The Piwi-interacting RNA (piRNA)-interacting Piwi protein is involved in 
transcriptional silencing of transposable elements in ovaries of Drosophila 
melanogaster. Here we characterized the genome-wide effect of nuclear Piwi 
elimination on the presence of the heterochromatic H3K9me3 mark and HP1a, as 
well as on the transcription-associated mark H3K4me2. Our results demonstrate 
that a significant increase in the H3K4me2 level upon nuclear Piwi loss is not 
accompanied by the alterations in H3K9me3 and HP1a levels for several 
germline-expressed transposons, suggesting that in this case Piwi prevents 
transcription by a mechanism distinct from H3K9 methylation. We found that the 
targets of Piwi-dependent chromatin repression are mainly related to the 
elements that display a higher level of H3K4me2 modification in the absence of 
silencing, i.e. most actively transcribed elements. We also show that 
Piwi-guided silencing does not significantly influence the chromatin state of 
dual-strand piRNA-producing clusters. In addition, host protein-coding gene 
expression is essentially not affected due to the nuclear Piwi elimination, but 
we noted an increase in small nuclear spliceosomal RNAs abundance and propose 
Piwi involvement in their post-transcriptional regulation. Our work reveals new 
aspects of transposon silencing in Drosophila, indicating that transcription of 
transposons can underpin their Piwi dependent silencing, while canonical 
heterochromatin marks are not obligatory for their repression.