| MicroRNAs (miRNAs) and other classes of short non-coding RNAs regulate essential processes in the development and function of the nervous system. Regulation of miRNAs by neural activity has also been reported. Recently, instances of piwi interacting RNA (piRNA) and endogenous short interfering RNA (esiRNA) mediated modulation of neural physiology have been reported. To better understand the role of miRNAs and other classes of short non-coding RNAs in long term memory (LTM) formation, we have conducted high throughput sequencing on 15-35nt RNAs isolated from heads of Drosophila that have been subjected to aversive olfactory conditioning. We developed genome wide profiles of miRNA, piRNA, and esiRNA, and tested for differential expression following conditioning. We find that 5 miRNAs exhibit significant regulation in the conditioned group. We identify several esiRNA generating loci within genes required for olfactory LTM formation. Our data reveal that an intron of the multiple wing hairs (mwh) gene forms secondary structures and generates esiRNAs following conditioning from regions that correspond to lysozyme family genes located within the mwh intron. We find that piRNAs are produced in fly heads, and that a small set of piRNA generating loci mapping to LTR retrotransposons are significantly down regulated following conditioning. In addition to the well characterized classes of short non coding RNAs, we describe a set of transcripts that produce large numbers of reads with a broad size distribution from the sense strand. We find that a subset of these are regulated following treatment and contain consensus elements that may be involved in their regulation. We investigate expression of one such gene with dramatically up-regulated reads following treatment, the Drosophila beta-site APP-cleaving enzyme (dBACE), and find that increased reads reflect increased mRNA levels. Further, we find that the target of dBACE protein, drosophila beta amyloid protein precursor-like (APPL), is subjected to increased cleavage following conditioning, and that dBACE is required for LTM formation, but not for learning or STM. |
