Epigenomic Landscape and Natural Variation in Transgenerational Inheritance in C. elegans – EpiMEV

Heredity is at the core of biology. Although hereditary variation is mostly based on DNA sequence, epigenetic heredity has now been described in a range of species. How epigenetic variation is molecularly transmitted over generations, and whether regulation of such epigenetic inheritance shows genetic variation in nature are key questions. Here we address these questions in an integrative manner by characterizing both the molecular mechanisms and natural genetic variation in epigenetic inheritance in the nematode Caenorhabditis elegans.

Over the past few years C. elegans has provided valuable insights on mechanisms of multigenerational inheritance dependent on germline nuclear small RNAs and histone post-translational modifications. We use two experimental paradigms to study epigenetic inheritance in C. elegans:
(1) Induction of progressive sterility by chronic exposure to high temperature (25°C) across multiple generations; this so-called mortal germline phenotype is displayed by a variety of small RNA and histone modification mutants and shows a characterized genetic variation among C. elegans wild isolates.
(2) Multigenerational memory of a trigger of RNA interference (RNAi); for example, the wildtype N2 reference strain displays memory of an RNAi trigger that lasts 4-5 generations when using GFP RNAi against a single-copy Ppie-1::GFP transgene. This memory is known to depend on the nuclear RNAi pathway, HRDE-1/Argonaute and H3K9 histone methyltransferases, but the involvement of H3K4 di-and tri-methylation, generally associated with actively transcribed genomic regions, has not been explored.

Preliminary data indicate that (a) multigenerational transmission likely involves the regulation of histone H3K4 methylation; (b) C. elegans shows natural genetic variation in the presence and degree of such multigenerational epigenetic transmission; (c) the microbial environment of C. elegans may suppress the mortal germline phenotype of both H3K4 methylation mutants and wild isolates.
The project will involve three research groups with complementary expertise in the fields of C. elegans developmental genetics, imaging, epigenetic inheritance through small RNAs and chromatin pathways, and evolutionary genetics.

The three principal objectives are:
Aim 1: Test whether and how H3K4 methylation plays a role in transgenerational memory. We will complement genetic approaches with the analysis of candidate molecular mechanisms involved in epigenetic inheritance: small RNAs, chromatin marks and chromatin organization.
Aim 2: Investigate the presence of evolutionary variation in RNAi inheritance, and characterize this evolutionary variation regarding small RNAs and chromatin pathways. For this aim, we will extend the assays used on the N2 reference strain to other wild isolates. We expect to uncover directly for the first time intraspecific evolution in transgenerational inheritance and the underlying genetic variation.
Aim 3: Characterize the effect of associated microorganisms on the mortal germline phenotype, as well as on transgenerational memory. We expect to establish the range and ecological relevance of the organisms that suppress multigenerational phenotypes and if possible, uncover metabolite(s) that participate in this suppression.

Significance: We have established experimental systems in C. elegans allowing the molecular study of non-genetic inheritance and the study of existing natural genetic variation in the species. We will characterize, for the first time, how natural genetic variation modulates molecular mechanisms of epigenetic inheritance systems. This project therefore addresses a fundamental question in current biological research with wide-ranging implications for multiple disciplines, including heredity, gene regulation, developmental biology and evolution.