Chromatin is probably the most complex molecular ensemble in the cell. It consists of hundreds of proteins that package the DNA and interact with regulatory elements such as enhancers and promoters. All of these components work in concert, and cannot be fully understood unless they are studied in their native context. In addition, the spatial organization of interphase chromosomes is thought to be of key importance for genome expression and maintenance. Yet, this three-dimensional chromosome organization and its impact on gene regulation and other functions are still poorly understood.
In order to gain insight into these fundamental processes, we develop and apply new genomics techniques to reveal the interplay of chromatin and regulatory elements, and to visualize the architecture of chromosomes inside the nucleus. Examples of such new techniques are our DamID and m6A-tracer methods to map and visualize protein - DNA interactions, the TRIP method for multiplexed measurements of chromatin context effects, and the TIDE method to quickly assess genome editing. We primarily use mammalian cultured cells as model systems.