High-throughput PRIME-editing screens identify functional DNA variants in the human genome
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Abstract
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.
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- Authors
- Ren, X., Yang, H., Nierenberg, J. L., Sun, Y., Chen, J., Beaman, C., Pham, T., Nobuhara, M., Takagi, M. A., Narayan, V., Li, Y., Ziv, E., & Shen, Y.
- Affiliations
- University of California, San Francisco (US)
- University of North Carolina at Chapel Hill (US)
- Corresponding author
- Shen, Yin
- ORCID
- Venue
- Molecular Cell
- Publisher
- Elsevier BV
- Published
- 2023-12
- Volume
- 83
- Issue
- 24
- Pages
- 4633-4645.e9
- ISSN
- 1097-2765 (ISSN-L)
- PMC
- PMC10766087
- OpenAlex
- W4390063959
- Cited by
- 70
- References
- 14
- Citations by year
- 2026: 15 · 2025: 29 · 2024: 21 · 2023: 5
- FWCI
- 6.24
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Molecular Cell (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion, other-oa)
- eScholarship (California Digital Library) (submittedVersion, cc-by)
- PubMed Central (submittedVersion, cc-by-nc-nd)
- Funders
- National Institutes of Health (1s10od028511-01)
- University of California, San Francisco
- National Institute on Aging (R01AG057497)
- National Institute on Drug Abuse (U01DA052713)
- National Human Genome Research Institute (UM1HG009402, U01HG011720)
- National Eye Institute (R01EY027789)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › CRISPR and Genetic Engineering
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA regulation and disease
- Keywords
- prime editing, non-coding variants, variants of uncertain significance, breast cancer, ClinVar variants, cell fitness, single-base resolution, genome annotation, disease risk prediction
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