PrEditR: A protein-centric platform for CRISPR-mediated base editor sgRNA design
- 1La Jolla Institute for Immunology
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.
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BibTeX
@misc{castro2026preditr,
title = {{PrEditR: A protein-centric platform for CRISPR-mediated base editor sgRNA design}},
author = {F. Vasquez Castro and L. D. Sanchez Solis and S. A. Myers},
howpublished = {bioRxiv},
year = {2026},
month = may,
doi = {10.64898/2026.05.15.725600},
url = {https://www.biorxiv.org/content/10.64898/2026.05.15.725600v3},
note = {CC BY},
}
RIS
TY - UNPB
TI - PrEditR: A protein-centric platform for CRISPR-mediated base editor sgRNA design
AU - F. Vasquez Castro
AU - L. D. Sanchez Solis
AU - S. A. Myers
PY - 2026
DA - 2026/05/15
PB - bioRxiv
DO - 10.64898/2026.05.15.725600
UR - https://www.biorxiv.org/content/10.64898/2026.05.15.725600v3
AB - 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.
ER -