Oncotarget

Research Papers:

Detection of canonical A-to-G editing events at 3’ UTRs and microRNA target sites in human lungs using next-generation sequencing

Ramani Soundararajan _, Timothy M. Stearns, Anthony J. Griswold, Arpit Mehta, Alexander Czachor, Jutaro Fukumoto, Richard F. Lockey, Benjamin L. King and Narasaiah Kolliputi

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Oncotarget. 2015; 6:35726-35736. https://doi.org/10.18632/oncotarget.6132

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Abstract

Ramani Soundararajan1, Timothy M. Stearns2, Anthony J. Griswold3, Arpit Mehta3, Alexander Czachor1, Jutaro Fukumoto1, Richard F. Lockey1, Benjamin L. King2 and Narasaiah Kolliputi1

1 Division of Allergy and Immunology, Department of Internal Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA

2 MDI Biological Laboratory, Salisbury Cove, ME, USA

3 Center for Genetic Epidemiology and Statistical Genetics, John P. Hussman Institute for Human Genomics, University of Miami, Miller School of Medicine, Miami, FL, USA

Correspondence to:

Narasaiah Kolliputi, email:

Keywords: RNA editing, RNA-seq, exome, 3’UTRs, microRNAs

Received: June 23, 2015 Accepted: September 14, 2015 Published: October 15, 2015

Abstract

RNA editing is a post-transcriptional modification of RNA. The majority of these changes result from adenosine deaminase acting on RNA (ADARs) catalyzing the conversion of adenosine residues to inosine in double-stranded RNAs (dsRNAs). Massively parallel sequencing has enabled the identification of RNA editing sites in human transcriptomes. In this study, we sequenced DNA and RNA from human lungs and identified RNA editing sites with high confidence via a computational pipeline utilizing stringent analysis thresholds. We identified a total of 3,447 editing sites that overlapped in three human lung samples, and with 50% of these sites having canonical A-to-G base changes. Approximately 27% of the edited sites overlapped with Alu repeats, and showed A-to-G clustering (>3 clusters in 100 bp). The majority of edited sites mapped to either 3’ untranslated regions (UTRs) or introns close to splice sites; whereas, only few sites were in exons resulting in non-synonymous amino acid changes. Interestingly, we identified 652 A-to-G editing events in the 3’ UTR of 205 target genes that mapped to 932 potential miRNA target binding sites. Several of these miRNA edited sites were validated in silico. Additionally, we validated several A-to-G edited sites by Sanger sequencing. Altogether, our study suggests a role for RNA editing in miRNA-mediated gene regulation and splicing in human lungs. In this study, we have generated a RNA editome of human lung tissue that can be compared with other RNA editomes across different lung tissues to delineate a role for RNA editing in normal and diseased states.


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