Skip to main content

Transgene Recombineering in Bacterial Artificial Chromosomes

  • Protocol
  • First Online:
Microinjection

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1874))

Abstract

Bacterial Artificial Chromosome (BAC) libraries are a valuable research resource. Any one of the clones in these libraries can carry hundreds of thousands of base pairs of genetic information. Often the entire coding sequence and significant upstream and downstream regions, including regulatory elements, can be found in a single BAC clone. BACs can be put to many uses, such as to study the function of human genes in knockout mice, to drive reporter gene expression in transgenic animals, and for gene discovery. In order to use BACs for experimental purposes it is often desirable to genetically modify them by introducing reporter elements or heterologous cDNA sequences. It is not feasible to use conventional DNA cloning approaches to modify BACs due to their size and complexity, thus a specialized field “recombineering” has developed to modify BAC clones through the use of homologous recombination in bacteria with short homology regions. Genetically engineered BACs can then be used in cell culture, mouse, or rat models to study cancer, neurology, and genetics.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 109.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 139.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 249.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Giraldo P, Montoliu L (2001) Size matters: use of YACs, BACs and PACs in transgenic animals. Transgenic Res 10:83–103

    Article  CAS  Google Scholar 

  2. Heaney JD, Bronson SK (2006) Artificial chromosome-based transgenes in the study of genome function. Mamm Genome 17:791–807

    Article  CAS  Google Scholar 

  3. Osoegawa K, Mammoser AG, Wu C, Frengen E, Zeng C, Catanese JJ, de Jong PJ (2001) A bacterial artificial chromosome library for sequencing the complete human genome. Genome Res 11:483–496

    Article  CAS  Google Scholar 

  4. Osoegawa K, Tateno M, Woon PY, Frengen E, Mammoser AG, Catanese JJ, Hayashizaki Y, de Jong PJ (2000) Bacterial artificial chromosome libraries for mouse sequencing and functional analysis. Genome Res 10:116–128

    CAS  PubMed  PubMed Central  Google Scholar 

  5. Van Keuren ML, Gavrilina GB, Filipiak WE, Zeidler MG, Saunders TL (2009) Generating transgenic mice from bacterial artificial chromosomes: transgenesis efficiency, integration and expression outcomes. Transgenic Res 18:769–785

    Article  CAS  Google Scholar 

  6. Alzhanov D, Rotwein P (2016) Characterizing a distal muscle enhancer in the mouse Igf2 locus. Physiol Genomics 48:167–172

    Article  CAS  Google Scholar 

  7. Deal KK, Cantrell VA, Chandler RL, Saunders TL, Mortlock DP, Southard-Smith EM (2006) Distant regulatory elements in a Sox10-betaGEO BAC transgene are required for expression of Sox10 in the enteric nervous system and other neural crest-derived tissues. Dev Dyn 235:1413–1432

    Article  CAS  Google Scholar 

  8. Dunnick WA, Shi J, Fontaine C, Collins JT (2013) Transgenes of the mouse immunoglobulin heavy chain locus, lacking distal elements in the 3′ regulatory region, are impaired for class switch recombination. PLoS One 8:e55842

    Article  CAS  Google Scholar 

  9. Davis SW, Keisler JL, Pérez-Millán MI, Schade V, Camper SA (2016) All hormone-producing cell types of the pituitary intermediate and anterior lobes derive from Prop1 expressing progenitors. Endocrinology 157:1385–1396

    Article  CAS  Google Scholar 

  10. Jones JM, Datta P, Srinivasula SM, Ji W, Gupta S, Zhang Z, Davies E, Hajnoczky G, Saunders TL, Van Keuren ML, Fernandes-Alnemri T, Meisler MH, Alnemri ES (2003) Loss of Omi mitochondrial protease activity causes the neuromuscular disorder of mnd2 mutant mice. Nature 425:721–727

    Article  CAS  Google Scholar 

  11. Khoriaty R, Everett L, Chase J, Zhu G, Hoenerhoff M, McKnight B, Vasievich MP, Zhang B, Tomberg K, Williams J, Maillard I, Ginsburg D (2016) Pancreatic SEC23B deficiency is sufficient to explain the perinatal lethality of germline SEC23B deficiency in mice. Sci Rep 6:27802

    Article  CAS  Google Scholar 

  12. Probst FJ, Fridell RA, Raphael Y, Wang A, Liang Y, Morell RJ, Touchman JW, Lyons RH, Noben-Trauth K, Friedman TB, Camper SA (1998) Correction of deafness in shaker-2 mice by an unconventional myosin in a BAC transgene. Science 280:1444–1447

    Article  CAS  Google Scholar 

  13. Antoch MP, Song EJ, Chang AM, Vitaterna MH, Zhao Y, Wilsbacher LD, Sangoram AM, King DP, Pinto LH, Takahashi JS (1997) Functional identification of the mouse circadian clock gene by transgenic BAC rescue. Cell 89:655–667

    Article  CAS  Google Scholar 

  14. Hu Y, Smith DE (2016) Species differences in the pharmacokinetics of cefadroxil as determined in wildtype and humanized PepT1 mice. Biochem Pharmacol 107:81–90

    Article  CAS  Google Scholar 

  15. Mensah-Osman E, Labut E, Zavros Y, El-Zaatari M, Law DJ, Merchant JL (2008) Regulated expression of the human gastrin gene in mice. Regul Pept 151:115–122

    Article  CAS  Google Scholar 

  16. Sarsero JP, Holloway TP, Li L, Finkelstein DI, Ioannou PA (2014) Rescue of the Friedreich ataxia knockout mutation in transgenic mice containing an FXN-EGFP genomic reporter. PLoS One 9:e93307

    Article  Google Scholar 

  17. Gong S, Zheng C, Doughty ML, Losos K, Didkovsky N, Schambra UB, Nowak NJ, Joyner A, Leblanc G, Hatten ME, Heintz N (2003) A gene expression atlas of the central nervous system based on bacterial artificial chromosomes. Nature 425:917–925

    Article  CAS  Google Scholar 

  18. Valjent E, Bertran-Gonzalez J, Hervé D, Fisone G, Girault JA (2009) Looking BAC at striatal signaling: cell-specific analysis in new transgenic mice. Trends Neurosci 32:538–547

    Article  CAS  Google Scholar 

  19. Witten IB, Steinberg EE, Lee SY, Davidson TJ, Zalocusky KA, Brodsky M, Yizhar O, Cho SL, Gong S, Ramakrishnan C, Stuber GD, Tye KM, Janak PH, Deisseroth K (2011) Recombinase-driver rat lines: tools, techniques, and optogenetic application to dopamine-mediated reinforcement. Neuron 72:721–733

    Article  CAS  Google Scholar 

  20. Keegan CE, Karolyi IJ, Knapp LT, Bourbonais FJ, Camper SA, Seasholtz AF (1994) Expression of corticotropin-releasing hormone transgenes in neurons of adult and developing mice. Mol Cell Neurosci 5:505–514

    Article  CAS  Google Scholar 

  21. Alon T, Zhou L, Pérez CA, Garfield AS, Friedman JM, Heisler LK (2009) Transgenic mice expressing green fluorescent protein under the control of the corticotropin-releasing hormone promoter. Endocrinology 150:5626–5632

    Article  CAS  Google Scholar 

  22. Deal KK, Cantrell VA, Chandler RL, Saunders TL, Mortlock DP, Southard-Smith EM (2006) Distant regulatory elements in a Sox10-beta GEO BAC transgene are required for expression of Sox10 in the enteric nervous system and other neural crest-derived tissues. Dev Dyn 235:1413–2432

    Article  CAS  Google Scholar 

  23. Dunnick WA, Shi J, Holden V, Fontaine C, Collins JT (2011) The role of germline promoters and I exons in cytokine-induced gene-specific class switch recombination. J Immunol 186:350–358

    Article  CAS  Google Scholar 

  24. Lehoczky JA, Innis JW (2008) BAC transgenic analysis reveals enhancers sufficient for Hoxa13 and neighborhood gene expression in mouse embryonic distal limbs and genital bud. Evol Dev 10:421–432

    Article  CAS  Google Scholar 

  25. Pérez-Millán MI, Zeidler MG, Saunders TL, Camper SA, Davis SW (2013) Efficient, specific, developmentally appropriate cre-mediated recombination in anterior pituitary gonadotropes and thyrotropes. Genesis 51:785–792

    Article  Google Scholar 

  26. Yu S, Zhou X, Hsiao JJ, Yu D, Saunders TL, Xue HH (2012) Fidelity of a BAC-EGFP transgene in reporting dynamic expression of IL-7Rα in T cells. Transgenic Res 21:201–215

    Article  CAS  Google Scholar 

  27. Lehoczky JA, Thomas PE, Patrie KM, Owens KM, Villarreal LM, Galbraith K, Washburn J, Johnson CN, Gavino B, Borowsky AD, Millen KJ, Wakenight P, Law W, Van Keuren ML, Gavrilina G, Hughes ED, Saunders TL, Brihn L, Nadeau JH, Innis JW (2013) A novel intergenic ETnII-β insertion mutation causes multiple malformations in polypodia mice. PLoS Genet 9:e1003967

    Article  Google Scholar 

  28. Watson CL, Mahe MM, Múnera J, Howell JC, Sundaram N, Poling HM, Schweitzer JI, Vallance JE, Mayhew CN, Sun Y, Grabowski G, Finkbeiner SR, Spence JR, Shroyer NF, Wells JM, Helmrath MA (2014) An in vivo model of human small intestine using pluripotent stem cells. Nat Med 20:1310–1314

    Article  CAS  Google Scholar 

  29. Albertsen HM, Abderrahim H, Cann HM, Dausset J, Le Paslier D, Cohen D (1990) Construction and characterization of a yeast artificial chromosome library containing seven haploid human genome equivalents. Proc Natl Acad Sci U S A 87:4256–4260

    Article  CAS  Google Scholar 

  30. Moreira PN, Pozueta J, Pérez-Crespo M, Valdivieso F, Gutiérrez-Adán A, Montoliu L (2007) Improving the generation of genomic-type transgenic mice by ICSI. Transgenic Res 16:163–168

    Article  CAS  Google Scholar 

  31. Brandt W, Khandekar M, Suzuki N, Yamamoto M, Lim KC, Engel JD (2008) Defining the functional boundaries of the Gata2 locus by rescue with a linked bacterial artificial chromosome transgene. J Biol Chem 283:8976–8983

    Article  CAS  Google Scholar 

  32. Sopher BL, La Spada AR (2006) Efficient recombination-based methods for bacterial artificial chromosome fusion and mutagenesis. Gene 12(371):136–143

    Article  Google Scholar 

  33. Montoliu L, Bock CT, Schutz G, Zentgraf H (1995) Visualization of large DNA molecules by electron microscopy with polyamines: application to the analysis of yeast endogenous and artificial chromosomes. J Mol Biol 246:486–492

    Article  CAS  Google Scholar 

  34. Montigny WJ, Phelps SF, Illenye S, Heintz NH (2003) Parameters influencing high-efficiency transfection of bacterial artificial chromosomes into cultured mammalian cells. BioTechniques 35:796–807

    Article  CAS  Google Scholar 

  35. Copeland NG, Jenkins NA, Court DL (2001) Recombineering: a powerful new tool for mouse functional genomics. Nat Rev Genet 2:769–779

    Article  CAS  Google Scholar 

  36. Court DL, Sawitzke JA, Thomason LC (2002) Genetic engineering using homologous recombination. Annu Rev Genet 36:361–388

    Article  CAS  Google Scholar 

  37. Zhang Y, Muyrers JP, Testa G, Stewart AF (2000) DNA cloning by homologous recombination in Escherichia coli. Nat Biotechnol 18:1314–1317

    Article  CAS  Google Scholar 

  38. Auwerx J, Avner P, Baldock R, Ballabio A, Balling R, Barbacid M, Berns A, Bradley A, Brown S, Carmeliet P, Chambon P, Cox R, Davidson D, Davies K, Duboule D, Forejt J, Granucci F, Hastie N, de Angelis MH, Jackson I, Kioussis D, Kollias G, Lathrop M, Lendahl U, Malumbres M, von Melchner H, Müller W, Partanen J, Ricciardi-Castagnoli P, Rigby P, Rosen B, Rosenthal N, Skarnes B, Stewart AF, Thornton J, Tocchini-Valentini G, Wagner E, Wahli W, Wurst W (2004) The European dimension for the mouse genome mutagenesis program. Nat Genet 36:925–927

    Article  CAS  Google Scholar 

  39. International Mouse Knockout Consortium, Collins FS, Rossant J, Wurst W (2007) A mouse for all reasons. Cell 128:9–13

    Article  Google Scholar 

  40. Skarnes WC, Rosen B, West AP, Koutsourakis M, Bushell W, Iyer V, Mujica AO, Thomas M, Harrow J, Cox T, Jackson D, Severin J, Biggs P, Fu J, Nefedov M, de Jong PJ, Stewart AF, Bradley A (2011) A conditional knockout resource for the genome-wide study of mouse gene function. Nature 474:337–342

    Article  CAS  Google Scholar 

  41. Testa G, Zhang Y, Vintersten K, Benes V, Pijnappel WW, Chambers I, Smith AJ, Smith AG, Stewart AF (2003) Engineering the mouse genome with bacterial artificial chromosomes to create multipurpose alleles. Nat Biotechnol 21:443–447

    Article  CAS  Google Scholar 

  42. Valenzuela DM, Murphy AJ, Frendewey D, Gale NW, Economides AN, Auerbach W, Poueymirou WT, Adams NC, Rojas J, Yasenchak J, Chernomorsky R, Boucher M, Elsasser AL, Esau L, Zheng J, Griffiths JA, Wang X, Su H, Xue Y, Dominguez MG, Noguera I, Torres R, Macdonald LE, Stewart AF, DeChiara TM, Yancopoulos GD (2003) High-throughput engineering of the mouse genome coupled with high-resolution expression analysis. Nat Biotechnol 21:652–659

    Article  CAS  Google Scholar 

  43. Hu Y, Xie Y, Wang Y, Chen X, Smith DE (2014) Development and characterization of a novel mouse line humanized for the intestinal peptide transporter PEPT1. Mol Pharm 11:3737–3746

    Article  CAS  Google Scholar 

  44. Warming S, Costantino N, Court DL, Jenkins NA, Copeland NG (2005) Simple and highly efficient BAC recombineering using galK selection. Nucleic Acids Res 33:e36

    Article  Google Scholar 

  45. Filipiak WE, Saunders TL (2006) Advances in transgenic rat production. Transgenic Res 15:673–686

    Article  CAS  Google Scholar 

  46. Becker K, Jerchow B (2011) Generation of transgenic mice by pronuclear microinjection. In: Pease S, Saunders TL (eds) Advanced protocols for animal Transgenesis: an ISTT manual. Springer-Verlag, Berlin

    Google Scholar 

  47. Ralser M, Querfurth R, Warnatz HJ, Lehrach H, Yaspo ML, Krobitsch S (2006) An efficient and economic enhancer mix for PCR. Biochem Biophys Res Commun 347:747–751

    Article  CAS  Google Scholar 

  48. St-Pierre F, Cui L, Priest DG, Endy D, Dodd IB, Shearwin KE (2013) One-step cloning and chromosomal integration of DNA. ACS Synth Biol 2:537–541

    Article  CAS  Google Scholar 

  49. Ye J, Coulouris G, Zaretskaya I, Cutcutache I, Rozen S, Madden T (2012) Primer-BLAST: a tool to design target-specific primers for polymerase chain reaction. BMC Bioinformatics 13:134

    Article  CAS  Google Scholar 

  50. Stratman JL, Barnes WM, Simon TC (2003) Universal PCR genotyping assay that achieves single copy sensitivity with any primer pair. Transgenic Res 12:521–552

    Article  CAS  Google Scholar 

  51. Lee EC, Yu D, Martinez de Velasco J, Tessarollo L, Swing DA, Court DL, Jenkins NA, Copeland NG (2001) A highly efficient Escherichia coli-based chromosome engineering system adapted for recombinogenic targeting and subcloning of BAC DNA. Genomics 73:56–65

    Article  CAS  Google Scholar 

  52. Schnütgen F, Ghyselinck NB (2007) Adopting the good reFLEXes when generating conditional alterations in the mouse genome. Transgenic Res 16:405–413

    Article  Google Scholar 

  53. Chuang K, Nguyen E, Sergeev Y, Badea TC (2016) Novel heterotypic Rox sites for combinatorial dre recombination strategies. G3 (Bethesda) 6:559–571

    Article  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Thomas L. Saunders .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2019 Springer Science+Business Media, LLC, part of Springer Nature

About this protocol

Check for updates. Verify currency and authenticity via CrossMark

Cite this protocol

Zeidler, M.G., Saunders, T.L. (2019). Transgene Recombineering in Bacterial Artificial Chromosomes. In: Liu, C., Du, Y. (eds) Microinjection. Methods in Molecular Biology, vol 1874. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-8831-0_3

Download citation

  • DOI: https://doi.org/10.1007/978-1-4939-8831-0_3

  • Published:

  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-8830-3

  • Online ISBN: 978-1-4939-8831-0

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics