Comprehensive analysis of RNA-Seq data reveals extensive RNA editing in a human transcriptome

被引：403

作者：

Peng, Zhiyu ^{[1
]}

Cheng, Yanbing ^{[1
]}

Tan, Bertrand Chin-Ming ^{[2
,3
]}

Kang, Lin ^{[1
]}

Tian, Zhijian ^{[1
]}

Zhu, Yuankun ^{[1
]}

Zhang, Wenwei ^{[1
]}

Liang, Yu ^{[1
]}

Hu, Xueda ^{[1
]}

Tan, Xuemei ^{[1
]}

Guo, Jing ^{[1
]}

Dong, Zirui ^{[1
]}

Liang, Yan ^{[1
]}

Bao, Li ^{[1
]}

Wang, Jun ^{[1
,4
,5
]}

机构：

[1] BGI Shenzhen, Shenzhen, Peoples R China

[2] Chang Gung Univ, Coll Med, Dept Biomed Sci, Tao Yuan, Taiwan

[3] Chang Gung Univ, Coll Med, Grad Inst Biomed Sci, Tao Yuan, Taiwan

[4] Univ Copenhagen, Novo Nordisk Fdn Ctr Basic Metab Res, Copenhagen, Denmark

[5] Univ Copenhagen, Dept Biol, Copenhagen, Denmark

来源：

NATURE BIOTECHNOLOGY | 2012年 / 30卷 / 03期

基金：

中国国家自然科学基金;

关键词：

NONCODING RNA; GENOME SEQUENCE; ADENOSINE; IDENTIFICATION; EXPRESSION; DISCOVERY; SITES; TOOL;

D O I：

10.1038/nbt.2122

中图分类号：

Q81 [生物工程学（生物技术）]; Q93 [微生物学];

学科分类号：

071005 ; 0836 ; 090102 ; 100705 ;

摘要：

RNA editing is a post-transcriptional event that recodes hereditary information. Here we describe a comprehensive profile of the RNA editome of a male Han Chinese individual based on analysis of similar to 767 million sequencing reads from poly(A)(+), poly(A)(-) and small RNA samples. We developed a computational pipeline that carefully controls for false positives while calling RNA editing events from genome and whole-transcriptome data of the same individual. We identified 22,688 RNA editing events in noncoding genes and introns, untranslated regions and coding sequences of protein-coding genes. Most changes (similar to 93%) converted A to I(G), consistent with known editing mechanisms based on adenosine deaminase acting on RNA (ADAR). We also found evidence of other types of nucleotide changes; however, these were validated at lower rates. We found 44 editing sites in microRNAs (miRNAs), suggesting a potential link between RNA editing and miRNA-mediated regulation. Our approach facilitates large-scale studies to profile and compare editomes across a wide range of samples.

引用

页码：253 / +

页数：10

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