Identification of A-to-I RNA Editing Sites in the Honey Bee (Apis mellifera) Brain Using RNAseq Data
RNA editing is a post-transcriptional modification process that leads to addition, substitution and deletion of certain bases in RNA molecules, and accordingly alters their biological properties. As the most widespread type of RNA editing in metazoans, A-to-I RNA editing refers to the conversion of adenosine (A) to inosine (I) through deamination catalyzed by adenosine deaminase acting on RNA (ADAR). Such editing sites can be detected as single nucleotide variations between genomic DNA and cDNA of the same individual.By taking advantage of the latest honey bee (Apis mellifera) genome assembly and Illumina-generated brain RNAseq data from ten honey bee individuals (five nurses and five foragers with two to three replicates per individual), I have performed computational identification and experimental validation of A-to-I RNA editing sites in the honey bee brain. A total of 68 candidate editing sites were identified, with 41 in coding exons, 22 in 3' UTRs, four in introns and one in 5' UTRs. Of these 68 candidate editing sites, genomic DNA and cDNA were successfully amplified and sequenced in 52, and 36 sites were confirmed as true editing sites. Guanosine was favored as the 3' most adjacent base and depleted as the 5' most adjacent base of validated editing sites, consistent with the base context preference previously shown as being recognized by ADAR. The 25 editing sites in coding exons did not show preference for a particular codon position, but 20 recoded amino acids. Two conserved editing sites were found in the honey bee gene orthologous to the quiver (qvr) gene in fruit fly (Drosophila melanogaster). Both conserved sites resulted in the same amino acid recoding in honey bee and fruit fly, the first one changing the amino acid from serine to glycine (AGU to GGU in both species), and the second one converting histidine to arginine (CAC to CGC in honey bee and CAU to CGU in fruit fly).This is the first RNAseq-based identification of A-to-I RNA editing sites in the honey bee brain, laying foundation for future studies on the functions of genes affected by A-to-I RNA editing.
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