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Abstract
Gene trapping is a technology originally developed for the simultaneous identification and mutation of genes by random integration in embryonic stem (ES) cells. While gene trapping was developed before efficient and high-throughput gene targeting, a significant proportion of the publically available mutant ES cell lines and mice were generated through a number of large-scale gene trapping initiatives. Moreover, elements of gene trap vectors continue to be incorporated into gene targeting vectors as a means to increase the efficiency of homologous recombination. Here, we review the current state of gene trapping technology and the applications of specific types of gene trap vector. As a component of this analysis, we consider the behavior of specific vector types both from the perspective of their application and how they can inform our annotation of the mammalian transcriptome. We consider the utility of gene trap vectors as tools for cell-based expression analysis, targeted screening in embryonic differentiation, and for use in cell lines derived from different lineages.
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Affiliation(s)
- Joshua M Brickman
- MRC Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
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52
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Okuno T, Nakatsuji Y, Moriya M, Takamatsu H, Nojima S, Takegahara N, Toyofuku T, Nakagawa Y, Kang S, Friedel RH, Sakoda S, Kikutani H, Kumanogoh A. Roles of Sema4D-plexin-B1 interactions in the central nervous system for pathogenesis of experimental autoimmune encephalomyelitis. THE JOURNAL OF IMMUNOLOGY 2009; 184:1499-506. [PMID: 20038643 DOI: 10.4049/jimmunol.0903302] [Citation(s) in RCA: 84] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Although semaphorins were originally identified as axonal guidance molecules during neuronal development, it is emerging that several semaphorins play crucial roles in various phases of immune responses. Sema4D/CD100, a class IV semaphorin, has been shown to be involved in the nervous and immune systems through its receptors plexin-B1 and CD72, respectively. However, the involvement of Sema4D in neuroinflammation still remains unclear. We found that Sema4D promoted inducible NO synthase expression by primary mouse microglia, the effects of which were abolished in plexin-B1-deficient but not in CD72-deficient microglia. In addition, during the development of experimental autoimmune encephalomyelitis (EAE), which was induced by immunization with myelin oligodendrocyte glycoprotein-derived peptides, we observed that the expression of Sema4D and plexin-B1 was induced in infiltrating mononuclear cells and microglia, respectively. Consistent with these expression profiles, when myelin oligodendrocyte glycoprotein-specific T cells derived from wild-type mice were adoptively transferred into plexin-B1-deficient mice or bone marrow chimera mice with plexin-B1-deficient CNS resident cells, the development of EAE was considerably attenuated. Furthermore, blocking Abs against Sema4D significantly inhibited neuroinflammation during EAE development. Collectively, our findings demonstrate the role of Sema4D-plexin-B1 interactions in the activation of microglia and provide their pathologic significance in neuroinflammation.
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Affiliation(s)
- Tatsusada Okuno
- Department of Immunopathology, Osaka University Graduate School of Medicine, Osaka University, Osaka, Japan
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53
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Tsakiridis A, Tzouanacou E, Rahman A, Colby D, Axton R, Chambers I, Wilson V, Forrester L, Brickman JM. Expression-independent gene trap vectors for random and targeted mutagenesis in embryonic stem cells. Nucleic Acids Res 2009; 37:e129. [PMID: 19692586 PMCID: PMC2770648 DOI: 10.1093/nar/gkp640] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2009] [Revised: 07/13/2009] [Accepted: 07/17/2009] [Indexed: 12/04/2022] Open
Abstract
Promoterless gene trap vectors have been widely used for high-efficiency gene targeting and random mutagenesis in embryonic stem (ES) cells. Unfortunately, such vectors are only effective for genes expressed in ES cells and this has prompted the development of expression-independent vectors. These polyadenylation (poly A) trap vectors employ a splice donor to capture an endogenous gene's polyadenylation sequence and provide transcript stability. However, the spectrum of mutations generated by these vectors appears largely restricted to the last intron of target loci due to nonsense-mediated mRNA decay (NMD) making them unsuitable for gene targeting applications. Here, we present novel poly A trap vectors that overcome the effect of NMD and also employ RNA instability sequences to improve splicing efficiency. The set of random insertions generated with these vectors show a significantly reduced insertional bias and the vectors can be targeted directly to a 5' intron. We also show that this relative positional independence is linked to the human beta-actin promoter and is most likely a result of its transcriptional activity in ES cells. Taken together our data indicate that these vectors are an effective tool for insertional mutagenesis that can be used for either gene trapping or gene targeting.
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Affiliation(s)
- Anestis Tsakiridis
- MRC Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, King's Buildings, West Mains Road and MRC Centre for Regenerative Medicine, Queens Medical Research Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh, UK
| | - Elena Tzouanacou
- MRC Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, King's Buildings, West Mains Road and MRC Centre for Regenerative Medicine, Queens Medical Research Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh, UK
| | - Afifah Rahman
- MRC Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, King's Buildings, West Mains Road and MRC Centre for Regenerative Medicine, Queens Medical Research Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh, UK
| | - Douglas Colby
- MRC Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, King's Buildings, West Mains Road and MRC Centre for Regenerative Medicine, Queens Medical Research Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh, UK
| | - Richard Axton
- MRC Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, King's Buildings, West Mains Road and MRC Centre for Regenerative Medicine, Queens Medical Research Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh, UK
| | - Ian Chambers
- MRC Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, King's Buildings, West Mains Road and MRC Centre for Regenerative Medicine, Queens Medical Research Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh, UK
| | - Valerie Wilson
- MRC Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, King's Buildings, West Mains Road and MRC Centre for Regenerative Medicine, Queens Medical Research Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh, UK
| | - Lesley Forrester
- MRC Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, King's Buildings, West Mains Road and MRC Centre for Regenerative Medicine, Queens Medical Research Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh, UK
| | - Joshua M. Brickman
- MRC Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, King's Buildings, West Mains Road and MRC Centre for Regenerative Medicine, Queens Medical Research Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh, UK
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54
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Targeting embryonic stem cells. Methods Mol Biol 2009. [PMID: 19504072 DOI: 10.1007/978-1-60327-019-9_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Gene targeting of mouse embryonic stem cells facilitates the deliberate engineering of the mouse genome. The gene targeting vector is introduced into cells by electroporation, and cell clones carrying the targeting vector are obtained by drug selection. Clones can be screened effectively for correct recombination events by either Southern blot analysis with external and internal probes, or by long-range PCR. Positive clones are subsequently expanded and prepared for the generation of chimeric mice.
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Schnütgen F, Hansen J, De-Zolt S, Horn C, Lutz M, Floss T, Wurst W, Noppinger PR, von Melchner H. Enhanced gene trapping in mouse embryonic stem cells. Nucleic Acids Res 2008; 36:e133. [PMID: 18812397 PMCID: PMC2582619 DOI: 10.1093/nar/gkn603] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Gene trapping is used to introduce insertional mutations into genes of mouse embryonic stem cells (ESCs). It is performed with gene trap vectors that simultaneously mutate and report the expression of the endogenous gene at the site of insertion and provide a DNA tag for rapid identification of the disrupted gene. Gene traps have been employed worldwide to assemble libraries of mouse ESC lines harboring mutations in single genes, which can be used to make mutant mice. However, most of the employed gene trap vectors require gene expression for reporting a gene trap event and therefore genes that are poorly expressed may be under-represented in the existing libraries. To address this problem, we have developed a novel class of gene trap vectors that can induce gene expression at insertion sites, thereby bypassing the problem of intrinsic poor expression. We show here that the insertion of the osteopontin enhancer into several conventional gene trap vectors significantly increases the gene trapping efficiency in high-throughput screens and facilitates the recovery of poorly expressed genes.
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Affiliation(s)
- Frank Schnütgen
- Department of Molecular Hematology, University of Frankfurt Medical School, Frankfurt am Main, Germany
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56
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Leighton PA, van de Lavoir MC, Diamond JH, Xia C, Etches RJ. Genetic modification of primordial germ cells by gene trapping, gene targeting, and phiC31 integrase. Mol Reprod Dev 2008; 75:1163-75. [PMID: 18213680 DOI: 10.1002/mrd.20859] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The genome of germline committed cells is thought to be protected by mechanisms of transcriptional silencing, posing a barrier to transgenesis using cultured germline cells. We found that selection for transgene integration into the primordial germ cell genome required that the transgenes be flanked by the chicken beta-globin insulator. However, integration frequency was low, and sequencing of the insertion sites revealed that the transgenes preferentially inserted into active promoter regions, implying that silencing prohibited recovery of insertions in other regions. Much higher frequencies of integration were achieved when the phiC31 integrase was used to insert transgenes into endogenous pseudo attP sites. Despite the evidence for transcriptional silencing in PGCs, gene targeting of a nonexpressed gene was also achieved. The ability to make genetic modifications in PGCs provides unprecedented opportunities to study the biology of PGCs, as well as produce transgenic chickens for applications in biotechnology and developmental biology.
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Affiliation(s)
- Philip A Leighton
- Origen Therapeutics, 1450 Rollins Road, Burlingame, California 94010, USA.
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57
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Moritz S, Lehmann S, Faissner A, von Holst A. An induction gene trap screen in neural stem cells reveals an instructive function of the niche and identifies the splicing regulator sam68 as a tenascin-C-regulated target gene. Stem Cells 2008; 26:2321-31. [PMID: 18617690 DOI: 10.1634/stemcells.2007-1095] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Neural stem cells (NSCs) reside in a niche that abounds in extracellular matrix (ECM) molecules. The ECM glycoprotein tenascin-C (Tnc) that occurs in more than 25 isoforms represents a major constituent of the privileged NSC milieu. To understand its role for NSCs, the induction gene trap technology was successfully applied to mouse embryonic NSCs, and a library of more than 500 NSC lines with independent gene trap vector integrations was established. Our pilot screen identified Sam68 as a target of Tnc signaling in NSCs. The Tnc-mediated downregulation of Sam68, which we found expressed at low levels in the niche along with Tnc, was independently confirmed on the protein level. Sam68 is a multifunctional RNA-binding protein, and its potential significance for cultured NSCs was studied by overexpression. Increased Sam68 levels caused a marked reduction in NSC cell proliferation. In addition, Sam68 is a signal-dependent regulator of alternative splicing, and its overexpression selectively increased the larger Tnc isoforms, whereas a mutated phosphorylation-deficient Sam68 variant did not. This emphasizes the importance of Sam68 for NSC biology and implicates an instructive rather than a purely permissive role for Tnc in the neural stem cell niche.
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Affiliation(s)
- Sören Moritz
- Department for Cell Morphology and Molecular Neurobiology, NDEF 05/339, Universitaetsstrasse 150, D-44780 Bochum, Germany
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58
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Maretto S, Müller PS, Aricescu AR, Cho KWY, Bikoff EK, Robertson EJ. Ventral closure, headfold fusion and definitive endoderm migration defects in mouse embryos lacking the fibronectin leucine-rich transmembrane protein FLRT3. Dev Biol 2008; 318:184-93. [PMID: 18448090 DOI: 10.1016/j.ydbio.2008.03.021] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2008] [Revised: 03/13/2008] [Accepted: 03/14/2008] [Indexed: 12/23/2022]
Abstract
The three fibronectin leucine-rich repeat transmembrane (FLRT) proteins contain 10 leucine-rich repeats (LRR), a type III fibronectin (FN) domain, followed by the transmembrane region, and a short cytoplasmic tail. XFLRT3, a Nodal/TGFbeta target, regulates cell adhesion and modulates FGF signalling during Xenopus gastrulation. The present study describes the onset and pattern of FLRT1-3 expression in the early mouse embryo. FLRT3 expression is activated in the anterior visceral endoderm (AVE), and during gastrulation appears in anterior streak derivatives namely the node, notochord and the emerging definitive endoderm. To explore FLRT3 function we generated a null allele via gene targeting. Early Nodal activities required for anterior-posterior (A-P) patterning, primitive streak formation and left-right (L-R) axis determination were unperturbed. However, FLRT3 mutant embryos display defects in headfold fusion, definitive endoderm migration and a failure of the lateral edges of the ventral body wall to fuse, leading to cardia bifida. Surprisingly, the mutation has no effect on FGF signalling. Collectively these experiments demonstrate that FLRT3 plays a key role in controlling cell adhesion and tissue morphogenesis in the developing mouse embryo.
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Affiliation(s)
- Silvia Maretto
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
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59
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Abstract
The knowledge about the complete genome sequences of mouse, human, and other organisms is only the first step toward the functional annotation of all genes. It facilitates the recognition of sequence conservation, which helps to distinguish between important and not important and also coding from noncoding sequence. Nevertheless, approximately only 50% of all mouse genes have been entirely annotated to date. In the postgenomic era, large-scale projects have been initiated to describe also the expression (Emap, Eurexpress) and the function (International Gene Trap Consortium, Eucomm, Norcomm, Komp) of all mouse genes. By building up on these resources, the average amount of time starting from a gene-coding sequence to finally studying its function in a living organism or embryo, has shortened significantly within the last decade. Several recent developments, namely, in bioinformatics and gene synthesis but also in targeted and random mutagenesis have contributed to the current status. This chapter will highlight the milestones that have been undertaken in order to saturate the mouse genome with gene trap mutations. We have no intention to cover the entire field but will instead focus on most recent vectors and protocols, which have turned out to be most useful in order to promote the technology. Therefore, we apologize upfront to the many studies that could not be mentioned here solely owing to space limitations but which nevertheless made significant contributions to our current understanding. This chapter will finally provide guidance on possible uses of conditional gene trap alleles as well as detailed protocols for the application of this recent technology.
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Affiliation(s)
- Thomas Floss
- Institute of Developmental Genetics, GSF-National Research Center for Environment and Health, Neuherberg, Germany
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60
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Abstract
PDGF-C is a newly identified member of the platelet-derived growth factor (PDGF) family, which is involved in multiple cellular functions by signaling through PDGF receptor (PDGFR)-alphaalpha and alphabeta dimers. PDGF-C deficiency is perinatal lethal due to the formation of cleft palate. To further characterize the cellular function of PDGF-C during both embryonic and postnatal development, we have generated two conditional alleles of the Pdgf-c gene in which two loxP sites flank exon 5. Global Cre-mediated excision of the floxed exon 5 in these alleles resulted in a complete loss of PDGF-C expression and caused embryonic defects identical to those previously described for the PDGF-C null embryos. These conditional alleles will therefore be the important genetic tools for dissecting the spatial and temporal roles of PDGF-C during development and in adult tissues. Furthermore, from this work, we have also described a simple approach for creating mouse conditional alleles in an efficient manner.
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Affiliation(s)
- Xiaoli Wu
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, Manitoba, Canada
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62
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Hernandez-Valladares M, Naessens J, Iraqi FA. Gene-knockout mice in malaria research: useful or misleading? Trends Parasitol 2007; 23:522-6. [PMID: 17951110 DOI: 10.1016/j.pt.2007.08.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2007] [Revised: 08/22/2007] [Accepted: 08/22/2007] [Indexed: 10/22/2022]
Abstract
Gene-knockout mice have been extensively used in the study of several malaria-induced pathologies. Some investigators believe that the deficient, infected mice mimic disease aspects produced in the absence of the target gene, but others believe that the deficient mice models mainly explain the effects of compensatory, related molecules. Comparison of some of the most relevant knockout mouse studies for understanding cerebral malaria and parasitemia and their related human reports shows that gene-knockout mice are useful tools that support conclusions from human genetic studies. These mice have helped to indicate new resistance genes against human malaria and have provided valuable information about mechanisms of malaria resistance in mice.
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63
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Lee T, Shah C, Xu EY. Gene trap mutagenesis: a functional genomics approach towards reproductive research. ACTA ACUST UNITED AC 2007; 13:771-9. [PMID: 17890780 DOI: 10.1093/molehr/gam069] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
We have entered a new era of genomics in biomedical research with the availability of genome-wide sequences and expression data, resulting in the identification of a huge number of novel reproductive genes. The challenge we are facing today is how to determine the function of those novel and known genes and their roles in normal reproductive physiology, such as gamete production, pregnancy and fertilization, and the disease physiology such as infertility, spontaneous abortion and gynecological cancers. Mouse genetics has contributed tremendously to our understanding of the genetic causes of human diseases in the past decades. The establishment of mouse mutations is an effective way to understand the function of many reproductive proteins. One of the fast-growing mouse mutagenesis technologies-gene trap mutagenesis-represents a cost-effective way to generate mutations because of the public availability of mouse embryonic stem (ES) cell lines carrying insertional mutations and the continuing expansion of those ES gene trap cell lines. We review here the gene trapping technology and in particular examine its efficacy in generating mouse mutations for reproductive research. Even with the existing gene trap cell lines, many of the genes important for reproductive function through traditional knockout and chemical mutagenesis have been trapped, demonstrating gene trapping's efficacy in mutating genes involved in reproductive development. Comparing genes expressed in specific reproductive sub-cellular organelles and in the entire testis and ovary with gene trap lines in the International Gene Trap Consortium (IGTC) database, we could identify a significant portion of those genes as having been trapped, representing a great resource for establishing mouse models for reproductive research. Establishment and analysis of these mouse models, for example, could help with identifying genetic abnormalities underlying male infertility and other reproductive diseases.
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Affiliation(s)
- Terrance Lee
- Division of Reproductive Biology Research, Department of Obstetrics and Gynecology, Center for Genetic Medicine, Feinberg School of Medicine, Northwestern University, Lurie 7-117, 303 E Superior Street, Chicago, IL 60611, USA
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64
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Gragerov A, Horie K, Pavlova M, Madisen L, Zeng H, Gragerova G, Rhode A, Dolka I, Roth P, Ebbert A, Moe S, Navas C, Finn E, Bergmann J, Vassilatis DK, Pavlakis GN, Gaitanaris GA. Large-scale, saturating insertional mutagenesis of the mouse genome. Proc Natl Acad Sci U S A 2007; 104:14406-11. [PMID: 17720809 PMCID: PMC1964832 DOI: 10.1073/pnas.0700608104] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
We describe the construction of a large-scale, orderly assembly of mutant ES cells, generated with retroviral insertions and having mutational coverage in >90% of mouse genes. We also describe a method for isolating ES cell clones with mutations in specific genes of interest from this library. This approach, which combines saturating random mutagenesis with targeted selection of mutations in the genes of interest, was successfully applied to the gene families of G protein-coupled receptors (GPCRs) and nuclear receptors. Mutant mouse strains in 60 different GPCRs were generated. Applicability of the technique for the GPCR genes, which on average represent fairly small targets for insertional mutagenesis, indicates the general utility of our approach for the rest of the genome. The method also allows for increased scale and automation for the large-scale production of mutant mice, which could substantially expedite the functional characterization of the mouse genome.
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Affiliation(s)
- Alexander Gragerov
- Omeros Corporation, 1420 Fifth Avenue, Suite 2600, Seattle, WA 98101, USA.
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65
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Nord AS, Vranizan K, Tingley W, Zambon AC, Hanspers K, Fong LG, Hu Y, Bacchetti P, Ferrin TE, Babbitt PC, Doniger SW, Skarnes WC, Young SG, Conklin BR. Modeling insertional mutagenesis using gene length and expression in murine embryonic stem cells. PLoS One 2007; 2:e617. [PMID: 17637833 PMCID: PMC1910612 DOI: 10.1371/journal.pone.0000617] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2007] [Accepted: 05/31/2007] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND High-throughput mutagenesis of the mammalian genome is a powerful means to facilitate analysis of gene function. Gene trapping in embryonic stem cells (ESCs) is the most widely used form of insertional mutagenesis in mammals. However, the rules governing its efficiency are not fully understood, and the effects of vector design on the likelihood of gene-trapping events have not been tested on a genome-wide scale. METHODOLOGY/PRINCIPAL FINDINGS In this study, we used public gene-trap data to model gene-trap likelihood. Using the association of gene length and gene expression with gene-trap likelihood, we constructed spline-based regression models that characterize which genes are susceptible and which genes are resistant to gene-trapping techniques. We report results for three classes of gene-trap vectors, showing that both length and expression are significant determinants of trap likelihood for all vectors. Using our models, we also quantitatively identified hotspots of gene-trap activity, which represent loci where the high likelihood of vector insertion is controlled by factors other than length and expression. These formalized statistical models describe a high proportion of the variance in the likelihood of a gene being trapped by expression-dependent vectors and a lower, but still significant, proportion of the variance for vectors that are predicted to be independent of endogenous gene expression. CONCLUSIONS/SIGNIFICANCE The findings of significant expression and length effects reported here further the understanding of the determinants of vector insertion. Results from this analysis can be applied to help identify other important determinants of this important biological phenomenon and could assist planning of large-scale mutagenesis efforts.
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Affiliation(s)
- Alex S. Nord
- Department of Medicine, MacDonald Medical Research Laboratories, University of California at Los Angeles, California, United States of America
- Gladstone Institute of Cardiovascular Disease, San Francisco, California, United States of America
- Departments of Biopharmaceutical Sciences and Pharmaceutical Chemistry, University of California at San Francisco, California, United States of America
- * To whom correspondence should be addressed. E-mail: (AN); (BC)
| | - Karen Vranizan
- Gladstone Institute of Cardiovascular Disease, San Francisco, California, United States of America
- Functional Genomics Laboratory, University of California at Berkeley, California, United States of America
| | - Whittemore Tingley
- Gladstone Institute of Cardiovascular Disease, San Francisco, California, United States of America
- Department of Medicine, University of California at San Francisco, California, United States of America
| | - Alexander C. Zambon
- Gladstone Institute of Cardiovascular Disease, San Francisco, California, United States of America
- Department of Medicine, University of California at San Francisco, California, United States of America
| | - Kristina Hanspers
- Gladstone Institute of Cardiovascular Disease, San Francisco, California, United States of America
- Department of Medicine, University of California at San Francisco, California, United States of America
| | - Loren G. Fong
- Department of Medicine, MacDonald Medical Research Laboratories, University of California at Los Angeles, California, United States of America
| | - Yan Hu
- Department of Medicine, MacDonald Medical Research Laboratories, University of California at Los Angeles, California, United States of America
| | - Peter Bacchetti
- Department of Epidemiology and Biostatistics, University of California at San Francisco, California, United States of America
| | - Thomas E. Ferrin
- Departments of Biopharmaceutical Sciences and Pharmaceutical Chemistry, University of California at San Francisco, California, United States of America
| | - Patricia C. Babbitt
- Departments of Biopharmaceutical Sciences and Pharmaceutical Chemistry, University of California at San Francisco, California, United States of America
| | - Scott W. Doniger
- Gladstone Institute of Cardiovascular Disease, San Francisco, California, United States of America
- Washington University School of Medicine, St. Louis, Missouri, United States of America
| | | | - Stephen G. Young
- Department of Medicine, MacDonald Medical Research Laboratories, University of California at Los Angeles, California, United States of America
| | - Bruce R. Conklin
- Gladstone Institute of Cardiovascular Disease, San Francisco, California, United States of America
- Department of Medicine, University of California at San Francisco, California, United States of America
- Department of Molecular and Cellular Pharmacology, University of California at San Francisco, California, United States of America
- * To whom correspondence should be addressed. E-mail: (AN); (BC)
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Specific expression of lacZ and cre recombinase in fetal thymic epithelial cells by multiplex gene targeting at the Foxn1 locus. BMC DEVELOPMENTAL BIOLOGY 2007; 7:69. [PMID: 17577402 PMCID: PMC1906761 DOI: 10.1186/1471-213x-7-69] [Citation(s) in RCA: 93] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2006] [Accepted: 06/18/2007] [Indexed: 02/03/2023]
Abstract
Background Thymic epithelial cells (TECs) promote thymocyte maturation and are required for the early stages of thymocyte development and for positive selection. However, investigation of the mechanisms by which TECs perform these functions has been inhibited by the lack of genetic tools. Since the Foxn1 gene is expressed in all presumptive TECs from the early stages of thymus organogenesis and broadly in the adult thymus, it is an ideal locus for driving gene expression in differentiating and mature TECs. Results We generated two knock-in alleles of Foxn1 by inserting IRES-Cre or IRES-lacZ cassettes into the 3' UTR of the Foxn1 locus. We simultaneously electroporated the two targeting vectors to generate the two independent alleles in the same experiment, demonstrating the feasibility of multiplex gene targeting at this locus. Our analysis shows that the knockin alleles drive expression of Cre or lacZ in all TECs in the fetal thymus. Furthermore, the knockin alleles express Cre or lacZ in a Foxn1-like pattern without disrupting Foxn1 function as determined by phenotype analysis of Foxn1 knockin/Foxn1 null compound heterozygotes. Conclusion These data show that multiplex gene targeting into the 3' UTR of the Foxn1 locus is an efficient method to express any gene of interest in TECs from the earliest stage of thymus organogenesis. The resulting alleles will make possible new molecular and genetic studies of TEC differentiation and function. We also discuss evidence indicating that gene targeting into the 3' UTR is a technique that may be broadly applicable for the generation of genetically neutral driver strains.
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Friedel RH, Kerjan G, Rayburn H, Schüller U, Sotelo C, Tessier-Lavigne M, Chédotal A. Plexin-B2 controls the development of cerebellar granule cells. J Neurosci 2007; 27:3921-32. [PMID: 17409257 PMCID: PMC6672405 DOI: 10.1523/jneurosci.4710-06.2007] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Cerebellar granule cell progenitors proliferate postnatally in the upper part of the external granule cell layer (EGL) of the cerebellum. Postmitotic granule cells differentiate and migrate, tangentially in the EGL and then radially through the molecular and Purkinje cell layers. The molecular control of the transition between proliferation and differentiation in cerebellar granule cells is poorly understood. We show here that the transmembrane receptor Plexin-B2 is expressed by proliferating granule cell progenitors. To study Plexin-B2 function, we generated a targeted mutation of mouse Plexin-B2. Most Plexin-B2(-/-) mutants die at birth as a result of neural tube closure defects. Some mutants survive but their cerebellum cytoarchitecture is profoundly altered. This is correlated with a disorganization of the timing of granule cell proliferation and differentiation in the EGL. Many differentiated granule cells migrate inside the cerebellum and keep proliferating. These results reveal that Plexin-B2 controls the balance between proliferation and differentiation in granule cells.
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Affiliation(s)
- Roland H. Friedel
- Department of Biological Sciences, Howard Hughes Medical Institute, Stanford University, Stanford, California 94305
| | - Géraldine Kerjan
- Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7102, Université Paris 6, 75005 Paris, France
| | - Helen Rayburn
- Department of Biological Sciences, Howard Hughes Medical Institute, Stanford University, Stanford, California 94305
| | - Ulrich Schüller
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, and
| | - Constantino Sotelo
- Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7102, Université Paris 6, 75005 Paris, France
- Cátedra de Neurobiología del Desarrollo “Remedios Caro Almela,” Instituto de Neurociencias de Alicante, Universidad Miguel Hernández de Elche, Consejo Superior de Investigaciones Científicas, 03550 San Juan de Alicante, Alicante, Spain
| | - Marc Tessier-Lavigne
- Department of Biological Sciences, Howard Hughes Medical Institute, Stanford University, Stanford, California 94305
| | - Alain Chédotal
- Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7102, Université Paris 6, 75005 Paris, France
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68
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Miller SFC, Summerhurst K, Rünker AE, Kerjan G, Friedel RH, Chédotal A, Murphy P, Mitchell KJ. Expression of Plxdc2/TEM7R in the developing nervous system of the mouse. Gene Expr Patterns 2007; 7:635-44. [PMID: 17280871 DOI: 10.1016/j.modgep.2006.12.002] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2006] [Revised: 11/14/2006] [Accepted: 12/10/2006] [Indexed: 02/04/2023]
Abstract
Plexin-domain containing 2 (Plxdc2) is a relatively uncharacterised transmembrane protein with an area of nidogen homology and a plexin repeat (PSI domain) in its extracellular region. Here, we describe Plxdc2 expression in the embryonic mouse, with particular emphasis on the developing central nervous system. Using light microscopy and optical projection tomography (OPT), we analyse RNA in situ hybridization patterns and expression of two reporter genes, beta-geo (a fusion of beta-galactosidase to neomycin phosphotransferase) and placental alkaline phosphatase (PLAP) in a Plxdc2 gene trap mouse line (KST37; [Leighton, P.A., Mitchell, K.J., Goodrich, L.V., Lu, X., Pinson, K., Scherz, P., Skarnes, W.C., Tessier-Lavigne, M., 2001. Defining brain wiring patterns and mechanisms through gene trapping in mice. Nature 410, 174-179]). At mid-embryonic stages (E9.5-E11.5) Plxdc2-betageo expression is prominent in a number of patterning centres of the brain, including the cortical hem, midbrain-hindbrain boundary and the midbrain floorplate. Plxdc2 is expressed in other tissues, most notably the limbs, lung buds and developing heart, as well as the spinal cord and dorsal root ganglia. At E15.5, expression is apparent in a large number of discrete nuclei and structures throughout the brain, including the glial wedge and derivatives of the cortical hem. Plxdc2-betageo expression is particularly strong in the developing Purkinje cell layer, especially in the posterior half of the cerebellum. The PLAP marker is expressed in a number of axonal tracts, including the posterior commissure, mammillotegmental tract and cerebellar peduncle. We compare Plxdc2-betageo expression in the embryonic brain with the much more restricted expression of the related gene Plxdc1 and with members of the Wnt family (Wnt3a, Wnt5a and Wnt8b) that show a striking overlap with Plxdc2 expression in certain areas.
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Affiliation(s)
- Suzanne F C Miller
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
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69
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Abstract
Three major mouse knockout programs are underway worldwide, working together to mutate all protein-encoding genes in the mouse using a combination of gene trapping and gene targeting in mouse embryonic stem (ES) cells. Although the current emphasis is on production of this valuable resource, there are significant efforts to facilitate program coordination, to enhance the availability of this resource, and to plan for future efforts in mouse genetics research.
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70
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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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71
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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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72
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Okada A, Charron F, Morin S, Shin DS, Wong K, Fabre PJ, Tessier-Lavigne M, McConnell SK. Boc is a receptor for sonic hedgehog in the guidance of commissural axons. Nature 2006; 444:369-73. [PMID: 17086203 DOI: 10.1038/nature05246] [Citation(s) in RCA: 227] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2006] [Accepted: 09/08/2006] [Indexed: 11/09/2022]
Abstract
In the spinal cord, sonic hedgehog (Shh) is secreted by the floor plate to control the generation of distinct classes of ventral neurons along the dorsoventral axis. Genetic and in vitro studies have shown that Shh also later acts as a midline-derived chemoattractant for commissural axons. However, the receptor(s) responsible for Shh attraction remain unknown. Here we show that two Robo-related proteins, Boc and Cdon, bind specifically to Shh and are therefore candidate receptors for the action of Shh as an axon guidance ligand. Boc is expressed by commissural neurons, and targeted disruption of Boc in mouse results in the misguidance of commissural axons towards the floor plate. RNA-interference-mediated knockdown of Boc impairs the ability of rat commissural axons to turn towards an ectopic source of Shh in vitro. Taken together, these data suggest that Boc is essential as a receptor for Shh in commissural axon guidance.
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Affiliation(s)
- Ami Okada
- Department of Biological Sciences, Stanford University, Stanford, California 94305, USA.
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73
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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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74
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De-Zolt S, Schnütgen F, Seisenberger C, Hansen J, Hollatz M, Floss T, Ruiz P, Wurst W, von Melchner H. High-throughput trapping of secretory pathway genes in mouse embryonic stem cells. Nucleic Acids Res 2006; 34:e25. [PMID: 16478711 PMCID: PMC1369290 DOI: 10.1093/nar/gnj026] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
High-throughput gene trapping is a random approach for inducing insertional mutations across the mouse genome. This approach uses gene trap vectors that simultaneously inactivate and report the expression of the trapped gene at the insertion site, and provide a DNA tag for the rapid identification of the disrupted gene. Gene trapping has been used by both public and private institutions to produce libraries of embryonic stem (ES) cells harboring mutations in single genes. Presently, ∼66% of the protein coding genes in the mouse genome have been disrupted by gene trap insertions. Among these, however, genes encoding signal peptides or transmembrane domains (secretory genes) are underrepresented because they are not susceptible to conventional trapping methods. Here, we describe a high-throughput gene trapping strategy that effectively targets secretory genes. We used this strategy to assemble a library of ES cells harboring mutations in 716 unique secretory genes, of which 61% were not trapped by conventional trapping, indicating that the two strategies are complementary. The trapped ES cell lines, which can be ordered from the International Gene Trap Consortium (), are freely available to the scientific community.
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Affiliation(s)
| | | | - Claudia Seisenberger
- Institute of Developmental Genetics, GSF-National Research Center for Environment and HealthNeuherberg, Germany
| | - Jens Hansen
- Institute of Developmental Genetics, GSF-National Research Center for Environment and HealthNeuherberg, Germany
| | - Melanie Hollatz
- Institute of Developmental Genetics, GSF-National Research Center for Environment and HealthNeuherberg, Germany
| | - Thomas Floss
- Institute of Developmental Genetics, GSF-National Research Center for Environment and HealthNeuherberg, Germany
| | - Patricia Ruiz
- Center for Cardiovascular Research, Charité UniversitätsmedizinBerlin, Germany
- Department of Vertebrate Genomics, Max-Planck Institute for Molecular GeneticsBerlin, Germany
| | - Wolfgang Wurst
- Institute of Developmental Genetics, GSF-National Research Center for Environment and HealthNeuherberg, Germany
- Department for Molecular Neurogenetics, Max-Planck Institute of PsychiatryMunich, Germany
| | - Harald von Melchner
- To whom correspondence should be addressed. Tel: +49 69 63016696; Fax: +49 69 63016390;
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75
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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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76
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Affiliation(s)
- William C Skarnes
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom.
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