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Assembly and Characterization of megaTALs for Hyperspecific Genome Engineering Applications

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Chromosomal Mutagenesis

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1239))

Abstract

Rare-cleaving nucleases have emerged as valuable tools for creating targeted genomic modification for both therapeutic and research applications. MegaTALs are novel monomeric nucleases composed of a site-specific meganuclease cleavage head with additional affinity and specificity provided by a TAL effector DNA binding domain. This fusion product facilitates the transformation of meganucleases into hyperspecific and highly active genome engineering tools that are amenable to multiplexing and compatible with multiple cellular delivery methods. In this chapter, we describe the process of assembling a megaTAL from a meganuclease, as well as a method for characterization of nuclease cleavage activity in vivo using a fluorescence reporter assay.

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References

  1. Hacein-Bey-Abina S, Garrigue A, Wang GP et al (2008) Insertional oncogenesis in 4 patients after retrovirus-mediated gene therapy of SCID-X1. J Clin Invest 118:3132–3142. doi:10.1172/JCI35700

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  2. Bushman F, Lewinski M, Ciuffi A et al (2005) Genome-wide analysis of retroviral DNA integration. Nat Rev Microbiol 3:848–858. doi:10.1038/nrmicro1263

    Article  CAS  PubMed  Google Scholar 

  3. Baum C, Kustikova O, Modlich U et al (2006) Mutagenesis and oncogenesis by chromosomal insertion of gene transfer vectors. Hum Gene Ther 17:253–263. doi:10.1089/hum.2006.17.253

    Article  CAS  PubMed  Google Scholar 

  4. Nowrouzi A, Glimm H, Von Kalle C, Schmidt M (2011) Retroviral vectors: post entry events and genomic alterations. Viruses 3:429–455. doi:10.3390/v3050429

    Article  PubMed Central  PubMed  Google Scholar 

  5. (2012) Method of the Year 2011. Nature Methods 9:1–1. doi: 10.1038/nmeth.1852

  6. Baker M (2012) Gene-editing nucleases. Nat Methods 9:23–26. doi:10.1038/nmeth.1807

    Article  CAS  PubMed  Google Scholar 

  7. McMahon MA, Rahdar M, Porteus M (2012) Gene editing: not just for translation anymore. Nat Methods 9:28–31. doi:10.1038/nmeth.1811

    Article  CAS  Google Scholar 

  8. Schiffer JT, Aubert M, Weber ND et al (2012) Targeted DNA mutagenesis for the cure of chronic viral infections. J Virol 86:8920–8936. doi:10.1128/JVI.00052-12

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  9. Lieber MR (2010) The mechanism of double-strand DNA break repair by the nonhomologous DNA end-joining pathway. Annu Rev Biochem 79:181–211. doi:10.1146/annurev.biochem.052308.093131

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  10. Shrivastav M, Haro LPD, Nickoloff JA (2008) Regulation of DNA double-strand break repair pathway choice. Cell Res 18:134–147. doi:10.1038/cr.2007.111

    Article  CAS  PubMed  Google Scholar 

  11. Paques F, Duchateau P (2007) Meganucleases and DNA double-strand break-induced recombination: perspectives for gene therapy. Curr Gene Ther 7:49–66. doi:10.2174/156652307779940216

    Article  CAS  PubMed  Google Scholar 

  12. Stoddard BL (2011) Homing endonucleases: from microbial genetic invaders to reagents for targeted DNA modification. Structure 19:7–15. doi:10.1016/j.str.2010.12.003

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  13. Mussolino C, Morbitzer R, Lutge F et al (2011) A novel TALE nuclease scaffold enables high genome editing activity in combination with low toxicity. Nucleic Acids Res 39:9283–9293. doi:10.1093/nar/gkr597

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  14. Ashworth J, Taylor GK, Havranek JJ et al (2010) Computational reprogramming of homing endonuclease specificity at multiple adjacent base pairs. Nucleic Acids Res 38:5601–5608

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  15. Takeuchi R, Lambert AR, Mak AN-S et al (2011) Tapping natural reservoirs of homing endonucleases for targeted gene modification. Proc Natl Acad Sci U S A 108:13077–13082. doi:10.1073/pnas.1107719108

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  16. Szeto MD, Boissel SJS, Baker D, Thyme SB (2011) Mining endonuclease cleavage determinants in genomic sequence data. J Biol Chem 286:32617–32627. doi:10.1074/jbc.M111.259572

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  17. Kim YG, Cha J, Chandrasegaran S (1996) Hybrid restriction enzymes: zinc finger fusions to Fok I cleavage domain. Proc Natl Acad Sci U S A 93:1156–1160

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  18. Klug A (2010) The discovery of zinc fingers and their applications in gene regulation and genome manipulation. Annu Rev Biochem 79:213–231. doi:10.1146/annurev-biochem-010909-095056

    Article  CAS  PubMed  Google Scholar 

  19. Christian M, Cermak T, Doyle EL et al (2010) Targeting DNA double-strand breaks with TAL effector nucleases. Genetics 186:757–761. doi:10.1534/genetics.110.120717

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  20. Li T, Huang S, Jiang WZ et al (2011) TAL nucleases (TALNs): hybrid proteins composed of TAL effectors and FokI DNA-cleavage domain. Nucleic Acids Res 39:359–372. doi:10.1093/nar/gkq704

    Article  PubMed Central  PubMed  Google Scholar 

  21. Cornu TI, Thibodeau-Beganny S, Guhl E et al (2008) DNA-binding specificity is a major determinant of the activity and toxicity of zinc-finger nucleases. Mol Ther 16:352–358. doi:10.1038/sj.mt.6300357

    Article  CAS  PubMed  Google Scholar 

  22. Gabriel R, Lombardo A, Arens A et al (2011) An unbiased genome-wide analysis of zinc-finger nuclease specificity. Nat Biotechnol 29:816–823. doi:10.1038/nbt.1948

    Article  CAS  PubMed  Google Scholar 

  23. Pattanayak V, Ramirez CL, Joung JK, Liu DR (2011) Revealing off-target cleavage specificities of zinc-finger nucleases by in vitro selection. Nat Methods 8:765–770. doi:10.1038/nmeth.1670

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  24. Söllü C, Pars K, Cornu TI et al (2010) Autonomous zinc-finger nuclease pairs for targeted chromosomal deletion. Nucleic Acids Res 38:8269–8276. doi:10.1093/nar/gkq720

    Article  PubMed Central  PubMed  Google Scholar 

  25. Holkers M, Maggio I, Liu J et al (2012) Differential integrity of TALE nuclease genes following adenoviral and lentiviral vector gene transfer into human cells. Nucleic Acids Res 41:e63. doi:10.1093/nar/gks1446

    Article  PubMed Central  PubMed  Google Scholar 

  26. Jinek M, Chylinski K, Fonfara I et al (2012) A programmable dual-RNA–guided DNA endonuclease in adaptive bacterial immunity. Science 337:816–821. doi:10.1126/science.1225829

    Article  CAS  PubMed  Google Scholar 

  27. Mali P, Yang L, Esvelt KM et al (2013) RNA-guided human genome engineering via Cas9. Science 339:823. doi:10.1126/science.1232033

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  28. Fu Y, Foden JA, Khayter C et al (2013) High-frequency off-target mutagenesis induced by CRISPR-Cas nucleases in human cells. Nat Biotechnol 31:822. doi:10.1038/nbt.2623

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  29. Cradick TJ, Fine EJ, Antico CJ, Bao G (2013) CRISPR/Cas9 systems targeting β-globin and CCR5 genes have substantial off-target activity. Nucleic Acids Res 41:9584. doi:10.1093/nar/gkt714

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  30. Boissel S, Jarjour J, Astrakhan A et al (2014) megaTALs: a rare-cleaving nuclease architecture for therapeutic genome engineering. Nucleic Acids Res 42:2591. doi:10.1093/nar/gkt1224

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  31. Takeuchi R. Choi M, Stoddard BL (2013) Efficient engineering of multiple meganucleases and MegaTALs using bioinformatics and in vitro compartmentalization (in press)

    Google Scholar 

  32. Wang Y, Khan I, Boissel S, Jarjour J, Pangallo J, Thyme S, Baker D, Scharenberg A, Rawlings D (2014) Progressive engineering of a homing endonuclease genome editing reagent for the murine X-linked immunodeficiency locus. Nucleic Acids Res 42:6463

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  33. Certo MT, Ryu BY, Annis JE et al (2011) Tracking genome engineering outcome at individual DNA breakpoints. Nat Methods 8:671–676. doi:10.1038/nmeth.1648

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  34. Kuhar R, Gwiazda KS, Humbert O et al (2013) Novel fluorescent genome editing reporters for monitoring DNA repair pathway utilization at endonuclease-induced breaks. Nucleic Acids Res 42:e4. doi:10.1093/nar/gkt872

    Article  PubMed Central  PubMed  Google Scholar 

  35. Cermak T, Doyle EL, Christian M et al (2011) Efficient design and assembly of custom TALEN and other TAL effector-based constructs for DNA targeting. Nucleic Acids Res 39:e82. doi:10.1093/nar/gkr218

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  36. Scalley-Kim M, McConnell-Smith A, Stoddard BL (2007) Coevolution of a homing endonuclease and its host target sequence. J Mol Biol 372:1305–1319. doi:10.1016/j.jmb.2007.07.052

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  37. Sethuraman J, Majer A, Friedrich NC et al (2009) Genes within genes: multiple LAGLIDADG homing endonucleases target the ribosomal protein S3 gene encoded within an rnl group I intron of Ophiostoma and related taxa. Mol Biol Evol 26:2299–2315. doi:10.1093/molbev/msp145

    Article  CAS  PubMed  Google Scholar 

  38. Römer P, Recht S, Strauß T et al (2010) Promoter elements of rice susceptibility genes are bound and activated by specific TAL effectors from the bacterial blight pathogen, Xanthomonas oryzae pv. oryzae. New Phytol 187:1048–1057

    Article  PubMed  Google Scholar 

  39. Scholze H, Boch J (2010) TAL effector-DNA specificity. Virulence 1:428–432. doi:10.4161/viru.1.5.12863

    Article  PubMed  Google Scholar 

  40. Mak AN-S, Bradley P, Cernadas RA et al (2012) The crystal structure of TAL effector PthXo1 bound to its DNA target. Science 335:716–719. doi:10.1126/science.1216211

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  41. De Lange O, Schreiber T, Schandry N et al (2013) Breaking the DNA-binding code of Ralstonia solanacearum TAL effectors provides new possibilities to generate plant resistance genes against bacterial wilt disease. New Phytol 199:773–786. doi:10.1111/nph.12324

    Article  PubMed  Google Scholar 

  42. Lamb BM, Mercer AC, Barbas CF 3rd (2013) Directed evolution of the TALE N-terminal domain for recognition of all 5′ bases. Nucleic Acids Res 41:9779–9785. doi:10.1093/nar/gkt754

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  43. Meckler JF, Bhakta MS, Kim M-S et al (2013) Quantitative analysis of TALE–DNA interactions suggests polarity effects. Nucleic Acids Res 41:4118–4128. doi:10.1093/nar/gkt085

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  44. Moscou MJ, Bogdanove AJ (2009) A simple cipher governs DNA recognition by TAL effectors. Science 326:1501. doi:10.1126/science.1178817

    Article  CAS  PubMed  Google Scholar 

  45. Boch J, Scholze H, Schornack S et al (2009) Breaking the code of DNA binding specificity of TAL-type III effectors. Science 326:1509–1512. doi:10.1126/science.1178811

    Article  CAS  PubMed  Google Scholar 

  46. Christian ML, Demorest ZL, Starker CG et al (2012) Targeting G with TAL effectors: a comparison of activities of TALENs constructed with NN and NK repeat variable di-residues. PLoS One 7:e45383. doi:10.1371/journal.pone.0045383

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  47. Streubel J, Blücher C, Landgraf A, Boch J (2012) TAL effector RVD specificities and efficiencies. Nat Biotechnol 30:593–595. doi:10.1038/nbt.2304

    Article  CAS  PubMed  Google Scholar 

  48. Colleaux L, D’Auriol L, Betermier M et al (1986) Universal code equivalent of a yeast mitochondrial intron reading frame is expressed into E. coli as a specific double strand endonuclease. Cell 44:521–533. doi:10.1016/0092-8674(86)90262-X

    Article  CAS  PubMed  Google Scholar 

  49. Takeuchi R, Certo M, Caprara MG et al (2009) Optimization of in vivo activity of a bifunctional homing endonuclease and maturase reverses evolutionary degradation. Nucleic Acids Res 37:877–890. doi:10.1093/nar/gkn1007

    Article  CAS  PubMed Central  PubMed  Google Scholar 

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Correspondence to Andrew M. Scharenberg .

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Boissel, S., Scharenberg, A.M. (2015). Assembly and Characterization of megaTALs for Hyperspecific Genome Engineering Applications. In: Pruett-Miller, S. (eds) Chromosomal Mutagenesis. Methods in Molecular Biology, vol 1239. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-1862-1_9

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  • DOI: https://doi.org/10.1007/978-1-4939-1862-1_9

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  • Print ISBN: 978-1-4939-1861-4

  • Online ISBN: 978-1-4939-1862-1

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