Effects of ADARs on small RNA processing pathways in C. elegans

Abstract

Adenosine deaminases that act on RNA (ADARs) are RNA editing enzymes that convert adenosine to inosine in doublestranded RNA (dsRNA). To evaluate effects of ADARs on small RNAs that derive from dsRNA precursors, we performed deep-sequencing, comparing small RNAs from wild-type and ADAR mutant Caenorhabditis elegans. While editing in small RNAs was rare, at least 40% of microRNAs had altered levels in at least one ADAR mutant strain, and miRNAs with significantly altered levels had mRNA targets with correspondingly affected levels. About 40% of siRNAs derived from endogenous genes (endo-siRNAs) also had altered levels in at least one mutant strain, including 63% of Dicer-dependent endo-siRNAs. The 26G class of endo-siRNAs was significantly affected by ADARs, and many altered 26G loci had intronic reads and histone modifications associated with transcriptional silencing. Our data indicate that ADARs, through both direct and indirect mechanisms, are important for maintaining wild-type levels of many small RNAs in C. elegans.

ADAR1 is required for differentiation and neural induction by regulating microRNA processing in a catalytically independent manner

“…Our data revealed that RNA editing has little correlation with mRNA expression changes in ADAR1 KD H9 cells (Supplementary information, Figure S4 and data not shown), which is in consistency with recent reports in other organisms [18][19][20]. We hypothesized that ADAR1 deficiency may lead to an altered miRNA repertoire, which in turn regulates mRNA expression in H9 cells and during differentiation.…”

“…It has been shown that at least 40% of miRNAs have altered levels in ADAR mutant C. elegans strains, although editing in small RNAs is rare [20]. Interestingly, a recent report found that despite the presence of a few sites in which editing is clearly beneficial, human RNA editing sites in coding regions are generally nonadaptive and evolutionarily poorly conserved, arguing against the physiological significance of these editing events in human [56].…”

“…Recent studies reported that non-enzymatic ADAR1 participates in small RNA biogenesis in different organisms [19,20]. ADAR1 was suggested to interact with DICER to promote miRNA processing [22] or to form a complex with DGCR8 to inhibit pri-miRNA processing [21].…”

“…ADARs are also important for maintaining many small RNAs in C. elegans through both editing and non-editing activities [20]. In addition, lack of ADARs in mouse embryos led to a general expansion of the miR-NA repertoire, which seems unrelated to editing events [18].…”

The spliceosome as a transposon sensor

“…One potential clue is the recent observation that a specific subset of 26G siRNA maps to both introns and exons of its target transcripts, suggesting that siRNA of this class can be triggered by incompletely spliced mRNA precursors. 49 A further motivation is the recent finding that nematode spliceosome components are enriched among proteins whose phylogenetic conservation correlates with that of RNA silencing factors. 48 Since proteins with similar conservation tend to act in the same pathways, 50 this finding suggests a conserved connection between splicing and small RNA function.…”