Systematic identification of abundant A-to-I editing sites in the human transcriptome

Abstract

RNA editing by members of the ADAR (adenosine deaminases acting on RNA) family leads to site-specific conversion of adenosine to inosine (A-to-I) in precursor messenger RNAs. Editing by ADARs is believed to occur in all metazoa, and is essential for mammalian development. Currently, only a limited number of human ADAR substrates are known, whereas indirect evidence suggests a substantial fraction of all pre-mRNAs being affected. Here we describe a computational search for ADAR editing sites in the human transcriptome, using millions of available expressed sequences. We mapped 12,723 A-to-I editing sites in 1,637 different genes, with an estimated accuracy of 95%, raising the number of known editing sites by two orders of magnitude. We experimentally validated our method by verifying the occurrence of editing in 26 novel substrates. A-to-I editing in humans primarily occurs in noncoding regions of the RNA, typically in Alu repeats. Analysis of the large set of editing sites indicates the role of editing in controlling dsRNA stability.

Editor meets silencer: crosstalk between RNA editing and RNA interference

“…Several groups have recently developed a systematic, computational analysis method for the genome-wide identification of new A→I RNA editing sites [6][7][8][9] . Reverse transcriptase recognizes inosine as if it were guanosine (FIG.…”

“…This is followed by the elimination of single nucleotide polymorphisms (SNPs) and the evaluation of data quality. With this technique, a much larger than expected number of human A→I RNA editing sites has been identified [6][7][8][9] . Most surprisingly, almost all of these new sites that were identified in the human transcriptome (∼15,000 sites, mapped in ∼2,000 different genes) reside in non-coding regions that consist of inversely oriented repetitive elements (FIG.…”

“…A→I RNA editing of a short dsRNA that has formed between a coding exon and nearby intron sequences can lead to a codon change and an alteration in the protein function. However, it was recently discovered that the most frequent targets of A→I RNA editing seem to be long, but partially double-stranded, RNAs that are formed from inverted Alu repeats and long interspersed element (LINE) repeats located in introns and untranslated regions (UTRs) of mRNAs [6][7][8][9] . Global editing of non-coding RNA might control the expression of genes that harbour these repeat sequences of retrotransposon origin.…”

Useful ‘junk’: Alu RNAs in the human transcriptome

“…Despite the apparent mass of inosine found in the transcriptome [38], very few positions edited by ADAR were identified until recently, when three independent groups discovered that embedded Alu RNAs were responsible for most (more than 90%) of the A-to-I editing events in the human transcriptome (for detailed reviews see [26,39,40]). Using elaborated genome-scale computational approaches, Kim and colleagues identified 30 085 substitutions in 2674 different transcripts [41], Levanon and colleagues identified 12 723 substitutions in 1637 different transcripts [42], and Athanasiadis and colleagues found 14 500 substitutions in 1445 mRNAs [43]. Most of the A-to-I substitutions occurred within Alu RNAs embedded in non-coding regions of mRNAs [42].…”

“…Using elaborated genome-scale computational approaches, Kim and colleagues identified 30 085 substitutions in 2674 different transcripts [41], Levanon and colleagues identified 12 723 substitutions in 1637 different transcripts [42], and Athanasiadis and colleagues found 14 500 substitutions in 1445 mRNAs [43]. Most of the A-to-I substitutions occurred within Alu RNAs embedded in non-coding regions of mRNAs [42]. To test the accuracy of these computational approaches, a certain number of previously unknown editing sites were experimentally confirmed [42].…”