Predicting sites of ADAR editing in double-stranded RNA

Abstract

ADAR (adenosine deaminase that acts on RNA) editing enzymes target coding and noncoding double-stranded RNA (dsRNA) and are essential for neuronal function. Early studies showed that ADARs preferentially target adenosines with certain 5′ and 3′ neighbours. Here we use current Sanger sequencing protocols to perform a more accurate and quantitative analysis. We quantified editing sites in an ∼800-bp dsRNA after reaction with human ADAR1 or ADAR2, or their catalytic domains alone. These large data sets revealed that neighbour preferences are mostly dictated by the catalytic domain, but ADAR2's dsRNA-binding motifs contribute to 3′ neighbour preferences. For all proteins, the 5′ nearest neighbour was most influential, but adjacent bases also affected editing site choice. We developed algorithms to predict editing sites in dsRNA of any sequence, and provide a web-based application. The predictive power of the algorithm on fully base-paired dsRNA, compared with biological substrates containing mismatches, bulges and loops, elucidates structural contributions to editing specificity.

Transcriptome-wide identification of A > I RNA editing sites by inosine specific cleavage

“…The majority of the sites (540 loci) were also located, as expected based on prior research (Athanasiadis et al 2004;Blow et al 2004;Kim et al 2004;Levanon et al 2004;Carmi et al 2011;Danecek et al 2012) in repeats including LINE1s and the B1 and B2 SINE elements. The analysis of the 5 ′ and 3 ′ neighbors of the editing sites showed an enrichment in U > A > C > G in 5 ′ , which is concordant with previous reports (Eggington et al 2011). For the 3 ′ , the enrichment was not as distinct with the following preference A ≈ G ≈ C > U, which is not concordant with previous reports but is due to the difference in site preference between Adar1 and Adar2 and the nondistinction between the sites edited by the two enzymes (Lehmann and Bass 2000;Eggington et al 2011).…”

“…The analysis of the 5 ′ and 3 ′ neighbors of the editing sites showed an enrichment in U > A > C > G in 5 ′ , which is concordant with previous reports (Eggington et al 2011). For the 3 ′ , the enrichment was not as distinct with the following preference A ≈ G ≈ C > U, which is not concordant with previous reports but is due to the difference in site preference between Adar1 and Adar2 and the nondistinction between the sites edited by the two enzymes (Lehmann and Bass 2000;Eggington et al 2011).…”

Solution structure of the N-terminal dsRBD of Drosophila ADAR and interaction studies with RNA

“…Those specifically modified substrates are typically formed by base pairing between edited exons and complementary sequences in flanking introns in pre-mRNA. Importantly, the structural determinants controlling this type of site-specific RNA editing are still not completely understood [5][6][7][8].…”

Dyschromatosis Symmetrica Hereditaria and RNA Editing Enzyme

“…New A-I editing sites have been found by next-generation sequencing [54]. Also, ADAR1 is now known to frequently target 5' and 3' untranslated regions (UTRs) and intronic retrotransposon elements, such as Alu and long interspersed elements (LINE/SINEs).…”