Talk by Olivia CHARMANT and Toni GOUHIER

Olivia CHARMANT
Sandra DUHARCOURT’s lab - Élimination programmée du génome, Institut Jacques Monod,CNRS, Université Paris Cité.

Title:
The PIWI-interacting protein Gtsf1 controls the selective degradation of small RNAs in Paramecium

Abstract:
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.

Toni GOUHIER
Herve Le Hir’s lab/Gwenael Badis

Title:

Nonsense-mediated decay (NMD) targets short poly(A)-tailed mRNAs for degradation

Abstract:
The nonsense-mediated mRNA decay (NMD) is a conserved eukaryotic cytoplasmic surveillance pathway that degrades aberrant mRNAs carrying premature termination codons (PTC). In yeast, the long distance between the poly(A) tail and the stop codon dictates mRNA detection by the central NMD factor Upf1 and its partners Upf2 and Upf3. The Upf proteins trigger the decapping and the 5’ to 3’ degradation of the targeted mRNA, independent of prior deadenylation. Some evidence suggest that Upf1 recognizes mRNAs other than archetypical PTC-containing mRNAs but the whole spectrum of Upf1 targets and the associated molecular mechanisms remain unclear. By direct Nanopore mRNA sequencing, we investigated the nature of Upf1-bound mRNAs in depth. Interestingly, we observed that the expected NMD substrates harbored long poly(A) tails, validating the deadenylation-independent degradation model of NMD. Strikingly, the largest fraction specifically associated to Upf1 corresponded to oligoadenylated mRNAs, a subfraction of many stable mRNAs likely at a particular stage of their life. Despite the absence of a PTC, the stability of these oligoadenylated mRNAs depends on the three Upf NMD factors. These results unveil a hitherto unknown major function of Upf1 and NMD cofactors in oligoadenylated mRNA decay.