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Lu H, Liu J, Feng T, Guo Z, Yin Y, Gao F, Cao G, Du X, Wu S. A HIT-trapping strategy for rapid generation of reversible and conditional alleles using a universal donor. Genome Res 2021; 31:900-909. [PMID: 33795333 PMCID: PMC8092013 DOI: 10.1101/gr.271312.120] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 03/30/2021] [Indexed: 11/24/2022]
Abstract
Targeted mutagenesis in model organisms is key for gene functional annotation and biomedical research. Despite technological advances in gene editing by the CRISPR-Cas9 systems, rapid and efficient introduction of site-directed mutations remains a challenge in large animal models. Here, we developed a robust and flexible insertional mutagenesis strategy, homology-independent targeted trapping (HIT-trapping), which is generic and can efficiently target-trap an endogenous gene of interest independent of homology arm and embryonic stem cells. Further optimization and equipping the HIT-trap donor with a site-specific DNA inversion mechanism enabled one-step generation of reversible and conditional alleles in a single experiment. As a proof of concept, we successfully created mutant alleles for 21 disease-related genes in primary porcine fibroblasts with an average knock-in frequency of 53.2%, a great improvement over previous approaches. The versatile HIT-trapping strategy presented here is expected to simplify the targeted generation of mutant alleles and facilitate large-scale mutagenesis in large mammals such as pigs.
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Affiliation(s)
- Hengxing Lu
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Jun Liu
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Tao Feng
- Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Chengdu 610200, China
| | - Zihang Guo
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Yunjun Yin
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Fei Gao
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Gengsheng Cao
- Henan Engineering Laboratory for Mammary Bioreactor, School of Life Science, Henan University, Kaifeng 475004, China
| | - Xuguang Du
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Sen Wu
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
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2
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Site-Specific Recombination with Inverted Target Sites: A Cautionary Tale of Dicentric and Acentric Chromosomes. Genetics 2020; 215:923-930. [PMID: 32586890 DOI: 10.1534/genetics.120.303394] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 06/22/2020] [Indexed: 11/18/2022] Open
Abstract
Site-specific recombinases are widely used tools for analysis of genetics, development, and cell biology, and many schemes have been devised to alter gene expression by recombinase-mediated DNA rearrangements. Because the FRT and lox target sites for the commonly used FLP and Cre recombinases are asymmetrical, and must pair in the same direction to recombine, construct design must take into account orientation of the target sites. Both direct and inverted configurations have been used. However, the outcome of recombination between target sites on sister chromatids is frequently overlooked. This is especially consequential with inverted target sites, where exchange between oppositely oriented target sites on sisters will produce dicentric and acentric chromosomes. By using constructs that have inverted target sites in Drosophila melanogaster and in mice, we show here that dicentric chromosomes are produced in the presence of recombinase, and that the frequency of this event is quite high. The negative effects on cell viability and behavior can be significant, and should be considered when using such constructs.
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3
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Chiou SH, Kim-Kiselak C, Risca VI, Heimann MK, Chuang CH, Burds AA, Greenleaf WJ, Jacks TE, Feldser DM, Winslow MM. A conditional system to specifically link disruption of protein-coding function with reporter expression in mice. Cell Rep 2014; 7:2078-86. [PMID: 24931605 DOI: 10.1016/j.celrep.2014.05.031] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Revised: 04/04/2014] [Accepted: 05/15/2014] [Indexed: 10/25/2022] Open
Abstract
Conditional gene deletion in mice has contributed immensely to our understanding of many biological and biomedical processes. Despite an increasing awareness of nonprotein-coding functional elements within protein-coding transcripts, current gene-targeting approaches typically involve simultaneous ablation of noncoding elements within targeted protein-coding genes. The potential for protein-coding genes to have additional noncoding functions necessitates the development of novel genetic tools capable of precisely interrogating individual functional elements. We present a strategy that couples Cre/loxP-mediated conditional gene disruption with faithful GFP reporter expression in mice in which Cre-mediated stable inversion of a splice acceptor-GFP-splice donor cassette concurrently disrupts protein production and creates a GFP fusion product. Importantly, cassette inversion maintains physiologic transcript structure, thereby ensuring proper microRNA-mediated regulation of the GFP reporter, as well as maintaining expression of nonprotein-coding elements. To test this potentially generalizable strategy, we generated and analyzed mice with this conditional knockin reporter targeted to the Hmga2 locus.
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Affiliation(s)
- Shin-Heng Chiou
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305-5120, USA
| | - Caroline Kim-Kiselak
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Viviana I Risca
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305-5120, USA
| | - Megan K Heimann
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Chen-Hua Chuang
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305-5120, USA
| | - Aurora A Burds
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - William J Greenleaf
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305-5120, USA
| | - Tyler E Jacks
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - David M Feldser
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA 19104-6160, USA; Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA 19104-6160, USA
| | - Monte M Winslow
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305-5120, USA; Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305-5324, USA; Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94305-5456, USA.
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4
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Parra S, Huang X, Charbeneau RA, Wade SM, Kaur K, Rorabaugh BR, Neubig RR. Conditional disruption of interactions between Gαi2 and regulator of G protein signaling (RGS) proteins protects the heart from ischemic injury. BMC Pharmacol Toxicol 2014; 15:29. [PMID: 24899231 PMCID: PMC4059092 DOI: 10.1186/2050-6511-15-29] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Accepted: 05/28/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Regulator of G protein signaling (RGS) proteins suppress G protein coupled receptor signaling by catalyzing the hydrolysis of Gα-bound guanine nucleotide triphosphate. Transgenic mice in which RGS-mediated regulation of Gαi2 is lost (RGS insensitive Gαi2G184S) exhibit beneficial (protection against ischemic injury) and detrimental (enhanced fibrosis) cardiac phenotypes. This mouse model has revealed the physiological significance of RGS/Gαi2 interactions. Previous studies of the Gαi2G184S mutation used mice that express this mutant protein throughout their lives. Thus, it is unclear whether these phenotypes result from chronic or acute Gαi2G184S expression. We addressed this issue by developing mice that conditionally express Gαi2G184S. METHODS Mice that conditionally express RGS insensitive Gαi2G184S were generated using a floxed minigene strategy. Conditional expression of Gαi2G184S was characterized by reverse transcription polymerase chain reaction and by enhancement of agonist-induced inhibition of cAMP production in isolated cardiac fibroblasts. The impact of conditional RGS insensitive Gαi2G184S expression on ischemic injury was assessed by measuring contractile recovery and infarct sizes in isolated hearts subjected to 30 min ischemia and 2 hours reperfusion. RESULTS We demonstrate tamoxifen-dependent expression of Gαi2G184S, enhanced inhibition of cAMP production, and cardioprotection from ischemic injury in hearts conditionally expressing Gαi2G184S. Thus the cardioprotective phenotype previously reported in mice expressing Gαi2G184S does not require embryonic or chronic Gαi2G184S expression. Rather, cardioprotection occurs following acute (days rather than months) expression of Gαi2G184S. CONCLUSIONS These data suggest that RGS proteins might provide new therapeutic targets to protect the heart from ischemic injury. We anticipate that this model will be valuable for understanding the time course (chronic versus acute) and mechanisms of other phenotypic changes that occur following disruption of interactions between Gαi2 and RGS proteins.
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Affiliation(s)
| | | | | | | | | | - Boyd R Rorabaugh
- Department of Pharmaceutical and Biomedical Sciences, Ohio Northern University College of Pharmacy, Ada, OH 45810, USA.
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5
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Abstract
Zebrafish has become a widely used model for analysis of gene function. Several methods have been used to create mutations in this organism and thousands of mutant lines are available. However, all the conventional zebrafish mutations affect the gene in all cells at all time, making it difficult to determine tissue-specific functions. We have adopted a FlEx Trap approach to generate conditional mutations in zebrafish by gene-trap mutagenesis. Combined with appropriate Cre or Flp lines, the insertional mutants not only allow spatial- and temporal-specific gene inactivation but also permit spatial- and temporal-specific rescue of the disrupted gene. We provide experimental details on how to generate and use such mutations.
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Affiliation(s)
- Lisette A Maddison
- Department of Molecular Physiology & Biophysics, Vanderbilt University School of Medicine, Nashville, TN, USA
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6
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Effective gene trapping mediated by Sleeping Beauty transposon. PLoS One 2012; 7:e44123. [PMID: 22952894 PMCID: PMC3432063 DOI: 10.1371/journal.pone.0044123] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2012] [Accepted: 07/30/2012] [Indexed: 01/14/2023] Open
Abstract
Gene trapping is a high-throughput approach to elucidate gene functions by disrupting and recapitulating expression of genes in a target genome. A number of transposon-based gene-trapping systems are developed for mutagenesis in cells and model organisms, but there is still much room for the improvement of their efficiency in gene disruption and mutation. Herein, a gene-trapping system mediated by Sleeping Beauty (SB) transposon was developed by inclusion of three functional cassettes. The mutation cassette can abrogate the splice of trapped genes and terminate their translation. Once an endogenous gene is captured, the finding cassette independently drives the translation of reporter gene in HeLa cells and zebrafish embryos. The efficiency cassette controls the remobilization of integrated traps through inducible expression of SB gene. Analysis of transposon-genome junctions indicate that most of trap cassettes are integrated into an intron without an obvious 3′ bias. The transcription of trapped genes was abrogated by alternative splicing of the mutation cassette. In addition, integrated transposons can be induced to excise from their original insertion sites. Furthermore, the Cre/LoxP system was introduced to delete the efficiency cassette for stabilization of gene interruption and bio-safety. Thus, this gene-trap vector is an alternative and effective tool for the capture and disruption of endogenous genes in vitro and in vivo.
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7
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Teta M, Choi YS, Okegbe T, Wong G, Tam OH, Chong MMW, Seykora JT, Nagy A, Littman DR, Andl T, Millar SE. Inducible deletion of epidermal Dicer and Drosha reveals multiple functions for miRNAs in postnatal skin. Development 2012; 139:1405-16. [PMID: 22434867 DOI: 10.1242/dev.070920] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
MicroRNAs (miRNAs) regulate the expression of many mammalian genes and play key roles in embryonic hair follicle development; however, little is known of their functions in postnatal hair growth. We compared the effects of deleting the essential miRNA biogenesis enzymes Drosha and Dicer in mouse skin epithelial cells at successive postnatal time points. Deletion of either Drosha or Dicer during an established growth phase (anagen) caused failure of hair follicles to enter a normal catagen regression phase, eventual follicular degradation and stem cell loss. Deletion of Drosha or Dicer in resting phase follicles did not affect follicular structure or epithelial stem cell maintenance, and stimulation of anagen by hair plucking caused follicular proliferation and formation of a primitive transient amplifying matrix population. However, mutant matrix cells exhibited apoptosis and DNA damage and hair follicles rapidly degraded. Hair follicle defects at early time points post-deletion occurred in the absence of inflammation, but a dermal inflammatory response and hyperproliferation of interfollicular epidermis accompanied subsequent hair follicle degradation. These data reveal multiple functions for Drosha and Dicer in suppressing DNA damage in rapidly proliferating follicular matrix cells, facilitating catagen and maintaining follicular structures and their associated stem cells. Although Drosha and Dicer each possess independent non-miRNA-related functions, the similarity in phenotypes of the inducible epidermal Drosha and Dicer mutants indicates that these defects result primarily from failure of miRNA processing. Consistent with this, Dicer deletion resulted in the upregulation of multiple direct targets of the highly expressed epithelial miRNA miR-205.
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Affiliation(s)
- Monica Teta
- Department of Dermatology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
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8
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Mayasari NI, Mukougawa K, Shigeoka T, Kawakami K, Kawaichi M, Ishida Y. Mixture of differentially tagged Tol2 transposons accelerates conditional disruption of a broad spectrum of genes in mouse embryonic stem cells. Nucleic Acids Res 2012; 40:e97. [PMID: 22447447 PMCID: PMC3401447 DOI: 10.1093/nar/gks262] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Among the insertional mutagenesis techniques used in the current international knockout mouse project (KOMP) on the inactivation of all mouse genes in embryonic stem (ES) cells, random gene trapping has been playing a major role. Gene-targeting experiments have also been performed to individually and conditionally knockout the remaining ‘difficult-to-trap’ genes. Here, we show that transcriptionally silent genes in ES cells are severely underrepresented among the randomly trapped genes in KOMP. Our conditional poly(A)-trapping vector with a common retroviral backbone also has a strong bias to be integrated into constitutively transcribed genome loci. Most importantly, conditional gene disruption could not be successfully accomplished by using the retrovirus vector because of the frequent development of intra-vector deletions/rearrangements. We found that one of the cut and paste-type DNA transposons, Tol2, can serve as an ideal platform for gene-trap vectors that ensures identification and conditional disruption of a broad spectrum of genes in ES cells. We also solved a long-standing problem associated with multiple vector integration into the genome of a single cell by incorporating a mixture of differentially tagged Tol2 transposons. We believe our strategy indicates a straightforward approach to mass-production of conditionally disrupted alleles for genes in the target cells.
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Affiliation(s)
- N Ika Mayasari
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma-shi, Nara 630-0192, Japan
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9
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Chen PC, Wakimoto H, Conner D, Araki T, Yuan T, Roberts A, Seidman CE, Bronson R, Neel BG, Seidman JG, Kucherlapati R. Activation of multiple signaling pathways causes developmental defects in mice with a Noonan syndrome–associated Sos1 mutation. J Clin Invest 2011; 120:4353-65. [PMID: 21041952 DOI: 10.1172/jci43910] [Citation(s) in RCA: 84] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2010] [Accepted: 09/15/2010] [Indexed: 02/06/2023] Open
Abstract
Noonan syndrome (NS) is an autosomal dominant genetic disorder characterized by short stature, unique facial features, and congenital heart disease. About 10%-15% of individuals with NS have mutations in son of sevenless 1 (SOS1), which encodes a RAS and RAC guanine nucleotide exchange factor (GEF). To understand the role of SOS1 in the pathogenesis of NS, we generated mice with the NS-associated Sos1E846K gain-of-function mutation. Both heterozygous and homozygous mutant mice showed many NS-associated pheno-types, including growth delay, distinctive facial dysmorphia, hematologic abnormalities, and cardiac defects. We found that the Ras/MAPK pathway as well as Rac and Stat3 were activated in the mutant hearts. These data provide in vivo molecular and cellular evidence that Sos1 is a GEF for Rac under physiological conditions and suggest that Rac and Stat3 activation might contribute to NS phenotypes. Furthermore, prenatal administration of a MEK inhibitor ameliorated the embryonic lethality, cardiac defects, and NS features of the homozygous mutant mice, demonstrating that this signaling pathway might represent a promising therapeutic target for NS.
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Affiliation(s)
- Peng-Chieh Chen
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
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10
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Maddison LA, Lu J, Chen W. Generating conditional mutations in zebrafish using gene-trap mutagenesis. Methods Cell Biol 2011; 104:1-22. [PMID: 21924154 DOI: 10.1016/b978-0-12-374814-0.00001-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
While several mutagenesis methods have been successfully applied in zebrafish, these mutations do not allow tissue- or temporal-specific functional analysis. We have developed a strategy that will allow tissue- or temporal-specific disruption of genes in zebrafish. This strategy combines gene-trap mutagenesis and FlEx modules containing target sites for site-specific recombinases. The gene-trap cassette is highly mutagenic in one orientation and nonmutagenic in the opposite orientation, with different fluorescent proteins as indicators of the orientation. The inclusion of the FlEx modules allows two rounds of stable inversion mediated by the Cre and Flp recombinases. This gene-trap cassette can be easily delivered via transposons. Through large-scale community-wide efforts, broad genome coverage can be obtained. This should allow investigation of cell/tissue-specific gene function of a wide range of genes.
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Affiliation(s)
- Lisette A Maddison
- Department of Molecular Physiology and Biophysics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
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11
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PhiC31 integrase induces efficient site-specific excision in zebrafish. Transgenic Res 2010; 20:183-9. [PMID: 20556509 DOI: 10.1007/s11248-010-9394-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2009] [Accepted: 04/01/2010] [Indexed: 01/09/2023]
Abstract
Site-specific recombinases catalyze recombination between specific targeting sites to delete, insert, invert, or exchange DNA with high fidelity. In addition to the widely used Cre and Flp recombinases, the phiC31 integrase system from Streptomyces phage may also be used for these genetic manipulations in eukaryotic cells. Unlike Cre and Flp, phiC31 recognizes two heterotypic sites, attB and attP, for recombination. While the phiC31 system has been recently applied in mouse and human cell lines and in Drosophila, it has not been demonstrated whether it can also catalyze efficient DNA recombination in zebrafish. Here we show that phiC31 integrase efficiently induces site-specific deletion of episomal targets as well as chromosomal targets in zebrafish embryos. Thus, the phiC31 system can be used in zebrafish for genetic manipulations, expanding the repertoire of available tools for genetic manipulation in this vertebrate model.
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12
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Abstract
Gene trapping in mouse embryonic stem (ES) cells is an efficient method for the mutagenesis of the mammalian genome. Insertion of a gene trap vector disrupts gene function, reports gene expression, and provides a convenient tag for the identification of the insertion site. The trap vector can be delivered to ES cells by electroporation of a plasmid, by retroviral infection, or by transposon-mediated insertion. Recent developments in trapping technology involve the utilization of site-specific recombination sites, which allow the induced modification of trap alleles in vitro and in vivo. Gene trapping strategies have also been successfully developed to screen for genes that are acting in specific biological pathways. In this chapter, we review different applications of gene trapping, and we provide detailed experimental protocols for gene trapping in ES cells by retroviral and transposon gene trap vectors.
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Affiliation(s)
- Roland H Friedel
- Department of Neurosurgery, Mount Sinai School of Medicine, New York, USA
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13
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Floxin, a resource for genetically engineering mouse ESCs. Nat Methods 2009; 7:50-2. [PMID: 19966808 PMCID: PMC2895430 DOI: 10.1038/nmeth.1406] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2009] [Accepted: 11/12/2009] [Indexed: 11/26/2022]
Abstract
We describe a method for the highly efficient and precise targeted modification of gene trap loci in mouse embryonic stem cells (ESCs). Through the Floxin method, gene trap mutations are reverted and new DNA sequences inserted using Cre recombinase and a shuttle vector, pFloxin. Floxin technology is applicable to the existing collection of 24,149 compatible gene trap cell lines, which should enable the high-throughput modification of many genes in mouse ESCs.
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14
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Gama Sosa MA, De Gasperi R, Elder GA. Animal transgenesis: an overview. Brain Struct Funct 2009; 214:91-109. [PMID: 19937345 DOI: 10.1007/s00429-009-0230-8] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2009] [Accepted: 11/06/2009] [Indexed: 10/20/2022]
Abstract
Transgenic animals are extensively used to study in vivo gene function as well as to model human diseases. The technology for producing transgenic animals exists for a variety of vertebrate and invertebrate species. The mouse is the most utilized organism for research in neurodegenerative diseases. The most commonly used techniques for producing transgenic mice involves either the pronuclear injection of transgenes into fertilized oocytes or embryonic stem cell-mediated gene targeting. Embryonic stem cell technology has been most often used to produce null mutants (gene knockouts) but may also be used to introduce subtle genetic modifications down to the level of making single nucleotide changes in endogenous mouse genes. Methods are also available for inducing conditional gene knockouts as well as inducible control of transgene expression. Here, we review the main strategies for introducing genetic modifications into the mouse, as well as in other vertebrate and invertebrate species. We also review a number of recent methodologies for the production of transgenic animals including retrovirus-mediated gene transfer, RNAi-mediated gene knockdown and somatic cell mutagenesis combined with nuclear transfer, methods that may be more broadly applicable to species where both pronuclear injection and ES cell technology have proven less practical.
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Affiliation(s)
- Miguel A Gama Sosa
- Department of Psychiatry, Mount Sinai School of Medicine, One Gustave L. Levy Place, New York, NY, 10029, USA.
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15
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Sivasubbu S, Balciunas D, Amsterdam A, Ekker SC. Insertional mutagenesis strategies in zebrafish. Genome Biol 2007; 8 Suppl 1:S9. [PMID: 18047701 PMCID: PMC2106850 DOI: 10.1186/gb-2007-8-s1-s9] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
We review here some recent developments in the field of insertional mutagenesis in zebrafish. We highlight the advantages and limitations of the rich body of retroviral methodologies, and we focus on the mechanisms and concepts of new transposon-based mutagenesis approaches under development, including prospects for conditional 'gene trapping' and 'gene breaking' approaches.
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Affiliation(s)
- Sridhar Sivasubbu
- Institute of Genomics and Integrative Biology, Council for Scientific and Industrial Research, Mall Road, Delhi 110007, India
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16
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Abstract
LINE1 (L1) retrotransposons are genetic elements that are present in all mammalian genomes. L1s are active in both humans and mice, and are capable of copying themselves and inserting the copy into a new genomic location. These de novo insertions occasionally result in disease. Endogenous L1 retrotransposons can be modified to increase their activity and mutagenic power in a variety of ways. Here we outline the advantages of using modified L1 retrotransposons for performing random mutagenesis in rodents and discuss several potential applications.
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Affiliation(s)
- Eric M Ostertag
- University of Pennsylvania School of Medicine, Department of Genetics, Curie Blvd, Philadelphia, Pennsylvania 19104, USA.
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17
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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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18
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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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19
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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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20
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Abstract
Over the past years new vectors and methodologies have been developed to carry out large-scale genome-wide insertional mutagenesis screens in the mouse. Gene trapping, the most commonly used technique, is based on the insertion of a retroviral- or plasmid-based vector into a gene, resulting in a loss-of-function mutation, while simultaneously reporting its expression pattern and providing a molecular tag to facilitate cloning. The discovery of vertebrate DNA transposons in the mouse and recent improvements has also led to their increased use in insertional mutagenesis screens. Several public resources have been set-up recently by the academic community to distribute information and materials generated from these large-scale screens. These new resources should accelerate the study and understanding of biological and developmental processes.
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Affiliation(s)
- Christopher S Raymond
- Program in Developmental Biology, Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
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21
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Schnütgen F, Stewart AF, von Melchner H, Anastassiadis K. Engineering embryonic stem cells with recombinase systems. Methods Enzymol 2006; 420:100-36. [PMID: 17161696 DOI: 10.1016/s0076-6879(06)20007-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The combined use of site-specific recombination and gene targeting or trapping in embryonic stem cells (ESCs) has resulted in the emergence of technologies that enable the induction of mouse mutations in a prespecified temporal and spatially restricted manner. Their large-scale implementation by several international mouse mutagenesis programs will lead to the assembly of a library of ES cell lines harboring conditional mutations in every single gene of the mouse genome. In anticipation of this unprecedented resource, this chapter will focus on site-specific recombination strategies and issues pertinent to ESCs and mice. The upcoming ESC resource and the increasing sophistication of site-specific recombination technologies will greatly assist the functional annotation of the human genome and the animal modeling of human disease.
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Affiliation(s)
- Frank Schnütgen
- Department for Molecular Hematology, University of Frankfurt Medical School, Frankfurt am Main, Germany
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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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