CRISPR-CBEI: a Designing and Analyzing Tool Kit for Cytosine Base Editor-Mediated Gene Inactivation

doi:10.1128/mSystems.00350-20

	CRISPR-CBEI: a Designing and Analyzing Tool Kit for Cytosine Base Editor-Mediated Gene Inactivation
	Yu, Haopeng 1,2,3; Wu, Zhaowei4 ; Chen, Xiangdan 1,2,3; Ji, Quanjiang4 ; Tao, Shiheng 1,2,3
	2020-09
发表期刊	MSYSTEMS
ISSN	2379-5077
卷号	5 期号:5
发表状态	已发表
DOI	10.1128/mSystems.00350-20
摘要	Base editing is a promising technique, allowing precise single-base mutagenesis in genomes without double-strand DNA breaks or donor templates. Cytosine base editors (CBEs) convert cytosine to thymidine. In particular, CBEs can transform four codons, CAA, CAG, CGA, and TGG, into stop codons, providing a new means to rapidly inactivate a gene of interest and enabling loss-of-function study in recombination-deficient species and the construction of gene-inactivation libraries. However, designing single guide RNAs (sgRNAs) for gene inactivation is more complicated and more restricted in applicability than using the lustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated (CRISPR/Cas9) system only, especially for researchers who do not specialize in the bioinformatics skills needed to design and evaluate sgRNAs. Here, we present a new user-friendly designing tool kit, namely, CRISPR-CBEI (cytosine base editor-mediated gene inactivation), including a Web tool and a command-line tool. The Web tool is dedicated to the design of sgRNAs for CBE-mediated gene inactivation and integrates various functions, including open reading frame (ORF) identification, CBE customization, sgRNA designing, summarizing, and front-end off-target searching against user-defined unlimited-file-size local genome files without the necessity of uploading to the server. The command-line version serves the same purpose but for a larger number of coding DNA sequences (CDSs), for instance, for designing a CBE-inactivation library in a target species which provides comprehensive evaluations of CBEs and target genomes. We envision that this tool would contribute to CBE-inactivation design.
关键词	base editing cytosine base editor CRISPR gene inactivation
URL	查看原文
收录类别	SCI ; SCIE
语种	英语
资助项目	National Natural Science Foundation of China[31771474][21922705][91753127][31700123] ; Shanghai Committee of Science and Technology, China[19QA1406000][17ZR1449200] ; China Postdoctoral Science Foundation[2019M651627]
WOS研究方向	Microbiology
WOS类目	Microbiology
WOS记录号	WOS:000579368300022
出版者	AMER SOC MICROBIOLOGY
引用统计
文献类型	期刊论文
条目标识符	https://kms.shanghaitech.edu.cn/handle/2MSLDSTB/123941
专题	物质科学与技术学院_PI研究组_季泉江组
通讯作者	Ji, Quanjiang; Tao, Shiheng
作者单位	1.Northwest A&F Univ, Coll Life Sci, Yangling, Shaanxi, Peoples R China 2.Northwest A&F Univ, State Key Lab Crop Stress Biol Arid Areas, Yangling, Shaanxi, Peoples R China 3.Northwest A&F Univ, Bioinformat Ctr, Yangling, Shaanxi, Peoples R China 4.ShanghaiTech Univ, Sch Phys Sci & Technol, Shanghai, Peoples R China
通讯作者单位	物质科学与技术学院
推荐引用方式 GB/T 7714	Yu, Haopeng,Wu, Zhaowei,Chen, Xiangdan,et al. CRISPR-CBEI: a Designing and Analyzing Tool Kit for Cytosine Base Editor-Mediated Gene Inactivation[J]. MSYSTEMS,2020,5(5).
APA	Yu, Haopeng,Wu, Zhaowei,Chen, Xiangdan,Ji, Quanjiang,&Tao, Shiheng.(2020).CRISPR-CBEI: a Designing and Analyzing Tool Kit for Cytosine Base Editor-Mediated Gene Inactivation.MSYSTEMS,5(5).
MLA	Yu, Haopeng,et al."CRISPR-CBEI: a Designing and Analyzing Tool Kit for Cytosine Base Editor-Mediated Gene Inactivation".MSYSTEMS 5.5(2020).