the genotypic level, systemic (assessing all organ systems) and systematic (analysing all mouse lines) phenotyping of existing and new mouse mutant resources, and assessing the effects of the environment on phenotypes.
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Affiliation(s)
- Johannes Beckers
- Institute of Experimental Genetics, Helmholtz Zentrum München, GmbH, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany.
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Brown SDM, Wurst W, Kühn R, Hancock JM. The functional annotation of mammalian genomes: the challenge of phenotyping. Annu Rev Genet 2009; 43:305-33. [PMID: 19689210 DOI: 10.1146/annurev-genet-102108-134143] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The mouse is central to the goal of establishing a comprehensive functional annotation of the mammalian genome that will help elucidate various human disease genes and pathways. The mouse offers a unique combination of attributes, including an extensive genetic toolkit that underpins the creation and analysis of models of human disease. An international effort to generate mutations for every gene in the mouse genome is a first and essential step in this endeavor. However, the greater challenge will be the determination of the phenotype of every mutant. Large-scale phenotyping for genome-wide functional annotation presents numerous scientific, infrastructural, logistical, and informatics challenges. These include the use of standardized approaches to phenotyping procedures for the population of unified databases with comparable data sets. The ultimate goal is a comprehensive database of molecular interventions that allows us to create a framework for biological systems analysis in the mouse on which human biology and disease networks can be revealed.
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Affiliation(s)
- Steve D M Brown
- MRC Mammalian Genetics Unit, MRC Harwell, Harwell Science and Innovation Campus, Oxfordshire OX11 0RD, United Kingdom.
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15
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ENU mutagenesis as a tool for understanding lung development and disease. Biochem Soc Trans 2009; 37:838-42. [PMID: 19614604 DOI: 10.1042/bst0370838] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
ENU (N-ethyl-N-nitrosourea) is a chemical mutagen that randomly induces point mutations in DNA. Since the 1990s ENU has been successfully used as a means to obtain mouse mutants using both gene-driven (reverse genetics) and phenotype-driven (forward genetics) approaches. A high-efficiency ENU approach results in approx. 25 functional mutations per genome; most of these will result in hypomorphic alleles. Our group has recently begun using ENU mutagenesis as a tool for understanding lung development and disease. In collaboration with other groups at MRC Harwell, we have undertaken a screen for recessive mutations affecting mouse lung development. We are currently pursuing two lines identified from this screen, Hel (head, eye and lung) and RecBA17. Both these lines exhibit lung defects and we believe that by studying the phenotypes and identifying the causative mutations, we may also shed light on lung disease pathogenesis. In collaboration with Bill Cookson and Miriam Moffatt, we are also taking a gene-driven approach for understanding asthma. Using the Harwell ENU sperm archive, we have recovered mouse lines harbouring mutations in the asthma-susceptibility genes Phf11 (PHD finger protein 11) and Dpp10 (dipeptidylpeptidase 10). Functional analyses of these alleles are currently under way.
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Labrie V, Fukumura R, Rastogi A, Fick LJ, Wang W, Boutros PC, Kennedy JL, Semeralul MO, Lee FH, Baker GB, Belsham DD, Barger SW, Gondo Y, Wong AHC, Roder JC. Serine racemase is associated with schizophrenia susceptibility in humans and in a mouse model. Hum Mol Genet 2009; 18:3227-43. [PMID: 19483194 DOI: 10.1093/hmg/ddp261] [Citation(s) in RCA: 139] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Abnormal N-methyl-d-aspartate receptor (NMDAR) function has been implicated in the pathophysiology of schizophrenia. d-serine is an important NMDAR modulator, and to elucidate the role of the d-serine synthesis enzyme serine racemase (Srr) in schizophrenia, we identified and characterized mice with an ENU-induced mutation that results in a complete loss of Srr activity and dramatically reduced d-serine levels. Mutant mice displayed behaviors relevant to schizophrenia, including impairments in prepulse inhibition, sociability and spatial discrimination. Behavioral deficits were exacerbated by an NMDAR antagonist and ameliorated by d-serine or the atypical antipsychotic clozapine. Expression profiling revealed that the Srr mutation influenced several genes that have been linked to schizophrenia and cognitive ability. Transcript levels altered by the Srr mutation were also normalized by d-serine or clozapine treatment. Furthermore, analysis of SRR genetic variants in humans identified a robust association with schizophrenia. This study demonstrates that aberrant Srr function and diminished d-serine may contribute to schizophrenia pathogenesis.
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Affiliation(s)
- Viviane Labrie
- Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada.
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17
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ENU-induced mutant mice for a next-generation gene-targeting system. PROGRESS IN BRAIN RESEARCH 2009. [PMID: 20302815 DOI: 10.1016/s0079-6123(09)17904-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register]
Abstract
By the N-ethyl-N-nitrosourea (ENU)-based gene-driven mutagenesis, it is now possible to obtain allelic series of mutant mouse strains, each of which carries a different base substitution in any target gene. This new reverse genetic tool has become available based on the ENU mutant mouse library. The ENU mutant mouse library consists of dual archives of frozen sperm and corresponding genomic DNA derived from Generation-1 (G1) male mice, each of which carries thousands of ENU-induced base substitutions. Firstly, ENU-induced mutations in the target gene are screened from the genomic DNA archive by using one of the high-throughput mutation discovery systems. The identified mutations are then revived as live mice by the in vitro fertilization (IVF) and embryo transfer (ET) technology. Just like the knockout (KO) mouse system, the revived mutant strains are finally subjected to the three-generation scheme to reveal the gene function(s) of the target gene. This new reverse genetics or "next-generation gene-targeting system" allows us to elucidate the biological roles of the mouse genome in terms of single base-pair effects not only for the protein-coding sequences but also for any genomic sequences.
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18
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Acevedo-Arozena A, Wells S, Potter P, Kelly M, Cox RD, Brown SDM. ENU mutagenesis, a way forward to understand gene function. Annu Rev Genomics Hum Genet 2008; 9:49-69. [PMID: 18949851 DOI: 10.1146/annurev.genom.9.081307.164224] [Citation(s) in RCA: 125] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Arguably, the main challenge for contemporary genetics is to understand the function of every gene in a mammalian genome. The mouse has emerged as a model for this task because its genome can be manipulated in a number of ways to study gene function or mimic disease states. Two complementary genetic approaches can be used to generate mouse models. A reverse genetics or gene-driven approach (gene to phenotype) starts from a known gene and manipulates the genome to create genetically modified mice, such as knockouts. Alternatively, a forward genetics or phenotype-driven approach (phenotype to gene) involves screening mice for mutant phenotypes without previous knowledge of the genetic basis of the mutation. N-ethyl-N-nitrosourea (ENU) mutagenesis has been widely used for both approaches to generate mouse mutants. Here we review progress in ENU mutagenesis screening, with an emphasis on creating mouse models for human disorders.
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van Boxtel R, Toonen PW, Verheul M, van Roekel HS, Nijman IJ, Guryev V, Cuppen E. Improved generation of rat gene knockouts by target-selected mutagenesis in mismatch repair-deficient animals. BMC Genomics 2008; 9:460. [PMID: 18840264 PMCID: PMC2567347 DOI: 10.1186/1471-2164-9-460] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2008] [Accepted: 10/07/2008] [Indexed: 01/15/2023] Open
Abstract
Background The laboratory rat (Rattus norvegicus) is one of the preferred model organisms in physiological and pharmacological research, although the availability of specific genetic models, especially gene knockouts, is limited. N-ethyl-N-nitrosourea (ENU)-driven target-selected mutagenesis is currently the most successful method in rats, although it is still very laborious and expensive. Results As ENU-induced DNA damage is normally recognized by the mismatch repair (MMR) system, we hypothesized that the effectiveness of the target-selected mutagenesis approach could be improved by using a MMR-deficient genetic background. Indeed, Msh6 knockout rats were found to be more sensitive to ENU treatment and the germ line mutation rate was boosted more than two-fold to 1 mutation per 585 kb. In addition, the molecular mutation spectrum was found to be changed in favor of generating knockout-type alleles by ~20%, resulting in an overall increase in efficiency of ~2.5 fold. The improved effectiveness was demonstrated by high throughput mutation discovery in 70 Mb of sequence in a set of only 310 mutant F1 rats. This resulted in the identification of 89 mutations of which four introduced a premature stopcodon and 64 resulted in amino acid changes. Conclusion Taken together, we show that the use of a MMR-deficient background considerably improves ENU-driven target-selected mutagenesis in the rat, thereby reducing animal use as well as screening costs. The use of a mismatch repair-deficient genetic background for improving mutagenesis and target-selected knockout efficiency is in principle applicable to any organism of interest.
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Affiliation(s)
- Ruben van Boxtel
- Hubrecht Institute for Developmental Biology and Stem Cell Research, Cancer Genomics Center, Royal Netherlands Academy of Sciences, Utrecht, The Netherlands.
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20
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Gondo Y. Trends in large-scale mouse mutagenesis: from genetics to functional genomics. Nat Rev Genet 2008; 9:803-10. [DOI: 10.1038/nrg2431] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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21
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Abstract
The auxiliary spliceosomal protein SCNM1 contributes to recognition of nonconsensus splice donor sites. SCNM1 was first identified as a modifier of the severity of a sodium channelopathy in the mouse. The most severely affected strain, C57BL/6J, carries the variant allele SCNM1R187X, which is defective in splicing the mutated donor site in the Scn8a(medJ) transcript. To further probe the in vivo function of SCNM1, we constructed a floxed allele and generated a mouse with constitutive deletion of exons 3-5. The SCNM1Delta3-5 protein is produced and correctly localized to the nucleus, but is more functionally impaired than the C57BL/6J allele. Deficiency of SCNM1 did not significantly alter other brain transcripts. We characterized an ENU-induced allele of Scnm1 and evaluated the ability of wild-type SCNM1 to rescue lethal mutations of I-mfa and Brunol4. The phenotypes of the Scnm1Delta3-5 mutant confirm the role of this splice factor in processing the Scn8a(medJ) transcript and provide a new allele of greater severity for future studies.
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22
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Aigner B, Rathkolb B, Herbach N, Hrabé de Angelis M, Wanke R, Wolf E. Diabetes models by screen for hyperglycemia in phenotype-driven ENU mouse mutagenesis projects. Am J Physiol Endocrinol Metab 2008; 294:E232-40. [PMID: 18056790 DOI: 10.1152/ajpendo.00592.2007] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
More than 150 million people suffer from diabetes mellitus worldwide, and this number is expected to rise substantially within the next decades. Despite its high prevalence, the pathogenesis of diabetes mellitus is not completely understood. Therefore, appropriate experimental models are essential tools to gain more insight into the genetics and pathogenesis of the disease. Here, we describe the current efforts to establish novel diabetes models derived from unbiased, phenotype-driven, large-scale N-ethyl-N-nitrosourea (ENU) mouse mutagenesis projects started a decade ago using hyperglycemia as a high-throughput screen parameter. Mouse lines were established according to their hyperglycemia phenotype over several generations, thereby revealing a mutation as cause for the aberrant phenotype. Chromosomal assignment of the causative mutation and subsequent candidate gene analysis led to the detection of the mutations that resulted in novel alleles of genes already known to be involved in glucose homeostasis, like glucokinase, insulin 2, and insulin receptor. Additional ENU-induced hyperglycemia lines are under genetic analysis. Improvements in screen for diabetic animals are implemented to detect more subtle phenotypes. Moreover, diet challenge assays are being employed to uncover interactions between genetic and environmental factors in the pathogenesis of diabetes mellitus. The new mouse mutants recovered in phenotype-driven ENU mouse mutagenesis projects complement the available models generated by targeted mutagenesis of candidate genes, all together providing the large resource of models required for a systematic dissection of the pathogenesis of diabetes mellitus.
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Affiliation(s)
- Bernhard Aigner
- Institute of Molecular Animal Breeding and Biotechnology, Hackerstrasse 27, Oberschleissheim, Germany.
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23
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Schneider B, Koppius A, Sedlmeier R. Use of an exon-trapping vector for the evaluation of splice-site mutations. Mamm Genome 2007; 18:670-6. [PMID: 17687606 DOI: 10.1007/s00335-007-9047-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2007] [Accepted: 06/07/2007] [Indexed: 10/23/2022]
Abstract
Prediction of the effects of splice-site variations by sequence analysis is difficult. In this study we provide the means for a rapid evaluation of the potential for splice-site mutations to interfere with RNA processing. The system may be useful in reverse genetics or mapping studies when isolation and characterization of mRNA is arduous or not possible. In the assay we cloned wild-type and mutant sequences of murine splice-site mutations into an exon-trapping vector and characterized splicing of both recombinant transcripts in a transient cell culture system. Results from this artificial assay were compared with in vivo data from the respective mouse models. We found that the exon-trapping system allows one to confidently predict whether a splice-site variation is going to have a splicing effect in vivo, but the system does not always reflect in vivo splicing in detail. In summary, the exon-trapping system is a reliable and easy-to-use tool for a first evaluation of splice effects.
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Affiliation(s)
- Boris Schneider
- Ingenium Pharmaceuticals AG, Fraunhoferstr 13, 82152, Martinsried, Germany
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24
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Clapcote SJ, Lipina TV, Millar JK, Mackie S, Christie S, Ogawa F, Lerch JP, Trimble K, Uchiyama M, Sakuraba Y, Kaneda H, Shiroishi T, Houslay MD, Henkelman RM, Sled JG, Gondo Y, Porteous DJ, Roder JC. Behavioral phenotypes of Disc1 missense mutations in mice. Neuron 2007; 54:387-402. [PMID: 17481393 DOI: 10.1016/j.neuron.2007.04.015] [Citation(s) in RCA: 403] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2006] [Revised: 03/01/2007] [Accepted: 04/18/2007] [Indexed: 01/25/2023]
Abstract
To support the role of DISC1 in human psychiatric disorders, we identified and analyzed two independently derived ENU-induced mutations in Exon 2 of mouse Disc1. Mice with mutation Q31L showed depressive-like behavior with deficits in the forced swim test and other measures that were reversed by the antidepressant bupropion, but not by rolipram, a phosphodiesterase-4 (PDE4) inhibitor. In contrast, L100P mutant mice exhibited schizophrenic-like behavior, with profound deficits in prepulse inhibition and latent inhibition that were reversed by antipsychotic treatment. Both mutant DISC1 proteins exhibited reduced binding to the known DISC1 binding partner PDE4B. Q31L mutants had lower PDE4B activity, consistent with their resistance to rolipram, suggesting decreased PDE4 activity as a contributory factor in depression. This study demonstrates that Disc1 missense mutations in mice give rise to phenotypes related to depression and schizophrenia, thus supporting the role of DISC1 in major mental illness.
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Affiliation(s)
- Steven J Clapcote
- Samuel Lunenfeld Research Institute at Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada.
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25
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Mutational pattern and frequency of induced nucleotide changes in mouse ENU mutagenesis. BMC Mol Biol 2007; 8:52. [PMID: 17584492 PMCID: PMC1914352 DOI: 10.1186/1471-2199-8-52] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2006] [Accepted: 06/20/2007] [Indexed: 11/16/2022] Open
Abstract
Background With the advent of sequence-based approaches in the mutagenesis studies, it is now possible to directly evaluate the genome-wide pattern of experimentally induced DNA sequence changes for a diverse array of organisms. To gain a more comprehensive understanding of the mutational bias inherent in mouse ENU mutagenesis, this study describes a detailed evaluation of the induced mutational pattern obtained from a sequence-based screen of ENU-mutagenized mice. Results Based on a large-scale screening data, we derive the sequence-based estimates of the nucleotide-specific pattern and frequency of ENU-induced base replacement mutation in the mouse germline, which are then combined with the pattern of codon usage in the mouse coding sequences to infer the spectrum of amino acid changes obtained by ENU mutagenesis. We detect a statistically significant difference between the mutational patterns in phenotype- versus sequence-based screens, which presumably reflects differential phenotypic effects caused by different amino acid replacements. We also demonstrate that the mutations exhibit strong strand asymmetry, and that this imbalance is generated by transcription, most likely as a by-product of transcription-coupled DNA repair in the germline. Conclusion The results clearly illustrate the biased nature of ENU-induced mutations. We expect that a precise understanding of the mutational pattern and frequency of induced nucleotide changes would be of practical importance when designing sequence-based screening strategies to generate mutant mouse strains harboring amino acid variants at specific loci. More generally, by enhancing the collection of experimentally induced mutations in unambiguously defined genomic regions, sequence-based mutagenesis studies will further illuminate the molecular basis of mutagenic and repair mechanisms that preferentially produce a certain class of mutational changes over others.
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26
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Oliver PL, Bitoun E, Davies KE. Comparative genetic analysis: the utility of mouse genetic systems for studying human monogenic disease. Mamm Genome 2007; 18:412-24. [PMID: 17514509 PMCID: PMC1998876 DOI: 10.1007/s00335-007-9014-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2007] [Revised: 03/19/2007] [Accepted: 03/22/2007] [Indexed: 12/23/2022]
Abstract
One of the long-term goals of mutagenesis programs in the mouse has been to generate mutant lines to facilitate the functional study of every mammalian gene. With a combination of complementary genetic approaches and advances in technology, this aim is slowly becoming a reality. One of the most important features of this strategy is the ability to identify and compare a number of mutations in the same gene, an allelic series. With the advent of gene-driven screening of mutant archives, the search for a specific series of interest is now a practical option. This review focuses on the analysis of multiple mutations from chemical mutagenesis projects in a wide variety of genes and the valuable functional information that has been obtained from these studies. Although gene knockouts and transgenics will continue to be an important resource to ascertain gene function, with a significant proportion of human diseases caused by point mutations, identifying an allelic series is becoming an equally efficient route to generating clinically relevant and functionally important mouse models.
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Affiliation(s)
- Peter L. Oliver
- Department of Physiology, Anatomy and Genetics, MRC Functional Genetics Unit, University of Oxford, South Parks Road, Oxford, OX1 3QX UK
| | - Emmanuelle Bitoun
- Department of Physiology, Anatomy and Genetics, MRC Functional Genetics Unit, University of Oxford, South Parks Road, Oxford, OX1 3QX UK
| | - Kay E. Davies
- Department of Physiology, Anatomy and Genetics, MRC Functional Genetics Unit, University of Oxford, South Parks Road, Oxford, OX1 3QX UK
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27
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Abstract
Despite the pre-eminence of the mouse in modelling human disease, several aspects of murine biology limit its routine use in large-scale genetic and therapeutic screening. Many researchers who are interested in an embryologically and genetically tractable disease model have now turned to zebrafish. Zebrafish biology allows ready access to all developmental stages, and the optical clarity of embryos and larvae allow real-time imaging of developing pathologies. Sophisticated mutagenesis and screening strategies on a large scale, and with an economy that is not possible in other vertebrate systems, have generated zebrafish models of a wide variety of human diseases. This Review surveys the achievements and potential of zebrafish for modelling human diseases and for drug discovery and development.
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Affiliation(s)
- Graham J Lieschke
- Cancer and Haematology Division, Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria, 3050, Australia.
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28
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Barbaric I, Wells S, Russ A, Dear TN. Spectrum of ENU-induced mutations in phenotype-driven and gene-driven screens in the mouse. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2007; 48:124-42. [PMID: 17295309 DOI: 10.1002/em.20286] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
N-ethyl-N-nitrosourea (ENU) mutagenesis in mice has become a standard tool for (i) increasing the pool of mutants in many areas of biology, (ii) identifying novel genes involved in physiological processes and disease, and (iii) in assisting in assigning functions to genes. ENU is assumed to cause random mutations throughout the mouse genome, but this presumption has never been analyzed. This is a crucial point, especially for large-scale mutagenesis, as a bias would reflect a constraint on identifying possible genetic targets. There is a significant body of published data now available from both phenotype-driven and gene-driven ENU mutagenesis screens in the mouse that can be used to reveal the effectiveness and limitations of an ENU mutagenesis approach. Analysis of the published data is presented in this paper. As expected for a randomly acting mutagen, ENU-induced mutations identified in phenotype-driven screens were in genes that had higher coding sequence length and higher exon number than the average for the mouse genome. Unexpectedly, the data showed that ENU-induced mutations were more likely to be found in genes that had a higher G + C content and neighboring base analysis revealed that the identified ENU mutations were more often directly flanked by G or C nucleotides. ENU mutations from phenotype-driven and gene-driven screens were dominantly A:T to T:A transversions or A:T to G:C transitions. Knowledge of the spectrum of mutations that ENU elicits will assist in positional cloning of ENU-induced mutations by allowing prioritization of candidate genes based on some of their inherent features.
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Affiliation(s)
- Ivana Barbaric
- Department of Biomedical Science, University of Sheffield, Sheffield, United Kingdom
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29
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Wyrobek AJ, Mulvihill JJ, Wassom JS, Malling HV, Shelby MD, Lewis SE, Witt KL, Preston RJ, Perreault SD, Allen JW, DeMarini DM, Woychik RP, Bishop JB. Assessing human germ-cell mutagenesis in the Postgenome Era: a celebration of the legacy of William Lawson (Bill) Russell. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2007; 48:71-95. [PMID: 17295306 PMCID: PMC2071946 DOI: 10.1002/em.20284] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Birth defects, de novo genetic diseases, and chromosomal abnormality syndromes occur in approximately 5% of all live births, and affected children suffer from a broad range of lifelong health consequences. Despite the social and medical impact of these defects, and the 8 decades of research in animal systems that have identified numerous germ-cell mutagens, no human germ-cell mutagen has been confirmed to date. There is now a growing consensus that the inability to detect human germ-cell mutagens is due to technological limitations in the detection of random mutations rather than biological differences between animal and human susceptibility. A multidisciplinary workshop responding to this challenge convened at The Jackson Laboratory in Bar Harbor, Maine. The purpose of the workshop was to assess the applicability of an emerging repertoire of genomic technologies to studies of human germ-cell mutagenesis. Workshop participants recommended large-scale human germ-cell mutation studies be conducted using samples from donors with high-dose exposures, such as cancer survivors. Within this high-risk cohort, parents and children could be evaluated for heritable changes in (a) DNA sequence and chromosomal structure, (b) repeat sequences and minisatellites, and (c) global gene expression profiles and pathways. Participants also advocated the establishment of a bio-bank of human tissue samples from donors with well-characterized exposure, including medical and reproductive histories. This mutational resource could support large-scale, multiple-endpoint studies. Additional studies could involve the examination of transgenerational effects associated with changes in imprinting and methylation patterns, nucleotide repeats, and mitochondrial DNA mutations. The further development of animal models and the integration of these with human studies are necessary to provide molecular insights into the mechanisms of germ-cell mutations and to identify prevention strategies. Furthermore, scientific specialty groups should be convened to review and prioritize the evidence for germ-cell mutagenicity from common environmental, occupational, medical, and lifestyle exposures. Workshop attendees agreed on the need for a full-scale assault to address key fundamental questions in human germ-cell environmental mutagenesis. These include, but are not limited to, the following: Do human germ-cell mutagens exist? What are the risks to future generations? Are some parents at higher risk than others for acquiring and transmitting germ-cell mutations? Obtaining answers to these, and other critical questions, will require strong support from relevant funding agencies, in addition to the engagement of scientists outside the fields of genomics and germ-cell mutagenesis.
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Affiliation(s)
| | - John J. Mulvihill
- University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma
| | - John S. Wassom
- YAHSGS, LLC, Richland, Washington
- Oak Ridge National Laboratory, Oak Ridge, Tennessee
| | - Heinrich V. Malling
- National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina
| | - Michael D. Shelby
- National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina
| | | | - Kristine L. Witt
- National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina
| | - R. Julian Preston
- US Environmental Protection Agency, Research Triangle Park, North Carolina
| | - Sally D. Perreault
- US Environmental Protection Agency, Research Triangle Park, North Carolina
| | - James W. Allen
- US Environmental Protection Agency, Research Triangle Park, North Carolina
| | - David M. DeMarini
- US Environmental Protection Agency, Research Triangle Park, North Carolina
| | | | - Jack B. Bishop
- National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina
- *Correspondence to: Dr. Jack B. Bishop, National Institute of Environmental Health Sciences, EC-01, PO Box 12233, Research Triangle Park, North Carolina, USA. E-mail:
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Puk O, Dalke C, Favor J, de Angelis MH, Graw J. Variations of eye size parameters among different strains of mice. Mamm Genome 2006; 17:851-7. [PMID: 16897341 DOI: 10.1007/s00335-006-0019-5] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2006] [Accepted: 04/10/2006] [Indexed: 10/24/2022]
Abstract
In the mouse, only a few genes have been definitively associated with a small-eye phenotype; the paired-box gene Pax6 and the gene coding for the microphthalmia-associated transcription factor (Mitf). Mutant alleles were recovered by crude phenotype screens and their effects on eye size are relatively large. This feature points to a bias during screening for eye-size mutants, selecting preferentially more severe phenotypes. An unbiased method determining eye-size parameters in an observer-independent, quantitative manner is expected to pick up variations in other genes, which will be confirmed as pathologic mutations in confirmation crosses. The present study used optical low coherent interferometry (OLCI) to compare the axial eye length, the cornea and lens thicknesses, and the anterior chamber depth in four common wild-type, laboratory inbred strains (C57BL/6J, C3HeB/FeJ, 129S2/SvPasCrl, and BALB/cByJ) between 4 and 15 weeks of age. There were no differences between left and right eyes; differences between the size parameters of males and females have been observed only in a few cases. An optimal screening age for OLCI measurements was defined as 11 weeks of age. At this age, we checked two other inbred strains (AKR/J and DBA/2NCrl) as well as CD-1 outbred mice. CD-1 mice have the largest axial length. The most impressive differences among inbred strains were, first, the anterior chamber depth, where the DBA mice have significantly lower values than the other strains. Second, the cornea in C3H mice is approximately 20% thicker than in the other inbred strains. Finally, wild-type intervals (mean +/- 3 SD) for axial length, anterior chamber depth, and cornea and lens thicknesses were calculated allowing a quick identification of pathologic outliers.
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Affiliation(s)
- Oliver Puk
- Institutes of Developmental Genetics, GSF-National Research Center for Environment and Health, D-85764, Neuherberg, Germany
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31
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Reue K, Vergnes L. Approaches to lipid metabolism gene identification and characterization in the postgenomic era. J Lipid Res 2006; 47:1891-907. [PMID: 16835441 DOI: 10.1194/jlr.r600020-jlr200] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
The availability of genomic resources has already had a tremendous impact on biomedical research. In this review, we describe how whole genome sequence and high-throughput functional genomics projects have facilitated the identification and characterization of important genes in lipid metabolism and disease. We review key approaches and lipid genes identified in the first years of this century and discuss how genomic resources are likely to streamline gene identification and functional characterization in the future.
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Affiliation(s)
- Karen Reue
- Department of Human Genetics and Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA.
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32
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Grosse J, Tarnow P, Römpler H, Schneider B, Sedlmeier R, Huffstadt U, Korthaus D, Nehls M, Wattler S, Schöneberg T, Biebermann H, Augustin M. N-ethyl-N-nitrosourea-based generation of mouse models for mutant G protein-coupled receptors. Physiol Genomics 2006; 26:209-17. [PMID: 16720677 DOI: 10.1152/physiolgenomics.00289.2005] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Chemical random mutagenesis techniques with the germ line supermutagen N-ethyl-N-nitrosourea (ENU) have been established to provide comprehensive collections of mouse models, which were then mined and analyzed in phenotype-driven studies. Here, we applied ENU mutagenesis in a high-throughput fashion for a gene-driven identification of new mutations. Selected members of the large superfamily of G protein-coupled receptors (GPCR), melanocortin type 3 (Mc3r) and type 4 (Mc4r) receptors, and the orphan chemoattractant receptor GPR33, were used as model targets to prove the feasibility of this approach. Parallel archives of DNA and sperm from mice mutagenized with ENU were screened for mutations in these GPCR, and in vitro assays served as a preselection step before in vitro fertilization was performed to generate the appropriate mouse model. For example, mouse models for inherited obesity were established by selecting fully or partially inactivating mutations in Mc4r. Our technology described herein has the potential to provide mouse models for a GPCR dysfunction of choice within <4 mo and can be extended to other gene classes of interest.
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MESH Headings
- Alkylating Agents/toxicity
- Animals
- COS Cells
- Chlorocebus aethiops
- DNA Mutational Analysis/methods
- Disease Models, Animal
- Enzyme-Linked Immunosorbent Assay
- Ethylnitrosourea/toxicity
- Female
- Green Fluorescent Proteins/genetics
- Green Fluorescent Proteins/metabolism
- Mice
- Mice, Inbred C3H
- Mice, Inbred C57BL
- Mice, Mutant Strains
- Mutagenesis/drug effects
- Mutation/genetics
- Phylogeny
- Receptor, Melanocortin, Type 3/genetics
- Receptor, Melanocortin, Type 3/physiology
- Receptor, Melanocortin, Type 4/genetics
- Receptor, Melanocortin, Type 4/physiology
- Receptors, G-Protein-Coupled/genetics
- Receptors, G-Protein-Coupled/physiology
- Signal Transduction/physiology
- Transfection
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33
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Peters T, Sedlmeier R. Current methods for high-throughput detection of novel DNA polymorphisms. DRUG DISCOVERY TODAY. TECHNOLOGIES 2006; 3:123-129. [PMID: 24980398 DOI: 10.1016/j.ddtec.2006.05.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
For research varying from the identification of specific disease loci to the investigation of protein function, the detection of DNA sequence variations requires reliable methods. Technologies enabling rapid and cost effective identification of novel genetic polymorphisms will significantly impact future work in genetic mapping studies, drug target discovery and validation and pharmacogenomics.:
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Affiliation(s)
- Thomas Peters
- Ingenium Pharmaceuticals AG, Fraunhoferstr. 13, 82152 Martinsried, Germany
| | - Reinhard Sedlmeier
- Ingenium Pharmaceuticals AG, Fraunhoferstr. 13, 82152 Martinsried, Germany.
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