The mechanobiology of nuclear phase separation

Abstract

The cell nucleus can be thought of as a complex, dynamic, living material, which functions to organize and protect the genome and coordinate gene expression. These functions are achieved via intricate mechanical and biochemical interactions among its myriad components, including the nuclear lamina, nuclear bodies, and the chromatin itself. While the biophysical organization of the nuclear lamina and chromatin have been thoroughly studied, the concept that liquid-liquid phase separation and related phase transitions play a role in establishing nuclear structure has emerged only recently. Phase transitions are likely to be intimately coupled to the mechanobiology of structural elements in the nucleus, but their interplay with one another is still not understood. Here, we review recent developments on the role of phase separation and mechanics in nuclear organization and discuss the functional implications in cell physiology and disease states.

FIG. 1.

The nucleus is host to a wide array of liquid-like nuclear condensates, e.g., nucleoli, PML bodies, nuclear speckles, and Cajal bodies, which form by phase separation, and is also largely filled with chromatin, which is highly structured and exhibits dynamic micrometer-scale correlations. Chromatin is a viscoelastic material with heterogeneous pore sizes and structure throughout the nuclear environment, and liquid-like condensates deform the chromatin matrix as they grow. These components directly interact in multiple contexts and elucidating the physical interplay between phase separation and nuclear mechanics is critical for understanding nuclear organization.

FIG. 2.

Viscoelasticity in the nucleus can be interrogated by a suite of methods known as microrheology. In passive microrheology (left column), tracer particles are tracked over time (a) and their movement is quantified by calculating a mean squared displacement (b), which typically scales as a power law in the time lag with exponent α. α = 1 indicates a purely viscous solution, while subdiffusion, i.e., α <1, which is typical of structures in the nucleus, is indicative of viscoelastic constraints, and α >1 is indicative of driven, active motion; these behaviors reflect local activity and mechanics, e.g., of chromatin. In active microrheology, a calibrated force is applied to the material and the deformation is used to infer the material's mechanical properties. For the nucleus, this is typically used to extract bulk mechanics via methods such as micropipette aspiration and atomic force microscopy (c). Typically, a force-extension curve is calculated, whose slope in the linear or elastic regime corresponds to the spring constant for displacements; nonlinearity indicates that the material is strain-stiffening or strain-softening (d). These techniques have defined the mechanical contributions of particular biological components of the nucleus such as the lamina and chromatin.

FIG. 3.

The thermodynamics of phase separation are traditionally understood using models of increasing complexity, building from a simple two-component “regular solution” colloidal system (a), to a multicomponent/multiphase system (b), and finally, to a polymeric system (c) containing components of differing lengths. These systems are typically understood by mapping phase diagrams with two or more components (d), or by calculating partition coefficients (e) in the case of multicomponent systems with intractably complex phase diagrams. Recent theoretical work has suggested that a local viscoelastic matrix can influence the equilibrium size, shape, and morphology of droplets, as a function of the ability of the droplet to wet the matrix and the mechanical stiffness of the matrix, quantified as the permeo-elastic number, p, and the elasto-capillary number, $h$, respectively (f).