Regulation of MORC-1 is key to the CSR-1-mediated germline gene licensing mechanism in C. elegans

The Argonaute CSR-1 is essential for germline development in C. elegans. Loss of CSR-1 leads to the downregulation of thousands of germline-expressed genes, supporting a model in which CSR-1 “licenses” gene expression via a poorly understood mechanism. In contrast, a small subset of genes is upregulated in csr-1 mutants, including morc-1, which encodes a conserved GHKL-type ATPase. We show that morc-1 is overexpressed in csr-1 mutants and accumulates over CSR-1 licensed targets, coinciding with aberrant gain of H3K9me3, reduced H3K36me3, and transcriptional repression. Strikingly, loss of morc-1 fully rescues these chromatin defects and partially restores gene expression and fertility in csr-1 mutants. Conversely, ectopic overexpression of MORC-1 in the wild-type germline is sufficient to repress CSR-1 licensed targets and severely compromise fertility. These findings support a model in which CSR-1 prevents MORC-1 overexpression and consequent misregulation of CSR-1 licensed genes. Overall design: RNA-seq data for two sets of experiments: (1) comparing gene expression in our two csr-1 mutants and in csr-1(G560R); morc-1 vs. matched controls to see csr-1 expression defects & their rescue by morc-1, and (2) comparing expression in various samples/treatments of our morcOE transgenic line (prefix "rna_morcOE") to see if germline MORC-1 overexpression causes expression defects. Experiment (1) samples were done in 4 replicates, and for csr-1(G560R) samples the control is wild-type (N2), for aid::csr-1 treated w/ 1mM auxin, the control is aid::csr-1 treated with 0mM auxin. In (2), morcOE worms were taken through three generations (P0, F1, F2), with F1 worms split into two separate batches processed in parallel, which were treated as biological replicates in all analyses. For each sample within each batch, most were done in triplicate, with a few in duplicate when worms were too sick. Some samples were maintained on neomycin to force transgene expression, whlie others were left on non-selective media and manually separated into transgene expressing (mCherry ON) vs. transgene off (mCherry OFF) samples in the F2 generation. All samples in (2) were compared to a control grown in parallel that lacks the transgene and just has a flag tag on the endogenous MORC-1 copy ("rna_morcOE_ctrl" samples).