Off-target genomic loci with partial sequence complementarity to the FXN guide RNA (FXN gRNA off-targets)

Off-target genomic loci with partial sequence complementarity to the FXN guide RNA represent unintended DNA sequences that may be recognized and modified by CRISPR-based gene editing tools designed to treat Friedreich's Ataxia (FA). In FA, the FXN gene contains expanded GAA repeats that suppress frataxin protein production, and therapeutic strategies often involve using guide RNAs (gRNAs) to direct Cas9 or other nucleases to excise these repeats or modulate the locus (Li et al., 2019, Nature Communications). However, because CRISPR systems can tolerate several mismatches between the gRNA and the genomic DNA, the nuclease may bind to and cleave "off-target" sites elsewhere in the genome that resemble the target FXN sequence (Fu et al., 2013, Nature Biotechnology). These off-target effects pose significant safety risks, including the potential for genotoxicity, chromosomal translocations, or the disruption of essential genes (Hsu et al., 2013, Nature Biotechnology). Rigorous assessment of these loci using high-throughput sequencing methods like GUIDE-seq or CIRCLE-seq is critical for the clinical development of FXN-targeted therapies to ensure high specificity and minimize the risk of secondary malignancies or other adverse cellular outcomes (Tsai et al., 2015, Nature Biotechnology).

Other names

CRISPR off-target sitesNon-specific genomic binding sitesUnintended FXN-related cleavage sitesFXN guide RNA off-target effects

Unintended binding and cleavage of DNA sequences that share partial homology with the FXN-specific guide RNA, leading to double-strand breaks or base modifications at non-target sites.