Molecular Epigenetics

Epigenetic modifications are a hallmark of gene regulation and thus govern a wide range of biological processes. We are interested in revealing the molecular interplay of chromatin modifying proteins, chromatin-reading proteins and epigenetic marks to understand the mechanisms underlying differentiation, ageing and DNA repair. To this aim we employ chromatin and protein biochemistry, ChIP and RNA deep sequencing techniques, stem cell biology, in vitro and in vivo techniques to obtain a detailed picture of the molecular events occurring at chromatin.

Epigenetic Mechanisms of Cellular Differentiation

Self-renewal and cellular differentiation of embryonic stem cells is controlled by a variety of distinct epigenetic modifications and multi-protein complexes. Silencing of genes is usually linked to methylation of histone H3K27 (H3K27me3) and ubiquitylation of histone H2A, which is brought about by Polycomb-Repressive complexes 1 and 2 (PRC1 and PRC2), respectively. During differentiation the epigenetic landscape changes dramatically and to transcriptionally activate genes the PRC complexes and their respective repressive marks have to be removed from chromatin. We have demonstrated that the protein ZRF1 acts at the onset of differentiation to remove PRC1 from chromatin and that it facilitates the deubiquitylation of histone H2A. ZRF1 acts as a switch protein that is crucial to converting chromatin from a silenced to a transcriptionally active state (Figure 1). In general, our laboratory is interested in the interplay between histone marks and novel epigenetic factors, which have an impact on differentiation. Recently, we started to study the function of ncRNAs since key developmental genes are typically regulated by ncRNAs. Interestingly, we have purified such ncRNAs as interactors of typical players of the Polycomb system and will now study their role in detail on a genome-wide basis in stem cells. Those ncRNAs are likely important for linking the functions of enhancer elements and promoters of Polycomb target genes. Our goal is to derive a deeper insight into the activation of genes and understand the integration of signals stemming from histone modifications, ncRNA and chromatin remodelling.

Figure 1: Model for ZRF1-dependent transcriptional activation. At the onset of cellular differentiation ZRF1 is specifically recruited to chromatin by binding the mono-ubiquitin mark at histone H2A (yellow balls). In a two-step mechanism it dislocates PRC1 complexes from chromatin and subsequently facilitates deubiquitination of histone H2A by USP21. Chromatin is thereby converted into a transcriptionally active state, which permits polymerase II to read through chromatin. For details see Richly et al., 2010 and Richly et al., 2011.

Molecular Epigenetics of Ageing

Ageing is certainly one of the most interesting but still less understood phenomena of biology. Tissues of different ages can easily be dissected and in the last couple of years cellular pathways and certain factors that act on longevity were discovered. However, how chromatin is modified during ageing stays enigmatic. Our laboratory is interested in unveiling the alterations of the chromatin landscape in the course of ageing. We use the nematode C. elegans as a model system and have discovered a specific histone-modification that seems to play a major role during ageing. The focus of this project consists of revealing the enzymes setting and removing the chromatin mark and epigenetic readers that transmit the ageing signal. Over the long-term we will turn our attention to mammals and investigate ageing in animal models and stem cells.

Signalling and Crosstalk at Chromatin during DNA Repair

Genomic integrity is central to homeostasis and facilitated by an intricate DNA damage response system. Damage of DNA by radiation leads to the activation of a signalling cascade driven by the ATM-ATR kinases, which leads to the ubiquitylation of histone H2A and H2AX at sites of double strand breaks. The ubiquitylated histone H2A recruits the E3 ligase RNF168, which is believed to add further ubiquitin residues to the substrate thus forming a Lys63-linked polyubiquitin chain. However, in vivo histones H2A and H2AX are predominantly mono-ubiquitylated during DNA damage. Recently the PRC1 complex was also shown to be involved in DNA double strand repair and thus parallel pathways exist to ensure a full-blown damage response. We are interested in identifying and characterizing novel H2A/H2AX-mono-ubiquitin-binding proteins to shed more light on the molecular mechanisms of double strand break repair.  Additionally we want to understand the crosstalk with other downstream acting protein complexes and modifications of the histone-tails in the course of DNA repair. Our goal is therefore to derive a better understanding of how chromatin modifications drive DNA repair by recruitment of multi-protein complexes.

Holger is an Associate Member of the EpiGeneSys network of scientists.