To understand inheritance patterns of health and disease, we must understand what information is passed between generations. There are a growing number of examples where some epigenetic modifications acquired during an individual’s lifetime are inherited from parent to offspring. This phenomenon is called transgenerational epigenetic inheritance (TEI) and could provide a mechanism for the inheritance of environmentally-acquired traits.
We are studying TEI using the nematode Caenorhabditis elegans. We have developed a system in which exposure to an environmental RNAi trigger induces robust TEI for multiple generations. We have previously shown that the putative histone H3 lysine 9 (H3K9) trimethyltransferase SET-25 and the putative histone methyltransferase SET-32 are required in the RNAi-exposed generation for effective transmission of silencing, but dispensable for long-term maintenance of silencing in subsequent generations. H3K9me3 deposition is associated with TEI, and lost at transgenerationally-silenced loci upon mutation of SET-25 and SET-32. It was therefore assumed that the SET domain which mediates methyltransferase activity is responsible for the role of SET-25 and SET-32 in TEI establishment. Here we show by LC-MS/MS that SET-25 deposits H3K9me3, and SET-32 deposits H3K23me3 – a recently-identified heterochromatic mark. We generated catalytically inactive SET-25 and SET-32 mutants by making point mutations in the SET domains with CRISPR-Cas9. The catalytic mutants show loss of the relevant histone modifications comparable with null mutants, confirming that the mutations abolish methyltransferase activity. Surprisingly however, the catalytic mutants were only partially defective in TEI, implicating other domains. Through protein structure and function prediction tools, we have identified a previously uncharacterised domain in SET-25 with homology to chromo and Tudor domains and show that it too contributes to TEI. We therefore propose that both the SET domain and chromo-like domain of SET-25 are required for efficient TEI establishment.