Skip to main content
SpringerLink
Log in

Gene Replacement

  • Chapter
  • First Online:
Diagnostics in Plant Breeding

  • 2790 Accesses

Abstract

Gene-targeting (GT) is a powerful tool for functional analysis of genes and for gene replacement in biotechnological applications, but unfortunately it is very inefficient in plants, because integration of foreign DNA mainly occurs via non-homologous recombination. Inactivation of the most conserved pathway of non-homologous recombination called non-homologous end-joining (NHEJ) did not result in much higher GT frequency. However, introduction of a double strand break (DSB) at the intended site of recombination significantly stimulated DNA recombination at this DSB site, which may lead to replacement of native DNA sequences with foreign DNA sequences. Artificial zinc finger nucleases (ZFNs) are nowadays the enzymes of choice to induce DSBs at specifically selected sites in the genome. Such DSB may lead to targeted mutagenesis through inaccurate repair via end-joining or to GT through repair via homologous recombination (HR).

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

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 169.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 219.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 219.99
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

  • Arnould S, Delenda C, Grizot S, Desseaux C, Pâques F, Silva GH, Smith J (2011) The I-CreI meganuclease and its engineered derivatives: applications from cell modification to gene therapy. Protein Eng Des Sel 24:27–31

    Article  PubMed  CAS  Google Scholar 

  • Audebert M, Salles B, Calsou P (2004) Involvement of poly(ADP-ribose) polymerase-1 and XRCC1/DNA ligase III in an alternative route for DNA double-strand breaks rejoining. J Biol Chem 279:55117–55126

    Article  PubMed  CAS  Google Scholar 

  • Beerli RR, Barbas CF (2002) Engineering polydactyl zinc-finger transcription factors. Nat Biotechnol 20:135–141

    Article  PubMed  CAS  Google Scholar 

  • Beumer K, Bhattacharyya G, Bibikova M, Trautman JK, Carroll D (2006) Efficient gene targeting in Drosophila with zinc-finger nucleases. Genetics 172:2391–2403

    Article  PubMed  CAS  Google Scholar 

  • Bhadauria V, Banniza S, Wei Y, Peng YL (2009) Reverse genetics for functional genomics of phytopathogenic fungi and oomycetes. Comp Funct Genom. doi:10.1155/2009/380719

    Google Scholar 

  • Bhakta MS, Segal DJ (2010) The generation of zinc finger proteins by modular assembly. In: Mackay JP, Segal DJ (eds) Engineered zinc finger proteins, Methods of molecular biology 649. Springer, New York, pp 3–30

    Chapter  Google Scholar 

  • Bibikova M, Carroll D, Segal DJ, Trautman JK, Smith J, Kim YG, Chandrasegaran S (2001) Stimulation of homologous recombination through targeted cleavage by chimeric nucleases. Mol Cell Biol 21:289–297

    Article  PubMed  CAS  Google Scholar 

  • Bibikova M, Golic M, Golic KG, Carroll D (2002) Targeted chromosomal cleavage and mutagenesis in Drosophila using zinc-finger nucleases. Genetics 161:1169–1175

    PubMed  CAS  Google Scholar 

  • Bitinaite J, Wah DA, Aggarwal AK, Schildkraut I (1998) FokI dimerization is required for DNA cleavage. Proc Natl Acad Sci USA 95:10570–10575

    Article  PubMed  CAS  Google Scholar 

  • Blancafort P, Magnenat L, Barbas CF (2003) Scanning the human genome with combinatorial transcription factor libraries. Nat Biotechnol 21:269–274

    Article  PubMed  CAS  Google Scholar 

  • Boch J, Scholze H, Schornack S, Landgraf A, Hahn S, Kay S, Lahaye T, Nickstadt A, Bonas U (2009) Breaking the code of DNA binding specificity of TAL-type III effectors. Science 326:1509–1512

    Article  PubMed  CAS  Google Scholar 

  • Bogdanove AJ, Schornack S, Lahaye T (2010) TAL effectors: finding plant genes for disease and defense. Curr Opin Plant Biol 13:394–401

    Article  PubMed  CAS  Google Scholar 

  • Bundock P, Hooykaas P (2002) Severe developmental defects, hypersensitivity to DNA-damaging agents, and lengthened telomeres in Arabidopsis MRE11 mutants. Plant Cell 14:2451–2462

    Article  PubMed  CAS  Google Scholar 

  • Bundock P, den Dulk-Ras A, Beijersbergen A, Hooykaas PJJ (1995) Trans-kingdom T-DNA transfer from Agrobacterium tumefaciens to Saccharomyces cerevisiae. EMBO J 14:3206–3214

    PubMed  CAS  Google Scholar 

  • Cai CQ, Doyon Y, Ainley WM, Miller JC, DeKelver RC, Moehle EA, Rock JM, Lee Y-L, Garrison R, Schulenberg L, Blue R, Worden A, Baker L, Faraji F, Zhang L, Holmes MC, Rebar EJ, Collingwood TN, Rubin-Wilson B, Gregory PD, Urnov FD, Petolino JF (2009) Targeted transgene integration in plant cells using designed zinc finger nucleases. Plant Mol Biol 69:699–709

    Article  PubMed  CAS  Google Scholar 

  • Cathomen T, Şöllü C (2010) In vitro assessment of zinc finger nuclease activity. In: Mackay JP, Segal DJ (eds) Engineered zinc finger proteins, Methods in molecular biology 649. Springer, New York, pp 227–235

    Chapter  Google Scholar 

  • Cermak T, Doyle EL, Christian M, Wang L, Zhang Y, Schmidt C, Baller JA, Somia NV, Bogdanove AJ, Voytas DF (2011) Efficient design and assembly of custom TALEN and other TAL effector-based constructs for DNA targeting. Nucl Acid Res. doi:10.1093/nar/gkr218

    Google Scholar 

  • Charbonnel C, Gallego ME, White CI (2010) Xrcc1-dependent and Ku-dependent DNA double-strand break repair kinetics in Arabidopsis plants. Plant J 64:280–290

    Article  PubMed  CAS  Google Scholar 

  • Choulika A, Perrin A, Dujon B, Nicolas J-F (1995) Induction of Homologous recombination in mammalian chromosomes by using the I-SceI system of Saccharomyces cerevisiae. Mol Cell Biol 15:1968–1973

    PubMed  CAS  Google Scholar 

  • Christian M, Cermak T, Doyle EL, Schmidt C, Zhang F, Hummel A, Bogdanove AJ, Voytas DF (2010) Targeted DNA double-strand breaks with TAL effector nucleases. Genetics 186:757–761

    Article  PubMed  CAS  Google Scholar 

  • Cornu TI, Thibodeau-Beganny S, Guhl E, Alwin S, Eichtinger M, Joung JK, Cathomen T (2008) DNA-binding specificity is a major determinant of the activity and toxicity of zinc-finger nucleases. Mol Ther 16:352–358

    Article  PubMed  CAS  Google Scholar 

  • Curtin SJ, Zhang F, Sander JD, Haun WJ, Starker C, Baltes NJ, Reyon D, Dahlborg EJ, Goodwin MJ, Coffman AP, Dobbs D, Joung JK, Voytas DF, Stupar RM (2011) Targeted mutagenesis of duplicated genes in soybean with zinc-finger nucleases. Plant Phys 156:466–473

    Article  CAS  Google Scholar 

  • De Boer P, Bastiaans J, Touw H, Kerkman R, Bronkhof J, van den Berg M, Offringa R (2010) Highly efficient gene targeting in Penicillium chrysogenum using the bi-partite approach in Δlig4 or Δku70 mutants. Fung Genet Biol 47:839–846

    Article  CAS  Google Scholar 

  • De Felipe P, Luke GA, Hughes LE, Gani D, Halpin C, Ryan MD (2006) E unum pluribus: multiple proteins from a self-processing polyprotein. Trends Biotechnol 24:68–75

    Article  PubMed  CAS  Google Scholar 

  • De Groot MJA, Bundock P, Beijersbergen AGM, Hooykaas PJJ (1998) Agrobacterium tumefaciens-mediated transformation of filamentous fungi. Nat Biotechnol 16:839–842

    Article  PubMed  Google Scholar 

  • De Pater S, Neuteboom LW, Pinas JE, Hooykaas PJJ, van der Zaal BJ (2009) ZFN-induced mutagenesis and gene-targeting in Arabidopsis through Agrobacterium-mediated floral dip transformation. Plant Biotechnol J 7:821–835

    Article  PubMed  CAS  Google Scholar 

  • Doyon Y, McCammon JM, Miller JC, Faraji F, Ngo C, Katibah GE, Amora R, Hocking TD, Zhang L, Rebar EJ, Gregory PD, Urnov FD, Amacher SL (2008) Heritable targeted gene disruption in zebrafish using designed zinc-finger nucleases. Nat Biotechnol 26:702–708

    Article  PubMed  CAS  Google Scholar 

  • Doyon Y, Vo TD, Mendel MC, Greenberg SG, Wang J, Xia DF, Miller JC, Urnov FD, Gregory PD, Holmes MC (2010) Enhancing zinc-finger-nuclease activity with improved obligate heterodimeric architectures. Nat Method 8:74–79

    Article  CAS  Google Scholar 

  • Dreier B, Segal DJ, Barbas CF (2000) Insights into the molecular recognition of the 5′-GNN-3′ family of DNA sequences by zinc finger domains. J Mol Biol 303:489–502

    Article  PubMed  CAS  Google Scholar 

  • Dreier B, Beerli RR, Segal DJ, Flippin JD, Barbas CF (2001) Development of zinc finger domains for recognition of the 5′-ANN-3′ family of DNA sequences and their use in the construction of artificial transcription factors. J Biol Chem 276:29466–29478

    Article  PubMed  CAS  Google Scholar 

  • Dreier B, Fuller RP, Segal DJ, Lund CV, Blancafort P, Huber A, Koksch B, Barbas CF (2005) Development of zinc finger domains for recognition of the 5′-CNN-3′ family DNA sequences and their use in the construction of artificial transcription factors. J Biol Chem 280:35588–35597

    Article  PubMed  CAS  Google Scholar 

  • Endo M, Osakabe K, Ono K, Handa H, Shimizu T, Toki S (2007) Molecular breeding of a novel herbicide-tolerant rice by gene targeting. Plant J 52:157–166

    Article  PubMed  CAS  Google Scholar 

  • Gorbunova V, Levy AA (1997) Non-homologous DNA end joining in plant cells is associated with deletions and filler DNA insertions. Nucl Acids Res 25:4650–4657

    Article  PubMed  CAS  Google Scholar 

  • Grizot S, Epinat J-C, Thomas S, Duclert A, Rolland S, Pâques F, Duchateau P (2010) Generation of redesigned homing endonucleases comprising DNA-binding domains derived from two different scaffolds. Nucl Acids Res 38:2006–2018

    Article  PubMed  CAS  Google Scholar 

  • Guo J, Gaj T, Barbas CF (2010) Directed evolution of an enhanced and highly efficient FokI cleavage domain for zinc finger nucleases. J Mol Biol 400:96–107

    Article  PubMed  CAS  Google Scholar 

  • Guschin DY, Waite AJ, Katibah GE, Miller JC, Holmes MC, Rebar EJ (2010) A rapid and general assay for monitoring endogenous gene modification. In: Mackay JP, Segal DJ (eds) Engineered zinc finger proteins, Methods in molecular biology 649. Springer, New York, pp 247–256

    Chapter  Google Scholar 

  • Halfter U, Morris PC, Willmitzer L (1992) Gene targeting in Arabidopsis thaliana. Mol Gen Genet 231:184–193

    Google Scholar 

  • Händel E-M, Alwin S, Cathomen T (2009) Expanding or restricting the target site repertoire of zinc-finger nucleases: the inter-domain linker as a major determinant of target site selectivity. Mol Ther 17:104–111

    Article  PubMed  CAS  Google Scholar 

  • Hanin M, Volrath S, Bogucki A, Briker M, Ward E, Paszkowski J (2001) Gene targeting in Arabidopsis. Plant J 28:671–677

    Article  PubMed  CAS  Google Scholar 

  • Herrmann F, Garriga-Canut M, Baumstark R, Fajardo-Sanchez E, Cotterell J, Minoche A, Himmelbauer H, Isalan M (2011) p53 gene repair with zinc finger nucleases optimised by yeast 1-hybrid and validated by Solexa sequencing. PLoS One 6:e20913

    Article  PubMed  CAS  Google Scholar 

  • Hiom K (2010) Coping with DNA double strand breaks. DNA Repair 9:1256–1263

    Article  PubMed  CAS  Google Scholar 

  • Hooykaas PJJ, van Attikum H, Bundock P (2001) Nucleic acid integration in eukaryotes. Patent EP 00204693.6

    Google Scholar 

  • Hoshaw JP, Unger-Wallace E, Zhang F, Voytas DF (2010) A transient assay for monitoring zinc finger nuclease activity at endogenous plant gene targets. In: Mackay JP, Segal DJ (eds) Engineered zinc finger proteins, Methods in molecular biology 649. Springer, New York, pp 299–314

    Chapter  Google Scholar 

  • Hrouda M, Paszkowski J (1994) High fidelity extrachromosomal recombination and gene targeting in plants. Mol Gen Genet 243:106–111

    Article  PubMed  CAS  Google Scholar 

  • Iida S, Terada R (2005) Modification of endogenous natural genes by gene targeting in rice and other higher plants. Plant Mol Biol 59:205–219

    Article  PubMed  CAS  Google Scholar 

  • Isalan M, Choo Y, Klug A (1997) Synergy between adjacent zinc fingers in sequence-specific DNA recognition. Proc Natl Acad Sci USA 94:5617–5621

    Article  PubMed  CAS  Google Scholar 

  • Jacob HJ, Lazar J, Dwinell MR, Moreno C, Geurts AM (2010) Gene targeting in the rat: advances and opportunities. Trends Genet 26:510–518

    Article  PubMed  CAS  Google Scholar 

  • Jasin M (1996) Genetic manipulation of genomes with rare-cutting endonucleases. Trends Genet 12:224–228

    Article  PubMed  CAS  Google Scholar 

  • Jia Q (2011) DNA repair and gene-targeting in plant end-joining mutants. Dissertation, Leiden University

    Google Scholar 

  • Jia Q, Bundock P, Hooykaas PJJ, de Pater S (2012) Agrobacterium tumefaciens T-DNA integration and gene targeting in Arabidopsis thaliana non-homologous end-joining mutants. J Bot. doi:10.1155/2012/989272

    Google Scholar 

  • Johzuka-Hisatomi Y, Terada R, Iida S (2008) Efficient transfer of base changes from a vector to the rice genome by homologous recombination: involvement of heteroduplex formation and mismatch correction. Nucl Acids Res 36:4727–4735

    Article  PubMed  CAS  Google Scholar 

  • Klug A (2010) The discovery of zinc fingers and their applications in gene regulation and genome manipulation. Ann Rev Biochem 79:213–231

    Article  PubMed  CAS  Google Scholar 

  • Kooistra R, Hooykaas PJJ, Steensma HY (2004) Efficient gene targeting in Kluyveromyces lactis. Yeast 21:781–792

    Article  PubMed  CAS  Google Scholar 

  • Lee KY, Lund P, Lowe K, Dunsmuir P (1990) Homologous recombination in plant cells after Agrobacterium-mediated transformation. Plant Cell 2:415–425

    PubMed  CAS  Google Scholar 

  • Li T, Huang S, Zhao X, Wright DA, Carpenter S, Spalding MH, Weeks DP, Yang B (2011) Modularly assembled designer TAL effector nucleases for targeted gene knockout and gene replacement in eukaryotes. Nucl Acids Res. doi:10.1093/nar/gkr188

    Google Scholar 

  • Liu Q, Xia Z, Case CC (2002) Validated zinc finger protein designs for all 16 GNN DNA triplet targets. J Biol Chem 277:3850–3856

    Article  PubMed  CAS  Google Scholar 

  • Lloyd A, Plaisier CL, Carroll D, Drews GN (2005) Targeted mutagenesis using zinc-finger nucleases in Arabidopsis. Proc Natl Acad Sci USA 102:2232–2237

    Article  PubMed  CAS  Google Scholar 

  • Lombardo A, Genovese P, Beausejour CM, Colleoni S, Lee Y-L, Kim KA, Ando D, Urnov FD, Galli C, Gregory PD, Holmes MC, Naldini L (2007) Gene editing in human stem cells using zinc finger nucleases and integrase-defective lentiviral vector delivery. Nat Biotechnol 25:1298–1306

    Article  PubMed  CAS  Google Scholar 

  • Maeder ML, Thibodeau-Beganny S, Osiak A, Wright DA, Reshma MA, Eichtinger M, Jiang T, Foley JE, Winfrey RJ, Townsend JA, Unger-Wallace E, Sander JD, Müller-Lerch F, Fu F, Pearlberg J, Göbel C, Dassie JP, Pruett-Miller SM, Porteus MH, Sgroi DC, Iafrate AJ, Dobbs D, McCray PB Jr, Cathomen T, Voytas DF, Joung JK (2008) Rapid “open-source” engineering of customized zinc-finger nucleases for highly efficient gene modification. Mol Cell 31:294–301

    Article  PubMed  CAS  Google Scholar 

  • Maeder ML, Thibodeau-Beganny S, Sander JD, Voytas DF, Joung JK (2009) Oligomerized pool engineering (OPEN): an ‘open-source’ protocol for making customized zinc-finger arrays. Nat Prot 4:1471–1501

    Article  CAS  Google Scholar 

  • Mahfouz MM, Li L, Shamimuzzaman M, Wibowo A, Fang X, Zhu J-K (2011) De novo-engineered transcription activator-like effector (TALE) hybrid nuclease with novel DNA binding specificity creates double-strand breaks. Proc Natl Acad Sci USA 108:2623–2628

    Article  PubMed  CAS  Google Scholar 

  • Mani M, Smith J, Kandavelou K, Berg JM, Chandrasegaran S (2005) Binding of two zinc finger nuclease monomers to two specific sites is required for effective double-strand DNA cleavage. Biochem Biophys Res Commun 334:1191–1197

    Article  PubMed  CAS  Google Scholar 

  • Marton I, Zuker A, Shklarman E, Zeevi V, Tovkach A, Roffe S, Ovadis M, Tzfira T, Vainstein A (2010) Nontransgenic genome modification in plant cells. Plant Phys 154:1079–1087

    Article  CAS  Google Scholar 

  • Meng X, Noyes MB, Zhu LJ, Lawson ND, Wolfe SA (2008) Targeted gene inactivation in zebrafish using engineered zinc-finger nucleases. Nat Biotechnol 26:695–701

    Article  PubMed  CAS  Google Scholar 

  • Meyer V, Arentshorst M, El-Ghezal A, Drews A-C, Kooistra R, van den Hondel CAMJJ, Ram AFJ (2007) Highly efficient gene targeting in the Aspergillus niger kusA mutant. J Biotechnol 128:770–775

    Article  PubMed  CAS  Google Scholar 

  • Miao ZH, Lam E (1995) Targeted disruption of the TGA3 locus in Arabidopsis thaliana. Plant J 7:359–365

    Article  PubMed  CAS  Google Scholar 

  • Michielse CB, Hooykaas PJJ, van den Hondel CAMJJ, Ram AFJ (2005) Agrobacterium-mediated transformation as a tool for functional genomics in fungi. Curr Genet 48:1–17

    Article  PubMed  CAS  Google Scholar 

  • Miller JC, Holmes MC, Wang J, Guschin DY, Lee Y-L, Rupniewski I, Beausejour CM, Waite AJ, Wang NS, Kim KA, Gregory PD, Pabo CO, Rebar EJ (2007) An improved zinc-finger nuclease architecture for highly specific genome editing. Nat Biotechnol 25:778–785

    Article  PubMed  CAS  Google Scholar 

  • Minczuk M, Papworth MA, Miller JC, Murphy MP, Klug A (2008) Development of a single-chain, quasi-dimeric zinc-finger nuclease for the selective degradation of mutated human mitochondrial DNA. Nucl Acids Res 36:3926–3938

    Article  PubMed  CAS  Google Scholar 

  • Mino T, Aoyama Y, Sera T (2009) Efficient double-stranded DNA cleavage by artificial zinc-finger nucleases composed of one zinc-finger protein and a single-chain FokI dimer. J Biotechnol 140:156–161

    Article  PubMed  CAS  Google Scholar 

  • Moehle E, Rock JM, Lee YL, Jouvenot Y, DeKelver RC, Gregory PD, Urnov FD, Holmes MC (2007) Targeted gene addition into a specified location in the human genome using designed zinc finger nucleases. Proc Natl Acad Sci USA 104:3055–3060

    Article  PubMed  CAS  Google Scholar 

  • Morton J, Davis MW, Jorgensen EM, Carroll D (2006) Induction and repair of zinc-finger nuclease-targeted double-strand breaks in Caenorhabditis elegans somatic cells. Proc Natl Acad Sci USA 103:16370–16375

    Article  PubMed  CAS  Google Scholar 

  • Neuteboom LW, Lindhout BI, Saman IL, Hooykaas PJJ, van der Zaal BJ (2006) Effects of different zinc finger transcription factors on genomic targets. Biochem Biophys Res Commun 339:263–270

    Article  PubMed  CAS  Google Scholar 

  • Ninomiya Y, Suzuki K, Ishii C, Inoue H (2004) Highly efficient gene replacements in Neurospora strains deficient for nonhomologous end-joining. Proc Natl Acad Sci USA 101:12248–12253

    Article  PubMed  CAS  Google Scholar 

  • Nussenzweig A, Nussenzweig MC (2007) A backup DNA repair pathway moves to the forefront. Cell 131:223–225

    Article  PubMed  CAS  Google Scholar 

  • Offringa R, de Groot MJA, Haagsman HJ, Does MP, van den Elzen PJM, Hooykaas PJJ (1990) Extrachromosomal homologous recombination and gene targeting in plant cells after Agrobacterium mediated transformation. EMBO J 9:3077–3084

    PubMed  CAS  Google Scholar 

  • Osakabe K, Osakabe Y, Toki S (2010) Site-directed mutagenesis in Arabidopsis using custom-designed zinc finger nucleases. Proc Natl Acad Sci USA 107:12034–12039

    Article  PubMed  CAS  Google Scholar 

  • Paszkowski J, Baur M, Bogucki A, Potrykus I (1988) Gene targeting in plants. EMBO J 7:4021–4026

    PubMed  CAS  Google Scholar 

  • Pruett-Miller SM, Reading DW, Porter SN, Porteus MH (2009) Attenuation of zinc finger nuclease toxicity by small-molecule regulation of protein levels. PLoS Genet 5:e1000376

    Article  PubMed  CAS  Google Scholar 

  • Puchta H, Dujon B, Hohn B (1996) Two different but related mechanisms are used in plants for the repair of genomic double-strand breaks by homologous recombination. Proc Natl Acad Sci USA 93:5055–5060

    Article  PubMed  CAS  Google Scholar 

  • Ramirez CL, Foley JE, Wright DA, Müller-Lerch F, Rahman SH, Cornu TI, Winfrey RJ, Sander JD, Fu F, Townsend JA, Cathomen T, Voytas DF, Joung JK (2008) Unexpected failure rates for modular assembly of engineered zinc fingers. Nat Method 5:374–375

    Article  CAS  Google Scholar 

  • Rémy S, Tesson L, Ménoret S, Usal C, Scharenberg AM, Anegon I (2010) Zinc-finger nucleases: a powerful tool for genetic engineering of animals. Transgenic Res 19:363–371

    Article  PubMed  CAS  Google Scholar 

  • Risseeuw E, Offringa R, Franke-van Dijk MEI, Hooykaas PJJ (1995) Targeted recombination in plants using Agobacterium coincides with additional rearrangements at the target locus. Plant J 7:109–119

    Article  PubMed  CAS  Google Scholar 

  • Rouet P, Smih F, Jasin M (1994) Introduction of double-strand breaks into the genome of mouse cells by expression of a rare-cutting endonuclease. Mol Cell Biol 14:8096–8106

    PubMed  CAS  Google Scholar 

  • Saika H, Oikawa A, Matsuda F, Onodera H, Saito K, Toki S (2011) Application of gene targeting to designed mutation breeding of high-tryptophan rice. Plant Phys 156:1269–1277

    Article  CAS  Google Scholar 

  • Sander JD, Dahlborg EJ, Goodwin MJ, Cade L, Zhang F, Cifuentes D, Curtin SJ, Blackburn JS, Thibodeau-Beganny S, Qi Y, Pierick CJ, Hoffman E, Maeder ML, Khayter C, Reyon D, Dobbs D, Langenau DM, Stupar RM, Giraldez AJ, Voytas DF, Peterson RT, Yeh J-RJ, Joung JK (2010a) Selection-free zinc-finger-nuclease engineering by context-dependent assembly (CoDA). Nat Method 8:67–69

    Article  CAS  Google Scholar 

  • Sander JD, Reyon D, Maeder ML, Foley JE, Thibodeau-Beganny S, Li X, Regan MR, Dahlborg EJ, Goodwin MJ, Fu F, Voytas DF, Joung JK, Dobbs D (2010b) Predicting success of oligomerized pool engineering (OPEN) for zinc finger target site sequences. BMC Bioinforma 11:543

    Article  CAS  Google Scholar 

  • Santiago Y, Chan E, Liu P-Q, Orlando S, Zhang L, Urnov FD, Holmes MC, Guschin D, Waite A, Miller JC, Rebar EJ, Gregory PD, Klug A, Collingwood TN (2008) Targeted gene knockout in mammalian cells by using engineered zinc-finger nucleases. Proc Natl Acad Sci USA 105:5809–5814

    Article  PubMed  CAS  Google Scholar 

  • Schaefer DG (2002) A new moss genetics: targeted mutagenesis in Physcomitrella patens. Ann Rev Plant Biol 53:477–501

    Article  CAS  Google Scholar 

  • Segal DJ, Dreier B, Beerli RR, Barbas CF (1999) Toward controlling gene expression at will: selection and design of zinc finger domains recognizing each of the 5′-GNN-3' DNA target sequences. Proc Natl Acad Sci USA 96:2758–2763

    Article  PubMed  CAS  Google Scholar 

  • Shaked H, Melamed-Bessudo C, Levy AA (2005) High-frequency gene targeting in Arabidopsis plants expressing the yeast RAD54 gene. Proc Natl Acad Sci USA 102:12265–12269

    Article  PubMed  CAS  Google Scholar 

  • Shimizu Y, Şöllü C, Meckler JF, Adriaenssens A, Zykovich A, Cathomen T, Segal DJ (2011) Adding fingers to an engineered zinc finger nuclease can reduce activity. Biochemistry 50:5033–5041

    Article  PubMed  CAS  Google Scholar 

  • Shrivastav M, De Haro LP, Nickoloff JA (2008) Regulation of DNA double-strand break repair pathway choice. Cell Res 18:134–147

    Article  PubMed  CAS  Google Scholar 

  • Shukla VK, Doyon Y, Miller JC, DeKelver RC, Moehle EA, Worden SE, Mitchell JC, Arnold NL, Gopalan S, Meng X, Choi VM, Rock JM, Wu Y-Y, Katibah GE, Zhifang G, McCaskill D, Simpson MA, Blakeslee B, Greenwalt SA, Butler HJ, Hinkley SJ, Zhang L, Rebar EJ, Gregory PD, Urnov FD (2009) Precise genome modification in the crop species Zea mays using zinc-finger nucleases. Nature 459:437–441

    Article  PubMed  CAS  Google Scholar 

  • Simsek D, Brunet E, Wong SY-W, Katyal S, Gao Y, McKinnon PJ, Lou J, Zhang L, Li J, Rebar EJ, Gregory PD, Holmes MC, Jasin M (2011) DNA ligase III promotes alternative nonhomologous end-joining during chromosomal translocation formation. PLoS Genet 7:e1002080

    Article  PubMed  CAS  Google Scholar 

  • 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  PubMed  CAS  Google Scholar 

  • Smith J, Bibikova M, Whitby FG, Reddy AR, Chandrasegaran S, Carroll D (2000) Requirements for double-strand cleavage by chimeric restriction enzymes with zinc finger DNA-recognition domains. Nucl Acids Res 28:3361–3369

    Article  PubMed  CAS  Google Scholar 

  • Şöllü C, Pars K, Cornu TI, Thibodeau-Beganny S, Maeder ML, Joung JK, Heilbronn R, Cathomen T (2010) Autonomous zinc-finger nuclease pairs for targeted chromosomal deletion. Nucl Acids Res 38:8269–8276

    Article  PubMed  CAS  Google Scholar 

  • Stoddard BL (2011) Homing endonucleases: from microbial genetic invaders to reagents for targeted DNA modification. Structure 19:7–15

    Article  PubMed  CAS  Google Scholar 

  • Stracker TH, Petrini JHJ (2011) The MRE11 complex: starting from the ends. Nat Rev Mol Cell Biol 12:90–103

    Article  PubMed  CAS  Google Scholar 

  • Szczepek M, Brondani V, Büchel J, Serrano L, Segal DJ, Cathomen T (2007) Structure-based redesign of the dimerization interface reduces the toxicity of zinc-finger nucleases. Nat Biotechnol 25:786–793

    Article  PubMed  CAS  Google Scholar 

  • Terada R, Johzuka-Hisatomi Y, Saitoh M, Asao H, Iida S (2007) Gene targeting by homologous recombination as a biotechnological tool for rice functional genomics. Plant Phys 144:846–856

    Article  CAS  Google Scholar 

  • Tovkach A, Zeevi V, Tzfira T (2009) A toolbox and procedural notes for characterizing novel zinc finger nucleases for genome editing in plant cells. Plant J 57:747–757

    Article  PubMed  CAS  Google Scholar 

  • Townsend JA, Wright DA, Winfrey RJ, Fu F, Maeder ML, Joung JK, Voytas DF (2009) High-frequency modification of plant genes using engineered zinc-finger nucleases. Nature 459:442–445

    Article  PubMed  CAS  Google Scholar 

  • Urnov FD, Miller JC, Lee Y-L, Beausejour CM, Rock JM, Augustus S, Jamieson AC, Porteus MH, Gregory PD, Holmes MC (2005) Highly efficient endogenous human gene correction using designed zinc-finger nucleases. Nature 435:646–651

    Article  PubMed  CAS  Google Scholar 

  • Van Attikum H, Hooykaas PJJ (2003) Genetic requirements for the targeted integration of Agrobacterium T-DNA in Saccharomyces cerevisiae. Nucl Acids Res 31:826–832

    Article  PubMed  CAS  Google Scholar 

  • Van Attikum H, Bundock P, Hooykaas PJJ (2001) Non-homologous end-joining proteins are required for Agrobacterium T-DNA integration. EMBO J 20:6550–6558

    Article  PubMed  Google Scholar 

  • Van Kregten M (2011) VirD2 of Agrobacterium tumefaciens: functional domains and biotechnological applications. Dissertation, Leiden University

    Google Scholar 

  • Vergunst AC, Schrammeijer B, den Dulk-Ras A, de Vlaam CMT, Regensburg-Tuink TJG, Hooykaas PJJ (2000) VirB/D4-dependent protein translocation from Agrobacterium into plant cells. Science 290:979–982

    Article  PubMed  CAS  Google Scholar 

  • Vergunst AC, van Lier MCM, den Dulk-Ras A, Grosse Stüve TA, Ouwehand A, Hooykaas PJJ (2005) Positive charge is an important feature of the C-terminal transport signal of the VirB/D4-translocated proteins of Agrobacterium. Proc Natl Acad Sci USA 102:832–837

    Article  PubMed  CAS  Google Scholar 

  • Wright DA, Townsend JA, Winfrey RJ, Irwin PA, Rajagopal J, Lonosky PM, Hall BD, Jondle MD, Voytas DF (2005) High-frequency homologous recombination in plants mediated by zinc-finger nucleases. Plant J 44:693–705

    Article  PubMed  CAS  Google Scholar 

  • Wright DA, Thibodeau-Beganny S, Sander JD, Winfrey RJ, Hirsh AS, Eichtinger M, Fu F, Porteus MH, Dobbs D, Voytas DF, Joung JK (2006) Standardized reagents and protocols for engineering zinc finger nucleases by modular assembly. Nat Prot 1:1637–1652

    Article  Google Scholar 

  • Yamauchi T, Johzuka-Hisatomi Y, Fukada-Tanaka S, Terada R, Nakamura I, Iida S (2009) Homologous recombination-mediated knock-in targeting of the MET1a gene for a maintenance DNA methyltransferase reproducibly reveals dosage-dependent spatiotemporal gene expression in rice. Plant J 60:386–396

    Article  PubMed  CAS  Google Scholar 

  • Zhang F, Maeder ML, Unger-Wallace E, Hoshaw JP, Reyon D, Christian M, Li X, Pierick CJ, Dobbs D, Peterson T, Joung JK, Voytas DF (2010) High frequency targeted mutagenesis in Arabidopsis thaliana using zinc finger nucleases. Proc Natl Acad Sci USA 107:12028–12033

    Article  PubMed  CAS  Google Scholar 

  • Zhang F, Cong L, Lodato S, Kosuri S, Church GM, Arlotta P (2011) Efficient construction of sequence-specific TAL effectors for modulating mammalian transcription. Nat Biotechnol 29:149–154

    Article  PubMed  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Department of Molecular and Developmental Genetics, Institute of Biology, Sylvius Laboratory, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands

    Sylvia de Pater & Paul J. J. Hooykaas

Authors
  1. Sylvia de Pater
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Paul J. J. Hooykaas
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Sylvia de Pater .

Editor information

Editors and Affiliations

  1. Dept. Agronomy, Iowa State University, Agronomy Hall 1204, Ames, 50011, Iowa, USA

    Thomas Lübberstedt

  2. ICRISAT, Centre of Excellence in Genomics (CEG), Patancheru, 502 324, Andra Pradesh, India

    Rajeev K. Varshney

Rights and permissions

Reprints and permissions

Copyright information

© 2013 Springer Science+Business Media Dordrecht

About this chapter

Cite this chapter

de Pater, S., Hooykaas, P.J.J. (2013). Gene Replacement. In: Lübberstedt, T., Varshney, R. (eds) Diagnostics in Plant Breeding. Springer, Dordrecht. https://doi.org/10.1007/978-94-007-5687-8_8

Download citation

Publish with us

Policies and ethics

Search

Navigation