| Project Detail |
From micro-scale chromatin activities to emergent macro-scale properties
The massive amount of DNA in a cell is wound around proteins like beads on a thread in a complex called chromatin. Increasing evidence suggests that the emergent material properties of chromatin regulate essential nuclear processes. Characterising these properties has been elusive because in vitro studies lack the complexity of the cell’s machinery whereas intact cell studies cannot access small-scale dynamics easily. The EU-funded SynthNuc project will bridge the scale gap with Xenopus laevis egg extracts and synthetic nuclei made of pre-engineered DNA sequences. High-tech experimental techniques will shed light on how collective small-scale chromatin activities give rise to the large-scale material properties of chromatin.
The main aim of this proposal is to resolve how the physics of molecular-scale activities result in the emergent material properties of chromatin and how those contribute to chromatin organization and function. Mounting evidence suggests that the material properties of chromatin regulate essential nuclear processes. Chromatin has been studied with two disconnected approaches; pure in vitro studies, perfectly suited for careful biophysical measurements on single DNA molecules but lacking the complexity of a cell, or intact cell measurements, with limited access to measure material properties and small-scale chromatin dynamics. The physical properties of chromatin, however, are emergent and result from the molecular activities that are in turn regulated by those properties. As a consequence, it is crucial to establish new experimental assays that connect these two scales and levels of complexity. Here, I will bridge the gap in scales and biochemistry between pure in vitro assays and measurements in intact cells by reconstituting chromatin processes in Xenopus laevis egg extracts across scales. I will combine quantitative microscopy, optical tweezer measurements, and theory to biophysically characterize the self-organization of protein-DNA co-condensation and loop extrusion and single chromatin molecules of increasing complexity. To bridge the microscopic and the macroscopic scales, I will assemble synthetic nuclei made of pre-engineered DNA sequences, which allows for exquisite control of DNA length, amount, and chromatin activities. In combination with microrheology, micropipette aspiration, and magnetic tweezers, I will unravel how the collective behavior of chromatin activities gives rise to the emergence of large-scale material properties of chromatin. This project will provide a physical description of the material state of chromatin across scales and contribute to reveal the basic physical principles that govern nuclear organization and function. |
