Research

Current projects:

1. Chemical synthesis of post-translationally modified proteins

The study of the function of post-translational modifications requires access to chemically defined samples. Thus, we develop and apply novel chemical methods to site-specifically modify proteins. We have recently developed methods that further allow to control the supramolecular assembly of macromolecular complexes. These methods were used to assemble nucleosomes, asymmetrically modified on H3 or H4.

Similar chemical approaches are being applied to synthesize post-translationally modified proteins involved in non-chromatin signaling pathways.

Relevant publications:

Traceless synthesis of asymetrically modified bivalent nucleosomes, 10.1002/anie.201510996

http://pubs.rsc.org/en/content/articlehtml/2017/cc/c7cc06180c

2. Dynamical processes in chromatin regulation

The structure of chromatin is organized over many length scales and highly dynamical. Its function is modulated by the combinatorial effect of histone post-translational modifications (PTMs). Specialized reader proteins interpret combinations of PTMs and result in structural transition in chromatin, recruitment of cellular machinery and gene regulation.

We develop chemical methods to site specifically introduce PTMs and fluorescent labels into reconstituted synthetic chromatin fibers to study conformational dynamics in chromatin as a function of histone marks and structural reader proteins on the single molecule scale.

We are interested in how proteins readers find their site of action in the highly complex environment of the cell. Thus, we characterize the binding thermodynamics and binding kinetics of protein readers with modified chromatin in vitro and study their diffusional properties and localization in cells.

Relevant publications:

Multivalency governs HP1α association dynamics with the silent chromatin state, 18 Jun 2015 | doi:10.1038/ncomms8313

https://academic.oup.com/nar/article/4064210/Single-molecule-kinetic-analysis-of-HP1-chromatin

https://www.nature.com/nsmb/journal/vaop/ncurrent/full/nsmb.3488.html

http://www.nature.com/nrg/journal/vaop/ncurrent/abs/nrg.2017.28.html

12-mer synthetic chromatin array. AFM image, w/ LBNI

 

3. Development of in vivo probes for chromatin modification patterns

Patterns of histone PTMs are the result of a highly regulated interplay between PTM writer, eraser and reader proteins. These patterns establish a landscape of distinct chromatin states and are associated with the regulation of gene expression, DNA replication and repair. A deeper knowledge of the function and dynamics of these combinatorial states is of critical importance, as misregulation may result in malignancy and disease.

We are interested in the molecular mechanisms how patterns of histone modifications are read out. We therefore use protein engineering approaches to design readers with novel binding affinities and study their effects on cell function.

We develop tools that allow to read out and alter epigenetic states in living cells. To this end, we are combining protein engineering, synthesis of modified chromatin and protein visualization. In vitro evaluation of candidate constructs then allows their application in cells to sense changes in cell differentiation state or report on the effects of epigenetic drugs.

Relevant publication:

http://www.cell.com/cell-chemical-biology/fulltext/S2451-9456(17)30389-6