Off-target genomic cytosines

Off-target genomic cytosines refer to unintended sites within the genome where cytosine-to-thymine (C-to-T) transitions occur during the use of base editing technologies, such as Cytosine Base Editors (CBEs) (Zuo et al., 2019, Science). These editors typically utilize a CRISPR-Cas9 nickase fused to a deaminase enzyme, such as APOBEC1, to convert cytosine to uracil, which is subsequently replaced by thymine during DNA replication or repair (Rees & Liu, 2018, Nature Reviews Genetics). While designed to target specific sequences, these enzymes can exhibit stochastic or sequence-dependent activity at non-target locations, leading to widespread genomic mutations (Jin et al., 2019, Science). Such off-target effects pose significant safety risks in gene therapy, including the potential for oncogenic transformation or the disruption of essential genes. Minimizing these unintended modifications is a primary focus in the development of next-generation base editors with higher precision and reduced DNA affinity. The detection of these off-targets often requires advanced whole-genome sequencing techniques to ensure the safety and specificity of the therapeutic intervention.

Other names

Off-target DNA deaminationUnintended cytosine deaminationOff-target base editingStochastic off-target editingGenome-wide off-target mutations

Unintended enzymatic deamination of cytosine to uracil at non-target genomic loci by base editing complexes, leading to permanent C-to-T or G-to-A transitions.