Intergenerationally Maintained Histone H4 Lysine 16 Acetylation Is Instructive for Future Gene Activation.

Before zygotic genome activation (ZGA), the quiescent genome undergoes reprogramming to transition into the transcriptionally active state. However, the mechanisms underlying euchromatin establishment during early embryogenesis remain poorly understood. Here, we show that histone H4 lysine 16 acetylation (H4K16ac) is maintained from oocytes to fertilized embryos in Drosophila and mammals.

OnTAD: hierarchical domain structure reveals the divergence of activity among TADs and boundaries.

The spatial organization of chromatin in the nucleus has been implicated in regulating gene expression. Maps of high-frequency interactions between different segments of chromatin have revealed topologically associating domains (TADs), within which most of the regulatory interactions are thought to occur. TADs are not homogeneous structural units but appear to be organized into a hierarchy.

Chromatin organization by an interplay of loop extrusion and compartmental segregation.

Mammalian chromatin is spatially organized at many scales showing two prominent features in interphase: () alternating regions (1-10 Mb) of active and inactive chromatin that spatially segregate into different compartments, and () domains (<1 Mb), that is, regions that preferentially interact internally [topologically associating domains (TADs)] and are central to gene regulation. There is growing evidence that TADs are formed by active extrusion of chromatin loops by cohesin, whereas compartmentalization is established according to local chromatin states. Here, we use polymer simulations to examine how loop extrusion and compartmental segregation work collectively and potentially interfere in shaping global chromosome organization.

Dynamics of sister chromatid resolution during cell cycle progression.

Faithful genome transmission in dividing cells requires that the two copies of each chromosome's DNA package into separate but physically linked sister chromatids. The linkage between sister chromatids is mediated by cohesin, yet where sister chromatids are linked and how they resolve during cell cycle progression has remained unclear. In this study, we investigated sister chromatid organization in live human cells using dCas9-mEGFP labeling of endogenous genomic loci.

A pathway for mitotic chromosome formation.

Mitotic chromosomes fold as compact arrays of chromatin loops. To identify the pathway of mitotic chromosome formation, we combined imaging and Hi-C analysis of synchronous DT40 cell cultures with polymer simulations. Here we show that in prophase, the interphase organization is rapidly lost in a condensin-dependent manner, and arrays of consecutive 60-kilobase (kb) loops are formed.

Adsorption-Desorption Kinetics of Soft Particles.

Adsorption-desorption processes are ubiquitous in physics, chemistry, and biology. Models usually assume hard particles, but within the realm of soft matter physics the adsorbing particles are compressible. A minimal 1D model reveals that softness fundamentally changes the kinetics: Below the desorption time scale, a logarithmic increase of the particle density replaces the usual Rényi jamming plateau, and the subsequent relaxation to equilibrium can be nonmonotonic and much faster than for hard particles.

Nucleosome spacing generated by ISWI and CHD1 remodelers is constant regardless of nucleosome density.

Arrays of regularly spaced nucleosomes are a hallmark of chromatin, but it remains unclear how they are generated. Recent genome-wide studies, in vitro and in vivo, showed constant nucleosome spacing even if the histone concentration was experimentally reduced. This counters the long-held assumption that nucleosome density determines spacing and calls for factors keeping spacing constant regardless of nucleosome density.

Replication-guided nucleosome packing and nucleosome breathing expedite the formation of dense arrays.

The first level of genome packaging in eukaryotic cells involves the formation of dense nucleosome arrays, with DNA coverage near 90% in yeasts. How cells achieve such high coverage within a short time, e.g.

Quantized ν = 5/2 state in a two-subband quantum hall system.

The evolution of the fractional quantum Hall state at filling 5/2 is studied in density tunable two-dimensional electron systems formed in wide wells in which it is possible to induce a transition from single- to two-subband occupancy. In 80 and 60 nm wells, the quantum Hall state at 5/2 filling of the lowest subband is observed even when the second subband is occupied. In a 50 nm well, the 5/2 state vanishes upon second subband population.

Parity-breaking bifurcation and global oscillation in patterns of ion channels.

Stationary spatiotemporal pattern formation emerging from the electric activity of biological membranes is widespread in cells and tissues. A known key instability comes from the self-aggregation of membrane channels. In a two-dimensional geometry, we show that the primary pattern undergoes four secondary instabilities: Eckhaus-like, period-halving, drift instabilities, and a global oscillation.

Cotransport-induced instability of membrane voltage in tip-growing cells.

A salient feature of stationary patterns in tip-growing cells is the key role played by the symports and antiports, membrane proteins that translocate two ionic species at the same time. It is shown that these cotransporters destabilize generically the membrane voltage if the two translocated ions diffuse differently and carry a charge of opposite (same) sign for symports (antiports). The orders of magnitude obtained for the time and length scale are in agreement with experiments.