EpiCOL_Ecological and evolutionary plant epigenetics

Differences in genetic information are widely analyzed in connection with phenotypic and physiological diversity in many organisms, including plants. Epigenetic information, which is not encoded in the DNA sequence but inherited in the form of regulatory switches and chromatin configuration, has so far been widely ignored as potentially additional source of biodiversity. The aim of EpiCOL is to determine the amount, stability and importance of epigenetic diversity. I want to combine the expertise of our lab in epigenetic inheritance and molecular analysis of chromatin features with that of partner labs contributing their competence in ecological and evolutionary biology. The contribution described below should be seen in connection with those of the other partners, as described in the full EEFG proposal. Our lab wants to characterize epigenetic differences between selected Arabidopsis accessions collected from different habitats, test the flexibility of epigenetic features under different environmental conditions and upon genetic transmission, and ask whether epigenetic features contribute to fitness and selection. We will compare the expression of known epigenetic target sequences (transposons, retrotransposons, protein-coding and non-protein-coding genes) and of epigenetic regulators (chromatin-modifying factors, microRNA and imprinted genes). We will perform gene-specific and genome-wide DNA methylation analysis (Southern blot, ms-PCR, bisulfite sequencing) and chromatin analysis (ChIP, QRT-PCR, deep sequencing) and apply bioinformatic methods to link epigenetic polymorphisms with genomic information. We will provide technology and experience to apply the molecular techniques to the Scabiosa material. Our lab will cooperate with the Colot lab in whole epigenome analysis and with the Ouborg / Bossdorf / Schmid labs in planning and performing experiments in extreme habitats and for fitness analysis of epigenetic variants. The results are expected to contribute to our understanding of plant evolution and adaptation to changing environments.

With the current immense interest in epigenetics, there are growing speculations and hot debates about the possibility that adverse environmental conditions and life style trigger heritable changes in the offspring for many generations. This would be in stark contrast to the paradigm that only genetic changes cause heritable effects. Plants are great model organisms for experimentally addressing such questions, as their germ line is much later determined than in most animals and much more exposed to environmental influences. Using Arabidopsis thaliana, a small flowering plant that has been studied as extensively as no other with respect to genetic, genomic, physiological, developmental and molecular features, we have (1) tested whether heat stress of plants exerts heritable effects on non-stressed progeny of the plants. While the chosen conditions cause strong phenotypic symptoms in the treated parent plants, we could not detect measurable effects on growth in non-stressed progeny, even if the stress had already been applied also to grandparents. We see this as some evidence against a simple epigenetic adaptation hypothesis. To refine the analysis to the molecular level, we are (2) setting up a system that allows switching epigenetic states and monitoring their maintenance and (3) studying the epigenetic configuration directly in the plants germ line cells.