The chromatin context differently impacts prime editors and base editors and controls the fidelity and purity of base editing

Base editors and prime editors allow changing specific eukaryotic DNA sequences without chromosomal breakage. However, the role of the chromatin environment and its underlying factors on the efficiency versus product fidelity and purity of prime editing and base editing is unknown. Here, using cellular systems that permit assessing the efficiency and fidelity of gene editing tools at isogenic target sites controlled by specific epigenetic factors, we report that heterochromatin mostly hinders prime editors over base editors with the extended portions of prime editing guide RNAs contributing to this outcome. Indeed, base editing performance at heterochromatin ranges in a target site-dependent manner from lower to, often, significantly higher than that observed at euchromatin. Additionally, the extent and types of byproducts accumulated after base editing is also contingent upon the epigenetic context of target sequences.