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Beijing Genomics Institute (BGI) Researchers Uncover Extensive RNA Editing in a Human Transcriptome by Comprehensive Analysis of RNA-seq Data  
2/13/2012 9:05:31 AM

February 12, 2012, Cambridge, MA and Shenzhen, China - In a new study published online in Nature Biotechnology, researchers from BGI, the world's largest genomics organization, reported evidence of extensive RNA editing in a human cell line by analysis of RNA-seq data, demonstrating the need for new robust methods to identify important post-transcriptional editing events.

RNA editing is a normal but not yet fully understood process in which small nucleotide changes occur after DNA has been transcribed into RNA. It is an integral step in generating diversity and plasticity of cellular RNA signature as a post-transciptional event that recodes hereditary information. RNA editing is an important area in the post-genomic era for its role in determining protein structure and function. It has become increasingly important in genetic research.

Last year, a study published in Science (Li, et al. Science, May 19, 2011) reported a large number of sequence differences between mRNA and DNA in the human transcriptome. This finding was startling because it implied that there might be a still undiscovered mechanism of 'RNA editing' that could disrupt the central dogma and affect our understanding of genetic variation. However, this view was strongly contested by other scientists because of the technical issue and lack of academic rigor, such as sequencing error or mis-mapping. In this latest study, BGI researchers developed a more rigorous pipeline for approaching these problems and answered some of the concerned questions, which contributed to paving the way for further studies in this field.

The whole-transcriptome data was obtained by RNA-seq from a lymphoblastoid cell line of a male Han Chinese individual (YH), whose genome sequence was previously reported as the first diploid genome of Han Chinese. RNA-seq, also known as "Whole Transcriptome Shotgun Sequencing", is a recently developed approach on transcriptome profiling that uses deep-sequencing technologies with the advantages of high-throughput data, low background, high sensitivity and repeatability. In a paper published in 2009 in Nature Reviews Genetics

(http://www.nature.com/nrg/journal/v10/n1/abs/nrg2484.html#top), RNA-seq is referred to as a revolutionary tool in transcriptomics.

"We used RNA-seq in the study to identify post-transcriptional editing events, and developed a computational and comprehensive pipeline to find the human RNA editing sites," said Zhiyu Peng, the leading author of the paper and Vice Director of Research & Cooperation Division of BGI. The pipeline was used to identify the extensive RNA editing from genome and whole transcriptome data by screening RNA-DNA differences of the same individual through successive quality control filters.

Through this pipeline, BGI researchers identified 22,688 RNA editing events, and found most editing events (~93%) convert adenosine (A) into inosine (I), which in turn is read as guanosine (G), in consistence with known editing mechanisms based on adenosine deaminase acting on RNA (ADAR). They also found 44 editing events in microRNAs (miRNA), suggesting there is a potential connection between RNA editing and miRNA-mediated regulation. Researchers also found in the study evidence of other types of nucleotide changes, but these were validated at lower rates.

"These findings demonstrate this multifilter molecular pipeline is an excellent approach in this study," said Peng. "With the multiple filters, false positive results can be controlled or eliminated while identifying RNA editing events, providing a more accurate and effective method to extensively analyze RNA editing. We now plan to apply this new methodology to larger-scale deep sequencing studies for more comprehensive analysis and profiling of editome, including studies with additional physiologically relevant samples."

"The evidence of extensive RNA editing identified in a human transcriptome underscores the necessity of an effective method to fully detect these events in order to further advance our understanding of human development and normal pathophysiological condition," said Jun Wang, Executive Director of BGI. "With continual improvement of the new approach, we believe this could be achieved in the near future."

About BGI

BGI was founded in Beijing, China on September 9th, 1999 with the mission of being a premier scientific partner to the global research community. The goal of BGI is to make leading-edge genomic science highly accessible through its investment in infrastructure that leverages the best available technology, economies of scale, and expert bioinformatics resources. BGI, and its affiliates, BGI Americas, based in Cambridge, MA and BGI Europe, based in Copenhagen, Denmark, have established partnerships and collaborations with leading academic and government research institutions as well as global biotechnology and pharmaceutical companies, supporting a variety of disease, agricultural, environmental, and related applications.

BGI has established a proven track record of excellence, delivering results with high efficiency and accuracy for innovative, high-profile research which has generated over 170 publications in top-tier journals such as Nature and Science. These accomplishments include sequencing one percent of the human genome for the International Human Genome Project, contributing 10 percent to the International Human HapMap Project, carrying out research to combat SARS and German deadly E. coli, playing a key role in the Sino-British Chicken Genome Project, and completing the sequence of the rice genome, the silkworm genome, the first Asian diploid genome, the potato genome, and, most recently, 1000 genomes and human Gut metagenome. For more information about BGI, please visit www.bgiamericas.com or www.genomics.cn .

Contact Information:

Zhiyu Peng

Vice Director of Research & Cooperation Division

BGI

pengzhiyu@genomics.cn

www.genomics.cn

Joyce Peng, Ph.D.

Marketing Director

BGI Americas Corporation

626-222-5584

joyce.peng@bgiamericas.com

www.bgiamericas.com

Bicheng Yang

Public Communication Officer

BGI

+86-755-82639701

yangbicheng@genomics.cn

www.genomics.cn