High-throughput PRIME-editing screens identify functional DNA variants in the human genome

Mol Cell. 2023 Dec 21;83(24):4633-4645.e9. doi: 10.1016/j.molcel.2023.11.021.


Despite tremendous progress in detecting DNA variants associated with human disease, interpreting their functional impact in a high-throughput and single-base resolution manner remains challenging. Here, we develop a pooled prime-editing screen method, PRIME, that can be applied to characterize thousands of coding and non-coding variants in a single experiment with high reproducibility. To showcase its applications, we first identified essential nucleotides for a 716 bp MYC enhancer via PRIME-mediated single-base resolution analysis. Next, we applied PRIME to functionally characterize 1,304 genome-wide association study (GWAS)-identified non-coding variants associated with breast cancer and 3,699 variants from ClinVar. We discovered that 103 non-coding variants and 156 variants of uncertain significance are functional via affecting cell fitness. Collectively, we demonstrate that PRIME is capable of characterizing genetic variants at single-base resolution and scale, advancing accurate genome annotation for disease risk prediction, diagnosis, and therapeutic target identification.

Keywords: disease variants; enhancer; high-throughput screens; prime editing; single-base resolution.

MeSH terms

  • CRISPR-Cas Systems
  • DNA
  • Gene Editing / methods
  • Genome, Human* / genetics
  • Genome-Wide Association Study*
  • Humans
  • Regulatory Sequences, Nucleic Acid
  • Reproducibility of Results


  • DNA