Enhanced prime editing systems by manipulating cellular determinants of editing outcomes. Author Peter Chen, Jeffrey Hussmann, Jun Yan, Friederike Knipping, Purnima Ravisankar, Pin-Fang Chen, Cidi Chen, James Nelson, Gregory Newby, Mustafa Sahin, Mark Osborn, Jonathan Weissman, Britt Adamson, David Liu Publication Year 2021 Type Journal Article Abstract While prime editing enables precise sequence changes in DNA, cellular determinants of prime editing remain poorly understood. Using pooled CRISPRi screens, we discovered that DNA mismatch repair (MMR) impedes prime editing and promotes undesired indel byproducts. We developed PE4 and PE5 prime editing systems in which transient expression of an engineered MMR-inhibiting protein enhances the efficiency of substitution, small insertion, and small deletion prime edits by an average 7.7-fold and 2.0-fold compared to PE2 and PE3 systems, respectively, while improving edit/indel ratios by 3.4-fold in MMR-proficient cell types. Strategic installation of silent mutations near the intended edit can enhance prime editing outcomes by evading MMR. Prime editor protein optimization resulted in a PEmax architecture that enhances editing efficacy by 2.8-fold on average in HeLa cells. These findings enrich our understanding of prime editing and establish prime editing systems that show substantial improvement across 191 edits in seven mammalian cell types. Keywords Humans, Models, Biological, Cell Line, Mutation, DNA, RNA, Female, Male, Reproducibility of Results, Genome, Human, CRISPR-Cas Systems, Gene Editing, DNA Mismatch Repair, Genes, Dominant, MutL Protein Homolog 1 Journal Cell Volume 184 Issue 22 Pages 5635-5652.e29 Date Published 2021 Oct 28 ISSN Number 1097-4172 DOI 10.1016/j.cell.2021.09.018 Alternate Journal Cell PMCID PMC8584034 PMID 34653350 PubMedPubMed CentralGoogle ScholarBibTeXEndNote X3 XML