The term „epigenetics“ was coined as a collective name for cases of alternate gene expression states that are heritable, but are not based on changes in DNA sequences. In order to elucidate the underlying mechanisms, we are employing genetic and molecular-biological methods in Arabidopsis thaliana and other plants as model systems. Our research addresses presently RNA-directed transcriptional gene silencing of transgenes, control of endogenous pararetroviruses and transgene-dependent alteration of nuclear architecture. Application of the gained knowledge is directly tested in efforts to optimise stable expression of recombinant proteins in plants by targeted modification of epigenetic mechanisms. 

RNA-directed transcriptional gene silencing
In RNA-directed transcriptional gene silencing (RdTGS), specific repression of transcription is induced in the presence of double stranded RNA with sequence-homology to a gene promoter. So far, work on this mechanism has mainly focused on molecular features of the silenced state such as DNA methylation patterns or the identity of RNAs and proteins involved. Recent observations suggested that the chromosomal location and the internal structure of targeted genes may also play an important role. We are currently investigating these aspects systematically in a transgene system in A. thaliana. Further approaches aim at the identification of factors counteracting RdTGS by introgression of known mutations in candidate genes and a new genetic screen for mutations enhancing silencing.

Epigenetic control of endogenous pararetroviruses
Pararetroviruses comprise a group of DNA viruses for which integration is not obligatory for their replication. Nevertheless, for some members of this group, related sequences were found to be integrated in plant genomes. These endogenous pararetroviruses are often fragmented or highly degenerated and therefore non-functional. However, integrants comprising complete and functional viral sequences can be activated under certain conditions and then lead to viral infections of plants. The possible involvement of epigenetic mechanisms in the control of endogenous pararetroviruses is under investigation.

Further research topics are related to the influence of epigenetic modifications on the local chromatin arrangement in nuclei of A. thaliana and to mechanisms of DNA double strand break repair in plants (in cooperation with  I. Schubert, Research Group Karyotype Evolution) as well as to the improvement of recombinant protein expression in plants (in cooperation with  J. Kumlehn, Research Group Plant Reproductive Biology).