C. elegans nuclear RNAi factor SET-32 is an H3K23 methyltransferase and deposits the transgenerational heritable modification of H3K23me3

Nuclear RNAi provides a highly tractable system to study RNA-mediated chromatin changes and epigenetic inheritance. Recent studies indicate that nuclear RNAi-mediated heterochromatin is highly complex in its regulation and function. The knowledge of histone modifications that are involved in nuclear RNAi and the corresponding histone modifying enzymes remains limited. In this study, we show that the heterochromatin mark H3K23me3 is induced by nuclear RNAi at both exogenous and endogenous targets in C. elegans. In addition, RNAi-induced H3K23me3 can be inherited for at least four generations. We also demonstrate that the histone methyltransferase SET-32, methylates H3K23 in vitro. Both set-32 and the germline nuclear RNAi Argonaute, hrde-1, are required for nuclear RNAi-induced H3K23me3 in vivo. Our data poise H3K23me3 as a chromatin modification involved in the nuclear RNAi pathway and provides the field with a new target for uncovering the role of heterochromatin in transgenerational epigenetic silencing. In this study we tested if H3K23me1/2/3 is induced by nuclear RNAi at both the exogenous and endogenous targets. We performed oma-1 dsRNA feeding and heritable RNAi experiments. We investigated the whole genome distribution of H3K23me3 and its overlap with H3K9me3. We tested its genetic requirements in the nuclear RNAi pathway and for three histone methyltransferases in vivo: MET-2, SET-25 and SET-32 by examining oma-1 and endogenous nuclear RNAi targets as well as whole genome changes in these mutants.