Molecular mechanisms of epigenetic gene regulation
The overarching goal of research in our lab is to elucidate how histone modifications regulategene expression. Ultimately, we are keen to understand how different histone modifiers and readers interact with other chromatin factors to establish complex regulatory systems that control development and affect disease states. We aim to take a multidisciplinary approach to tackle these questions, combining powerful biochemistry with proteomic, genomic, cell- biological, imaging-based, and systems biology-inspired techniques.
We currently focus on determining the mechanisms that govern the interplay between Polycomb and Trithorax group proteins at bivalent domains and poised enhancers, in order to resolve how these complexes regulate expression of developmental genes in embryonic stem (ES) cells. Bivalent domains harbour a distinctive histone modification signature containing both the active histone H3 lysine 4 trimethylation (H3K4me3) mark and the repressive H3K27me3 mark (Figure 1A). They are presumed to maintain developmental genes in a poised state, allowing for timely expression upon differentiation signals, while keeping them repressed in ES cells. Bivalent nucleosomes adopt a previously unknown asymmetric conformation, carrying the active and repressive mark on opposite copies of histone H3 (Voigt et al., Cell, 2012). However, it remains unclear how bivalent domains are established and subsequently interpreted in ES cells and whether they are essential for proper ES cell differentiation and development.
We have set up methods to generate recombinant chromatin templates carrying defined modifications. We are utilising these templates to determine which factors are binding to asymmetric, bivalent nucleosomes in ES cells to clarify how this mark signature is decoded by the cell and how it is translated to a poised state of expression. These recombinant chromatin templates further allow us to study how different histone marks affect the placement of other marks. We have purified native MLL2 complexes from ES cells by CRISPR-based endogenous tagging. Preliminary results indicate that placement of H3K4me3 is inhibited by H3K27me3, pointing to a mechanism by which this mark may repress transcription.
We are further setting up quantitative, systems biology-inspired approaches to define the physiological functions of bivalent domains. Specifically, we are testing the hypothesis that bivalency may represent a dynamic state in between activation and repression that allows plasticity for genes to be activated at the correct time during development (Figure 1B). As both temporal and spatial accuracy of expression patterns is essential for development, bivalency may be indispensable to proper embryonic development.
Brewster, R. C., Gavins, G. C., Günthardt, B., Farr, S., Webb. K. M., Voigt, P., & Hulme, A. N. (2016). Chloromethyl-triazole: a new motif for site-selective pseudo-acylation of proteins. Chem. Commun. 52, 12230–12232.
Voigt, P., Tee, W.-W., and Reinberg, D. (2013). A double take on bivalent promoters. Genes Dev. 27, 1318–1338.
Voigt, P., Leroy, G., Drury, W. J., Zee, B. M., Son, J., Beck, D B., Young, N. L., Garcia, B A., and Reinberg, D. (2012). Asymmetrically Modified Nucleosomes. Cell 151, 181–193.