Abstract
The circadian system of Drosophila is composed of discrete populations of neurons. Previous studies purified two of these populations, the sLNvs and lLNvs, and characterized their expression using microarrays. These studies were useful in elucidating the functions of these cells and identifying new circadian genes. However, microarray data is limited and cannot provide information regarding isoform expression, alternative splicing, or RNA-editing. Therefore, using the same purification method, we sought to create RNA-sequencing libraries from these populations and use the data to identify RNA-editing sites. Overall, we were able to create 3'-biased libraries by extracting RNA from cells and amplifying the mRNA using dT-priming. We did this for PDF- and TH-expressing cells, which encompass the sLNvs/lLNvs and dopaminergic neurons in the brain, respectively. Using the sequencing data from these cells we identified potential editing sites, which we then verified using site-specific PCR. In this manner we identified a total of 20 editing sites. 17 of these sites had been previously identified in heads, and 3 were novel and fly strain specific. Additionally, some of the edited sites found in both cell types showed variations in editing levels and cycling across two time-points. These results suggest that RNA-editing may be regulated in a tissue-specific manner and that the circadian system may control some aspects of this regulation.