PrEditR: A protein-centric platform for CRISPR-mediated base editor sgRNA design

Abstract

Motivation: Post-translational modifications (PTMs) are critical to protein activity, yet the biological role of most known modification sites remains uncharacterized. CRISPR-mediated phenotypic screens using base editors offer a powerful approach to dissecting PTM function at scale. However, existing sgRNA design tools for base editing applications are DNA-centric and lack the throughput required to integrate seamlessly with mass-spectrometry-based proteomics experimental outputs. Results: We introduce protein editing in R, PrEditR, an open-source, protein-centric tool for high throughput sgRNA design for custom base editor screens. PrEditR enables users to designate specific amino acid residues in proteins and design protospacer sequences that target the corresponding gene and annotate every resulting amino acid change (missense, nonsense, or silent), including bystander edits. Availability and Implementation: PrEditR is available on GitHub and Docker Hub.