The cells of our body contain nearly the same genetic information but greatly differ in function. Accordingly, each cell interprets its genetic information in a distinct way. This involves chemical modifications of the DNA and the histone proteins, which are in close contact with the DNA, and the spatial organization of the genomic DNA within the cell nucleus. These features, which are often called “epigenetic”, are linked to the cellular gene expression program and the cellular identity. Epigenetic dysregulation is often found in diseased cells, indicating that their faithful regulation is important for our health.
DNA and histone modifications as well as the spatial organization of the genome are on the one hand dynamic, as they can change in response to different signals from outside. On the other hand, they are stable enough so that the cellular identity they encode can be maintained over time. How this balance between plasticity and stability is mechanistically regulated is a key question. As many cellular proteins are involved in the regulation of DNA/histone modifications and spatial genome organization, which have multiple functions and are often redundant, it is difficult to study this system using loss-of-function approaches in cells.
The objective of this project was to reconstitute minimal systems to investigate the formation and maintenance of domains of modified chromatin, both in vitro and in living cells. On the one hand, this entailed the development of bulk and single-molecule microscopy assays to visualize chromatin-associated proteins and histone modifications on chromatinized templates in the test tube to assess their biophysical properties. On the other hand, this comprised the implementation of "synthetic biology" approaches to generate ectopic domains in living cells to study their dynamics.
In this project, we have established the above-mentioned assays and have studied the mechanisms underlying the dynamics of modified chromatin domains. Our results have shed light on the question how phase separation and the action of read-write proteins regulate modified chromatin domains, and how this impacts cellular function. We anticipate that our results will be helpful for upcoming applications, for example in the context of condensate-modifying epigenetic drugs.
