By Bio-IT World Staff
February 13, 2012 | In a study published online in Nature Biotechnology, BGI researchers have reported evidence of extensive RNA editing in human cells. The paper is a follow up study to last May's Science paper that initially reported sequence differences between mRNA and DNA.
The team, headed by Zhiyu Peng, Vice Director of Research & Cooperation Division of BGI, developed a more rigorous pipeline for comparing RNA and DNA for this study. They began with whole-transcriptome data by RNA-seq from a cell line from a previously-sequenced Han Chinese male, YH. (see, "The Bedrock of BGI: Huanming Yang")
"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 Peng in a press release. 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.
The new pipeline identified more than 22,000 RNA editing events and 44 microRNA editing events. Most of the RNA editing events (about 93%) converted adenosine into inosine, which is read as guanosine. This corresponds with a known editing mechanism based on adenosine deaminase acting on RNA (ADAR). Other nucleotide changes were validated at lower rates.
"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," said Peng.
"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."