Co-surveillance of ribosomal RNA by the exosome complex and nucleolar RNAi inC. elegans

Abstract

Eukaryotic cells express a wide variety of endogenous small regulatory RNAs that function in the nucleus. We previously found that erroneous rRNAs induce the generation of antisense ribosomal siRNAs (risiRNAs) which silence the expression of rRNAs via the nuclear RNAi defective (Nrde) pathway. To further understand the biological roles and mechanisms of this class of small regulatory RNAs, we conducted forward genetic screening to identify factors involved in risiRNA generation in Caenorhabditis elegans. We found that risiRNAs accumulated in the RNA exosome mutants. risiRNAs directed a NRDE-dependent silencing of pre-rRNAs in the nucleolus. In the presence of risiRNA, NRDE-2 accumulated in the nucleolus and colocalized with RNA polymerase I. risiRNA inhibited the transcription elongation of RNA polymerase I by decreasing RNAP I occupancy downstream of the site of RNAi. Meanwhile, exosome mislocalized from the nucleolus to nucleoplasm in suppressor of siRNA (susi) mutants, in which erroneous rRNAs accumulated. These results establish a novel model of rRNA surveillance by combining ribonuclease-mediated RNA degradation with small RNA-directed nucleolar RNAi system.

Two parallel sRNA amplification cycles contribute to RNAi inheritance in C. elegans

“…We speculate that the initial increase in FISH signal reflects stalling of RNA polymerase II and/or stalling of pre-mRNA processing causing nascent transcripts to accumulate at the locus. Stalling of RNA polymerase has previously been implicated in nuclear RNAi (Guang et al, 2010; Liao et al, 2020).…”

Phosphatidylcholine mediates the crosstalk between LET-607 and DAF-16 stress response pathways

“…DIS-3 is a component of C . elegans nuclear RNA exosome complex that is enriched in the nucleoplasm but not in the nucleoli [ 15 ]. It was identified that LET-607::GFP overlapped well with DIS-3:: mCHERRY specifically in the nucleoplasm ( Fig 1B ).…”