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

Journal

bioRxiv : the preprint server for biology
Titre abrégé: bioRxiv
Pays: United States
ID NLM: 101680187

Informations de publication

Date de publication:
12 Jul 2023
Historique:
pubmed: 28 7 2023
medline: 28 7 2023
entrez: 28 7 2023
Statut: epublish

Résumé

Despite tremendous progress in detecting DNA variants associated with human disease, interpreting their functional impact in a high-throughput and base-pair resolution manner remains challenging. Here, we develop a novel pooled prime editing screen method, PRIME, which 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

Identifiants

DOI: 10.1101/2023.07.12.548736 PMID: 37502948 PMC: PMC10370011
pubmed: 37502948
doi: 10.1101/2023.07.12.548736
pmc: PMC10370011
pii:
doi:

Types de publication

Preprint

Langues

eng

Subventions

Organisme : NIA NIH HHS
ID : R01 AG057497
Pays : United States
Organisme : NEI NIH HHS
ID : R01 EY027789
Pays : United States
Organisme : NIH HHS
ID : S10 OD028511
Pays : United States
Organisme : NHGRI NIH HHS
ID : UM1 HG009402
Pays : United States
Organisme : NHGRI NIH HHS
ID : U01 HG011720
Pays : United States
Organisme : NIDA NIH HHS
ID : U01 DA052713
Pays : United States

Déclaration de conflit d'intérêts

Competing interests statement X.R., H.Y., and Y.S. have filed a patent application related to pooled prime editing screens. Code availability statement A copy of the custom code used for data analysis and figure generation in this study is available upon request.

Auteurs

Xingjie Ren (X)

Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA.

Han Yang (H)

Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA.

Jovia L Nierenberg (JL)

Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA.

Yifan Sun (Y)

Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA.

Jiawen Chen (J)

Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.

Cooper Beaman (C)

Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA.

Thu Pham (T)

Pharmaceutical Sciences and Pharmacogenomics Graduate Program, University of California, San Francisco, San Francisco, CA, USA.

Mai Nobuhara (M)

Pharmaceutical Sciences and Pharmacogenomics Graduate Program, University of California, San Francisco, San Francisco, CA, USA.

Maya Asami Takagi (MA)

Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA.

Vivek Narayan (V)

Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA.

Yun Li (Y)

Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
Department of Genetics, University of North Carolina, Chapel Hill, NC, USA.
Department of Computer Science, University of North Carolina, Chapel Hill, NC, USA.

Elad Ziv (E)

Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA.
Division of General Internal Medicine, Department of Medicine, and Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA.

Yin Shen (Y)

Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA.
Department of Neurology, University of California, San Francisco, San Francisco, CA, USA.
Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA.

Classifications MeSH