Programmable RNA editing with compact CRISPR-Cas13 systems from uncultivated microbes

doi:10.1038/s41592-021-01124-4

	Programmable RNA editing with compact CRISPR-Cas13 systems from uncultivated microbes
	Xu, Chunlong 1; Zhou, Yingsi 1; Xiao, Qingquan 1,2; He, Bingbing 1,2; Geng, Guannan 1; Wang, Zikang 1; Cao, Birong 2,3; Dong, Xue 1; Bai, Weiya 4; Wang, Yifan 1
刊名	NATURE METHODS
	2021-05-03
页码	29
ISSN号	1548-7091
DOI	10.1038/s41592-021-01124-4
通讯作者	Zhou, Yingsi(yszhou@ion.ac.cn) ; Lai, Jinsheng(jlai@cau.edu.cn) ; Yang, Hui(huiyang@ion.ac.cn)
英文摘要	Competitive coevolution between microbes and viruses has led to the diversification of CRISPR-Cas defense systems against infectious agents. By analyzing metagenomic terabase datasets, we identified two compact families (775 to 803 amino acids (aa)) of CRISPR-Cas ribonucleases from hypersaline samples, named Cas13X and Cas13Y. We engineered Cas13X.1 (775 aa) for RNA interference experiments in mammalian cell lines. We found Cas13X.1 could tolerate single-nucleotide mismatches in RNA recognition, facilitating prophylactic RNA virus inhibition. Moreover, a minimal RNA base editor, composed of engineered deaminase (385 aa) and truncated Cas13X.1 (445 aa), exhibited robust editing efficiency and high specificity to induce RNA base conversions. Our results suggest that there exist untapped bacterial defense systems in natural microbes that can function efficiently in mammalian cells, and thus potentially are useful for RNA-editing-based research. This work describes the identification of Cas13 proteins from two families by mining public metagenomic data. The newly identified Cas13X.1 shows efficient target knockdown and can be used to degrade SARS-CoV-2 and H1N1 genomes. In addition, the truncated Cas13X.1 offers an advantage in generating mini-RNA base editors.
资助项目	Chinese Academy of Sciences[ZDBS-LY-SM001] ; R&D Program of China[2017YFC1001300] ; R&D Program of China[2018YFC2000100] ; CAS Strategic Priority Research Program[XDB32060000] ; National Natural Science Foundation of China[31871502] ; National Natural Science Foundation of China[31925016] ; National Natural Science Foundation of China[91957122] ; National Natural Science Foundation of China[31901047] ; National Natural Science Foundation of China[82021001] ; Shanghai Municipal Science and Technology Major Project[2018SHZDZX05] ; Shanghai City Committee of Science and Technology Project[18411953700] ; Shanghai City Committee of Science and Technology Project[18JC1410100] ; Shanghai City Committee of Science and Technology Project[19XD1424400] ; Shanghai City Committee of Science and Technology Project[19YF1455100] ; International Partnership Program of Chinese Academy of Sciences[153D31KYSB20170059]
WOS关键词	EVOLUTIONARY CLASSIFICATION ; DISCOVERY ; DATABASE
WOS研究方向	Biochemistry & Molecular Biology
语种	英语
出版者	NATURE RESEARCH
WOS记录号	WOS:000646531300002
内容类型	期刊论文
源URL	[http://119.78.100.183/handle/2S10ELR8/296693]
专题	中国科学院上海药物研究所
通讯作者	Zhou, Yingsi; Lai, Jinsheng; Yang, Hui
作者单位	1.Chinese Acad Sci, Shanghai Res Ctr Brain Sci & Brain Inspired Intel, Shanghai Inst Biol Sci,CAS Ctr Excellence Brain S, Inst Neurosci,State Key Lab Neurosci,Key Lab Prim, Shanghai, Peoples R China 2.Univ Chinese Acad Sci, Coll Life Sci, Beijing, Peoples R China 3.Chinese Acad Sci, Shanghai Inst Mat Med, CAS Key Lab Receptor Res, Shanghai, Peoples R China 4.Huigene Therapeut Inc, Shanghai, Peoples R China 5.Fudan Univ, Shanghai Publ Hlth Clin Ctr, Shanghai, Peoples R China 6.Tianjin Med Univ, Sch Basic Med Sci, Dept Pathogen Biol, Tianjin, Peoples R China 7.Chinese Acad Agr Sci, Agr Genome Inst Shenzhen, Ctr Anim Genom, Shenzhen, Peoples R China 8.China Agr Univ, Dept Plant Genet & Breeding, State Key Lab Agrobiotechnol, Beijing, Peoples R China 9.China Agr Univ, Dept Plant Genet & Breeding, Natl Maize Improvement Ctr, Beijing, Peoples R China
推荐引用方式 GB/T 7714	Xu, Chunlong,Zhou, Yingsi,Xiao, Qingquan,et al. Programmable RNA editing with compact CRISPR-Cas13 systems from uncultivated microbes[J]. NATURE METHODS,2021:29.
APA	Xu, Chunlong.,Zhou, Yingsi.,Xiao, Qingquan.,He, Bingbing.,Geng, Guannan.,...&Yang, Hui.(2021).Programmable RNA editing with compact CRISPR-Cas13 systems from uncultivated microbes.NATURE METHODS,29.
MLA	Xu, Chunlong,et al."Programmable RNA editing with compact CRISPR-Cas13 systems from uncultivated microbes".NATURE METHODS (2021):29.