Chromatin Organization and Dynamics

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)

Micron-scale coherence in interphase chromatin dynamics

Chromatin structure and dynamics control all aspects of DNA biology yet are poorly understood, especially at large length scales. We developed an approach, displacement correlation spectroscopy (DCS) based on time-resolved image correlation analysis, to map chromatin dynamics simultaneously across the whole interphase nucleus in cultured human cells.

This method revealed that chromatin movement was coherent across large regions (4–5 μm) for several seconds. Regions of coherent motion extended beyond the boundaries of single-chromosome territories, suggesting elastic coupling of motion over length scales much larger than those of genes. These large-scale, coupled motions were ATP-dependent and unidirectional for several seconds, perhaps accounting for ATP-dependent directed movement of single genes.

Perturbation of major nuclear ATPases such as DNA polymerase, RNA polymerase II, and topoisomerase II eliminated micron-scale coherence, while causing rapid, local movement to increase; i. e. , local motions accelerated but became uncoupled from their neighbors. We observe similar trends in chromatin dynamics upon inducing a direct DNA damage; thus we hypothesize that this may be due to DNA damage responses that physically relax chromatin and block long-distance communication of forces.

A. Zidovska, D. A. Weitz and T. J. Mitchison, Proc. Natl. Acad. Sci. USA, 110: 15555 (2013)

Interphase Chromatin Undergoes a Local Sol-Gel Transition upon Cell Differentiation

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.

I. Eshghi, J.A. Eaton and A. Zidovska, Phys. Rev. Lett., 126: 228101 (2021)

Mechanical stress affects dynamics and rheology of the human genome

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.

C.M. Caragine, N. Kanellakopoulos and A. Zidovska, Soft Matter, 18: 107-116 (2022)