Skip to main content
SpringerLink
Log in

Designing and Testing the Activities of TAL Effector Nucleases

  • Protocol
  • First Online:
Gene Correction

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1114))

Abstract

Transcription activator-like effector nucleases (TALENs) have rapidly developed into a powerful tool for genome editing. To avoid labor-intensive and time-consuming experimental screening for active TALENs, a scoring system can help select optimal target sites. Here we describe a procedure to design active TALENs using a scoring system named Scoring Algorithm for Predicted TALEN Activity (SAPTA) and a method to test the activity of individual and pairs of TALENs.

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

Access this chapter

Log in via an institution

Subscribe and save

Springer+ Basic
$34.99 /Month
  • Get 10 units per month
  • Download Article/Chapter or eBook
  • 1 Unit = 1 Article or 1 Chapter
  • Cancel anytime
Subscribe now

Buy Now

Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 89.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 119.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 169.99
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

Similar content being viewed by others

References

  1. 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, 1178811 [pii]

    Article  CAS  PubMed  Google Scholar 

  2. Boch J, Bonas U (2009) Xanthomonas AvrBs3 family-type III effectors: discovery and function. Annu Rev Phytopathol 48:419–436. doi:10.1146/annurev-phyto-080508-081936

    Article  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  4. Schornack S, Meyer A, Römer P, Jordan T, Lahaye T (2006) Gene-for-gene-mediated recognition of nuclear-targeted AvrBs3-like bacterial effector proteins. J Plant Physiol 163(3):256–272. doi:10.1016/j.jplph.2005.12.001, S0176-1617(05)00462-1 [pii]

    Article  CAS  PubMed  Google Scholar 

  5. 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. doi:10.1093/nar/gkr218, gkr218 [pii]

    PubMed Central  PubMed  Google Scholar 

  6. 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 (2010) A TALE nuclease architecture for efficient genome editing. Nat Biotechnol 29(2):143–148. doi:10.1038/nbt.1755, nbt.1755 [pii]

    Article  PubMed  Google Scholar 

  7. Tesson L, Usal C, Ménoret S, Leung E, Niles BJ, Remy S, Santiago Y, Vincent AI, Meng X, Zhang L, Gregory PD, Anegon I, Cost GJ (2011) Knockout rats generated by embryo microinjection of TALENs. Nat Biotechnol 29(8):695–696. doi:10.1038/nbt.1940, nbt.1940 [pii]

    Article  CAS  PubMed  Google Scholar 

  8. 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(2):757–761. doi:10.1534/genetics.110.120717, genetics.110.120717 [pii]

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  9. Li T, Huang S, Jiang WZ, Wright D, Spalding MH, Weeks DP, Yang B (2010) TAL nucleases (TALNs): hybrid proteins composed of TAL effectors and FokI DNA-cleavage domain. Nucleic Acids Res 39(1):359–372. doi:10.1093/nar/gkq704, gkq704 [pii]

    Article  PubMed Central  PubMed  Google Scholar 

  10. Mahfouz MM, Li L, Shamimuzzaman M, Wibowo A, Fang X, Zhu JK (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(6):2623–2628. doi:10.1073/pnas.1019533108, 1019533108 [pii]

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  11. Wood AJ, Lo TW, Zeitler B, Pickle CS, Ralston EJ, Lee AH, Amora R, Miller JC, Leung E, Meng X, Zhang L, Rebar EJ, Gregory PD, Urnov FD, Meyer BJ (2011) Targeted genome editing across species using ZFNs and TALENs. Science 333(6040):307. doi:10.1126/science.1207773, science.1207773 [pii]

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  12. Sander JD, Cade L, Khayter C, Reyon D, Peterson RT, Joung JK, Yeh JR (2011) Targeted gene disruption in somatic zebrafish cells using engineered TALENs. Nat Biotechnol 29(8):697–698. doi:10.1038/nbt.1934, nbt.1934 [pii]

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  13. Huang P, Xiao A, Zhou M, Zhu Z, Lin S, Zhang B (2011) Heritable gene targeting in zebrafish using customized TALENs. Nat Biotechnol 29(8):699–700. doi:10.1038/nbt.1939, nbt.1939 [pii]

    Article  PubMed  Google Scholar 

  14. Mussolino C, Morbitzer R, Lütge F, Dannemann N, Lahaye T, Cathomen T (2011) A novel TALE nuclease scaffold enables high genome editing activity in combination with low toxicity. Nucleic Acids Res 39(21):9283–9293. doi:10.1093/nar/gkr597, gkr597 [pii]

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  15. Hockemeyer D, Wang H, Kiani S, Lai CS, Gao Q, Cassady JP, Cost GJ, Zhang L, Santiago Y, Miller JC, Zeitler B, Cherone JM, Meng X, Hinkley SJ, Rebar EJ, Gregory PD, Urnov FD, Jaenisch R (2011) Genetic engineering of human pluripotent cells using TALE nucleases. Nat Biotechnol 29(8):731–734. doi:10.1038/nbt.1927, nbt.1927 [pii]

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  16. Lin Y, Fine EJ, Zheng Z, Antico CJ, Voit RA, Porteus MH, Cradick TJ, Bao G (in press) SAPTA: a new design tool for improving TALE nuclease activity. Nucleic Acids Research

    Google Scholar 

  17. Porteus MH (2006) Mammalian gene targeting with designed zinc finger nucleases. Mol Ther 13(2):438–446. doi:10.1016/j.ymthe.2005.08.003

    Article  CAS  PubMed  Google Scholar 

  18. Guschin DY, Waite AJ, Katibah GE, Miller JC, Holmes MC, Rebar EJ (2010) A rapid and general assay for monitoring endogenous gene modification. Methods Mol Biol 649:247–256. doi:10.1007/978-1-60761-753-2_15

    Article  CAS  PubMed  Google Scholar 

  19. 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(2):149–153. doi:10.1038/nbt.1775, nbt.1775 [pii]

    Article  PubMed Central  PubMed  Google Scholar 

  20. 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, gks624 [pii]

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  21. 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, nbt.2170 [pii]

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  22. Schmid-Burgk JL, Schmidt T, Kaiser V, Höning K, Hornung V (2013) A ligation-independent cloning technique for high-throughput assembly of transcription activator–like effector genes. Nat Biotechnol 31(1):76–81. doi:10.1038/nbt.2460

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  23. Kim Y, Kweon J, Kim A, Chon JK, Yoo JY, Kim HJ, Kim S, Lee C, Jeong E, Chung E, Kim D, Lee MS, Go EM, Song HJ, Kim H, Cho N, Bang D, Kim JS (2013) A library of TAL effector nucleases spanning the human genome. Nat Biotechnol 31(3):251–258. doi:10.1038/nbt.2517

    Article  CAS  PubMed  Google Scholar 

  24. Deng D, Yin P, Yan C, Pan X, Gong X, Qi S, Xie T, Mahfouz M, Zhu JK, Yan N, Shi Y (2012) Recognition of methylated DNA by TAL effectors. Cell Res. doi:10.1038/cr.2012.127, cr2012127 [pii]

    Google Scholar 

  25. Valton J, Dupuy A, Daboussi F, Thomas S, Maréchal A, Macmaster R, Melliand K, Juillerat A, Duchateau P (2012) Overcoming transcription activator-like effector (TALE) DNA binding domain sensitivity to cytosine methylation. The Journal of biological chemistry 287(46):38427–38432. doi:10.1074/jbc.C112.408864

    Article  CAS  PubMed Central  PubMed  Google Scholar 

Download references

Acknowledgments

This work was supported by the National Institutes of Health as an NIH Nanomedicine Development Center Award (PN2EY018244 to G.B.).

Author information

Authors and Affiliations

  1. Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA, USA

    Yanni Lin, Thomas J. Cradick & Gang Bao

Authors
  1. Yanni Lin
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Thomas J. Cradick
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Gang Bao
    View author publications

    You can also search for this author in PubMed Google Scholar

Editor information

Editors and Affiliations

  1. Georgia Institute of Technology, Atlanta, Georgia, USA

    Francesca Storici

Rights and permissions

Reprints and permissions

Copyright information

© 2014 Springer Science+Business Media, LLC

About this protocol

Cite this protocol

Lin, Y., Cradick, T.J., Bao, G. (2014). Designing and Testing the Activities of TAL Effector Nucleases. In: Storici, F. (eds) Gene Correction. Methods in Molecular Biology, vol 1114. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-761-7_13

Download citation

  • DOI: https://doi.org/10.1007/978-1-62703-761-7_13

  • Published:

  • Publisher Name: Humana Press, Totowa, NJ

  • Print ISBN: 978-1-62703-760-0

  • Online ISBN: 978-1-62703-761-7

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics

Search

Navigation