Non-catalytic function of PRC2 in the control of small RNA dynamics during programmed genome elimination in Paramecium

To limit transposable element (TE) mobilization, most eukaryotes have evolved small RNAs to silence TE activity via homology-dependent mechanisms. Small RNAs, 20-30 nucleotides in length, bind to PIWI proteins and guide them to nascent transcripts by sequence complementarity, triggering the recruitment of histone methyltransferase enzymes on chromatin to repress the transcriptional activity of TEs and other repeats. In the ciliate Paramecium tetraurelia, 25-nt scnRNAs corresponding to TEs recruit Polycomb Repressive Complex 2 (PRC2), and trigger their elimination during the formation of the somatic nucleus. Here, we sequenced sRNAs during the entire sexual cycle with unprecedented precision. Our data confirmed that scnRNAs are produced from the entire germline genome, from TEs and non-TE sequences, during meiosis. Non-TE sRNAs are selectively degraded, which results in the specific selection of TE-scnRNAs.  We provide important mechanistic insight into the scnRNA selection pathway by identifying PRC2 and its cofactors as essential for the selective degradation of non-TE-scnRNAs. Our findings reveal a new mechanism for PRC2 that involves a non-methyltransferase function for regulating small RNA dynamics during development.