Abstract
Using engineered nucleases, such as Zinc Finger Nucleases (ZFNs) or Transcription Activator-Like Effector Nucleases (TALENs), to make targeted genomic modifications has become a common technique to create new model organisms and custom cell lines, and has shown great promise for disease treatment. However, these nucleases have the potential for off-target cleavage that could confound interpretation of experimental results and be detrimental for therapeutic use. Here, we describe a method to test for nuclease cleavage at potential off-target sites predicted by bioinformatics models.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Humbert O, Davis L, Maizels N (2012) Targeted gene therapies: tools, applications, optimization. Crit Rev Biochem Mol Biol 47(3):264–281
Gabriel R, Lombardo A, Arens A, Miller JC, Genovese P, Kaeppel C et al (2011) An unbiased genome-wide analysis of zinc-finger nuclease specificity. Nat Biotechnol 29(9):816–823
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(9):765–770
Gupta A, Meng X, Zhu LJ, Lawson ND, Wolfe SA (2011) Zinc finger protein-dependent and -independent contributions to the in vivo off-target activity of zinc finger nucleases. Nucleic Acids Res 39(1):381–392
Fine EJ, Cradick TJ, Zhao CL, Lin Y, Bao G (in press) An online bioinformatics tool predicts zinc finger and TALE nuclease off-target cleavage. Nucleic Acids Research
Hockemeyer D, Wang H, Kiani S, Lai CS, Gao Q, Cassady JP et al (2011) Genetic engineering of human pluripotent cells using TALE nucleases. Nat Biotechnol 29(8):731–734
Tesson L, Usal C, Ménoret S, Leung E, Niles BJ, Remy S et al (2011) Knockout rats generated by embryo microinjection of TALENs. Nat Biotechnol 29(8):695–696
Schneider CA, Rasband WS, Eliceiri KW (2012) NIH Image to ImageJ: 25 years of image analysis. Nat Methods 9(7):671–675
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
Carlson DF, Tan W, Lillico SG, Stverakova D, Proudfoot C, Christian M et al (2012) Efficient TALEN-mediated gene knockout in livestock. Proc Natl Acad Sci U S A 109(43):17382–17387
Acknowledgements
This work was supported by the National Institutes of Health as an NIH Nanomedicine Development Center Award (PN2EY018244 to GB). E.J.F. was additionally supported by an NSF Graduate Research Fellowship under Grant No. DGE-1148903.
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2014 Springer Science+Business Media, LLC
About this protocol
Cite this protocol
Fine, E.J., Cradick, T.J., Bao, G. (2014). Identification of Off-Target Cleavage Sites of Zinc Finger Nucleases and TAL Effector Nucleases Using Predictive Models. 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_24
Download citation
DOI: https://doi.org/10.1007/978-1-62703-761-7_24
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