In humans, a two-meter-long DNA polymer is physically folded into a micron-sized nucleus. Fundamental biological processes such as transcription or condensation of chromatin during mitosis require to physically bring distant DNA sequences together in space. For this to happen, the local material properties of chromatin need to be properly tuned in space and time. The physical properties of chromatin, however, are emergent and result from the molecular activities that are in turn regulated by those properties. Molecular processes make chromatin and active material. For example, DNA can be actively extruded into loops, a process thought to regulate gene expression by bringing together enhancer and promoters or packaging chromatin into stacked loops during chromatid formation. Phase separation regulated by the transcription machinery is thought to physically bring distant regulatory sequences together and to segregate chromatin into active and inactive compartments at large scales. However, the physics of these molecular processes and how they contribute to the emergence of the large-scale organization of chromatin and its material state is not well understood. In this project, we aim to understand how the physics of molecular-scale activities result in the emergent material properties of chromatin and how those contribute to chromatin organization and function. One of the major limitations in this field is the lack of methods to quantitatively explore chromatin across scales. To achieve this goal, we will bridge the gap in scales and biochemistry between previous pure in vitro assays and measurements in intact cells by reconstituting chromatin processes in Xenopus laevis egg extracts across scales.
