Prediction of constitutive A-to-I editing sites from human transcriptomes in the absence of genomic sequences

	Prediction of constitutive A-to-I editing sites from human transcriptomes in the absence of genomic sequences
	Zhu, SS; Xiang, JF; Chen, T; Chen, LL; Yang, L
刊名	BMC GENOMICS
	2013
卷号	14 期号:1 页码:206-206
关键词	RNA-seq RNA editing Potential SNP score Constitutive editing Editing box
通讯作者	Chen, LL (reprint author), Chinese Acad Sci, Shanghai Inst Biol Sci, Inst Biochem & Cell Biol, State Key Lab Mol Biol, Shanghai 200031, Peoples R China.,linglingchen@sibcb.ac.cn ; liyang@picb.ac.cn
英文摘要	Background: Adenosine-to-inosine (A-to-I) RNA editing is recognized as a cellular mechanism for generating both RNA and protein diversity. Inosine base pairs with cytidine during reverse transcription and therefore appears as guanosine during sequencing of cDNA. Current approaches of RNA editing identification largely depend on the comparison between transcriptomes and genomic DNA (gDNA) sequencing datasets from the same individuals, and it has been challenging to identify editing candidates from transcriptomes in the absence of gDNA information. Results: We have developed a new strategy to accurately predict constitutive RNA editing sites from publicly available human RNA-seq datasets in the absence of relevant genomic sequences. Our approach establishes new parameters to increase the ability to map mismatches and to minimize sequencing/mapping errors and unreported genome variations. We identified 695 novel constitutive A-to-I editing sites that appear in clusters (named "editing boxes") in multiple samples and which exhibit spatial and dynamic regulation across human tissues. Some of these editing boxes are enriched in non-repetitive regions lacking inverted repeat structures and contain an extremely high conversion frequency of As to Is. We validated a number of editing boxes in multiple human cell lines and confirmed that ADAR1 is responsible for the observed promiscuous editing events in non-repetitive regions, further expanding our knowledge of the catalytic substrate of A-to-I RNA editing by ADAR enzymes. Conclusions: The approach we present here provides a novel way of identifying A-to-I RNA editing events by analyzing only RNA-seq datasets. This method has allowed us to gain new insights into RNA editing and should also aid in the identification of more constitutive A-to-I editing sites from additional transcriptomes.
学科主题	Biotechnology & Applied Microbiology; Genetics & Heredity
类目[WOS]	Biotechnology & Applied Microbiology ; Genetics & Heredity
关键词[WOS]	RNA-SEQ DATA ; HUMAN BRAIN ; SYSTEMATIC IDENTIFICATION ; ACCURATE IDENTIFICATION ; ADENOSINE DEAMINASES ; NUCLEAR RETENTION ; ADAR DEAMINASES ; NONCODING RNAS ; MESSENGER-RNAS ; ALIGNMENT
收录类别	SCI
语种	英语
WOS记录号	WOS:000318517900002
内容类型	期刊论文
版本	出版稿
源URL	[http://202.127.25.143/handle/331003/488]
专题	上海生化细胞研究所_上海生科院生化细胞研究所
推荐引用方式 GB/T 7714	Zhu, SS,Xiang, JF,Chen, T,et al. Prediction of constitutive A-to-I editing sites from human transcriptomes in the absence of genomic sequences[J]. BMC GENOMICS,2013,14(1):206-206.
APA	Zhu, SS,Xiang, JF,Chen, T,Chen, LL,&Yang, L.(2013).Prediction of constitutive A-to-I editing sites from human transcriptomes in the absence of genomic sequences.BMC GENOMICS,14(1),206-206.
MLA	Zhu, SS,et al."Prediction of constitutive A-to-I editing sites from human transcriptomes in the absence of genomic sequences".BMC GENOMICS 14.1(2013):206-206.