The Paramecium PRC2 complex physically interacts with the RNAi pathway. PARAMECIUM_PRC2_CPLX

The repression of transposable elements in eukaryotes often involves their transcriptional silencing via small RNA-targeted chromatin modifications. In plants and animals, these repressive modifications include DNA and/or H3K9 methylation. In the ciliate Paramecium tetraurelia, transposable elements are enriched for H3K9me3 and H3K27me3, both of which are catalyzed by the Polycomb Enhancer-of-zeste-like protein Ezl1. To understand how the Ezl1 enzyme is recruited to transposable elements and how its activity is regulated, we performed tandem affinity purification from nuclear extracts combined with mass spectrometry and identified the proteins that physically interact with Ezl1. We showed that the Paramecium PRC2-Ezl1 core complex is formed around four subunits, which co-immunoprecipitate in a heterologous expression system and co-elute. We further demonstrated that these proteins are required in vivo for Ezl1 catalytic activity. Additionally, we identified PRC2-Ezl1 cofactors, which are required for the correct targeting of H3K9me3 and H3K27me3 on transposable elements. Interestingly, we found that the small RNA binding protein Ptiwi09 interacts with the PRC2-Ezl1 complex, and this interaction is mediated by a RING finger protein PRC2-Ezl1 cofactor. Altogether our data suggest that, in Paramecium, the PRC2 complex is recruited to transposable elements by physical interaction with the RNAi pathway, a mechanism that has been described for the recruitment of H3K9 methylation SU(VAR)3–9 enzymes.