Nuclear dynamical deformation induced hetero- and euchromatin positioning

Polymeric nature of tandemly repeated genes enhances assembly of constitutive heterochromatin in fission yeast

Motivated by our recent experiments that demonstrate that the tandemly repeated genes become heterochromatin, here we show a theory of heterochromatin assembly by taking into account the connectivity of these genes along the chromatin in the kinetic equations of small RNA production and histone methylation, which are the key biochemical reactions involved in the heterochromatin assembly. Our theory predicts that the polymeric nature of the tandemly repeated genes ensures the steady production of small RNAs because of the stable binding of nascent RNAs produced from the genes to RDRC/Dicers at the surface of nuclear membrane. This theory also predicts that the compaction of the tandemly repeated genes suppresses the production of small RNAs, consistent with our recent experiments. This theory can be extended to the small RNA-dependent gene silencing in higher organisms.

Epigenetic-structural changes in X chromosomes promote Xic pairing during early differentiation of mouse embryonic stem cells

X chromosome inactivation center (Xic) pairing occurs during the differentiation of embryonic stem (ES) cells from female mouse embryos, and is related to X chromosome inactivation, the circadian clock, intra-nucleus architecture, and metabolism. However, the mechanisms underlying the identification and approach of X chromosome pairs in the crowded nucleus are unclear. To elucidate the driving force of Xic pairing, we developed a coarse-grained molecular dynamics model of intranuclear chromosomes in ES cells and in cells 2 days after the onset of differentiation (2-day cells) by considering intrachromosomal epigenetic-structural feature-dependent mechanics. The analysis of the experimental data showed that X-chromosomes exhibit the rearrangement of their distributions of open/closed chromatin regions on their surfaces during cell differentiation. By simulating models where the excluded volume effects of closed chromatin regions are stronger than those of open chromatin regions, such rearrangement of open/closed chromatin regions on X-chromosome surfaces promoted the mutual approach of the Xic pair. These findings suggested that local intrachromosomal epigenetic features may contribute to the regulation of cell species-dependent differences in intranuclear architecture.

Polymer models for the mechanisms of chromatin 3D folding: review and perspective

In this perspective paper, classical physical models for mammalian interphase chromatin folding are reviewed.

The biology and polymer physics underlying large-scale chromosome organization

Chromosome large-scale organization is a beautiful example of the interplay between physics and biology. DNA molecules are polymers and thus belong to the class of molecules for which physicists have developed models and formulated testable hypotheses to understand their arrangement and dynamic properties in solution, based on the principles of polymer physics. Biologists documented and discovered the biochemical basis for the structure, function and dynamic spatial organization of chromosomes in cells. The underlying principles of chromosome organization have recently been revealed in unprecedented detail using high-resolution chromosome capture technology that can simultaneously detect chromosome contact sites throughout the genome. These independent lines of investigation have now converged on a model in which DNA loops, generated by the loop extrusion mechanism, are the basic organizational and functional units of the chromosome.

Transcription dynamics stabilizes nucleus-like layer structure in chromatin brush

We use a brush of DNA in a solution of transcriptional machinery and histone proteins to theoretically predict that this brush shows phase separation due to the instability arising from the disassembly of nucleosomes during transcription. In the two-phase coexistent state, collapsed chains (with relatively large nucleosome occupancy) lie at the grafting surface and swollen chains (with relatively small nucleosome occupancy) are distributed at the space above the collapsed chains, analogous to the structure of chromatin in differentiated cells. This layer structure is stabilized by the lateral osmotic pressure of swollen chains. For a relatively small grafting density, DNA brushes show tricritical points because the entropic elasticity with respect to the lateral excursion of swollen chains balances with the lateral osmotic pressure of these chains. At the tricritical points, DNA brushes show large fluctuations of local nucleosome concentration, which may be reminiscent of the fluctuations observed in embryonic stem cells.