Developmental mRNA clearance by PIWI-bound endo-siRNAs in Paramecium

The clearance of untranslated mRNAs by Argonaute proteins is essential for embryonic development in metazoans. However, it is currently unknown whether similar processes exist in unicellular eukaryotes. The ciliate Paramecium tetraurelia harbors a vast array of PIWI-clade Argonautes involved in various small RNA (sRNA) pathways, many of which have not yet been investigated. Here, we investigate the function of a PIWI protein, Ptiwi08, whose expression is limited to a narrow time window during development, concomitant with the start of zygotic transcription. We show that Ptiwi08 acts in an endogenous small interfering RNA (endo-siRNA) pathway involved in the clearance of untranslated mRNAs. These endo-siRNAs are found in clusters that are strictly antisense to their target mRNAs and are a subset of siRNA-producing clusters (SRCs). Furthermore, the endo-siRNAs are 2′-O-methylated by Hen1 and require Dcr1 for their biogenesis. Our findings suggest that sRNA-mediated developmental mRNA clearance extends beyond metazoans and may be a more widespread mechanism than previously anticipated. [Display omitted] •Discovery of a small-RNA-mediated mRNA clearance pathway in a unicellular eukaryote•Endo-siRNAs display a strict strand bias and are antisense to their target mRNAs•Endo-siRNAs are Dicer dependent and bound by a PIWI-clade Argonaute protein, Ptiwi08•Untranslated mRNAs are likely targeted for degradation by the Ptiwi08 pathway Solberg et al. describe a small-RNA-mediated mRNA clearance pathway at the start of zygotic genome activation in the unicellular eukaryote Paramecium tetraurelia. In this pathway, the endo-siRNAs are strictly antisense to their target mRNAs, require Dicer1 for their production, and are bound by the PIWI-clade Argonaute protein Ptiwi08.