Profiling the RNA editomes of wild-type C. elegans and ADAR mutants

Abstract

RNA editing increases transcriptome diversity through post-transcriptional modifications of RNA. Adenosine deaminases that act on RNA (ADARs) catalyze the adenosine-to-inosine (A-to-I) conversion, the most common type of RNA editing in higher eukaryotes. Caenorhabditis elegans has two ADARs, ADR-1 and ADR-2, but their functions remain unclear. Here, we profiled the RNA editomes of C. elegans at different developmental stages of wild-type and ADAR mutants. We developed a new computational pipeline with a ''bisulfite-seq-mapping-like'' step and achieved a threefold increase in identification sensitivity. A total of 99.5% of the 47,660 A-to-I editing sites were found in clusters. Of the 3080 editing clusters, 65.7% overlapped with DNA transposons in noncoding regions and 73.7% could form hairpin structures. The numbers of editing sites and clusters were highest at the L1 and embryonic stages. The editing frequency of a cluster positively correlated with the number of editing sites within it. Intriguingly, for 80% of the clusters with 10 or more editing sites, almost all expressed transcripts were edited. Deletion of adr-1 reduced the editing frequency but not the number of editing clusters, whereas deletion of adr-2 nearly abolished RNA editing, indicating a modulating role of ADR-1 and an essential role of ADR-2 in A-to-I editing. Quantitative proteomics analysis showed that adr-2 mutant worms altered the abundance of proteins involved in aging and lifespan regulation. Consistent with this finding, we observed that worms lacking RNA editing were short-lived. Taken together, our results reveal a sophisticated landscape of RNA editing and distinct modes of action of different ADARs.

Genome-wide profiling of the C. elegans dsRNAome

“…Prior to this study, only 10 hyperedited substrates were known in C. elegans (Morse and Bass 1999;Morse et al 2002), although studies have identified transcripts with multiple editing sites (Wu et al 2011;Washburn et al 2014;Zhao et al 2015). Our final list of 664 GNUMAP +Repeat EERs extends this list considerably.…”

“…Nonsynonymous editing of codons, which is known to have important functions in other organisms (Bass 2002;Nishikura 2010), although rare, has recently been observed in C. elegans transcripts (Washburn et al 2014;Zhao et al 2015). To determine whether any sites, both inside EERs and outside, resulted in nonsynonymous codon changes, we used the program Annovar to annotate all observed A-to-G changes in coding exons (Wang et al 2010).…”

Aging and Alzheimer’s disease: Comparison and associations from molecular to system level

“…In C. elegans , the RNA editomes of wild‐type and ADAR mutants were profiled. Worms lacking RNA editing were short‐lived, potentially due to alteration of the abundance of proteins, as determined by quantitative proteomics (Zhao et al, 2015). In AD, RNA editing was studied in a site‐specific manner (Gaisler‐Salomon et al, 2014; Khermesh et al, 2016).…”

The emerging role of RNA editing in plasticity

“…A recent estimate using multiple strains uncovered ∼50 (Danecek et al, 2012), 34 of which are conserved across mammals (Pinto et al, 2014). In C. elegans, only eight recoding sites were identified (Zhao et al, 2014). In leaf-cutter ants there are thousands of sites, many of which are caste-specific; however, only 57 sites recode and in the diamondback moth there were 152 recoding sites .…”