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Original Research ARTICLE Provisionally accepted The full-text will be published soon. Notify me

Front. Genet. | doi: 10.3389/fgene.2019.00211

Genomic positional dissection of RNA Editomes in tumor and normal samples

 Michael Chigaev1, Hui Yu1, David Samuels2, Quanhu Sheng3,  Olufunmilola Oyebamiji1, Scott Ness1, Wei Yue1,  Ying-Yong Zhao4 and  Yan Guo1*
  • 1University of New Mexico, United States
  • 2Vanderbilt University, United States
  • 3Vanderbilt University Medical Center, United States
  • 4Northwest University, China

RNA editing is a phenomenon that occurs in both protein coding and non-coding RNAs. Increasing evidence shows that adenosine-to-inosine RNA editing can potentially render substantial functional effects throughout the genome. Using RNA editing datasets from two large consortiums: The Cancer Genome Atlas (TCGA) and the Genotype-Tissue Expression (GTEx) project, we quantitatively analyzed human genome-wide RNA editing events derived from tumor or normal tissues. We found that most common RNA editing sites tend to have a higher level of editing in tumors as compared to normal samples. Of the 14 tumor-normal-paired cancer types examined, 11 of the 14 cancers tested had elevated RNA editing levels in tumors. The editomes in cancer or normal tissues were dissected by genomic locations, and significant RNA editing locational differences were found between cancerous and healthy specimens. Our results indicated a significant correlation between the RNA editing rate and the gene density across chromosomes. Visualization of running RNA editing rates along chromosomes highlighted clusters of hyper RNA editing regions. We identified hyper RNA edited genes (protein-coding genes, lincRNAs, and pseudogenes) that embodied a large portion of cancer prognostic predictors. This study reinforces the potential functional effects of RNA editing in protein-coding genes, and also makes a strong foundation for further exploration of the role of RNA editing in non-coding regions.

Keywords: RNA Editing, A to I, adenosine to inosine, Cancer, non-coding RNAs, TCGA, GTEx

Received: 31 Aug 2018; Accepted: 27 Feb 2019.

Edited by:

Zhifu Sun, Mayo Clinic, United States

Reviewed by:

Meng How Tan, Nanyang Technological University, Singapore
Leng Han, University of Texas Health Science Center at Houston, United States  

Copyright: © 2019 Chigaev, Yu, Samuels, Sheng, Oyebamiji, Ness, Yue, Zhao and Guo. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

* Correspondence: Dr. Yan Guo, University of New Mexico, Albuquerque, 87131, New Mexico, United States, yanguo1978@gmail.com