The Mi-2 nucleosome remodeler and the Rpd3 histone deacetylase are involved in piRNA-guided heterochromatin formation

In eukaryotes, trimethylation of lysine 9 on histone H3 (H3K9) is associated with transcriptional silencing of transposable elements (TEs). In drosophila ovaries, this heterochromatic repressive mark is thought to be deposited by SetDB1 on TE genomic loci after the initial recognition of nascent transcripts by PIWI-interacting RNAs (piRNAs) loaded on the Piwi protein. Here, we show that the nucleosome remodeler Mi-2, in complex with its partner MEP-1, forms a subunit that is transiently associated, in a MEP-1 C-terminus-dependent manner, with known Piwi interactors, including a recently reported SUMO ligase Su(var)2-10. Together with the histone deacetylase Rpd3, this module is involved in the piRNA-dependent TE silencing, correlated with H3K9 deacetylation and trimethylation. Therefore. drosophila piRNA-mediated transcriptional silencing involves three epigenetic effectors, a remodeler, Mi-2, an eraser, Rpd3 and a writer, SetDB1, in addition to the Su(var)2-10 SUMO ligase. Transcriptome-wide examination of gene expression changes in Piwi, Mi-2, Rpd3-depleted OSCs. Knockdowns of Piwi, Mi-2, and Rpd3 were treated for 4 days in OSCs. siEGFP was used as a control. Isolated total RNAs were analyzed by deep sequencing using Illumina HiSeq 2500. Sequences were mapped to dm6 Drosophila genome, and then FPKMs were calculated. Upon depletion of Mi-2 and Rpd3 in OSCs, Piwi-targeted transposons were derepressed.