title: Chromosomal context and epigenetic mechanisms control the efficacy of genome editing by rare-cutting designer endonucleases.
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.
authors.affiliation: CELLECTIS S.A., Paris, France.
authors.forename: Fayza
authors.initials: F
authors.lastname: Daboussi
authors.forename: Mikhail
authors.initials: M
authors.lastname: Zaslavskiy
authors.forename: Laurent
authors.initials: L
authors.lastname: Poirot
authors.forename: Mariana
authors.initials: M
authors.lastname: Loperfido
authors.forename: Agnès
authors.initials: A
authors.lastname: Gouble
authors.forename: Valerie
authors.initials: V
authors.lastname: Guyot
authors.forename: Sophie
authors.initials: S
authors.lastname: Leduc
authors.forename: Roman
authors.initials: R
authors.lastname: Galetto
authors.forename: Sylvestre
authors.initials: S
authors.lastname: Grizot
authors.forename: Danusia
authors.initials: D
authors.lastname: Oficjalska
authors.forename: Christophe
authors.initials: C
authors.lastname: Perez
authors.forename: Fabien
authors.initials: F
authors.lastname: Delacôte
authors.forename: Aurélie
authors.initials: A
authors.lastname: Dupuy
authors.forename: Isabelle
authors.initials: I
authors.lastname: Chion-Sotinel
authors.forename: Diane
authors.initials: D
authors.lastname: Le Clerre
authors.forename: Céline
authors.initials: C
authors.lastname: Lebuhotel
authors.forename: Olivier
authors.initials: O
authors.lastname: Danos
authors.forename: Frédéric
authors.initials: F
authors.lastname: Lemaire
authors.forename: Kahina
authors.initials: K
authors.lastname: Oussedik
authors.forename: Frédéric
authors.initials: F
authors.lastname: Cédrone
authors.forename: Jean-Charles
authors.initials: JC
authors.lastname: Epinat
authors.forename: Julianne
authors.initials: J
authors.lastname: Smith
authors.forename: Rafael J
authors.initials: RJ
authors.lastname: Yáñez-Muñoz
authors.forename: George
authors.initials: G
authors.lastname: Dickson
authors.forename: Linda
authors.initials: L
authors.lastname: Popplewell
authors.forename: Taeyoung
authors.initials: T
authors.lastname: Koo
authors.forename: Thierry
authors.initials: T
authors.lastname: VandenDriessche
authors.forename: Marinee K
authors.initials: MK
authors.lastname: Chuah
authors.forename: Aymeric
authors.initials: A
authors.lastname: Duclert
authors.forename: Philippe
authors.initials: P
authors.lastname: Duchateau
authors.forename: Frédéric
authors.initials: F
authors.lastname: Pâques
mesh_terms: D000818:Animals; D016466:CHO Cells; D002460:Cell Line; D055012:Chromosomal Position Effects; D006224:Cricetinae; D003412:Cricetulus; D004262:DNA Restriction Enzymes / Q000737:chemistry / Q000378:metabolism*; D018390:Gene Targeting; D005818:Genetic Engineering; D015894:Genome, Human; D006801:Humans; D016296:Mutagenesis
chemical_list: D004262:DNA Restriction Enzymes; C048901:endodeoxyribonuclease CreI