Evolutionarily significant A-to-I RNA editing events originated through G-to-A mutations in primates

Ni A An; Wanqiu Ding; Xin-Zhuang Yang; Jiguang Peng; Bin Z He; Qing Sunny Shen; Fujian Lu; Aibin He; Yong E Zhang; Bertrand Chin-Ming Tan; Jia-Yu Chen; Chuan-Yun Li

doi:10.1186/s13059-019-1638-y

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Evolutionarily significant A-to-I RNA editing events originated through G-to-A mutations in primates

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Evolutionarily significant A-to-I RNA editing events originated through G-to-A mutations in primates

Ni A An, Wanqiu Ding, Xin-Zhuang Yang, Jiguang Peng, Bin Z He, Qing Sunny Shen, Fujian Lu, Aibin He, Yong E Zhang, Bertrand Chin-Ming Tan, …

Genome biology, Vol.20(1), pp.24-24

02/04/2019

DOI: 10.1186/s13059-019-1638-y

PMCID: PMC6360793

PMID: 30712515

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Abstract

Recent studies have revealed thousands of A-to-I RNA editing events in primates, but the origination and general functions of these events are not well addressed. Here, we perform a comparative editome study in human and rhesus macaque and uncover a substantial proportion of macaque A-to-I editing sites that are genomically polymorphic in some animals or encoded as non-editable nucleotides in human. The occurrence of these recent gain and loss of RNA editing through DNA point mutation is significantly more prevalent than that expected for the nearby regions. Ancestral state analyses further demonstrate that an increase in recent gain of editing events contribute to the over-representation, with G-to-A mutation site as a favorable location for the origination of robust A-to-I editing events. Population genetics analyses of the focal editing sites further reveal that a portion of these young editing events are evolutionarily significant, indicating general functional relevance for at least a fraction of these sites. Overall, we report a list of A-to-I editing events that recently originated through G-to-A mutations in primates, representing a valuable resource to investigate the features and evolutionary significance of A-to-I editing events at the population and species levels. The unique subset of primate editome also illuminates the general functions of RNA editing by connecting it to particular gene regulatory processes, based on the characterized outcome of a gene regulatory level in different individuals or primate species with or without these editing events.

G-to-A mutation

Primate evolution

RNA editing

Origination

Population genetics

Details

Title: Subtitle: Evolutionarily significant A-to-I RNA editing events originated through G-to-A mutations in primates
Creators: Ni A An - Laboratory of Bioinformatics and Genomic Medicine, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Peking University, Beijing, 100871, China
Wanqiu Ding - Laboratory of Bioinformatics and Genomic Medicine, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Peking University, Beijing, 100871, China
Xin-Zhuang Yang - Department of Central Research Laboratory, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
Jiguang Peng - Laboratory of Bioinformatics and Genomic Medicine, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Peking University, Beijing, 100871, China
Bin Z He - Biology Department, University of Iowa, Iowa City, IA, USA
Qing Sunny Shen - Laboratory of Bioinformatics and Genomic Medicine, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Peking University, Beijing, 100871, China
Fujian Lu - Laboratory of Bioinformatics and Genomic Medicine, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Peking University, Beijing, 100871, China
Aibin He - Laboratory of Bioinformatics and Genomic Medicine, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Peking University, Beijing, 100871, China
Yong E Zhang - State Key Laboratory of Integrated Management of Pest Insects and Rodents & Key Laboratory of the Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
Bertrand Chin-Ming Tan - Molecular Medicine Research Center, Chang Gung University, Tao-Yuan, Taiwan
Jia-Yu Chen - Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, 92093-0651, USA. jic386@ucsd.edu
Chuan-Yun Li - Laboratory of Bioinformatics and Genomic Medicine, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Peking University, Beijing, 100871, China. chuanyunli@pku.edu.cn
Resource Type: Journal article
Publication Details: Genome biology, Vol.20(1), pp.24-24
DOI: 10.1186/s13059-019-1638-y
PMID: 30712515
PMCID: PMC6360793
NLM abbreviation: Genome Biol
ISSN: 1474-7596
eISSN: 1474-760X
Grant note: DOI: 10.13039/501100001809, name: National Natural Science Foundation of China, award: 31522032, 31821091, 31871272; DOI: 10.13039/501100001809, name: National Natural Science Foundation of China, award: 31471240; name: National Young Top-Notch Talent Support Program of China
Language: English
Date published: 02/04/2019
Academic Unit: Biology
Record Identifier: 9984217540402771

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