Changes in gene expression in fruitfly ovaries in mutants affecting components of rasiRNA system

rasiRNA (rasiRNAs, repeat-associated short interfering RNAs) system is a mechanism of silencing of mobile element transpositions in germline of a number of species including Drosophila melanogaster. rasiRNA itself is a short RNAs which participate in transposon transcription repression and mRNA degradation. Defects in rasiRNA system lead to increased transposition rate and developmental abnormalities due to accumulation of double-strand DNA breaks in fruitfly testes and ovaries. A number of proteins participate in rasiRNA-mediated repression including SPN-E (homeless), PIWI and ARMI. Mutations in the genes of these proteins lead to significant mobile element mRNA accumulation. We performed microarray-based study of effects of spn-E mutation on expression in fruitfly ovaries - one of the organs where rasiRNA system work. Our goal was the identification of other (besides mobile elements) targets of rasiRNA system regulation Total RNA samples were extracted from ovaries of 1) spn-E1/spn-Ehls03987 trans-heterozygotes and mix of heterozygotes spn-E1/TM3 and spn-Ehls03987/TM3 (spn-E/+ hereafter). 2) Piwi2/PiwiNT trans-heterozygotes and mix of heterozygotes PiwiNT/CyO and Piwi2/CyO (Piwi/+ hereafter). Samples were reverse transcribed, IVT-amplified and labeled with Cy3 or Cy5. Mix of differently labeled aRNAs was hybridized to Oligo14Kv2 microarray slides (CDMC), washed, scanned and treated in GenePix 6 (Molecular Devices) and subsequently in FlexArray 1.6.2 (McGill University and Génome Québec Innovation Centre). Three biological replica (one sample dye-swapped) were produced and analyzed.