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Online Tools for TALEN Design

  • Protocol
TALENs

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1338))

Abstract

Transcription activator-like effector nucleases (TALENs) can be exquisitely specific and highly effective genome editing reagents. Specificity and efficacy depend however on good design for minimal off-targeting and strong binding. Several online tools are accessible to aid in this process. Here, we tabulate those tools, noting their functions and key features.

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References

  1. Carroll D (2014) Genome engineering with targetable nucleases. Annu Rev Biochem 83:409–439. doi:10.1146/annurev-biochem-060713-035418

    Article  CAS  PubMed  Google Scholar 

  2. Moscou MJ, Bogdanove AJ (2009) A simple cipher governs DNA recognition by TAL effectors. Science 326(5959):1501. doi:10.1126/science.1178817

    Article  CAS  PubMed  Google Scholar 

  3. 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(5959):1509–1512. doi:10.1126/science.1178811

    Article  CAS  PubMed  Google Scholar 

  4. Mak AN, Bradley P, Cernadas RA, Bogdanove AJ, Stoddard BL (2012) The crystal structure of TAL effector PthXo1 bound to its DNA target. Science 335(6069):716–719. doi:10.1126/science.1216211

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  5. Deng D, Yan C, Pan X, Mahfouz M, Wang J, Zhu JK, Shi Y, Yan N (2012) Structural basis for sequence-specific recognition of DNA by TAL effectors. Science 335(6069):720–723. doi:10.1126/science.1215670

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  6. Doyle EL, Stoddard BL, Voytas DF, Bogdanove AJ (2013) TAL effectors: highly adaptable phytobacterial virulence factors and readily engineered DNA-targeting proteins. Trends Cell Biol 23:390–398. doi:10.1016/j.tcb.2013.04.003

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  7. 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. Nucleic Acids Res 39(12):e82. doi:10.1093/nar/gkr218

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  8. 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 29:149–153. doi:10.1038/nbt.1775

    Article  PubMed Central  PubMed  Google Scholar 

  9. Reyon D, Tsai SQ, Khayter C, Foden JA, Sander JD, Joung JK (2012) FLASH assembly of TALENs for high-throughput genome editing. Nat Biotechnol 30(5):460–465. doi:10.1038/nbt.2170

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  10. Weber E, Gruetzner R, Werner S, Engler C, Marillonnet S (2011) Assembly of designer TAL effectors by Golden Gate cloning. PLoS One 6(5):e19722. doi:10.1371/journal.pone.0019722

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  11. Wang Z, Li J, Huang H, Wang G, Jiang M, Yin S, Sun C, Zhang H, Zhuang F, Xi JJ (2012) An integrated chip for the high-throughput synthesis of transcription activator-like effectors. Angew Chem Int Ed Engl 51(34):8505–8508. doi:10.1002/anie.201203597

    Article  CAS  PubMed  Google Scholar 

  12. Li L, Atef A, Piatek A, Ali Z, Piatek M, Aouida M, Sharakuu A, Mahjoub A, Wang G, Khan S, Fedoroff NV, Zhu JK, Mahfouz MM (2013) Characterization and DNA-binding specificities of Ralstonia TAL-like effectors. Mol Plant 6(4):1318–1330. doi:10.1093/mp/sst006

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  13. Briggs AW, Rios X, Chari R, Yang L, Zhang F, Mali P, Church GM (2012) Iterative capped assembly: rapid and scalable synthesis of repeat-module DNA such as TAL effectors from individual monomers. Nucleic Acids Res 40(15):e117. doi:10.1093/nar/gks624

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  14. Morbitzer R, Elsaesser J, Hausner J, Lahaye T (2011) Assembly of custom TALE-type DNA binding domains by modular cloning. Nucleic Acids Res 39(13):5790–5799. doi:10.1093/nar/gkr151

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  15. Christian M, Cermak T, Doyle EL, Schmidt C, Zhang F, Hummel A, Bogdanove AJ, Voytas DF (2010) Targeting DNA double-strand breaks with TAL effector nucleases. Genetics 186:757–761. doi:10.1534/genetics.110.120717

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  16. Miller JC, Tan S, Qiao G, Barlow KA, Wang J, Xia DF, Meng X, Paschon DE, Leung E, Hinkley SJ, Dulay GP, Hua KL, Ankoudinova I, Cost GJ, Urnov FD, Zhang HS, Holmes MC, Zhang L, Gregory PD, Rebar EJ (2011) A TALE nuclease architecture for efficient genome editing. Nat Biotechnol 29:143–148. doi:10.1038/nbt.1755

    Article  CAS  PubMed  Google Scholar 

  17. Streubel J, Blucher C, Landgraf A, Boch J (2012) TAL effector RVD specificities and efficiencies. Nat Biotechnol 30(7):593–595. doi:10.1038/nbt.2304

    Article  CAS  PubMed  Google Scholar 

  18. Meckler JF, Bhakta MS, Kim MS, Ovadia R, Habrian CH, Zykovich A, Yu A, Lockwood SH, Morbitzer R, Elsaesser J, Lahaye T, Segal DJ, Baldwin EP (2013) Quantitative analysis of TALE-DNA interactions suggests polarity effects. Nucleic Acids Res 41(7):4118–4128. doi:10.1093/nar/gkt085

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  19. Montague TG, Cruz JM, Gagnon JA, Church GM, Valen E (2014) CHOPCHOP: a CRISPR/Cas9 and TALEN web tool for genome editing. Nucleic Acids Res 42(Web Server issue):W401–W407. doi:10.1093/nar/gku410

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  20. Heigwer F, Kerr G, Walther N, Glaeser K, Pelz O, Breinig M, Boutros M (2013) E-TALEN: a web tool to design TALENs for genome engineering. Nucleic Acids Res 41(20):e190. doi:10.1093/nar/gkt789

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  21. Neff KL, Argue DP, Ma AC, Lee HB, Clark KJ, Ekker SC (2013) Mojo Hand, a TALEN design tool for genome editing applications. BMC Bioinformatics 14:1. doi:10.1186/1471-2105-14-1

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  22. Fine EJ, Cradick TJ, Zhao CL, Lin Y, Bao G (2014) An online bioinformatics tool predicts zinc finger and TALE nuclease off-target cleavage. Nucleic Acids Res 42(6):e42. doi:10.1093/nar/gkt1326

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  23. Lin Y, Fine EJ, Zheng Z, Antico CJ, Voit RA, Porteus MH, Cradick TJ, Bao G (2014) SAPTA: a new design tool for improving TALE nuclease activity. Nucleic Acids Res 42(6):e47. doi:10.1093/nar/gkt1363

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  24. Doyle EL, Booher NJ, Standage DS, Voytas DF, Brendel VP, Vandyk JK, Bogdanove AJ (2012) TAL Effector-Nucleotide Targeter (TALE-NT) 2.0: tools for TAL effector design and target prediction. Nucleic Acids Res 40(Web Server issue):W117–W122. doi:10.1093/nar/gks608

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  25. Grau J, Boch J, Posch S (2013) TALENoffer: genome-wide TALEN off-target prediction. Bioinformatics 29(22):2931–2932. doi:10.1093/bioinformatics/btt501

    Article  CAS  PubMed  Google Scholar 

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Acknowledgement

Research on TAL effectors in our laboratory is supported by grants from the National Science Foundation (IOS 1238189) and the National Institutes of Health (R01 GM098861).

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Authors and Affiliations

  1. Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, 334 Plant Science, Ithaca, NY, 14853, USA

    Adam J. Bogdanove & Nicholas J. Booher

Authors
  1. Adam J. Bogdanove
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  2. Nicholas J. Booher
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Corresponding author

Correspondence to Adam J. Bogdanove .

Editor information

Editors and Affiliations

  1. Max-Delbrück-Center for Molecular Medicine, Berlin, Germany

    Ralf Kühn

  2. Institute of Developmental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany

    Wolfgang Wurst

  3. Institute of Developmental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany

    Benedikt Wefers

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Bogdanove, A.J., Booher, N.J. (2016). Online Tools for TALEN Design. In: Kühn, R., Wurst, W., Wefers, B. (eds) TALENs. Methods in Molecular Biology, vol 1338. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-2932-0_4

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  • DOI: https://doi.org/10.1007/978-1-4939-2932-0_4

  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-2931-3

  • Online ISBN: 978-1-4939-2932-0

  • eBook Packages: Springer Protocols

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