Liquid Condensates in the Nucleus

Surface Fluctuations and Coalescence of Nucleolar Droplets in the Cell Nucleus

Material properties of the cell nucleus and its constituents are critical for all cellular processes, directly impacting the central dogma of biology. For example, the rheological behavior of the nucleoplasm affects the length scales and timescales of molecular and organelle transport inside the nucleus, yet its measurement proves nontrivial. Microrheology gave us a rare glimpse into the physical properties of the nucleoplasm, however, such approaches are invasive, requiring an injection of foreign particles into the nucleus, which only a few cells survive.

Moreover, injected nuclei are in distress that can change their physical properties. We developed an alternative strategy of using physiological dynamics and events inside the human cell nucleus to infer material properties of the nucleus and its constituents in live cells. Such an approach employing natural probes is completely noninvasive.

Specifically, we investigate surface fluctuations and fusion of nucleoli, the largest structures inside the nucleus, which not only reveal that nucleoli behave as liquid droplets in human cells, but also inform on the rheological behavior of the surrounding nucleoplasm. By analyzing surface dynamics and fusion kinetics of human nucleoli in vivo, we find that the nucleolar surface exhibits subtle, but measurable, shape fluctuations and that the radius of the neck connecting two fusing nucleoli grows in time as r(t) ∼ t^1/2. This is consistent with liquid droplets with low surface tension ∼10^−6 Nm^−1 coalescing within an outside fluid of high viscosity ∼10^3 Pas. Our study presents a noninvasive approach of using natural probes and their dynamics to investigate material properties of the cell and its constituents.

C. M. Caragine, S. C. Haley and A. Zidovska, Phys. Rev. Lett., 121: 148101 (2018)

Nucleolar dynamics and interactions with nucleoplasm in living cells

Liquid-liquid phase separation (LLPS) has been recognized as one of the key cellular organizing principles and was shown to be responsible for formation of membrane-less organelles such as nucleoli. Although nucleoli were found to behave like liquid droplets, many ramifications of LLPS including nucleolar dynamics and interactions with the surrounding liquid remain to be revealed.

Here, we study the motion of human nucleoli in vivo, while monitoring the shape of the nucleolus-nucleoplasm interface. We reveal two types of nucleolar pair dynamics: an unexpected correlated motion prior to coalescence and an independent motion otherwise. This surprising kinetics leads to a nucleolar volume distribution, p(V) ~ V^-1, unaccounted for by any current theory. Moreover, we find that nucleolus-nucleoplasm interface is maintained by ATP-dependent processes and susceptible to changes in chromatin transcription and packing. Our results extend and enrich the LLPS framework by showing the impact of the surrounding nucleoplasm on nucleoli in living cells.

C. M. Caragine, S. C. Haley and A. Zidovska, eLife, 8:e47533 (2019)

The self-stirred genome: large-scale chromatin dynamics, its biophysical origins and implications

The organization and dynamics of the human genome govern all cellular processes — directly impacting the central dogma of biology — yet are poorly understood, especially at large length scales. Chromatin, the functional form of DNA in cells, undergoes frequent local remodeling and rearrangements to accommodate processes such as transcription, replication and DNA repair. How these local activities contribute to nucleus- wide coherent chromatin motion, where micron-scale regions of chromatin move together over several seconds, remains unclear. Activity of nuclear enzymes was found to drive the coherent chromatin dynamics, however, its biological nature and physical mechanism remain to be revealed. The coherent dynamics leads to a perpetual stirring of the genome, leading to collective gene dynamics over microns and seconds, thus likely contributing to local and global gene-expression patterns. Hence, a possible biological role of chromatin coherence may involve gene regulation.

A. Zidovska, Curr. Opin. Genet. Dev., 61: 83-90 (2020)