The viscoelastic properties of chromatin and the nucleoplasm revealed by scale-dependent protein mobility

TL;DR

This study characterizes the viscoelastic properties of the nucleus in living human cells by measuring protein mobility, revealing scale-dependent behavior that influences DNA target search processes.

Contribution

It provides the first detailed analysis of nuclear viscoelasticity using inert protein tracers, showing scale-dependent properties and implications for chromatin dynamics.

Findings

Nuclear interior behaves as viscous on small and large scales.

Intermediate scales show viscoelastic behavior dependent on protein size.

Chromatin forms a random obstacle network affecting molecular diffusion.

Abstract

The eukaryotic cell nucleus harbors the DNA genome that is organized in a dynamic chromatin network and embedded in a viscous crowded fluid. This environment directly affects enzymatic reactions and target search processes that access the DNA sequence information. However, its physical properties as a reaction medium are poorly understood. Here, we exploit mobility measurements of differently sized inert green fluorescent tracer proteins to characterize the viscoelastic properties of the nuclear interior of a living human cell. We find that it resembles a viscous fluid on small and large scales, but appears viscoelastic on intermediate scales that change with protein size. Our results are consistent with simulations of diffusion through polymers and suggest that chromatin forms a random obstacle network rather than a self-similar structure with fixed fractal dimension. By calculating how long molecules remember their previous position in dependence on their size, we evaluate how the nuclear environment affects search processes of chromatin targets.