EMA1 RNAi experiments

Ciliates undergo developmentally programmed genome elimination, in which small RNAs direct the removal of transposable elements during the development of the somatic nucleus. 25-nt scnRNAs are produced from the entire germline genome and transported to the maternal somatic nucleus, where selection of scnRNAs corresponding to germline-specific sequences is thought to take place. Selected scnRNAs then guide the elimination of transposable elements in the developing somatic nucleus. How germline-specific scnRNAs are selected remains to be determined. Here, we provide important mechanistic insights into the scnRNA selection pathway by identifying a Paramecium homolog of Gtsf1 as essential for the selective degradation of scnRNAs corresponding to retained somatic sequences. Consistently, we also show that Gtsf1 is localized in the maternal somatic nucleus where it associates with the scnRNA-binding protein Ptiwi09. Furthermore, we demonstrate that the scnRNA selection process is critical for genome elimination. We propose that Gtsf1 is required for the coordinated degradation of Ptiwi09-scnRNA complexes that pair with target RNA via the ubiquitin pathway, similarly to the mechanism suggested for microRNA target-directed degradation in metazoans. Funding : Centre National de la Recherche Scientifique (CNRS); Agence Nationale de la Recherche (ANR) [ANR-18-CE12-0005 to S.D. and M.B.; ANR-19-CE12-0015 to S.D. and O.A.; ANR-23-CE12-0027 to S.D. and G.C.; and ANR-21-CE12-0019 to M.B.]; LABEX Who Am I? [ANR-11-LABX-0071 and ANR-11-IDEX-0005-02 to S.D.]; Fondation de la Recherche Médicale [FRM EQU202203014643 to S.D., FRM EQU202103012766 to M.B. and FDT202204014919 to O.C.]; National Science Centre, Poland [2019/32/C/NZ2/00472 to J.G., and 2019/33/B/NZ2/01062 and 2022/45/B/NZ2/03058 to J.N.]; EUR G.E.N.E. [ANR-17-EURE-0013 to O.C.]; Université Paris Cité [IdEx #ANR-18-IDEX-0001 to O.C.]. Exchange grants from the CNRS and the Polish Academy of Sciences.