Title |
Comprehensive analysis of RNA-Seq data reveals extensive RNA editing in a human transcriptome
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Published in |
Nature Biotechnology, February 2012
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DOI | 10.1038/nbt.2122 |
Pubmed ID | |
Authors |
Zhiyu Peng, Yanbing Cheng, Bertrand Chin-Ming Tan, Lin Kang, Zhijian Tian, Yuankun Zhu, Wenwei Zhang, Yu Liang, Xueda Hu, Xuemei Tan, Jing Guo, Zirui Dong, Yan Liang, Li Bao, Jun Wang |
Abstract |
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. |
X Demographics
Geographical breakdown
Country | Count | As % |
---|---|---|
United States | 10 | 32% |
Canada | 2 | 6% |
United Kingdom | 2 | 6% |
Spain | 1 | 3% |
Switzerland | 1 | 3% |
Germany | 1 | 3% |
Ireland | 1 | 3% |
Hong Kong | 1 | 3% |
China | 1 | 3% |
Other | 3 | 10% |
Unknown | 8 | 26% |
Demographic breakdown
Type | Count | As % |
---|---|---|
Members of the public | 15 | 48% |
Scientists | 14 | 45% |
Science communicators (journalists, bloggers, editors) | 2 | 6% |
Mendeley readers
Geographical breakdown
Country | Count | As % |
---|---|---|
United States | 21 | 3% |
Germany | 6 | <1% |
Italy | 5 | <1% |
Netherlands | 4 | <1% |
Spain | 4 | <1% |
United Kingdom | 4 | <1% |
France | 3 | <1% |
Hong Kong | 3 | <1% |
China | 3 | <1% |
Other | 20 | 3% |
Unknown | 623 | 90% |
Demographic breakdown
Readers by professional status | Count | As % |
---|---|---|
Researcher | 193 | 28% |
Student > Ph. D. Student | 187 | 27% |
Student > Master | 57 | 8% |
Student > Bachelor | 44 | 6% |
Professor > Associate Professor | 40 | 6% |
Other | 105 | 15% |
Unknown | 70 | 10% |
Readers by discipline | Count | As % |
---|---|---|
Agricultural and Biological Sciences | 386 | 55% |
Biochemistry, Genetics and Molecular Biology | 138 | 20% |
Computer Science | 25 | 4% |
Medicine and Dentistry | 24 | 3% |
Immunology and Microbiology | 8 | 1% |
Other | 37 | 5% |
Unknown | 78 | 11% |