Plastic germline reprogramming of heritable small RNAs enables maintenance or erasure of epigenetic memories.

In Caenorhabditis elegans small RNAs can regulate genes across generations. The mysterious tendency of heritable RNA interference (RNAi) responses to terminate after 3-5 generations has been referred to as "the bottleneck to RNAi inheritance." We have recently shown that the re-setting of epigenetic inheritance after 3-5 generations is not due to passive dilution of the original RNA trigger, but instead results from an active, multigenerational, and small RNA-mediated regulatory pathway. In this "Point of View" manuscript we suggest that the process that leads to the erasure of the ancestral small RNA-encoded memory is a specialized type of germline reprogramming mechanism, analogous to the processes that robustly remove parental DNA methylation and histone modifications early in development in different organisms. Traditionally, germline reprogramming mechanisms that re-set chromatin are thought to stand in the way of inheritance of memories of parental experiences. We found that reprogramming of heritable small RNAs takes multiple generations to complete, enabling long-term inheritance of small RNA responses. Moreover, the duration of this reprogramming process can be prolonged significantly if new heritable RNAi responses are provoked. A dedicated signaling pathway that is responsive to environmental cues can tune the epigenetic state of the RNAi inheritance system, so that inheritance of particular small RNA species can be extended.

A Tunable Mechanism Determines the Duration of the Transgenerational Small RNA Inheritance in C. elegans.

In C. elegans, small RNAs enable transmission of epigenetic responses across multiple generations. While RNAi inheritance mechanisms that enable "memorization" of ancestral responses are being elucidated, the mechanisms that determine the duration of inherited silencing and the ability to forget the inherited epigenetic effects are not known. We now show that exposure to dsRNA activates a feedback loop whereby gene-specific RNAi responses dictate the transgenerational duration of RNAi responses mounted against unrelated genes, elicited separately in previous generations. RNA-sequencing analysis reveals that, aside from silencing of genes with complementary sequences, dsRNA-induced RNAi affects the production of heritable endogenous small RNAs, which regulate the expression of RNAi factors. Manipulating genes in this feedback pathway changes the duration of heritable silencing. Such active control of transgenerational effects could be adaptive, since ancestral responses would be detrimental if the environments of the progeny and the ancestors were different.

Starvation-induced transgenerational inheritance of small RNAs in C. elegans.

Evidence from animal studies and human famines suggests that starvation may affect the health of the progeny of famished individuals. However, it is not clear whether starvation affects only immediate offspring or has lasting effects; it is also unclear how such epigenetic information is inherited. Small RNA-induced gene silencing can persist over several generations via transgenerationally inherited small RNA molecules in C. elegans, but all known transgenerational silencing responses are directed against foreign DNA introduced into the organism. We found that starvation-induced developmental arrest, a natural and drastic environmental change, leads to the generation of small RNAs that are inherited through at least three consecutive generations. These small, endogenous, transgenerationally transmitted RNAs target genes with roles in nutrition. We defined genes that are essential for this multigenerational effect. Moreover, we show that the F3 offspring of starved animals show an increased lifespan, corroborating the notion of a transgenerational memory of past conditions.