Epigenetics, Metabolism, and Acclimation


Cells in a complex organism specialize on different tasks, but they all share the same genomic blueprint. As the cells divide, what determines their fate and how do they remember their assigned functions? In the field of epigenetics, we address these questions by focusing on chemical modifications of histone proteins and DNA - the main constituents of chromatin. DNA methylation and different histone modifications are transmitted during cell division and can regulate the activities of genes by influencing their surrounding chromatin structure. Exploring these chromatin dynamics is not only central to cell differentiation during development, but also sheds light on how cells memorize cues from their surroundings and acclimatize to environmental changes.


In our group, we study (I) how environmental changes influence epigenetic regulation and (II) how chromatin dynamics contribute to acclimation and stress memory. We thereby pay particular attention to the roles of central metabolic pathways. Chromatin modifications are added or removed by enzymes, which require certain metabolites to do their jobs. Looking further, it turns out that metabolic pathways are not just suppliers of chemical groups, but they play active roles in epigenetic regulation, for example by also inhibiting chromatin-associated enzymes. The links between metabolism and epigenetics might seem inherent, but we are just starting to recognize the scope of implications in different diseases and stress responses. Read more about our current DYNAMET project here.


We use Arabidopsis thaliana as model organism in our lab to study epigenetics mechanisms and the effects of epigenetic changes. This small plant has proven to be very useful in research and we can take advantage of the vast data and genetic resources that are available. Ethical barriers for genetic and phenotypic studies do not apply and handling and maintenance of the germplasm is convenient. In contrast to mammals, Arabidopsis tolerates genome-wide losses of DNA methylation, which makes genetic dissection of the involved mechanisms much easier. Moreover, epigenetic patterns in mammals are reset in each generation, whereas in plants, changes in DNA methylation can lead to epialleles that are heritable over many generations. This enables us to stably manipulate DNA methylation patterns and follow the phenotypic changes.


Integral to our studies is the identification of epigenetic factors and subsequent biochemical characterization of their functions. For this, we use interdisciplinary approaches, including genetic and chemical screening, “omics” technologies (genomics, metabolomics, proteomics), and computational tools. We apply state-of-the-art phenotyping systems to accelerate the discovery of traits that are influenced by epigenetic and metabolic changes in Arabidopsis and important crop species, including wheat. We also make use of the unique chambers for environmental simulation at our institute to test the effects of different climate parameters, light regimes, and gas concentration.