Live-cell 3D single-molecule tracking reveals how NuRD modulates enhancer dynamics

Enhancer-promoter dynamics are critical for the spatiotemporal control of gene expression, but it remains unclear how these dynamics are controlled by chromatin regulators, such as the nucleosome remodelling and deacetylase (NuRD) complex. Here, we show that the intact NuRD complex increases CTCF/Cohesin binding and the probability of the interaction of intermediate-range (~1Mb) interactions in Hi-C experiments. To understand how NuRD alters 3D genome structure in this way, we developed a novel approach to segment and extract key biophysical parameters from trajectories of the NuRD complex determined using live-cell 3D single-molecule imaging. Unexpectedly, this revealed that the intact NuRD complex decompacts chromatin structure, makes NuRD-bound sequences move faster, and thus increases the overall volume of the nucleus that they explore. Interestingly, we also uncovered a rare fast-diffusing state of chromatin that exhibits directed motion. The intact NuRD complex reduces the amount of time that enhancers/promoters remain in this fast state, which we propose would otherwise reset enhancer-promoter proximity. Thus, we uncover an intimate connection between a chromatin regulator and the spatial dynamics of the local region of the genome to which it binds.