Diffusion of nuclear proteins and its link to 3d chromatin organization

The interaction of proteins with chromatin regulates many cellular functions. Most DNA-binding proteins interact both non-specifically and transiently with many chromatin sites, as well as specifically and more stably with cognate binding sites. These interactions and chromatin structure are important in governing protein dynamics. These questions can be addressed theoretically using diffusion models. I will show how that the dynamics of proteins is determined by the 3d organization of chromatin in the nucleus. The time to find a chromatin target depends on chromatin organization around it, which determines the local association and disassociation rates.

These ideas can be applied to study the dynamics of nuclear proteins and infer from single particle trajectories the geometry of the structures with which they interact.