Selective degradation of small RNAs during programmed genome elimination in Paramecium – SELECTION

Due to their capacity to jump from one site to another, transposable elements (TEs) are a significant threat to genome integrity. To limit TE mobilization, most eukaryotes have evolved small RNAs (sRNAs) to silence TE activity via homology-dependent mechanisms. sRNAs guide PIWI proteins to which they bind to homologous TE sequences, recruit histone-modifying enzymes, and repress the transcriptional activity of TEs. However, how small RNA-PIWI complexes recruit downstream effectors remains elusive. We will address this important question using the sRNA-guided genome elimination paradigm in ciliates. In the ciliate Paramecium, massive and reproducible elimination of TEs occurs during the development of the somatic genome from the germline genome at each sexual cycle. The specific recognition of TEs involves sRNAs which direct heterochromatin formation and subsequent TE elimination. sRNAs are produced from the entire germline genome, from TEs and non-TE sequences, by a developmental-specific RNAi interference pathway. Non-TEs sRNAs, which represent a large fraction of the sRNA population, are degraded, while sRNAs corresponding to TEs will remain and recruit Polycomb Repressive Complex 2 (PRC2) and trigger TE elimination. How non-TEs sRNAs are massively degraded and TE sRNAs are selected is currently unknown. In this proposal, we aim at uncovering how sRNAs are selectively degraded in Paramecium, an exquisite model because of the abundance and precise developmental timing of sRNA degradation. Our preliminary data identified new factors required for the process. We will use multidisciplinary, cutting-edge approaches, combining functional genomics and proteomics, to decipher the mode of action of these factors and the pathways involved.