Site-Specific Recombinases pp 1-19

Part of the Methods in Molecular Biology book series (MIMB, volume 1642) | Cite as

Generating Genetically Modified Mice: A Decision Guide

Protocol

Abstract

The generation of a new genetically modified mouse strain is a big hurdle to take for many researchers. It is often unclear which steps and decisions have to be made prior to obtaining the desired mouse model. This review aims to help researchers by providing a decision guide that answers the essential questions that need to be asked before generating the most suitable genetically modified mouse line in the most optimal timeframe. The review includes the latest technologies in both the stem cell culture and gene editing tools, particularly CRISPR/Cas9, and provides compatibility guidelines for selecting among the different types of genetic modifications that can be introduced in the mouse genome and the various routes for introducing these modifications into the mouse germline.

Key words

Transgenesis Genetic engineering Mouse models CRISPR/Cas9 Embryonic stem cell Zygote Gene targeting Recombinase Transposon GEMM-ESC 

References

  1. 1.
    Heyer J, Kwong LN, Lowe SW, Chin L (2010) Non-germline genetically engineered mouse models for translational cancer research. Nat Rev Cancer 10:470–480CrossRefPubMedPubMedCentralGoogle Scholar
  2. 2.
    Zender L, Xue W, Zuber J, Semighini CP, Krasnitz A, Ma B, Zender P, Kubicka S, Luk JM, Schirmacher P, McCombie WR, Wigler M, Hicks J, Hannon GJ, Powers S, Lowe SW (2008) An oncogenomics-based in vivo RNAi screen identifies tumor suppressors in liver cancer. Cell 135:852–864CrossRefPubMedPubMedCentralGoogle Scholar
  3. 3.
    Maddalo D, Manchado E, Concepcion CP, Bonetti C, Vidigal JA, Han YC, Ogrodowski P, Crippa A, Rekhtman N, de Stanchina E, Lowe SW, Ventura A (2014) In vivo engineering of oncogenic chromosomal rearrangements with the CRISPR/Cas9 system. Nature 516:423–427CrossRefPubMedPubMedCentralGoogle Scholar
  4. 4.
    Platt RJ, Chen S, Zhou Y, Yim MJ, Swiech L, Kempton HR, Dahlman JE, Parnas O, Eisenhaure TM, Jovanovic M, Graham DB, Jhunjhunwala S, Heidenreich M, Xavier RJ, Langer R, Anderson DG, Hacohen N, Regev A, Feng G, Sharp PA, Zhang F (2014) CRISPR-Cas9 knockin mice for genome editing and cancer modeling. Cell 159:440–455CrossRefPubMedPubMedCentralGoogle Scholar
  5. 5.
    Eppig JT, Motenko H, Richardson JE, Richards-Smith B, Smith CL (2015) The International Mouse Strain Resource (IMSR): cataloging worldwide mouse and ES cell line resources. Mamm Genome 26:448–455CrossRefPubMedPubMedCentralGoogle Scholar
  6. 6.
    Rosen B, Schick J, Wurst W (2015) Beyond knockouts: the International Knockout Mouse Consortium delivers modular and evolving tools for investigating mammalian genes. Mamm Genome 26:456–466CrossRefPubMedGoogle Scholar
  7. 7.
    Bradley A, Anastassiadis K, Ayadi A, Battey JF, Bell C, Birling MC, Bottomley J, Brown SD, Burger A, Bult CJ, Bushell W, Collins FS, Desaintes C, Doe B, Economides A, Eppig JT, Finnell RH, Fletcher C, Fray M, Frendewey D, Friedel RH, Grosveld FG, Hansen J, Herault Y, Hicks G, Horlein A, Houghton R, Hrabe de Angelis M, Huylebroeck D, Iyer V, de Jong PJ, Kadin JA, Kaloff C, Kennedy K, Koutsourakis M, Lloyd KC, Marschall S, Mason J, McKerlie C, McLeod MP, von Melchner H, Moore M, Mujica AO, Nagy A, Nefedov M, Nutter LM, Pavlovic G, Peterson JL, Pollock J, Ramirez-Solis R, Rancourt DE, Raspa M, Remacle JE, Ringwald M, Rosen B, Rosenthal N, Rossant J, Ruiz Noppinger P, Ryder E, Schick JZ, Schnutgen F, Schofield P, Seisenberger C, Selloum M, Simpson EM, Skarnes WC, Smedley D, Stanford WL, Stewart AF, Stone K, Swan K, Tadepally H, Teboul L, Tocchini-Valentini GP, Valenzuela D, West AP, Yamamura K, Yoshinaga Y, Wurst W (2012) The mammalian gene function resource: the International Knockout Mouse Consortium. Mamm Genome 23:580–586CrossRefPubMedPubMedCentralGoogle Scholar
  8. 8.
    Wang X (2009) Cre transgenic mouse lines. Methods Mol Biol 561:265–273CrossRefPubMedGoogle Scholar
  9. 9.
    Trujillo ME, Pajvani UB, Scherer PE (2005) Apoptosis through targeted activation of caspase 8 (“ATTAC-mice”): novel mouse models of inducible and reversible tissue ablation. Cell Cycle 4:1141–1145CrossRefPubMedGoogle Scholar
  10. 10.
    Abe T, Fujimori T (2013) Reporter mouse lines for fluorescence imaging. Dev Growth Differ 55:390–405CrossRefPubMedGoogle Scholar
  11. 11.
    Zhang J, Zhao J, Jiang WJ, Shan XW, Yang XM, Gao JG (2012) Conditional gene manipulation: Cre-ating a new biological era. J Zhejiang Univ Sci B 13:511–524CrossRefPubMedPubMedCentralGoogle Scholar
  12. 12.
    Akagi K, Sandig V, Vooijs M, Van der Valk M, Giovannini M, Strauss M, Berns A (1997) Cre-mediated somatic site-specific recombination in mice. Nucleic Acids Res 25:1766–1773CrossRefPubMedPubMedCentralGoogle Scholar
  13. 13.
    Feil R, Wagner J, Metzger D, Chambon P (1997) Regulation of Cre recombinase activity by mutated estrogen receptor ligand-binding domains. Biochem Biophys Res Commun 237:752–757CrossRefPubMedGoogle Scholar
  14. 14.
    Dow LE, Premsrirut PK, Zuber J, Fellmann C, McJunkin K, Miething C, Park Y, Dickins RA, Hannon GJ, Lowe SW (2012) A pipeline for the generation of shRNA transgenic mice. Nat Protoc 7:374–393CrossRefPubMedPubMedCentralGoogle Scholar
  15. 15.
    Seibler J, Kleinridders A, Kuter-Luks B, Niehaves S, Bruning JC, Schwenk F (2007) Reversible gene knockdown in mice using a tight, inducible shRNA expression system. Nucleic Acids Res 35:e54CrossRefPubMedPubMedCentralGoogle Scholar
  16. 16.
    Dickins RA, McJunkin K, Hernando E, Premsrirut PK, Krizhanovsky V, Burgess DJ, Kim SY, Cordon-Cardo C, Zender L, Hannon GJ, Lowe SW (2007) Tissue-specific and reversible RNA interference in transgenic mice. Nat Genet 39:914–921CrossRefPubMedPubMedCentralGoogle Scholar
  17. 17.
    Gay L, Karfilis KV, Miller MR, Doe CQ, Stankunas K (2014) Applying thiouracil tagging to mouse transcriptome analysis. Nat Protoc 9:410–420CrossRefPubMedPubMedCentralGoogle Scholar
  18. 18.
    Day CP, Merlino G, Van Dyke T (2015) Preclinical mouse cancer models: a maze of opportunities and challenges. Cell 163:39–53CrossRefPubMedPubMedCentralGoogle Scholar
  19. 19.
    Jonkers J, Berns A (2002) Conditional mouse models of sporadic cancer. Nat Rev Cancer 2:251–265CrossRefPubMedGoogle Scholar
  20. 20.
    Kawase E, Suemori H, Takahashi N, Okazaki K, Hashimoto K, Nakatsuji N (1994) Strain difference in establishment of mouse embryonic stem (ES) cell lines. Int J Dev Biol 38:385–390PubMedGoogle Scholar
  21. 21.
    Czechanski A, Byers C, Greenstein I, Schrode N, Donahue LR, Hadjantonakis AK, Reinholdt LG (2014) Derivation and characterization of mouse embryonic stem cells from permissive and nonpermissive strains. Nat Protoc 9:559–574CrossRefPubMedPubMedCentralGoogle Scholar
  22. 22.
    Nichols J, Jones K, Phillips JM, Newland SA, Roode M, Mansfield W, Smith A, Cooke A (2009) Validated germline-competent embryonic stem cell lines from nonobese diabetic mice. Nat Med 15:814–818CrossRefPubMedGoogle Scholar
  23. 23.
    Meissner A, Eminli S, Jaenisch R (2009) Derivation and manipulation of murine embryonic stem cells. Methods Mol Biol 482:3–19CrossRefPubMedGoogle Scholar
  24. 24.
    Ying QL, Wray J, Nichols J, Batlle-Morera L, Doble B, Woodgett J, Cohen P, Smith A (2008) The ground state of embryonic stem cell self-renewal. Nature 453:519–523CrossRefPubMedPubMedCentralGoogle Scholar
  25. 25.
    Huijbers IJ, Bin Ali R, Pritchard C, Cozijnsen M, Kwon MC, Proost N, Song JY, de Vries H, Badhai J, Sutherland K, Krimpenfort P, Michalak EM, Jonkers J, Berns A (2014) Rapid target gene validation in complex cancer mouse models using re-derived embryonic stem cells. EMBO Mol Med 6:212–225PubMedPubMedCentralGoogle Scholar
  26. 26.
    Yang H, Wang H, Jaenisch R (2014) Generating genetically modified mice using CRISPR/Cas-mediated genome engineering. Nat Protoc 9:1956–1968CrossRefPubMedGoogle Scholar
  27. 27.
    Inui M, Miyado M, Igarashi M, Tamano M, Kubo A, Yamashita S, Asahara H, Fukami M, Takada S (2014) Rapid generation of mouse models with defined point mutations by the CRISPR/Cas9 system. Sci Rep 4:5396CrossRefPubMedPubMedCentralGoogle Scholar
  28. 28.
    Yang H, Wang H, Shivalila CS, Cheng AW, Shi L, Jaenisch R (2013) One-step generation of mice carrying reporter and conditional alleles by CRISPR/Cas-mediated genome engineering. Cell 154:1370–1379CrossRefPubMedPubMedCentralGoogle Scholar
  29. 29.
    Wang H, Yang H, Shivalila CS, Dawlaty MM, Cheng AW, Zhang F, Jaenisch R (2013) One-step generation of mice carrying mutations in multiple genes by CRISPR/Cas-mediated genome engineering. Cell 153:910–918CrossRefPubMedPubMedCentralGoogle Scholar
  30. 30.
    Vanden Berghe T, Hulpiau P, Martens L, Vandenbroucke RE, Van Wonterghem E, Perry SW, Bruggeman I, Divert T, Choi SM, Vuylsteke M, Shestopalov VI, Libert C, Vandenabeele P (2015) Passenger mutations confound interpretation of all genetically modified congenic mice. Immunity 43:200–209CrossRefPubMedCentralGoogle Scholar
  31. 31.
    Dow LE, Nasr Z, Saborowski M, Ebbesen SH, Manchado E, Tasdemir N, Lee T, Pelletier J, Lowe SW (2014) Conditional reverse tet-transactivator mouse strains for the efficient induction of TRE-regulated transgenes in mice. PLoS One 9:e95236CrossRefPubMedPubMedCentralGoogle Scholar
  32. 32.
    Dow LE, Fisher J, O'Rourke KP, Muley A, Kastenhuber ER, Livshits G, Tschaharganeh DF, Socci ND, Lowe SW (2015) Inducible in vivo genome editing with CRISPR-Cas9. Nat Biotechnol 33:390–394CrossRefPubMedPubMedCentralGoogle Scholar
  33. 33.
    Dankort D, Filenova E, Collado M, Serrano M, Jones K, McMahon M (2007) A new mouse model to explore the initiation, progression, and therapy of BRAFV600E-induced lung tumors. Genes Dev 21:379–384CrossRefPubMedPubMedCentralGoogle Scholar
  34. 34.
    Tuveson DA, Shaw AT, Willis NA, Silver DP, Jackson EL, Chang S, Mercer KL, Grochow R, Hock H, Crowley D, Hingorani SR, Zaks T, King C, Jacobetz MA, Wang L, Bronson RT, Orkin SH, DePinho RA, Jacks T (2004) Endogenous oncogenic K-ras(G12D) stimulates proliferation and widespread neoplastic and developmental defects. Cancer Cell 5:375–387CrossRefPubMedGoogle Scholar
  35. 35.
    Chen CM, Krohn J, Bhattacharya S, Davies B (2011) A comparison of exogenous promoter activity at the ROSA26 locus using a PhiiC31 integrase mediated cassette exchange approach in mouse ES cells. PLoS One 6:e23376CrossRefPubMedPubMedCentralGoogle Scholar
  36. 36.
    Choi T, Huang M, Gorman C, Jaenisch R (1991) A generic intron increases gene expression in transgenic mice. Mol Cell Biol 11:3070–3074CrossRefPubMedPubMedCentralGoogle Scholar
  37. 37.
    Jackson EL, Willis N, Mercer K, Bronson RT, Crowley D, Montoya R, Jacks T, Tuveson DA (2001) Analysis of lung tumor initiation and progression using conditional expression of oncogenic K-ras. Genes Dev 15:3243–3248CrossRefPubMedPubMedCentralGoogle Scholar
  38. 38.
    Muzumdar MD, Tasic B, Miyamichi K, Li L, Luo L (2007) A global double-fluorescent Cre reporter mouse. Genesis 45:593–605CrossRefPubMedGoogle Scholar
  39. 39.
    Kim JH, Lee SR, Li LH, Park HJ, Park JH, Lee KY, Kim MK, Shin BA, Choi SY (2011) High cleavage efficiency of a 2A peptide derived from porcine teschovirus-1 in human cell lines, zebrafish and mice. PLoS One 6:e18556CrossRefPubMedPubMedCentralGoogle Scholar
  40. 40.
    Bochkov YA, Palmenberg AC (2006) Translational efficiency of EMCV IRES in bicistronic vectors is dependent upon IRES sequence and gene location. Biotechniques 41: 283, 284, 286, 288 passimGoogle Scholar
  41. 41.
    Friedrich G, Soriano P (1991) Promoter traps in embryonic stem cells: a genetic screen to identify and mutate developmental genes in mice. Genes Dev 5:1513–1523CrossRefPubMedGoogle Scholar
  42. 42.
    Beard C, Hochedlinger K, Plath K, Wutz A, Jaenisch R (2006) Efficient method to generate single-copy transgenic mice by site-specific integration in embryonic stem cells. Genesis 44:23–28CrossRefPubMedGoogle Scholar
  43. 43.
    Pardo B, Gomez-Gonzalez B, Aguilera A (2009) DNA repair in mammalian cells: DNA double-strand break repair: how to fix a broken relationship. Cell Mol Life Sci 66:1039–1056CrossRefPubMedGoogle Scholar
  44. 44.
    Shrivastav M, De Haro LP, Nickoloff JA (2008) Regulation of DNA double-strand break repair pathway choice. Cell Res 18:134–147CrossRefPubMedGoogle Scholar
  45. 45.
    Hall B, Limaye A, Kulkarni AB (2009) Overview: generation of gene knockout mice. Curr Protoc Cell Biol. Chapter 19: Unit 19.12 19.12.1–17Google Scholar
  46. 46.
    Ivics Z, Izsvak Z (2015) Sleeping beauty transposition. Microbiol Spectr 3:MDNA3-0042-2014CrossRefPubMedGoogle Scholar
  47. 47.
    Ivics Z, Mates L, Yau TY, Landa V, Zidek V, Bashir S, Hoffmann OI, Hiripi L, Garrels W, Kues WA, Bosze Z, Geurts A, Pravenec M, Rulicke T, Izsvak Z (2014) Germline transgenesis in rodents by pronuclear microinjection of Sleeping Beauty transposons. Nat Protoc 9:773–793CrossRefPubMedGoogle Scholar
  48. 48.
    Tasic B, Hippenmeyer S, Wang C, Gamboa M, Zong H, Chen-Tsai Y, Luo L (2011) Site-specific integrase-mediated transgenesis in mice via pronuclear injection. Proc Natl Acad Sci U S A 108:7902–7907CrossRefPubMedPubMedCentralGoogle Scholar
  49. 49.
    Seibler J, Schubeler D, Fiering S, Groudine M, Bode J (1998) DNA cassette exchange in ES cells mediated by Flp recombinase: an efficient strategy for repeated modification of tagged loci by marker-free constructs. Biochemistry 37:6229–6234CrossRefPubMedGoogle Scholar
  50. 50.
    Hanahan D, Wagner EF, Palmiter RD (2007) The origins of oncomice: a history of the first transgenic mice genetically engineered to develop cancer. Genes Dev 21:2258–2270CrossRefPubMedGoogle Scholar
  51. 51.
    Chu VT, Weber T, Graf R, Sommermann T, Petsch K, Sack U, Volchkov P, Rajewsky K, Kuhn R (2016) Efficient generation of Rosa26 knock-in mice using CRISPR/Cas9 in C57BL/6 zygotes. BMC Biotechnol 16:4CrossRefPubMedPubMedCentralGoogle Scholar
  52. 52.
    Huijbers IJ, Del Bravo J, Bin Ali R, Pritchard C, Braumuller TM, van Miltenburg MH, Henneman L, Michalak EM, Berns A, Jonkers J (2015) Using the GEMM-ESC strategy to study gene function in mouse models. Nat Protoc 10:1755–1785CrossRefPubMedGoogle Scholar
  53. 53.
    Premsrirut PK, Dow LE, Kim SY, Camiolo M, Malone CD, Miething C, Scuoppo C, Zuber J, Dickins RA, Kogan SC, Shroyer KR, Sordella R, Hannon GJ, Lowe SW (2011) A rapid and scalable system for studying gene function in mice using conditional RNA interference. Cell 145:145–158CrossRefPubMedPubMedCentralGoogle Scholar
  54. 54.
    Huijbers IJ, Krimpenfort P, Berns A, Jonkers J (2011) Rapid validation of cancer genes in chimeras derived from established genetically engineered mouse models. Bioessays 33:701–710CrossRefPubMedPubMedCentralGoogle Scholar
  55. 55.
    Mitrecic D, Huzak M, Curlin M, Gajovic S (2005) An improved method for determination of gene copy numbers in transgenic mice by serial dilution curves obtained by real-time quantitative PCR assay. J Biochem Biophys Methods 64:83–98CrossRefPubMedGoogle Scholar
  56. 56.
    Pham CT, MacIvor DM, Hug BA, Heusel JW, Ley TJ (1996) Long-range disruption of gene expression by a selectable marker cassette. Proc Natl Acad Sci U S A 93:13090–13095CrossRefPubMedPubMedCentralGoogle Scholar
  57. 57.
    Iyer V, Shen B, Zhang W, Hodgkins A, Keane T, Huang X, Skarnes WC (2015) Off-target mutations are rare in Cas9-modified mice. Nat Methods 12:479CrossRefPubMedGoogle Scholar
  58. 58.
    Pattanayak V, Lin S, Guilinger JP, Ma E, Doudna JA, Liu DR (2013) High-throughput profiling of off-target DNA cleavage reveals RNA-programmed Cas9 nuclease specificity. Nat Biotechnol 31:839–843CrossRefPubMedPubMedCentralGoogle Scholar
  59. 59.
    Liang Q, Conte N, Skarnes WC, Bradley A (2008) Extensive genomic copy number variation in embryonic stem cells. Proc Natl Acad Sci U S A 105:17453–17456CrossRefPubMedPubMedCentralGoogle Scholar
  60. 60.
    Shen B, Zhang W, Zhang J, Zhou J, Wang J, Chen L, Wang L, Hodgkins A, Iyer V, Huang X, Skarnes WC (2014) Efficient genome modification by CRISPR-Cas9 nickase with minimal off-target effects. Nat Methods 11:399–402CrossRefPubMedGoogle Scholar
  61. 61.
    Slaymaker IM, Gao L, Zetsche B, Scott DA, Yan WX, Zhang F (2016) Rationally engineered Cas9 nucleases with improved specificity. Science 351:84–88CrossRefPubMedGoogle Scholar
  62. 62.
    Kleinstiver BP, Pattanayak V, Prew MS, Tsai SQ, Nguyen NT, Zheng Z, Joung JK (2016) High-fidelity CRISPR-Cas9 nucleases with no detectable genome-wide off-target effects. Nature 529:490–495CrossRefPubMedPubMedCentralGoogle Scholar

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© Springer Science+Business Media LLC 2017

Authors and Affiliations

  1. 1.Mouse Clinic for Cancer and Aging, The Netherlands Cancer InstituteAmsterdamThe Netherlands

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