Target-specific requirements for RNA interference can be explained by a single regulatory network

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.