Dual roles for nuclear RNAi Argonautes in Caenorhabditis elegans dosage compensation

Abstract Dosage compensation involves chromosome-wide gene regulatory mechanisms which impact higher order chromatin structure and are crucial for organismal health. Using a genetic approach, we identified Argonaute genes which promote dosage compensation in Caenorhabditis elegans. Dosage compensation in C. elegans hermaphrodites is initiated by the silencing of xol-1 and subsequent activation of the dosage compensation complex which binds to both hermaphrodite X chromosomes and reduces transcriptional output by half. A hallmark phenotype of dosage compensation mutants is decondensation of the X chromosomes. We characterized this phenotype in Argonaute mutants using X chromosome paint probes and fluorescence microscopy. We found that while nuclear Argonaute mutants hrde-1 and nrde-3, as well as mutants for the piRNA Argonaute prg-1, exhibit derepression of xol-1 transcripts, they also affect X chromosome condensation in a xol-1-independent manner. We also characterized the physiological contribution of Argonaute genes to dosage compensation using genetic assays and found that hrde-1 and nrde-3 contribute to healthy dosage compensation both upstream and downstream of xol-1. RNA-interference is a conserved process, but its endogenous roles are enigmatic. In C. elegans, the dosage compensation complex binds the two X chromosomes of hermaphrodites to repress gene expression by half. Here, Davis et al. show that the nuclear RNAi machinery contributes to dosage compensation, revealing that nuclear Argonautes contribute to both gene-specific repression of the master regulator of dosage compensation xol-1, as well as to the chromosome-wide gene repression of the X chromosomes.