Comprehensive analysis of RNA-Seq data reveals extensive RNA editing in a human transcriptome.
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 ∼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 (∼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.
BGI-Shenzhen, Shenzhen, China.
Zhiyu
Z
Peng
Yanbing
Y
Cheng
Bertrand Chin-Ming
BC
Tan
Lin
L
Kang
Zhijian
Z
Tian
Yuankun
Y
Zhu
Wenwei
W
Zhang
Yu
Y
Liang
Xueda
X
Hu
Xuemei
X
Tan
Jing
J
Guo
Zirui
Z
Dong
Yan
Y
Liang
Li
L
Bao
Jun
J
Wang
D019295:Computational Biology; D006801:Humans; D037181:Lectins, C-Type / Q000235:genetics / Q000378:metabolism; D035683:MicroRNAs / Q000235:genetics / Q000378:metabolism; D011061:Poly A / Q000235:genetics / Q000378:metabolism; D020641:Polymorphism, Single Nucleotide; D012313:RNA / Q000235:genetics* / Q000378:metabolism; D017393:RNA Editing; D011956:Receptors, Cell Surface / Q000235:genetics / Q000378:metabolism; D017423:Sequence Analysis, RNA; D059467:Transcriptome
C400041:CLEC2D protein, human; D037181:Lectins, C-Type; D035683:MicroRNAs; D011956:Receptors, Cell Surface; D011061:Poly A; D012313:RNA