BEtarget: A versatile web-based tool to design guide RNAs for base editing in plants

Xianrong Xie; Fuquan Li; Xiyu Tan; Dongchang Zeng; Weizhi Liu; Wanyong Zeng; Qinlong Zhu; Yao-Guang Liu

doi:10.1016/j.csbj.2022.07.046

BEtarget: A versatile web-based tool to design guide RNAs for base editing in plants

Comput Struct Biotechnol J. 2022 Jul 29:20:4009-4014. doi: 10.1016/j.csbj.2022.07.046. eCollection 2022.

Authors

Xianrong Xie^{1

2}, Fuquan Li¹, Xiyu Tan¹, Dongchang Zeng¹, Weizhi Liu¹, Wanyong Zeng¹, Qinlong Zhu^{1

2}, Yao-Guang Liu^{1

2}

Affiliations

¹ State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China.
² Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China.

Abstract

CRISPR-dependent base editors enable direct nucleotide conversion without the introduction of double-strand DNA break or donor DNA template, thus expanding the CRISPR toolbox for genetic manipulation. However, designing guide RNAs (gRNAs) for base editors to enable gene correction or inactivation is more complicated than using the CRISPR system for gene disruption. Here, we present a user-friendly web tool named BEtarget dedicated to the design of gRNA for base editing. It is currently supported by 46 plant reference genomes and 5 genomes of non-plant model organisms. BEtarget supports the design of gRNAs with different types of protospacer adjacent motifs (PAM) and integrates various functions, including automatic identification of open reading frame, prediction of potential off-target sites, annotation of codon change, and assessment of gRNA quality. Moreover, the program provides an interactive interface for users to selectively display information about the desired target sites. In brief, we have developed a flexible and versatile web-based tool to simplify complications associated with the design of base editing technology. BEtarget is freely accessible at https://skl.scau.edu.cn/betarget/.

Keywords: ABE, adenine base editor; Base editing; CBE, cytosine base editor; CDS, coding sequence; CRISPR; CRISPR, clustered regularly interspaced short palindromic repeats; DSB, double-strand break; Genome editing; NHEJ, non-homologous end joining; ORF, open reading frame; PAM, protospacer adjacent motif; gRNA design; gRNA, guide RNA.