Integrated MINFLUX tracking reveals two distinct chromatin dynamics classes across cell types

Authors:

Matteo Mazzocca, Domenic N. Narducci, Simon Grosse-Holz, Jessica Matthias, Tatiana S. Karpova, Anders S. Hansen

Keywords:

Chromatin; chromatin dynamics; DNA double-strand break repair; enhancer–promoter search

Abstract:

Chromatin dynamics control the timescales of essential biological processes and reflect how chromatin is organized in the nucleus. Previous studies have reported widely varying degrees of chromatin subdiffusion without consensus. For robust subdiffusion measurements, chromatin should be tracked across a sufficiently large dynamic range. Here we track chromatin movement across seven orders of magnitude in time by integrating MINFLUX microscopy with single-molecule and locus tracking in five mouse and human cell types. We discover two fundamentally different dynamics classes that are cell type specific and not described by common chromatin polymer models. In one class, chromatin displays strong subdiffusion across all timescales (α ~0.3), indicating that the local environment is more quickly searched than the distal. In the other class, chromatin shifts from strongly subdiffusive at short timescales to less subdiffusive, making search less local over long timescales. Both classes are only moderately sensitive to perturbations. Search times under these observed dynamics are extremely short for nearby loci (<100 nm) but almost impossibly long over larger distances (>1 µm); this has important implications for processes involving two-locus contacts, such as enhancer–promoter search and DNA double-strand break repair.

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