Abstract
Since double-stranded RNA (dsRNA) is effective for silencing a wide variety of genes, all genes are typically considered equivalent targets for such RNA interference (RNAi). Yet, loss of some regulators of RNAi in the nematode C. elegans can selectively impair the silencing of some genes, raising the possibility of gene-specific specialization of the RNAi mechanism. Here we dissect the silencing of two somatic genes in detail to show that such selective regulation can be explained by a single network of regulators acting on genes with differences in their RNA metabolism. In this network, the Maelstrom domain-containing protein RDE-10, the intrinsically disordered protein MUT-16, and the Argonaute protein NRDE-3 work together so that any two are required for silencing one gene, but each is singly required for silencing the other gene. While numerous features could distinguish one gene from another, quantitative models suggest that, for the same steady state abundance of mRNA, genes with higher rates of mRNA production are more difficult to knockdown with a single dose of dsRNA and recovery from knockdown can occur if all intermediates of RNA silencing undergo turnover. Consistent with such dissipation of RNA silencing, animals recover after silencing by a pulse of dsRNA and show restricted production of templates for amplifying small RNAs. The loss of NRDE-3 can be overcome by enhancing dsRNA processing, which supports a quantitative contribution of this regulator to RNA silencing. These insights explain selectivity in the requirements for specific regulators without invoking different mechanisms for different sets of genes.
Significance Statement RNA interference (RNAi) is a widely used mechanism for silencing the expression of genes to combat disease or improve agriculture. We show that different genes can show stark differences in their requirements for particular regulators of RNAi despite silencing relying on a single regulatory network. These differences are explained by genes having different thresholds for silencing such that genes with high thresholds for silencing require multiple regulators of RNA silencing for efficient knockdown. When such genes are targeted, resistance through mutations becomes more likely, necessitating another round of drug development. Anticipating these mechanisms for the development of resistance before widespread use of an RNAi-based drug or treatment will be crucial for avoiding futile cycles of innovation.
Competing Interest Statement
The authors have declared no competing interest.
Footnotes
Competing Interest Statement: The authors declare no conflict of interest.