Systematic dissection of Cas12a-mediated precision genome editing defines design principles for genome-scale variant engineering

Abstract

Cas9 precision editing is increasingly predictable because guide, donor and target-context effects have been systematically characterized. Extending this framework to other nucleases is essential for installing variants outside convenient Cas9 target space. Cas12a provides a T-rich protospacer-adjacent motif (PAM) alternative, but determinants of efficient donor-templated Cas12a editing remain poorly defined. Here, we systematically dissected Cas12a precision editing in Saccharomyces cerevisiae across nuclease, direct repeat, expression, crRNA, donor, genomic context and time-course variables. Reporter and amplicon-sequencing assays showed that cleavage activity alone did not predict precise editing. Highly active configurations often reduced viability or lost edited alleles over time, whereas attenuated configurations better preserved programmed edits. Enhanced AsCas12a edited rapidly and tolerated shorter crRNAs, resulting in a narrower editing window, while an attenuated FnCas12a configuration edited more slowly but maintained higher viability and better distal-edit recovery. Alternative repair outcomes were rare, target-dependent, and further suppressed by LexA-FHA donor recruitment. To define design parameters at scale, we established a pooled Cas12a platform with 530 barcoded edit cassettes and recovered programmed edits for 70.2% of designs. Successful editing was reduced with TTTG PAMs, a C upstream of the PAM and at distal edit positions. Excluding these features increased the edited fraction to 85.4% and adding high predicted cleavage scores further elevated it to 91.4%. Applied retrospectively, these criteria also identified poorly edited loci in the targeted panels. Together, these data define design principles for Cas12a-mediated precision editing and establish a scalable platform for genome-scale pooled variant engineering and phenotyping in yeast.