Histone H3K9 methylation is dispensable for Caenorhabditis elegans development but required for RNA:DNA hybrid-associated repeat stability

Histone H3K9 methylation is a conserved modification that generally represses transcription. In C. elegans it is enriched on silent tissue-specific genes and repetitive elements. In met-2 set-25 double mutants, which lack all H3K9 methylation, embryos differentiate normally although mutant adults are sterile due to extensive DNA damage-driven apoptosis in the germline. Transposons and simple repeats are derepressed in both germline and somatic tissues. This unprogrammed transcription correlates with increased rates of repeat-specific insertions and deletions, copy-number variation, R-loops, and enhanced sensitivity to replication stress. We propose that H3K9me2/3 stabilizes and protects complex, repeat-rich genomes by suppressing replication stress.