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: Contains two sets of ChIP-seq experiments. (1) The H3K9me3 and H3K36me3 ChIPs were done identically to the ones published in Weiser et al. 2017, except adding csr-1 RNAi. These were used to check for rescue of csr-1 chromatin defects by morc-1. For these experiments, two replicates were performed for each genotype/condition/antibody, as well as two input samples per genotype/condition. (2) The MORC-1::FLAG ChIPs used a FLAG tagged into the endogenous morc-1 locus, in order to investigate the genome-wide distribution of wild-type MORC-1, as well as the distribution of MORC-1 in two different csr-1 mutants csr-1(G560R) and aid::csr-1. For the FLAG experiments, control experiments were performed using wild-type worms lacking FLAG (N2). All MORC-1::FLAG ChIPs were performed with two replicates, each with a matched input sample.