5434 Nucleic Acids Research, 2007, Vol. 35, No. 16 Figure 3. Increase of retrotransposon transcript abundance in homo- zygous spn-E1, piwi2 and armi1 ovaries, but not in somatic tissues. The steady-state level of transcripts corresponding to HeT-A, I element and copia retrotransposons and house-keeping genes (rp49 and Adh) was detected by quantitative RT–PCR in ovaries and carcasses (ﬂies without ovaries) of heterozygous or homozygous mutant females. Bars indicate the ratio of transcript amount in homozygous ﬂies to heterozygous ones normalized to Adh transcript amount. piwi2 mutation produces less pronounced eﬀects that may result from the severe morphological ovarian defects induced by this mutation. variegated repression of a white reporter carried by the 1360 element (40) in somatic tissues. The origin of short RNAs in these cases remains unknown. We investigated the regulation of Het-A, I element and copia in somatic tissues of ﬂies, carrying mutations in the spn-E, piwi and armi genes, which control the rasiRNA pathway (3). The steady-state levels of HeT-A, I element and copia related to rp49 and Adh transcripts were comparable in ovaries, heads and carcasses (ﬂies without ovaries) of spn-E1/+, piwi2/+ and armi1/+ heterozygous ﬂies, indicating that tested retrotransposons are not exclusively germ-line transcribed. Nevertheless, we observed up-regulation of retrotransposon transcripts only in ovaries, but not in carcasses or heads of homozygous spn-E1, piwi2 and armi1 ﬂies (Figure 3;data not shown). Furthermore, we found no eﬀects of the spn-E1 mutation on the histone modiﬁcations in carcasses (Figure 4). To extend the analysis of retrotransposon expression in somatic tissues, we used a transgenic copiaLTR-lacZ construct (Figure 5A). Activity of b-gal increased 10, 9 and 13 times in extracts of homozygous spn-E1/hls3987, Figure 4. ChIP assay in carcasses. The occupancy of histone modiﬁca- tions in the chromatin of retrotransposons in spn-E1/spn-E1 (light bars) and spn-E1/+ ovaries (dark bars). piwi2 and armi1 ovaries, respectively, as compared to heterozygous ovaries, whereas the expression level remained unchanged in carcasses (Figure 5B). Expression of the construct was dramatically increased in germinal nurse cells and developing oocytes of spn-E1, piwi2, armi1