SWISS: multiplexed orthogonal genome editing in plants with a Cas9 nickase and engineered CRISPR RNA scaffolds

Chao Li; Yuan Zong; Shuai Jin; Haocheng Zhu; Dexing Lin; Shengnan Li; Jin-Long Qiu; Yanpeng Wang; Caixia Gao

doi:10.1186/s13059-020-02051-x

SWISS: multiplexed orthogonal genome editing in plants with a Cas9 nickase and engineered CRISPR RNA scaffolds

Genome Biol. 2020 Jun 16;21(1):141. doi: 10.1186/s13059-020-02051-x.

Authors

Chao Li^{1

2}, Yuan Zong¹, Shuai Jin^{1

2}, Haocheng Zhu^{1

2}, Dexing Lin^{1

2}, Shengnan Li³, Jin-Long Qiu^{2

3}, Yanpeng Wang^{4

5}, Caixia Gao^{6

7}

Affiliations

¹ State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Genome Editing, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China.
² College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China.
³ State Key Laboratory of Plant Genomics, Institute of Microbiology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China.
⁴ State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Genome Editing, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China. yanpengwang@genetics.ac.cn.
⁵ College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China. yanpengwang@genetics.ac.cn.
⁶ State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Genome Editing, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China. cxgao@genetics.ac.cn.
⁷ College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China. cxgao@genetics.ac.cn.

Abstract

We describe here a CRISPR simultaneous and wide-editing induced by a single system (SWISS), in which RNA aptamers engineered in crRNA scaffold recruit their cognate binding proteins fused with cytidine deaminase and adenosine deaminase to Cas9 nickase target sites to generate multiplexed base editing. By using paired sgRNAs, SWISS can produce insertions/deletions in addition to base editing. Rice mutants are generated using the SWISS system with efficiencies of cytosine conversion of 25.5%, adenine conversion of 16.4%, indels of 52.7%, and simultaneous triple mutations of 7.3%. The SWISS system provides a powerful tool for multi-functional genome editing in plants.

Keywords: ABE; CBE; Cas9 nickase; Indels; Multiplexed orthogonal genome editing; RNA scaffolds.

Publication types

Evaluation Study
Research Support, Non-U.S. Gov't

MeSH terms

CRISPR-Cas Systems*
Gene Editing / methods*
Genome, Plant*
Oryza