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.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
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
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
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
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
(2012) Method of the Year 2011. Nature Methods 9:1–1. doi: 10.1038/nmeth.1852
Baker M (2012) Gene-editing nucleases. Nat Methods 9:23–26. doi:10.1038/nmeth.1807
McMahon MA, Rahdar M, Porteus M (2012) Gene editing: not just for translation anymore. Nat Methods 9:28–31. doi:10.1038/nmeth.1811
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
Mali P, Yang L, Esvelt KM et al (2013) RNA-guided human genome engineering via Cas9. Science 339:823. doi:10.1126/science.1232033
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
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
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
Takeuchi R. Choi M, Stoddard BL (2013) Efficient engineering of multiple meganucleases and MegaTALs using bioinformatics and in vitro compartmentalization (in press)
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
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
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
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
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
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
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
Scholze H, Boch J (2010) TAL effector-DNA specificity. Virulence 1:428–432. doi:10.4161/viru.1.5.12863
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
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
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
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
Moscou MJ, Bogdanove AJ (2009) A simple cipher governs DNA recognition by TAL effectors. Science 326:1501. doi:10.1126/science.1178817
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
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
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
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
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
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2015 Springer Science+Business Media New York
About this protocol
Cite this protocol
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
Download citation
DOI: https://doi.org/10.1007/978-1-4939-1862-1_9
Published:
Publisher Name: Humana Press, New York, NY
Print ISBN: 978-1-4939-1861-4
Online ISBN: 978-1-4939-1862-1
eBook Packages: Springer Protocols