Epigenetic modifications acquired by an individual during its lifetime can be inherited for multiple generations. We have developed a transgenerational epigenetic inheritance (TEI) sensor in the model organism Caenorhabditis elegans in which RNAi-induced silencing of a GFP transgene is robustly inherited for multiple generations. We previously showed that the putative histone methyltransferases SET-32 and SET-25 are required for establishment of transgenerational silencing but are dispensable for long-term maintenance of silencing. The molecular nature of the establishment signals are not yet certain.
Here we show that another two putative histone methyltransferases, SET-9 and SET-26, are involved in establishment and long-term maintenance of silencing, respectively. Intriguingly, the methyltransferase domain of these two proteins is not well conserved and their ability to act as histone lysine methyltransferases is controversial. SET-9 and SET-26 also contain PHD finger domains that we show bind H3K4me3 with high affinity in vitro. TEI assays performed on SET-26 strains in which either the putative methyltransferase or PHD finger domains were mutated suggest that the methyltransferase domain is required for establishment of silencing, while the PHD finger’s role is mainly in maintenance of silencing.
Interestingly, we also show that mutations that render the methyltransferase domains of SET-32 and SET-25 catalytically inactive only cause a partial defect in TEI, implicating a role for other protein domains. Using AlphaFold2 we have identified a previously uncharacterised domain in SET-25 that has the characteristics of a chromodomain. Chromodomains are well known to have methyl-lysine binding activity.
Taken together these data suggest a model whereby SET-25, SET-9 and SET-26 bind methylated lysines using their chromodomain and PHD finger domains, and then alongside SET-32 methylate neighbouring histones to nucleate and spread the silencing signal. Effective establishment and transmission of the epigenetic mark between generations requires both methyltransferase activity and methyl reader activity.