TY - JOUR
T1 - Chromosomal context and epigenetic mechanisms control the efficacy of genome editing by rare-cutting designer endonucleases
AU - Daboussi, Fayza
AU - Zaslavskiy, Mikhail
AU - Poirot, Laurent
AU - Loperfido, Mariana
AU - Gouble, Agnès
AU - Guyot, Valerie
AU - Leduc, Sophie
AU - Galetto, Roman
AU - Grizot, Sylvestre
AU - Oficjalska, Danusia
AU - Perez, Christophe
AU - Delacôte, Fabien
AU - Dupuy, Aurélie
AU - Chion-Sotinel, Isabelle
AU - Le Clerre, Diane
AU - Lebuhotel, Céline
AU - Danos, Olivier
AU - Lemaire, Frédéric
AU - Oussedik, Kahina
AU - Cédrone, Frédéric
AU - Epinat, Jean-Charles
AU - Smith, Julianne
AU - Yáñez-Muñoz, Rafael J
AU - Dickson, George
AU - Popplewell, Linda
AU - Koo, Taeyoung
AU - VandenDriessche, Thierry
AU - Chuah, Marinee K
AU - Duclert, Aymeric
AU - Duchateau, Philippe
AU - Pâques, Frédéric
PY - 2012/7/1
Y1 - 2012/7/1
N2 - The ability to specifically engineer the genome of living cells at precise locations using rare-cutting designer endonucleases has broad implications for biotechnology and medicine, particularly for functional genomics, transgenics and gene therapy. However, the potential impact of chromosomal context and epigenetics on designer endonuclease-mediated genome editing is poorly understood. To address this question, we conducted a comprehensive analysis on the efficacy of 37 endonucleases derived from the quintessential I-CreI meganuclease that were specifically designed to cleave 39 different genomic targets. The analysis revealed that the efficiency of targeted mutagenesis at a given chromosomal locus is predictive of that of homologous gene targeting. Consequently, a strong genome-wide correlation was apparent between the efficiency of targeted mutagenesis (≤ 0.1% to ≈ 6%) with that of homologous gene targeting (≤ 0.1% to ≈ 15%). In contrast, the efficiency of targeted mutagenesis or homologous gene targeting at a given chromosomal locus does not correlate with the activity of individual endonucleases on transiently transfected substrates. Finally, we demonstrate that chromatin accessibility modulates the efficacy of rare-cutting endonucleases, accounting for strong position effects. Thus, chromosomal context and epigenetic mechanisms may play a major role in the efficiency rare-cutting endonuclease-induced genome engineering.
AB - The ability to specifically engineer the genome of living cells at precise locations using rare-cutting designer endonucleases has broad implications for biotechnology and medicine, particularly for functional genomics, transgenics and gene therapy. However, the potential impact of chromosomal context and epigenetics on designer endonuclease-mediated genome editing is poorly understood. To address this question, we conducted a comprehensive analysis on the efficacy of 37 endonucleases derived from the quintessential I-CreI meganuclease that were specifically designed to cleave 39 different genomic targets. The analysis revealed that the efficiency of targeted mutagenesis at a given chromosomal locus is predictive of that of homologous gene targeting. Consequently, a strong genome-wide correlation was apparent between the efficiency of targeted mutagenesis (≤ 0.1% to ≈ 6%) with that of homologous gene targeting (≤ 0.1% to ≈ 15%). In contrast, the efficiency of targeted mutagenesis or homologous gene targeting at a given chromosomal locus does not correlate with the activity of individual endonucleases on transiently transfected substrates. Finally, we demonstrate that chromatin accessibility modulates the efficacy of rare-cutting endonucleases, accounting for strong position effects. Thus, chromosomal context and epigenetic mechanisms may play a major role in the efficiency rare-cutting endonuclease-induced genome engineering.
U2 - 10.1093/nar/gks268
DO - 10.1093/nar/gks268
M3 - Article
C2 - 22467209
SN - 0305-1048
VL - 40
SP - 6367
EP - 6379
JO - Nucleic Acids Research
JF - Nucleic Acids Research
IS - 13
ER -