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 L. Griswold, Arpit Mehta, Alexander Czachor, Jutaro Fukumoto, Richard F. Lockey, Benjamin L. King, Narasaiah Kolliputi

Research output: Contribution to journalArticle

9 Scopus citations

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.

Original languageEnglish (US)
Pages (from-to)35726-35736
Number of pages11
JournalOncotarget
Volume6
Issue number34
DOIs
StatePublished - 2015
Externally publishedYes

Keywords

  • 3'UTRs
  • Exome
  • MicroRNAs
  • RNA editing
  • RNA-seq

ASJC Scopus subject areas

  • Oncology

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    Soundararajan, R., Stearns, T. M., Griswold, A. L., Mehta, A., Czachor, A., Fukumoto, J., Lockey, R. F., King, B. L., & Kolliputi, N. (2015). Detection of canonical A-to-G editing events at 3' UTRs and microRNA target sites in human lungs using next-generation sequencing. Oncotarget, 6(34), 35726-35736. https://doi.org/10.18632/oncotarget.6132