Identification of putative miRNA involved in Drosophila melanogaster immune response

MicroRNAs (miRNAs) are small endogenous non-coding RNAs that post-transcriptionally regulate gene expression in eukaryotes. They are known to play diverse roles in physiological processes such as homeostasis, development, cancer and immune response. In Drosophila melanogaster up to 176 miRNAs have been identified; yet, their biological functions remain unknown. Here, we describe an in silico screening strategy to identify miRNAs involved in a specific immune signaling pathway that is based on: (i) the potential capability of miRNAs to target mRNAs of a given pathway; (ii) the sequence conservation of miRNAs across species and (iii) the expression profile of miRNAs. Using this strategy, we have defined a subset of seven Drosophila miRNAs that are likely to participate in the immune response. Interestingly, some of these miRNAs target peptidoglycan receptor proteins (PGRPs) for which no regulators are known yet. miRNA-mediated regulation may explain how PGRPs are controlled in the immune signaling pathway.