Chromosomal context and epigenetic mechanisms control the efficacy of genome editing by rare-cutting designer endonucleases

Daboussi, Fayza; Zaslavskiy, Mikhail; Poirot, Laurent; Loperfido, Mariana; Gouble, Agnès; Guyot, Valerie; Leduc, Sophie; Galetto, Roman; Grizot, Sylvestre; Oficjalska, Danusia; Perez, Christophe; Delacôte, Fabien; Dupuy, Aurélie; Chion-Sotinel, Isabelle; Le Clerre, Diane; Lebuhotel, Céline; Danos, Olivier; Lemaire, Frédéric; Oussedik, Kahina; Cédrone, Frédéric; Epinat, Jean-Charles; Smith, Julianne; Yáñez-Muñoz, Rafael J; Dickson, George; Popplewell, Linda; Koo, Taeyoung; Vandendriessche, Thierry; Chuah, Marinee; Duclert, Aymeric; Duchateau, Philippe; Pâques, Frédéric

doi:10.1093/nar/gks268

Chromosomal context and epigenetic mechanisms control the efficacy of genome editing by rare-cutting designer endonucleases

Author:

Daboussi, Fayza

Zaslavskiy, Mikhail ; Poirot, Laurent ; Loperfido, Mariana ; Gouble, Agnès ; Guyot, Valerie ; Leduc, Sophie ; Galetto, Roman ; Grizot, Sylvestre ; Oficjalska, Danusia ; Perez, Christophe ; Delacôte, Fabien ; Dupuy, Aurélie ; Chion-Sotinel, Isabelle ; Le Clerre, Diane ; Lebuhotel, Céline ; Danos, Olivier ; Lemaire, Frédéric ; Oussedik, Kahina ; Cédrone, Frédéric ; Epinat, Jean-Charles ; Smith, Julianne ; Yáñez-Muñoz, Rafael J ; Dickson, George ; Popplewell, Linda ; Koo, Taeyoung ; Vandendriessche, Thierry ; Chuah, Marinee ; Duclert, Aymeric ; Duchateau, Philippe ; Pâques, Frédéric

Keywords:

Animals, CHO Cells, Cell Line, Chromosomal Position Effects, Cricetinae, Cricetulus, DNA Restriction Enzymes, Gene Targeting, Genetic Engineering, Genome, Human, Humans, Mutagenesis, Science & Technology, Life Sciences & Biomedicine, Biochemistry & Molecular Biology, ZINC-FINGER NUCLEASES, DOUBLE-STRAND BREAKS, HOMING ENDONUCLEASES, REPAIR PATHWAY, GENE, RECOMBINATION, CELLS, MEGANUCLEASES, PERSPECTIVES, 05 Environmental Sciences, 06 Biological Sciences, 08 Information and Computing Sciences, Developmental Biology, 31 Biological sciences, 34 Chemical sciences, 41 Environmental sciences

Abstract:

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.