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Identify Key Sequence Features to Improve CRISPR sgRNA Efficacy

文献类型：期刊论文

作者Chen, Lei1; Wang, Shaopeng3; Li, Jiarui3; Cai, Yu-Dong3; Zhang, Yu-Hang2; Xing, Zhi-Hao2; Huang, Tao2; Yang, Jialiang4; ,
刊名IEEE ACCESS
出版日期2017
卷号5期号:-页码:26582-26590
关键词CRISPR/Cas9 system sgRNAs maximal-relevance-minimal-redundancy incremental feature selection protein disorder
ISSN号2169-3536
DOI10.1109/ACCESS.2017.2775703
文献子类Article
英文摘要The CRISPR/Cas9 system is a creative and innovative gene editing biotechnology tool in genetic engineering. Although several achievements have been attained using the CRISPR/Cas9 system, it is still a challenge to avoid off-target effects and improve the editing efficacy. Previous efforts on evaluating the efficacy and designing the guide RNA mainly focused on DNA properties. However, some DNA features have not been characterized but can be reflected by protein properties, such as the disorder features and the sequence conservation. In this paper, we provided a computational framework to identify important features related to the efficacy of CRISPR/Cas9 focusing on the properties of the proteins encoded by the target DNA fragments. The feature selection method, maximal-relevance-minimal-redundancy, was adopted to analyze these features. And incremental feature selection together with support vector machine, were employed to extract optimal features, on which an optimal classifier can be constructed. As a result, 152 important features were extracted, with which an optimal classifier based on support vector machine was built. This classifier obtained the highest MCC value of 0.355. Finally, a series of detailed biological analyses were performed on the optimal features. From the results, we found that some key factors may differentially affect the binding activity of sgRNAs to their targets. Among them, the disorder status of the target protein sequences was found to be a major factor that is related to the efficacy of sgRNAs, suggesting the DNA features associated with the protein disorder status could also affect the CRISPR/Cas9 efficacy.
学科主题Computer Science ; Engineering ; Telecommunications
WOS关键词FEATURE-SELECTION ; MOLECULAR FRAGMENTS ; GENE ONTOLOGY ; OFF-TARGET ; SYSTEM ; PREDICTION ; TOOL ; CLASSIFICATION ; IDENTIFICATION ; ENDONUCLEASE
语种英语
WOS记录号WOS:000418881100043
出版者IEEE-INST ELECTRICAL ELECTRONICS ENGINEERS INC
版本出版稿
源URL[http://202.127.25.144/handle/331004/1166]  
专题中国科学院上海生命科学研究院营养科学研究所
作者单位1.Shanghai Maritime Univ, Coll Informat Engn, Shanghai 201306, Peoples R China;
2.Chinese Acad Sci, Shanghai Inst Biol Sci, Inst Hlth Sci, Shanghai 200031, Peoples R China;
3.Shanghai Univ, Sch Life Sci, Shanghai 200444, Peoples R China;
4.Icahn Sch Med Mt Sinai, Dept Genet & Genom Sci, New York, NY 10029 USA,
推荐引用方式
GB/T 7714		 Chen, Lei,Wang, Shaopeng,Li, Jiarui,et al. Identify Key Sequence Features to Improve CRISPR sgRNA Efficacy[J]. IEEE ACCESS,2017,5(-):26582-26590.
APA Chen, Lei.,Wang, Shaopeng.,Li, Jiarui.,Cai, Yu-Dong.,Zhang, Yu-Hang.,...&,.(2017).Identify Key Sequence Features to Improve CRISPR sgRNA Efficacy.IEEE ACCESS,5(-),26582-26590.
MLA Chen, Lei,et al."Identify Key Sequence Features to Improve CRISPR sgRNA Efficacy".IEEE ACCESS 5.-(2017):26582-26590.

入库方式： OAI收割

来源：上海营养与健康研究所

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