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The European dimension for the mouse mutagenesis program

The European Mouse Mutagenesis Consortium is the European initiative contributing to the international effort on functional annotation of the mouse genome. Its objectives are to establish and integrate mutagenesis platforms, expression resources, phenotyping units, storage and distribution centers and resources. The combined efforts will accelerate our understanding of gene function and of human health and disease.

The sequencing of mammalian has that will require an extraordinary range of (EBI), for database generation and dissemi- http://www.nature.com/naturegenetics shown that their gene catalogs are unexpect- expertise and tools. It will depend on the nation of results. Since December 2002, sev- edly small, with ∼28,000 . Owing to the maximal integration of basic biological and eral European Community–sponsored development of mouse embryonic stem (ES) clinical data alongside the development and pan-European discussions have focused on cells1,2 and a variety of mutagenic technolo- application of efficient and standardized further development and coordination of gies3–12, it is now possible to plan a system- methodologies. mouse functional in Europe. From atic assault on the mouse genome to Already, discussions in the international these discussions has emerged Priorities for document function. The most straightfor- mouse research community have considered Research in Mouse Genetics in Europe ward way to start this program is to create the new challenges and underlined the (PRIME), a forum whose remit has been to and characterize null alleles in the germ line. importance of large-scale mouse mutagene- weigh the new challenges, consider the But null mutants in the germ line identify sis and its potential benefit to biomedical sci- opportunities and economies of greater only the earliest function in development, ence13,14. The scale of a comprehensive coordination and build on existing accom- and later functions are often occluded. undertaking to add functional understand- plishments and resources. In two meetings Furthermore, many genes are expressed with ing to the mammalian gene catalog clearly (15 July 2003 and 9 January 2004), PRIME © 2004 Nature Publishing Group temporal and spatial (tissue) specificities, requires the development of cooperative agreed on a primary focus for European and many are expressed as alterna- structures akin to present-day research con- efforts in mouse genome mutagenesis. tive or post-translationally modified forms. sortia in physics and astronomy. In Europe, Therefore, a straightforward analysis of the requirement for integrated programs to A European mouse mutagenesis program 28,000 null-allele mutants will be far from tackle elements of the greater task has been We present an initial working plan for a pan- functionally exhaustive. Strategies for condi- met so far by the establishment of various European effort in mouse mutagenesis that tional mutagenesis in the mouse permit the national and European Community–funded builds on existing resources in mutagenesis, discovery and dissection of gene function programs including EUMORPHIA, an inte- phenotyping, expression studies and infor- throughout the life cycle and in a chosen cell grated network of centers for standardized matics to make a first step towards a compre- type. Because health and disease are often phenotyping; EURExpress15,16, a program to hensive annotation of gene function in the related to aging, spatially and temporally document thousands of expression patterns mouse genome. There are several important controlled conditional mutagenesis is also at mid-gestation allied to EMAGE, the mouse early priorities of this plan: (i) continued crucial for the medical and social relevance of atlas project; the German and British Gene work to establish a complete catalog of null mutational studies in the mouse. Therefore, a Trap Consortia, parts of the International reporter alleles in ES cells through the systematic program of functional documen- Gene Trap Consortium, which has estab- International Gene Trap Consortium; (ii) fur- tation in the mouse will ideally combine the lished banks of ES cells mutated with ther development of centers that archive and advantages of null- and conditional-allele sequence-verified gene traps17; ENU mutage- distribute mutant resources (ES cell lines, approaches while recognizing the disadvan- nesis centers in Germany and the UK, under- sperm, oocytes; these centers will also gener- tages of each. taking broad-based -driven ate mouse lines from the mutant resources A comprehensive assembly of mammalian mutagenesis programs; European condi- and document initial aspects of phenotype); gene functional data is a far-reaching project tional mouse mutagenesis centers, undertak- and (iii) integration of European mouse func- ing spatially and temporally controlled, tional genomics and expression pattern data The European Mouse Mutagenesis Consortium* site-specific somatic mutagenesis; the sets, logically through EBI, with other inter- *Authors and their affiliations are listed at the European mouse mutant archive (EMMA); national initiatives to create a unified global end of the paper. and the European Bioinformatics Institute database.

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The integration of European mouse ated with human diseases, because they are and freeze gametes for distribution. Priorities research programs with international initia- well-suited to analysis using the power of for the generation of mice from ES cells will tives to create a coordinated global research conditional mutagenesis and are of medical be determined by demand from committed program will maximize the collective effort relevance. The development of ‘recombi- scientists who will pay a cost-covering charge and public access and minimize redundancy. neering’ technology and the availability of and by the gene subsets selected by The early establishment of an efficient inter- bioinformatics resources as an outcome of EUCOMM for systematic conditional muta- national infrastructure and standardized, the genome-sequencing project have greatly genesis. Many of these centers are also user-friendly practices will deliver down- reduced the time and costs involved in the involved with the development and applica- stream benefits for the more demanding establishment of targeted conditional alle- tion of high-throughput phenotyping plat- challenges to come. Furthermore, existing les22–25. Nevertheless, to generate a large forms, in particular the development of new mutant resources from the German and number of conditional alleles efficiently, first-line screens such as the European British gene trap programs and the European gene-targeting units need to be established. Comprehensive First-Line Phenotyping pro- Community–sponsored EUMORPHIA, as These units will complement existing tocol. We therefore envisage that these cen- well as expression and functional data from European strengths in gene traps, expression ters will engage in both resource and EURExpress and other programs, should be analysis, ENU mutagenesis and phenotyp- phenotyping activities to document a first- built into a unified, publicly accessible, inter- ing26,27 and will add capacity for the eco- line annotation of the mouse genome. For national effort as soon as possible. nomical production of precise , mouse production, the centers will generate such as point mutations or isoform-specific heterozygous mutant mouse lines and then EUCOMM knockouts. They will also facilitate the estab- breed them, to secure embryos and sperm for Conditional mutagenesis in Europe is lishment of the complete null-allele set by archiving and further dissemination, to strong, in large part due to the local develop- targeting those genes that prove recalcitrant determine developmental lethality in the ment of key technologies, including applica- to mutagenesis by gene trapping. The collec- homozygote and to apply, where appropriate, tions of site-specific recombination3,8,12 and tion of transgenic mouse lines expressing Cre first-line phenotyping screens. In addition, http://www.nature.com/naturegenetics ligand-inducible switches18–21. Because con- recombinase needs to be expanded, most the centers may interact with dedicated units ditional mutagenesis is required for the efficiently by exploiting characterized expres- that document heterozygous reporter expres- accurate functional analysis of most genes, it sion patterns and taking advantage of cas- sion patterns in a generic manner. Providing is rational to build the European contribu- sette exchange technology, and housed in first-line phenotyping information on any tion to international efforts on existing central distribution centers such as EMMA. scale will place a considerable demand on the European strengths. In addition, EUCOMM aims to maintain a existing phenotyping platforms. But the syn- The goals of the European Conditional strong emphasis on further technology ergies between archiving, distribution and Mouse Mutagenesis Program (EUCOMM) development so that the program can rapidly phenotyping and the opportunity, as each are as follows: (i) develop generic conditional incorporate improvements that facilitate mouse is generated, to develop FLAGs, will strategies, using conditional gene traps and achievement of the overall goals. Such tech- add substantial value to each mutant and multipurpose targeting cassettes, for the nology developments include alternative stimulate individual researchers to acquire rapid creation of conditional alleles in ES approaches to mutagenesis, such as ENU mice of interest and embrace further analysis. cells; (ii) establish dedicated gene targeting gene-driven screens or conditional RNA Even the archiving and dissemination of © 2004 Nature Publishing Group and conditional gene trap units; (iii) use gene knock-down strategies. these new ES cell resources will require a con- targeting with multipurpose conditional alle- siderable investment in and expansion of les to help complete the null reporter allele Planting FLAGs in the mouse genome existing facilities in Europe. set; (iv) comprehensively expand, archive and A main goal of the mouse mutagenesis pro- The principles governing access to the distribute the collection of transgenic mouse gram is to promote hypothesis-driven mouse mutant resource are those that have lines expressing Cre recombinase; (v) focus research by as broad a range of scientists as been applied to the human genome sequenc- coordinated efforts of conditional mutagene- possible, including not only experienced ing program. The science is best served by sis and phenotyping on particular subsets of mouse researchers but also those who do not unrestricted access to all the resources gener- genes (including, for example, genes known have the facilities or expertise to generate ated and rapid deposition of information to be involved in human disease or new mice from ES cells. Therefore, the archiving into the public domain. mammalian transcribed sequences); (vi) and distribution centers will also generate continue to explore and incorporate technol- mice. Furthermore, by harnessing mouse The global context ogy advances in functional genomics (e.g., production to initial phenotyping to add The European priorities elaborated here the use of point mutagenesis, RNA interfer- FLAGs (first-line functional annotations of complement the initiative launched at the ence and other emergent technologies that the genome) to the mutant collection, we will Banbury meeting on the Knockout Mouse operate at the RNA level) to complement null enhance hypothesis-driven use of the muta- Project (from 30 September to 1 October and conditional mutagenesis and enrich the genesis resources. 2003; ref. 28). In this paper, The depth of the mutant resources. We envisage that the existing European Comprehensive Knockout Mouse Project Conditional analyses require a greater distribution centers for mouse strains will Consortium outlines a hierarchy of practical investment than does null mutagenesis in the expand to archive and distribute the mutant steps, dividing goals into short- and long- germ line. Therefore, it makes sense at this resources. New centers may also emerge, and term objectives. There is substantial concor- stage to prioritize genes for conditional all will need to be coordinated, logically dance between the Knockout Mouse Project mutagenesis and phenotyping. For example, under the auspices of EMMA. The centers and EUCOMM with regard to the short-term one possible focus of EUCOMM might be will not only archive and distribute ES cells, objectives, particularly those relating to the the OMIM list of genes known to be associ- but also use their expertise to generate mice establishment of a centralized bioinformatics

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platform for data deposition and a global URLs. The German Genetrap Consortium is avail- Biotechnol. 16, 657–662 (1998). expression atlas, as well as extending capaci- able at http://www.genetrap.de/. The Sanger Institute 13. Battey, J., Jordan, E., Cox, D. & Dove, W. Nat. Genet. Gene Trap Resource is available at http://www. 21, 73–75 (1999). ties for central storage and distribution cen- 14. Nadeau, J.H. et al. Science 291, 1251–1255 (2001). ters for mice and ES cells. In addition, sanger.ac.uk/genetrap/. The Harwell Mouse 15. Reymond, A. et al. Nature 420, 582–586 (2002). Mutagenesis Programme is available at http://www. 16. Gitton, Y. et al. Nature 420, 586–590 (2002). European efforts in gene trap mutagenesis, as mgu.har.mrc.ac.uk/. The Institut Clinique de la 17. The International Gene Trap Consortium. Nat. Genet. part of the International Gene Trap Souris is available at http://www-mci.u-strasbg.fr/. 36, 543–544 (2004). Consortium, will contribute substantially to 18. Gossen, M & Bujard, H. Proc. Natl. Acad. Sci. USA 89, 5547–5551 (1992). the planned bank of 28,000 null reporter alle- 1. Evans, M.J. & Kaufman, M.H. Nature 292,154–156 19. Logie, C. & Stewart, A.F. Proc. Natl. Acad. Sci. USA 92, les in ES cells. Due to existing European (1981). 5940–5944 (1995). strengths in conditional mutagenesis and 2. Bradley, A., Evans, M., Kaufman, M.H. & Robertson, E. 20. Feil, R. et al. Proc. Natl. Acad. Sci. USA 93, Nature 309, 255–256 (1984). 10887–10890 (1996). phenotyping platforms, the European pro- 3. Branda, C.S. & Dymecki, S.M. Dev. Cell 6, 7–28 (2004) 21. Metzger, D. & Chambon, P. Methods 24, 71–80 posal differs from the Knockout Mouse 4. Thomas, K.R. & Capecchi, M.R. Cell 51, 503–512 (2001). (1987). 22. Zhang, Y., Buchholz, F., Muyrers, J.P.P. & Stewart, A.F. Project proposal with respect to overall strat- 5. Doetschman, T. et al. Nature 330, 576–578 (1987). Nat. Genet. 20, 123–128 (1998). egy and priority emphasis. We regard this 6. te Riele, H., Maandag, E.R. & Berns, A. H Proc. Natl. 23. Angrand, P.-O., Daigle, N., van der Hoeven, F., diversity as a strengthening factor for the Acad. Sci. USA 89, 5128–5132 (1992). Schoeler, H.R. & Stewart, A.F. Nucleic Acids Res. 27, 7. Gossler, A., Joyner, A.L., Rossant, J. & Skarnes, W.C. e16 (1999). forthcoming international collaboration. Science 244, 463–465 (1989). 24. Copeland, N.G., Jenkins, N.A. & Court, D.L. Nat. Rev. The immediate task at hand is to begin the 8. Gu, H., Zou, Y.R. & Rajewsky, K. Cell 73, 1155–1164 Genet. 2, 769–779 (2001). process of coordination and integration, (1993). 25. Valenzuela, D.M. et al. Nat. Biotechnol. 21, 652–659 9. Wiles, M.V. et al. Nat. Genet. 24, 13–14 (2000). (2003). developing detailed structural plans and har- 10. Hansen, J. et al. Proc. Natl. Acad. Sci. USA 100, 26. Nolan, P.M. et al. Nat. Genet. 25, 440–443 (2000). nessing the wider expertise of the commu- 9918–9922 (2003). 27. Hrabe de Angelis, M.H. et al. Nat. Genet. 25, 444–447 11. Stryke, D. et al. Nucleic Acids Res. 31, 278–281 (2000). nity, so that this milestone can be achieved (2003). 28. The Comprehensive Knockout Mouse Project with speed, quality and economy. 12. Buchholz, F., Angrand, P.O. & Stewart, A.F. Nat. Consortium. Nat. Genet. 36, 921–924 (2004). http://www.nature.com/naturegenetics

Johan Auwerx1, Phil Avner2, Richard Baldock3, Andrea Ballabio4, Rudi Balling5, Mariano Barbacid6, Anton Berns7, Allan Bradley8, Steve Brown9,33, Peter Carmeliet10, Pierre Chambon2, Roger Cox9, Duncan Davidson3, Kay Davies11, Denis Duboule12, Jiri Forejt13, Francesca Granucci14, Nick Hastie3, Martin Hrabé de Angelis15, Ian Jackson3, Dimitris Kioussis16, George Kollias17, Mark Lathrop18, Urban Lendahl19, Marcos Malumbres20, Harald von Melchner21, Werner Müller22, Juha Partanen23, Paola Ricciardi-Castagnoli14, Peter Rigby24, Barry Rosen25, Nadia Rosenthal26, Bill Skarnes25, A Francis Stewart27,33, Janet Thornton28, Glauco Tocchini-Valentini29, Erwin Wagner30, Walter Wahli31 & Wolfgang Wurst32,33

1IGBMC, Illkirch, Strasbourg, France. 2Unité Génétique Moléculaire Murine, Institut Pasteur, Paris, France. 3MRC Human Genetics Unit, Western General Hospital, Edinburgh, UK. 4TIGEM Institute, Napoli, Italy. 5Molecular , GBF-Gesellschaft für Biotechnologische Forschung mbH, Braunschweig, Germany. 6CNIO, Madrid, Spain. 7The Netherlands Cancer Institute, Amsterdam, The Netherlands. 8The Sanger Centre, Hinxton, Cambridge, UK. 9MRC , MRC Mouse Genome Centre, Harwell, OX11 ORD, UK. 10Center for Transgene Technology and © 2004 Nature Publishing Group Gene Therapy, University of Leuven, Leuven, Belgium. 11MRC Functional Genetics Unit, Department of Human Anatomy and Genetics, University of Oxford, Oxford, UK. 12Department of Zoology, University of Geneva, Geneva, Switzerland. 13Institute of Molecular Genetics, ASCR, Prague, Czech Republic. 14Department of Biotechnology and Bioscience, University of Milano-Bicocca, Milano, Italy. 15Institute of Experimental Genetics, GSF- National Research Center for Environment and Health, GmbH, Munich/Neuherberg, Germany. 16Division of Molecular Immunology, MRC NIMR, London, UK. 17Biomedical Sciences Research Center ‘Alexander Fleming’, Athens, Greece. 18Consortium National de Recherche en Génomique, Centre National de Génotypage, Evry, France. 19Department of Cell and , Karolinska Institute, Stockholm, Sweden. 20Centro Nacional de Investigaciones Oncologicas, Madrid, Spain. 21Molecular Hematology, Goethe-University Frankfurt, Frankfurt/Main, Germany. 22Experimental Immunology, GBF-Gesellschaft für Biotechnologische Forschung mbH, Braunschweig, Germany. 23Institute of Biotechnology, University of Helsinki, Finland. 24Institute of Cancer Research, Chester Beatty Laboratories, London, UK. 25Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK. 26EMBL Monterotondo, Mouse Biology Programme, Monterotondo Scalo (Rome), Italy. 27Genomics, Technical University Dresden, BioInnovationZentrum, Am Tatzberg 47, 01307 Dresden, Germany. 28European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK. 29Istituto di Biologia Cellulare, CNR, Monterotondo Scalo (Rome), Italy. 30Research Institute of Molecular Pathology, University of Vienna, Vienna, Austria. 31Institute of Animal Biology, University of Lausanne, Lausanne-Dorigny, Switzerland. 32Institute of Developmental Genetics, GSF-National Research Center for Environment and Health, Ingolstädter Landstr. 1, GmbH, 85764 Munich/Neuherberg, Germany. 33These authors contributed equally to this work. Correspondence should be addressed to W.W. ([email protected]).

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