Search for: All records

Chromatin – the functional form of DNA in the cell – exists in the form of a polymer immersed in a nucleoplasmic fluid inside the cell nucleus. Both chromatin and nucleoplasm are subject to active forces resulting from local biological processes. This activity leads to non-equilibrium phenomena, affecting chromatin organization and dynamics, yet the underlying physics is far from understood. Here, we expand upon a previously developed two-fluid model of chromatin and nucleoplasm by considering three types of activity in the form of force dipoles – two with both forces of the dipole acting on the same fluid (either polymer or nucleoplasm) and a third, with two forces pushing chromatin and solvent in opposite directions. We find that this latter type results in the most significant flows, dominating over most length scales of interest. Due to the friction between the fluids and their viscosity, we observe emergent screening length scales in the active flows of this system. We predict that the presence of different activity types and their relative strengths can be inferred from observing the power spectra of hydrodynamic fluctuations in the chromatin and the nucleoplasm. 

Material properties of the genome are critical for proper cellular function – they directly affect timescales and length scales of DNA transactions such as transcription, replication and DNA repair, which in turn impact all cellular processes via the central dogma of molecular biology. Hence, elucidating the genome's rheology in vivo may help reveal physical principles underlying the genome's organization and function. Here, we present a novel noninvasive approach to study the genome's rheology and its response to mechanical stress in form of nuclear injection in live human cells. Specifically, we use Displacement Correlation Spectroscopy to map nucleus-wide genomic motions pre/post injection, during which we deposit rheological probes inside the cell nucleus. While the genomic motions inform on the bulk rheology of the genome pre/post injection, the probe's motion informs on the local rheology of its surroundings. Our results reveal that mechanical stress of injection leads to local as well as nucleus-wide changes in the genome's compaction, dynamics and rheology. We find that the genome pre-injection exhibits subdiffusive motions, which are coherent over several micrometers. In contrast, genomic motions post-injection become faster and uncorrelated, moreover, the genome becomes less compact and more viscous across the entire nucleus. In addition, we use the injected particles as rheological probes and find the genome to condense locally around them, mounting a local elastic response. Taken together, our results show that mechanical stress alters both dynamics and material properties of the genome. These changes are consistent with those observed upon DNA damage, suggesting that the genome experiences similar effects during the injection process. 

Cell differentiation, the process by which stem cells become specialized cells, is associated with chromatin reorganization inside the cell nucleus. Here, we measure the chromatin distribution and dynamics in embryonic stem cells in vivo before and after differentiation. We find that undifferentiated chromatin is less compact, more homogeneous, and more dynamic than differentiated chromatin. Furthermore, we present a noninvasive rheological analysis using intrinsic chromatin dynamics, which reveals that undifferentiated chromatin behaves like a Maxwell fluid, while differentiated chromatin shows a coexistence of fluidlike (sol) and solidlike (gel) phases. Our data suggest that chromatin undergoes a local sol-gel transition upon cell differentiation, corresponding to the formation of the more dense and transcriptionally inactive heterochromatin. 

Abstract The cell nucleus stores the genetic material essential for life, and provides the environment for transcription, maintenance, and replication of the genome. Moreover, the nucleoplasm is filled with subnuclear bodies such as nucleoli that are responsible for other vital functions. Overall, the nucleus presents a highly heterogeneous and dynamic environment with diverse functionality. Here, we propose that its biophysical complexity can be organized around three inter-related and interactive facets: heterogeneity, activity, and rheology. Most nuclear constituents are sites of active, ATP-dependent processes and are thus inherently dynamic: The genome undergoes constant rearrangement, the nuclear envelope flickers and fluctuates, nucleoli migrate and coalesce, and many of these events are mediated by nucleoplasmic flows and interactions. And yet there is spatiotemporal organization in terms of hierarchical structure of the genome, its coherently moving regions and membrane-less compartmentalization via phase-separated nucleoplasmic constituents. Moreover, the non-equilibrium or activity-driven nature of the nucleus gives rise to emergent rheology and material properties that impact all cellular processes via the central dogma of molecular biology. New biophysical insights into the cell nucleus can come from appreciating this rich inner life. 

The inside of a cell is very organized. Just as bodies contain internal organs, cells contain many different compartments, called ‘organelles’, each with its own specific role. Most organelles are surrounded by a membrane that keeps their contents separate from the cytoplasm, the water-based liquid inside the rest of the cell. Some organelles, however, are not bounded by a membrane. Instead, they act like tiny drops of oil in water, retaining their structure because they have different physical properties from the fluid around them, a phenomenon called liquid-liquid phase separation. One such organelle is the nucleolus, which sits inside the cell’s nucleus (a membrane-bound organelle containing all the genetic material of the cell in the form of DNA). The nucleolus’s job is to produce ribosomes, the cellular machines that, once transported out of the nucleus, will make proteins. Human cells start with 10 small nucleoli in the nucleus, which fuse together until only one or two larger ones remain. Previous research showed that nucleoli form and persist thanks to liquid-liquid phase separation, and they behave like liquid droplets. Despite this, exactly how nucleoli interact with each other and with the fluid environment in the rest of the nucleus remained unknown. Caragine et al. set out to measure the behavior and interactions of nucleoli in living human cells. Microscopy experiments using human cells grown in the laboratory allowed the positions, size and shape of nucleoli to be tracked over time. This also yielded detailed information about the smoothness of their surface. Mathematical analysis revealed that pairs of nucleoli normally moved independently of each other, unless they were about to fuse, when they invariably slowed down and coordinated their movements. In addition, altering the state of DNA in the surrounding nucleus also affected the nucleoli. For example, when DNA was less densely packed, nucleoli shrank and their surfaces became smoother. These results build on our knowledge of how cells are organized by showing, for the first time, that the environment within the nucleus directly shapes the behavior of nucleoli. In the future, a better understanding of how cells maintain healthy nucleoli may help develop new treatments for human diseases such as cancer, which are characterized by problems with this organelle.