Genomic DNA cytosines at off-target or bystander sites

Genomic DNA cytosines at off-target or bystander sites refer to unintended locations within the genome that undergo chemical modification by base editing technologies. Bystander editing occurs when multiple cytosine residues are present within the activity window of a base editor, leading to unintended deamination near the desired target nucleotide (Komor et al., 2016). Off-target editing involves modifications at genomic sites that either resemble the target sequence or are processed by the deaminase in a guide RNA-independent manner (Zuo et al., 2019). These unintended modifications are a significant concern in therapeutic development because they can lead to permanent mutations in the host genome. Such mutations may result in the loss of function of essential genes or the activation of proto-oncogenes, posing a risk of genotoxicity or malignancy (Rees & Liu, 2018). Consequently, these sites are not therapeutic targets but rather safety liabilities that researchers aim to minimize through the engineering of high-fidelity enzymes and optimized delivery methods. Monitoring these sites is critical for the safety assessment and regulatory approval of CRISPR-based base editing platforms (Kim et al., 2019).

Other names

Off-target cytosinesBystander cytosinesUnintended deamination sitesNon-target genomic cytosines

Unintended enzymatic deamination of cytosine to uracil by base editing complexes, leading to C-to-T transitions during DNA replication or repair (Komor et al., 2016).