Novel insights into gene silencing mechanisms in Zea mays and Arabidopsis thaliana

Gene activity is positively or negatively regulated by transcription factors that bind to cis-acting regulatory sequences. In addition, gene expression is enforced by epigenetics, DNA interactions, and chromatin domains through mechanisms that span from modifications of the underlying DNA sequence up to higher order chromatin organization in the nucleus. This thesis discusses two gene silencing mechanisms in maize and Arabidopsis.
The RNA-directed DNA methylation (RdDM) pathway is, among others, involved in the in trans repression of sequences by homologous paramutagenic loci. The investigation of DNA methylation and chromatin structure of two RdDM-dependent, paramutagenic loci in maize revealed two distinct, extreme profiles, representing the endpoints of a negative correlation among RdDM loci in maize between the levels of DNA methylation in CHH context (where H = A,T or C) and histone H3-dimethylation at lysine 9. The inverse gradient of the two silencing marks emphasizes the variability of RdDM loci.
Additionally, it was investigated whether polycomb-dependent chromatin cluster as they exist in vertebrates can be found as well in Arabidopsis. Polycomb silencing at the FLC gene is induced by cold treatment, which allowed a spatial-temporal study of this gene upon repression. During the cold treatment a general, transient increase of interactions with sequences on other chromosomes was noticed, indicating a cold-stress induced chromatin decompaction that results in changes in the higher-order chromatin organization. Furthermore, once the FLC gene is repressed by polycomb, it interacts preferably with other closely located polycomb targets rather than with non-polycomb targets.