Profiling the RNA editomes of wild-type C. elegans and ADAR mutants

doi:10.1101/gr.176107.114

CORC > 北京大学 > 生命科学学院

	Profiling the RNA editomes of wild-type C. elegans and ADAR mutants
	Zhao, Han-Qing ; Zhang, Pan ; Gao, Hua ; He, Xiandong ; Dou, Yanmei ; Huang, August Y. ; Liu, Xi-Ming ; Ye, Adam Y. ; Dong, Meng-Qiu ; Wei, Liping
刊名	genome research
	2015
关键词	CAENORHABDITIS-ELEGANS MESSENGER-RNA ADENOSINE DEAMINASES EDITING SITES MASS-SPECTRA TARGETS SEQ IDENTIFICATION PATHWAYS QUANTIFICATION
DOI	10.1101/gr.176107.114
英文摘要	RNA editing increases transcriptome diversity through post-transcriptional modifications of RNA. Adenosine deaminases that act on RNA (ADARs) catalyze the adenosine-to-inosine (A-to-I) conversion, the most common type of RNA editing in higher eukaryotes. Caenorhabditis elegans has two ADARs, ADR-1 and ADR-2, but their functions remain unclear. Here, we profiled the RNA editomes of C. elegans at different developmental stages of wild-type and ADAR mutants. We developed a new computational pipeline with a "bisulfite-seq-mapping-like" step and achieved a threefold increase in identification sensitivity. A total of 99.5% of the 47,660 A-to-I editing sites were found in clusters. Of the 3080 editing clusters, 65.7% overlapped with DNA transposons in noncoding regions and 73.7% could form hairpin structures. The numbers of editing sites and clusters were highest at the L1 and embryonic stages. The editing frequency of a cluster positively correlated with the number of editing sites within it. Intriguingly, for 80% of the clusters with 10 or more editing sites, almost all expressed transcripts were edited. Deletion of adr-1 reduced the editing frequency but not the number of editing clusters, whereas deletion of adr-2 nearly abolished RNA editing, indicating a modulating role of ADR-1 and an essential role of ADR-2 in A-to-I editing. Quantitative proteomics analysis showed that adr-2 mutant worms altered the abundance of proteins involved in aging and lifespan regulation. Consistent with this finding, we observed that worms lacking RNA editing were short-lived. Taken together, our results reveal a sophisticated landscape of RNA editing and distinct modes of action of different ADARs.; Biochemistry & Molecular Biology; Biotechnology & Applied Microbiology; Genetics & Heredity; SCI(E); PubMed; 1; ARTICLE; dongmengqiu@nibs.ac.cn; weilp@mail.cbi.pku.edu.cn; 1; 66-75; 25
语种	英语
内容类型	期刊论文
源URL	[http://ir.pku.edu.cn/handle/20.500.11897/188560]
专题	生命科学学院
推荐引用方式 GB/T 7714	Zhao, Han-Qing,Zhang, Pan,Gao, Hua,et al. Profiling the RNA editomes of wild-type C. elegans and ADAR mutants[J]. genome research,2015.
APA	Zhao, Han-Qing.,Zhang, Pan.,Gao, Hua.,He, Xiandong.,Dou, Yanmei.,...&Wei, Liping.(2015).Profiling the RNA editomes of wild-type C. elegans and ADAR mutants.genome research.
MLA	Zhao, Han-Qing,et al."Profiling the RNA editomes of wild-type C. elegans and ADAR mutants".genome research (2015).