Scalable variant-to-function screens using prime editing perturb-seq

Prime editing perturb-seq (PEP-seq) uses 2,164 guides to generate 749,110 time-resolved single-cell transcriptomes, enabling precise endogenous mapping of variant effects.

• Why it matters: Linking genetic variants to functional consequences at scale is difficult because perturb-seq variant installation is limited and prime editing has mostly supported simpler readouts.
• What they did: The authors designed 2,164 prime editing guides targeting common eQTLs, premature termination codons, and position-matched synonymous controls, producing 749,110 time-resolved single-cell transcriptomes.
• The result: PEP-seq precisely detected nonsense-mediated decay, and for eQTLs a locus-size-corrected specificity metric showed the intended target was frequently the most affected transcript within a 1 Mb window, with effects linked to open chromatin near the edit site.