H3K9me3 is Required for Inheritance of Small RNAs that Target a Unique Subset of Newly Evolved Genes

In Caenorhabditis elegans, RNA interference (RNAi) responses can transmit across generations via heritable small RNAs. Heritable RNAi memory is associated with Histone-3-Lysine-9 tri-methylation (H3K9me3) of the targeted genes. In other organisms, maintenance of silencing responses requires a feed-forward loop between H3K9me3 and small RNAs. In C. elegans, however, we find that the effect of H3K9 methyltransferase mutants on heritable RNAi is more complex. In this paper, we show that not only that H3K9me3 is unnecessary for inheritance, the effect of this modification depends on the identity of the RNAi-targeted gene. We found an asymmetry in the requirement for H3K9me3 and the two main worm H3K9me3 methyltransferases, SET-25 and SET-32. Both methyltransferases promote heritable silencing of the foreign gene gfp, but are dispensable for silencing of the endogenous gene oma-1. Genome-wide examination of heritable endogenous small interfering RNAs (endo-siRNAs) revealed that the heritable endo-siRNAs which are lost in set-25 mutants target newly acquired and highly H3K9me3 marked C. elegans genes. Thus, "repressive" chromatin marks could be important specifically for heritable RNAi silencing of genes which are flagged as "foreign", such as gfp.