Distinct regulatory mechanisms by the nuclear Argonautes HRDE-1 and NRDE-3 in the soma of Caenorhabditis elegans.

Histone H3 lysine 9 methylation (H3K9me) and nuclear RNAi are two processes with roles in repression of repetitive elements and regulation of gene expression. Recently, they were also implicated in dosage compensation, a mechanism that accommodates for the differences in gene dosage between the biological sexes. In Caenorhabditis elegans, dosage compensation is achieved via epigenetic modifications on both X chromosomes of hermaphrodites, effectively dampening their expression by half to match the single X chromosome in males. This chromosome-wide process also relies on the anchoring and compaction of the X chromosomes near the nuclear lamina, mediated by the H3K9 histone methyltransferases MET-2, SET-25 and SET-32. H3K9me is also involved in gene silencing during nuclear RNAi, and recent evidence suggests that mutations in the nuclear RNAi machinery impact X chromosome compaction and dosage compensation. The nuclear Argonautes HRDE-1 and NRDE-3 are responsible for the recruitment of the H3K9 histone methyltransferases to targets in the germline and the soma, respectively, during nuclear RNAi. We investigated the impact of the loss of nuclear Argonautes and/or H3K9 methyltransferases on both dosage compensation and global gene expression during somatic development. Our immunofluorescence and bioinformatic analyses suggest that the nuclear RNAi and H3K9me pathways are involved in the packaging of the X chromosomes during dosage compensation, without consequence to their transcriptional output. Instead, mutant RNAi mutants exhibit global transcriptional differences, in which HRDE-1 and NRDE-3 affect expression of their native targets through different modes of regulation and different relationships between each nuclear Argonaute and H3K9 methylation. RNA-seq profiles of L1 larval stage C. elegans samples. The genotypes included are: N2 Bristol strain (wild-type), CSS419 set-32 (red11); met-2 (n4256) set-25 (n5021), EKM89 hrde-1 (tm1200), CSS415 set-32 (red11); hrde-1 (tm1200) met-2 (n4256) set-25 (n5021), WM156 nrde-3 (tm1116) and EKM205 set-32 (red11); met-2 (n4256) set-25 (n5021); nrde-3 (tm1116).