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Updated: Oct 16, 2025

Generation of Genomic Deletions in Mammalian Cell Lines via CRISPR/Cas9

Generation of Genomic Deletions in Mammalian Cell Lines via CRISPR/Cas9

Published on: January 3, 2015

Precise genomic deletions using paired prime editing.

Junhong Choi^1,2, Wei Chen^3,4, Chase C Suiter^3,5

¹Department of Genome Sciences, University of Washington, Seattle, WA, USA. junhongc@uw.edu.

Nature Biotechnology

|October 15, 2021

Summary

This summary is machine-generated.

A new prime editing-based method, PRIME-Del, offers precise genomic deletions up to 10kb, overcoming limitations of CRISPR-Cas9. This advance enables flexible gene editing for various applications.

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Area of Science:

Molecular Biology
Genomics
Gene Editing Technologies

Background:

Current clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9 methods for genomic deletion are often inefficient and imprecise.
Existing methods can result in unintended indels, large deletions, and complex genomic rearrangements.

Purpose of the Study:

To introduce PRIME-Del, a novel prime editing-based system for precise genomic deletions.
To evaluate the efficiency and precision of PRIME-Del compared to CRISPR-Cas9.

Main Methods:

Utilizing a pair of prime editing sgRNAs (pegRNAs) targeting opposite DNA strands to program specific genomic deletions.
Programming both nicking sites and repair outcomes for controlled deletion induction.
Assessing deletion efficiency and precision for deletions up to 10kb.

Main Results:

PRIME-Del demonstrates significantly higher precision in programming deletions compared to CRISPR-Cas9 and sgRNA pairs.
Achieved editing efficiency for PRIME-Del ranges from 1-30%.
PRIME-Del allows coupling genomic deletions with short insertions and deletions at non-protospacer-adjacent motif sites.

Conclusions:

PRIME-Del offers a precise and flexible alternative for programming genomic deletions.
The method can be enhanced by extended expression of prime editing components without compromising precision.
PRIME-Del holds potential for applications including epitope tagging and programming genomic rearrangements.