Comprehensive analysis of the specificity of transcription activator-like effector nucleases

TY - JOUR

T1 - Comprehensive analysis of the specificity of transcription activator-like effector nucleases

AU - Juillerat, Alexandre

AU - Dubois, Gwendoline

AU - Valton, Julien

AU - Thomas, Séverine

AU - Stella, Stefano

AU - Maréchal, Alan

AU - Langevin, Stéphanie

AU - Benomari, Nassima

AU - Bertonati, Claudia

AU - Silva, George H

AU - Daboussi, Fayza

AU - Epinat, Jean-Charles

AU - Montoya, Guillermo

AU - Duclert, Aymeric

AU - Duchateau, Philippe

PY - 2014/4

Y1 - 2014/4

N2 - A key issue when designing and using DNA-targeting nucleases is specificity. Ideally, an optimal DNA-targeting tool has only one recognition site within a genomic sequence. In practice, however, almost all designer nucleases available today can accommodate one to several mutations within their target site. The ability to predict the specificity of targeting is thus highly desirable. Here, we describe the first comprehensive experimental study focused on the specificity of the four commonly used repeat variable diresidues (RVDs; NI:A, HD:C, NN:G and NG:T) incorporated in transcription activator-like effector nucleases (TALEN). The analysis of >15 500 unique TALEN/DNA cleavage profiles allowed us to monitor the specificity gradient of the RVDs along a TALEN/DNA binding array and to present a specificity scoring matrix for RVD/nucleotide association. Furthermore, we report that TALEN can only accommodate a relatively small number of position-dependent mismatches while maintaining a detectable activity at endogenous loci in vivo, demonstrating the high specificity of these molecular tools. We thus envision that the results we provide will allow for more deliberate choices of DNA binding arrays and/or DNA targets, extending our engineering capabilities.

AB - A key issue when designing and using DNA-targeting nucleases is specificity. Ideally, an optimal DNA-targeting tool has only one recognition site within a genomic sequence. In practice, however, almost all designer nucleases available today can accommodate one to several mutations within their target site. The ability to predict the specificity of targeting is thus highly desirable. Here, we describe the first comprehensive experimental study focused on the specificity of the four commonly used repeat variable diresidues (RVDs; NI:A, HD:C, NN:G and NG:T) incorporated in transcription activator-like effector nucleases (TALEN). The analysis of >15 500 unique TALEN/DNA cleavage profiles allowed us to monitor the specificity gradient of the RVDs along a TALEN/DNA binding array and to present a specificity scoring matrix for RVD/nucleotide association. Furthermore, we report that TALEN can only accommodate a relatively small number of position-dependent mismatches while maintaining a detectable activity at endogenous loci in vivo, demonstrating the high specificity of these molecular tools. We thus envision that the results we provide will allow for more deliberate choices of DNA binding arrays and/or DNA targets, extending our engineering capabilities.

KW - Amino Acids

KW - Animals

KW - Base Sequence

KW - CHO Cells

KW - Cricetinae

KW - Cricetulus

KW - DNA

KW - DNA Cleavage

KW - DNA-Binding Proteins

KW - Deoxyribonucleases

KW - Mutation

KW - Protein Array Analysis

KW - Protein Engineering

KW - Yeasts

U2 - 10.1093/nar/gku155

DO - 10.1093/nar/gku155

M3 - Journal article

C2 - 24569350

SN - 0305-1048

VL - 42

SP - 5390

EP - 5402

JO - Nucleic Acids Research

JF - Nucleic Acids Research

IS - 8

ER -