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.
Highlights
In recent years, the focus of molecular biology has been radically shifted from the “central dogma” (DNA to RNA to protein) to encompass the role of modifications of RNA nucleotides via co- or post-transcription mechanisms termed “RNA editing”
This study demonstrates that RNA editing is widespread in normal human lungs, and the majority of events are canonical A-to-G editing that map to introns and 3’ untranslated regions (UTRs) of target genes
For DNA sequencing, we generated an average of 110 million reads per sample of which ~98% aligned uniquely to the human reference genome. 79% of reads aligned to the targeted exome giving an exome coverage of 69X. 92% of targeted bases were covered at 10X coverage and 81% at 20X
Summary
The focus of molecular biology has been radically shifted from the “central dogma” (DNA to RNA to protein) to encompass the role of modifications of RNA nucleotides via co- or post-transcription mechanisms termed “RNA editing”. We investigated RNA editing in three normal human lungs using high-throughput (exome) DNA- and RNA-sequencing data from the same sample and computational pipeline.
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