Accurate inference of the full base-pairing structure of RNA by deep mutational scanning and covariation-induced deviation of activity

doi:10.1093/nar/gkz1192

	Accurate inference of the full base-pairing structure of RNA by deep mutational scanning and covariation-induced deviation of activity
	Zhang, Zhe 1,2,3; Xiong, Peng 3; Zhang, Tongchuan 3; Wang, Junfeng 1,4; Zhan, Jian 3; Zhou, Yaoqi 3,5
刊名	NUCLEIC ACIDS RESEARCH
	2020-02-20
卷号	48
ISSN号	0305-1048
DOI	10.1093/nar/gkz1192
通讯作者	Wang, Junfeng(junfeng@hmfl.ac.cn) ; Zhan, Jian(j.zhan@griffith.edu.au) ; Zhou, Yaoqi(yaoqi.zhou@griffith.edu.au)
英文摘要	Despite the large number of noncoding RNAs in human genome and their roles in many diseases include cancer, we know very little about them due to lack of structural clues. The centerpiece of the structural clues is the full RNA base-pairing structure of secondary and tertiary contacts that can be precisely obtained only from costly and time-consuming 3D structure determination. Here, we performed deep mutational scanning of self-cleaving CPEB3 ribozyme by error-prone PCR and showed that a library of <5 x 10(4) single-to-triple mutants is sufficient to infer 25 of 26 base pairs including non-nested, nonhelical, and noncanonical base pairs with both sensitivity and precision at 96%. Such accurate inference was further confirmed by a twister ribozyme at 100% precision with only noncanonical base pairs as false negatives. The performance was resulted from analyzing covariation-induced deviation of activity by utilizing both functional and nonfunctional variants for unsupervised classification, followed by Monte Carlo (MC) simulated annealing with mutation-derived scores. Highly accurate inference can also be obtained by combining MC with evolution/direct coupling analysis, R-scape or epistasis analysis. The results highlight the usefulness of deep mutational scanning for high-accuracy structural inference of self-cleaving ribozymes with implications for other structured RNAs that permit high-throughput functional selections.
资助项目	Australia Research Council (ARC)[DP180102060] ; National Health and Medical Research Council of Australia[1121629] ; National Natural Science Foundation of China[U1532269] ; National Natural Science Foundation of China[U1632274] ; High Magnetic Field Laboratory of Anhui Province ; ARC[DP180102060]
WOS关键词	SECONDARY STRUCTURE ; STRUCTURE PREDICTION ; PROTEIN INTERACTIONS ; TERTIARY STRUCTURE ; SEQUENCE ; RIBOZYMES ; GENOME ; TRANSCRIPTION ; LANDSCAPE ; REVEALS
WOS研究方向	Biochemistry & Molecular Biology
语种	英语
出版者	OXFORD UNIV PRESS
WOS记录号	WOS:000515121900038
资助机构	Australia Research Council (ARC) ; National Health and Medical Research Council of Australia ; National Natural Science Foundation of China ; High Magnetic Field Laboratory of Anhui Province ; ARC
内容类型	期刊论文
源URL	[http://ir.hfcas.ac.cn:8080/handle/334002/103895]
专题	中国科学院合肥物质科学研究院
通讯作者	Wang, Junfeng; Zhan, Jian; Zhou, Yaoqi
作者单位	1.Chinese Acad Sci, Hefei Inst Phys Sci, High Magnet Field Lab, Key Lab High Magnet Field & Ion Beam Phys Biol, Hefei 230031, Anhui, Peoples R China 2.Univ Chinese Acad Sci, Beijing 101408, Peoples R China 3.Griffith Univ, Inst Glyc, Parklands Dr, Southport, Qld 4222, Australia 4.Anhui Univ, Inst Phys Sci & Informat Technol, Hefei 230031, Anhui, Peoples R China 5.Griffith Univ, Sch Informat & Commun Technol, Parklands Dr, Southport, Qld 4222, Australia
推荐引用方式 GB/T 7714	Zhang, Zhe,Xiong, Peng,Zhang, Tongchuan,et al. Accurate inference of the full base-pairing structure of RNA by deep mutational scanning and covariation-induced deviation of activity[J]. NUCLEIC ACIDS RESEARCH,2020,48.
APA	Zhang, Zhe,Xiong, Peng,Zhang, Tongchuan,Wang, Junfeng,Zhan, Jian,&Zhou, Yaoqi.(2020).Accurate inference of the full base-pairing structure of RNA by deep mutational scanning and covariation-induced deviation of activity.NUCLEIC ACIDS RESEARCH,48.
MLA	Zhang, Zhe,et al."Accurate inference of the full base-pairing structure of RNA by deep mutational scanning and covariation-induced deviation of activity".NUCLEIC ACIDS RESEARCH 48(2020).