Curated loci prime editing (cliPE) for accessible multiplexed assays of variant effect (MAVEs)

TL;DR

The paper introduces cliPE, a low-cost, accessible pipeline for multiplexed variant effect assays using prime editing, along with a user-friendly design tool, to enhance the adoption of MAVEs in genomic research.

Contribution

It presents a novel, standardized protocol and a design app for efficient, multiplexed prime editing-based MAVEs, improving accessibility and reproducibility.

Findings

Developed a low-cost, standardized prime editing pipeline (cliPE)

Created a user-friendly pegRNA design app (pegRNA Designer)

Demonstrated effective multiplexed variant editing in target genes

Abstract

Multiplexed assays of variant effect (MAVEs) perform simultaneous characterization of many variants. Prime editing has been recently adopted for introducing many variants in their native genomic contexts. However, robust protocols and standards are limited, preventing widespread uptake. Herein, we describe curated loci prime editing (cliPE) which is an accessible, low-cost experimental pipeline to perform MAVEs using prime editing of a target gene, as well as a companion Shiny app (pegRNA Designer) to rapidly and easily design user-specific MAVE libraries.