Transcriptional silencing of transposable elements by Piwi and its impact on chromatin and gene expression

Eukaryotic genomes are colonized by transposable elements whose uncontrolled activity results in genomic instability. The piRNA pathway silences transposons in animal gonads, yet how this is achieved molecularly remains controversial. We assign an essential role to the HMG protein Maelstrom in the process of Piwi mediated silencing in Drosophila. Genome wide assays revealed highly correlated changes in RNA Polymerase II recruitment, nascent RNA output and steady state RNA levels of transposons upon loss of Piwi or Maelstrom. Our data demonstrate piRNA-mediated trans- silencing of hundreds of transposon copies at the transcriptional level. We show that Piwi is required for establishing heterochromatic H3K9me3 marks on transposons and their genomic surrounding. In contrast, loss of Maelstrom impacts transposon H3K9me3 patterns only marginally yet leads to increased heterochromatin spreading, suggesting that Maelstrom acts downstream of or in parallel to H3K9me3. Our work uncovers the widespread influence of transposons and the piRNA pathway on chromatin patterns and gene expression programs. Overall design: RNA Polymerase II and H3K9me3 occupancy, and steady-state and nascent RNA levels in wild-type ovarian somatic cells (OSC) and RNAi knock-downs of the piRNA pathway components. RNA Polymerase II occupancy in tissue-specific knockdowns of tejas (control) and armi in somatic cells of Drosophila ovary.