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

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 Overall design: 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.