首页|Systematic Exploration of Optimized Base Editing gRNA Design and Pleiotropic Effects with BExplorer

Systematic Exploration of Optimized Base Editing gRNA Design and Pleiotropic Effects with BExplorer

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Base editing technology is being increasingly applied in genome engineering,but the cur-rent strategy for designing guide RNA(gRNA)relies substantially on empirical experience rather than a dependable and efficient in silico design.Furthermore,the pleiotropic effect of base editing on disease treatment remains unexplored,which prevents its further clinical usage.Here,we pre-sented BExplorer,an integrated and comprehensive computational pipeline to optimize the design of gRNAs for 26 existing types of base editors in silico.Using BExplorer,we described its results for two types of mainstream base editors,BE3 and ABE7.10,and evaluated the pleiotropic effects of the corresponding base editing loci.BExplorer revealed 524 and 900 editable pathogenic single nucleotide polymorphism(SNP)loci in the human genome together with the selected optimized gRNAs for BE3 and ABE7.10,respectively.In addition,the impact of 707 edited pathogenic SNP loci following base editing on 131 diseases was systematically explored by revealing their pleio-tropic effects,indicating that base editing should be carefully utilized given the potential pleiotropic effects.Collectively,the systematic exploration of optimized base editing gRNA design and the cor-responding pleiotropic effects with BExplorer provides a computational basis for applying base editing in disease treatment.

Gene editingBase editingPleiotropyCRISPR/Cas9gRNA design

Gongchen Zhang、Chenyu Zhu、Xiaohan Chen、Jifang Yan、Dongyu Xue、Zixuan Wei、Guohui Chuai、Qi Liu

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Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine,Shanghai East Hospital,Bioinformatics Department,School of Life Sciences and Technology,Tongji University,Shanghai 200092,China

National Key Research and Development Program of ChinaNational Natural Science Foundation of ChinaNational Natural Science Foundation of ChinaShanghai Natural Science Foundation ProgramShanghai Artificial Intelligence Technology Standard ProjectShanghai Shuguang scholars projectWeBank scholars projectFundamental Research Funds for the Central Universities

2021YFF1201200319706386157236117ZR144940019DZ2200900

2023

10.1016/j.gpb.2022.06.005

基因组蛋白质组与生物信息学报(英文版)
中国科学院北京基因组研究所

基因组蛋白质组与生物信息学报(英文版)

CSTPCDCSCD
影响因子：0.495
ISSN：1672-0229
年,卷(期)：2023.6(6)
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