Dr. M.E. (Maike) Stam

Epigenetic and chromatin regulation of gene expression

Eukaryotic gene regulation is a very complex process in which a wide range of molecules and mechanisms come together, such as different types of DNA sequences, proteins and RNAs, genetic and epigenetic mechanisms. The tremendously rapid advances in high-throughput sequencing, but also advances in other techniques have enabled many exciting new discoveries in the field of gene regulation. Research in my team focuses on gene regulation through cis-regulatory sequences, and epigenetic and chromatin-based mechanisms. We use plants (maize, tomato, Arabidopsis, and oilseed rape) as a model system and mainly focus on two research lines: 1) Regulation by epigenetic mechanisms & chromatin structure, 2) Control of gene expression by cis-regulatory sequences.

Regulation by epigenetic mechanisms & chromatin structure

Plant and animal breeding has been done for thousands of years and forms the basis of food production and other human activities. It is based on the heritability of desirable traits and the reiterated process of crossing and selection. Most differences in heritable traits are due to genetic variation, which are DNA sequence differences between individuals. In addition, epigenetic variation can result in trait variation and contribute to the diversity we know of today. Epigenetic variation refers to mitotically and/or meiotically heritable changes in genome function based on chromatin modifications instead of changes in the DNA sequence. Examples of such modifications are DNA methylation and histone modifications. Epigenetic modifications are heritable, but not as stable as the genetic code. At particular DNA sequences the epigenetic information can be remodeled, among others under the influence of homologous DNA sequences carrying different epigenetic marks. The latter is well known to occur between individual alleles in a process called paramutation, but has also been indicated to occur at a genome-wide scale in heterosis, a phenomenon extensively exploited in agricultural breeding in which F1 hybrids between two parents display superior phenotypes compared to that of their parents. Currently, the contribution of epigenetic variation to beneficial traits displayed by crop plants and livestock, as well as the molecular basis underlying heterosis are still largely unknown. The aim of this research line is to unravel the mechanisms underlying the transfer of epigenetic information, both between specific alleles as genome-wide.