Intraspecific variation in the duration of epigenetic inheritance in wild isolates of C. elegans

Epigenetic inheritance is generally less stable across generations than DNA sequence-based heredity. One common form of epigenetic inheritance, found in plants, fungi, and animals, is the transgenerational memory of gene silencing mediated by small RNAs. These small RNAs can be amplified through RNA-dependent RNA polymerases, thus maintaining the silenced state across multiple generations. Such molecular mechanisms raise questions regarding their natural variation and evolutionary impact. Here, we ask whether the presence and duration of epigenetic inheritance vary within a species. We use the ability of the nematode Caenorhabditis elegans to silence genes for multiple generations after an initial RNA interference trigger. We find that the duration of silencing memory varies across C. elegans wild strains as a quantitative trait expressed in number of generations. Strikingly, several wild strains show no memory, while some display a longer memory than the reference strain. Natural DNA sequence polymorphisms, such as in the set-24 gene, affect the duration of small RNA inheritance. We further show that the silencing memory duration in wild strains increases with temperature and that memory is retained upon early starvation arrest and passage through dauer diapause. Altogether, these results demonstrate intraspecific diversity in the regulation of small RNA-based heredity, a prerequisite for selection acting on genetic variants affecting epigenetic inheritance duration.