RNA A-to-I editing sites as determined from short sequencing reads of cDNA prepared from 30 different developmental stages. The frequency of editing at each site throughout development is analyzed and the effects of editing on the amino acids encoded are predicted.
To identify potential sites of RNA editing, short poly(A)+ RNA-Seq reads that mapped to annotated transcripts were compared to the reference genome to find instances in which a 'G' aligned to an 'A' (for plus strand transcripts) or a 'C' aligned to a 'T' (for minus strand). The first or last six bases of reads were not examined because they were easily mismapped to introns rather than across splice junctions. Only positions with at least five reads showing a substitution from any single developmental stage were considered further. A dataset of potential editing sites with the number of edited reads and the number of non-edited reads for each sample was created. To prevent a polymorphism in the sequenced strain from being reported as editing, at least 100 reads having an exact match to the genome were necessary for further consideration of a potential editing site. Only those sites with at least 5% of reads in at least two independent adult samples showing evidence of editing are reported.
927 A-to-I RNA editing sites are listed in Table S29 of the Supplementary Information.
Editing at 972 positions was observed within the transcripts of 597 genes.
Expressed sequence tags, long poly(A) RNA-Seq and cDNAs cross-validate nearly one-quarter (214) of the newly discovered A-to-I RNA editing sites.
For most A-to-I RNA editing sites, the frequency of editing increases throughout development and does not correlate with overall expression levels.
RNA editing typically begins in late pupal stages, although some transcripts seem to be edited in late embryogenesis.
Three potential editing-associated sequence motifs were identified by computational analysis.