Genome-wide mapping of Cas9-induced sister chromatid exchange across single and over 200 genomic sites in human cells.

Cas9-induced DNA double-strand breaks strongly enrich sister chromatid exchange at the break site, reaching up to 41% in the same cell cycle in human cells.

• Why it matters: Understanding how CRISPR/Cas9 editing provokes sister chromatid exchange is crucial because these exchanges can lead to structural chromosome alterations that are invisible to standard sequencing, impacting genome editing safety and fidelity.
• What they did: Using sci-L3-Strand-seq, a single-cell template-strand sequencing method, the study mapped SCE across targeted loci, including 237 Alu sites and specific breakpoints, in human cells.
• The result: Findings show Cas9-induced DSBs are potent local triggers of SCE, with structural alterations observed at SCE junctions, and disruption of key repair proteins did not significantly change SCE frequency, indicating complex repair dynamics.