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Illuminating the Mechanism of Nucleolar RNA

In a bid to further understand ribosomal siRNA in gene silencing, scientists looked into C. elegans and unveiled the nucleolar RNA interference mechanism, granting us greater insight into the biological roles of these small regulatory RNAs.

In eukaryotic cells, the processing of ribosomal RNAs is extremely complex. Erroneous ribosomal RNAs will have to be degraded by multiple surveillance machinery. This involves the interference of a small double-stranded non-coding RNA about 20 to 30 nucleotides long called the siRNA, or small interfering RNA. Such small regulatory RNAs direct sequence-specific regulation of genes through a process known as RNA interference (RNAi). InC. elegans, it is known that siRNAs silence nuclear-localised RNAs through the Nrde pathway. However, the detailed mechanism of ribosomal siRNA-mediated pre-RNA silencing is still not well understood.

Here, scientists from the University of Science and Technology of China (USTC) of the China Academy of Sciences and the First Affiliated Hospital of USTC revealed the nucleolar RNAi mechanism in C. elegans.

Through genetic screening, the researchers identified a series of suppressors of siRNA (SUSI) factors that inhibit endogenous siRNA production in C. elegans and found that SUSI-5 gene suppressed the production of ribosomal siRNA. SUSI-5 encodes a core catalytic subunit of RNA exosomes called DIS-3. To find out if other components of the exosome complex are crucial to inhibiting ribosomal siRNA production, the team utilised mutants obtained from the National Bioresource Project, the Caenorhabditis Genetics Center, and ones generated by CRISPR gene-editing technology. They observed that in all the mutants, NRDE-3 accumulated in the nucleus in seam cells, which indicates the production of ribosomal siRNA.

This confirms that any functional defect of any subunit of the RNA exosome will result in the accumulation of ribosomal siRNA, which will go on to induce two nuclear RNA interference key factors, NRDE-2 and NRDE-3, to enter the nucleolus, bind to ribosomal RNA precursors, and suppress the transcriptional activity of RNA polymerase.

Furthermore, the team found that cells could maintain ribosomal RNA homeostasis through the change in RNA exosome subcellular localisation. As established, RNA exosomes play a critical role in processing and metabolising a variety of RNA and are mainly found in the nucleolus. An imbalance of intracellular ribosomal RNA homeostasis would trigger the transfer of RNA exosomes from the nucleolus to the nucleoplasm. The correct localisation of RNA exosomes is required to inhibit the production of ribosomal siRNA.

This study has shown that C. elegans have in place a backup system, nucleolar RNAi, where RNA homeostasis can be maintained and erroneous ribosomal RNAs do not accumulate, giving us greater insight into the biological roles and mechanisms of ribosomal siRNAs. [APBN]

Source: Liao et al. (2021). Antisense ribosomal siRNAs inhibit RNA polymerase I-directed transcription in C. elegans. Nucleic Acids Research, 49(16), 9194-9210.