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Target Specificity of the CRISPR-Cas9 System in Arabidopsis thaliana, Oryza sativa, and Glycine max Genomes

文献类型： 外文期刊

作者： Zou, Pan 1 ; Duan, Lijin 1 ; Zhang, Shasha 1 ; Bai, Xue 1 ; Liu, Zhenghui 1 ; Jin, Fengmei 3 ; Sun, Haibo 3 ; Xu, Wentao; 1 ;

作者机构： 1.Tianjin Acad Agr Sci, Tianjin Inst Agr Qual Stand & Testing Technol, Tianjin 300381, Peoples R China

2.Hebei Univ Engn, Coll Life Sci & Food Engn, Handan, Peoples R China

3.Tianjin Acad Agr Sci, Tianjin Res Ctr Agr Biotechnol, Tianjin, Peoples R China

4.China Agr Univ, Key Lab Assessment Genetically Modified Organism, Minist Agr & Rural Affairs, Beijing, Peoples R China

关键词： Arabidopsis thaliana; CRISPR-Cas9; Glycine max; off-target effect; Oryza sativa; specificity

期刊名称：JOURNAL OF COMPUTATIONAL BIOLOGY （ 影响因子：1.479； 五年影响因子：1.377 ）

ISSN： 1066-5277

年卷期：

页码：

收录情况： SCI

摘要： Clustered regularly interspaced short palindromic repeats (CRISPR), a class of immune-associated sequences in bacteria, have been developed as a powerful tool for editing eukaryotic genomes in diverse cells and organisms in recent years. The CRISPR-Cas9 system can recognize upstream 20 nucleotides (guide sequence) adjacent to the protospacer-adjacent motif site and trigger double-stranded DNA cleavage as well as DNA repair mechanisms, which eventually result in knockout, knockin, or site-specific mutagenesis. However, off-target effect caused by guide sequence misrecognition is the major drawback and restricts its widespread application. In this study, global analysis of specificities of all guide sequences in Arabidopsis thaliana, Oryza sativa (rice), and Glycine max (soybean) were performed. As a result, a simple pipeline and three genome-wide databases were established and shared for the scientific society. For each target site of CRISPR-Cas9, specificity score and off-target number were calculated and evaluated. The mean values of off-target numbers for A. thaliana, rice, and soybean were determined as 27.5, 57.3, and 174.7, respectively. Comparative analysis among these plants suggested that the frequency of off-target effects was correlated to genome size, chromosomal locus, gene density, and guanine-cytosine (GC) content. Our results contributed to the better understanding of CRISPR-Cas9 system in plants and would help to minimize the off-target effect during its applications in the future.

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