Convergent pairs of highly transcribed genes restrict chromatin looping in Dictyostelium discoideum.

Dictyostelium discoideum is a unicellular slime mold, developing into a multicellular fruiting body upon starvation. Development is accompanied by large-scale shifts in gene expression program, but underlying features of chromatin spatial organization remain unknown. Here, we report that the Dictyostelium 3D genome is organized into positionally conserved, largely consecutive, non-hierarchical and weakly insulated loops at the onset of multicellular development.

Long non-coding RNAs direct the SWI/SNF complex to cell type-specific enhancers.

The coordination of chromatin remodeling is essential for DNA accessibility and gene expression control. The highly conserved and ubiquitously expressed SWItch/Sucrose Non-Fermentable (SWI/SNF) chromatin remodeling complex plays a central role in cell type- and context-dependent gene expression. Despite the absence of a defined DNA recognition motif, SWI/SNF binds lineage specific enhancers genome-wide where it actively maintains open chromatin state.

A genome-wide nucleosome-resolution map of promoter-centered interactions in human cells corroborates the enhancer-promoter looping model.

The enhancer-promoter looping model, in which enhancers activate their target genes via physical contact, has long dominated the field of gene regulation. However, the ubiquity of this model has been questioned due to evidence of alternative mechanisms and the lack of its systematic validation, primarily owing to the absence of suitable experimental techniques. In this study, we present a new MNase-based proximity ligation method called MChIP-C, allowing for the measurement of protein-mediated chromatin interactions at single-nucleosome resolution on a genome-wide scale.

Tuning polymer micelle size and dynamics with solvophobic block structure.

Hypothesis: Micelles formed by copolymers with mixed solvophobic blocks have attracted much attention lately. It is expected that changing the mixed blocks sequence can be used as a tool to influence the micellization behavior in a way that is not equivalent to simply varying the incompatibility parameter for pure diblock-copolymers. Simulations: By using coarse-grained simulations, the micellization behavior of copolymers with twelve types of solvophobic blocks, which differed in the fraction f as well as the sequence of solvophilic units in the solvophobic blocks, was studied.

Cohesin-Dependent Loop Extrusion: Molecular Mechanics and Role in Cell Physiology.

The most prominent representatives of multisubunit SMC complexes, cohesin and condensin, are best known as structural components of mitotic chromosomes. It turned out that these complexes, as well as their bacterial homologues, are molecular motors, the ATP-dependent movement of these complexes along DNA threads leads to the formation of DNA loops. In recent years, we have witnessed an avalanche-like accumulation of data on the process of SMC dependent DNA looping, also known as loop extrusion.

Cohesin Complex: Structure and Principles of Interaction with DNA.

Accurate duplication and separation of long linear genomic DNA molecules is associated with a number of purely mechanical problems. SMC complexes are key components of the cellular machinery that ensures decatenation of sister chromosomes and compaction of genomic DNA during division. Cohesin, one of the essential eukaryotic SMC complexes, has a typical ring structure with intersubunit pore through which DNA molecules can be threaded.

Effect of ion distribution on stress relaxation in polyelectrolyte complex gels.

Solutions of polyelectrolytes consisting of polycations and polyanions in equal proportions were studied in the present work. Due to the physical cross-links formed by the charged groups, physical gels were formed in such systems. The mechanical properties and structure of the obtained gels depending on the charge arrangement along the backbone and the dimensionless Bjerrum length λ were investigated.

Copolymers with Nonblocky Sequences as Novel Materials with Finely Tuned Properties.

The copolymer sequence can be considered as a new tool to shape the resulting system properties on demand. This perspective is devoted to copolymers with "partially segregated" (or nonblocky) sequences. Such copolymers include gradient copolymers and copolymers with random sequences as well as copolymers with precisely controlled sequences.

Effect of the counterion size on microphase separation in charged-neutral diblock copolymers.

In this work, the question of the influence of the counterion size on the self-assembly in melts of diblock copolymers with one charged block was studied using coarse-grained molecular dynamics simulations. It was assumed that the blocks were fully compatible, i.e.

Phase Diagrams of Polymerization-Induced Self-Assembly Are Largely Determined by Polymer Recombination.

In the current work, atom transfer radical polymerization-induced self-assembly (ATRP PISA) phase diagrams were obtained by the means of dissipative particle dynamics simulations. A fast algorithm for determining the equilibrium morphology of block copolymer aggregates was developed. Our goal was to assess how the chemical nature of ATRP affects the self-assembly of diblock copolymers in the course of PISA.

Recurrent Translocations in Topoisomerase Inhibitor-Related Leukemia Are Determined by the Features of DNA Breaks Rather Than by the Proximity of the Translocating Genes.

Topoisomerase inhibitors are widely used in cancer chemotherapy. However, one of the potential long-term adverse effects of such therapy is acute leukemia. A key feature of such therapy-induced acute myeloid leukemia (t-AML) is recurrent chromosomal translocations involving or genes.

Correction: Effect of network topology and crosslinker reactivity on microgel structure and ordering at liquid-liquid interface.

Correction for 'Effect of network topology and crosslinker reactivity on microgel structure and ordering at liquid-liquid interface' by Rustam A. Gumerov , , 2022, , 3738-3747, https://doi.org/10.

Effect of network topology and crosslinker reactivity on microgel structure and ordering at liquid-liquid interface.

Polymer microgels synthesized were studied at a liquid-liquid interface mesoscopic computer simulations and compared to microgels with ideal (diamond-like) structure. The effect of crosslinkers reactivity ratio on the single particle morphology at the interface and monolayer behavior was examined. It was demonstrated that single particles deform into an explicit core-corona morphology when adsorbed at the interface.

An exotic microstructured globular state formed by a single multiblock copolymer chain.

In this work, we studied the equilibrium structures formed by a single (AB) multiblock copolymer chain. Within our model, the interactions between the A-type beads were repulsive and the B-type beads could form pairwise reversible bonds with each other (BB-bonds). Our goal was to investigate how the formation of pairwise reversible bonds between the A-type beads and the B-type beads (AB-bonds) affected the structure of the chain.

RedChIP identifies noncoding RNAs associated with genomic sites occupied by Polycomb and CTCF proteins.

Nuclear noncoding RNAs (ncRNAs) are key regulators of gene expression and chromatin organization. The progress in studying nuclear ncRNAs depends on the ability to identify the genome-wide spectrum of contacts of ncRNAs with chromatin. To address this question, a panel of RNA-DNA proximity ligation techniques has been developed.

The effect of explicit polarity on the conformational behavior of a single polyelectrolyte chain.

In this work using dissipative particle dynamics simulations with explicit treatment of polar species we demonstrate that the molecular nature of dielectric media has a significant impact on swelling and collapse of a polyelectrolyte chain in a dilute solution. We show that the small-scale effects related to the presence of polar species lead to the intensification of the electrostatic interactions when the charges are close to each other and/or their density is high enough. As a result, the electrostatic strength , usually regarded as the main parameter governing the polyelectrolyte chain collapse, does not have a universal meaning: the value of at which the coil-to-globule transition occurs is found to be dependent on the specific fixed value of the solvent bulk permittivity while varying the monomer unit charge and .

Sensitivity of cohesin-chromatin association to high-salt treatment corroborates non-topological mode of loop extrusion.

Cohesin is a key organizer of chromatin folding in eukaryotic cells. The two main activities of this ring-shaped protein complex are the maintenance of sister chromatid cohesion and the establishment of long-range DNA-DNA interactions through the process of loop extrusion. Although the basic principles of both cohesion and loop extrusion have been described, we still do not understand several crucial mechanistic details.

Transformations of wormlike surfactant micelles induced by a water-soluble monomer.

Hypothesis: Wormlike surfactant micelles (WLMs) are prospective as nanoreactors for micellar copolymerization of hydrophilic and hydrophobic monomers. Hydrophilic monomers can destroy WLMs. Large size and cylindrical shape of micelles can be preserved by high salt content favoring closer packing of surfactant heads.

Non-coding RNAs in chromatin folding and nuclear organization.

One of the most intriguing questions facing modern biology concerns how the genome directs the construction of cells, tissues, and whole organisms. It is tempting to suggest that the part of the genome that does not encode proteins contains architectural plans. We are still far from understanding how these plans work at the level of building tissues and the body as a whole.

Suppression of liquid-liquid phase separation by 1,6-hexanediol partially compromises the 3D genome organization in living cells.

Liquid-liquid phase separation (LLPS) contributes to the spatial and functional segregation of molecular processes within the cell nucleus. However, the role played by LLPS in chromatin folding in living cells remains unclear. Here, using stochastic optical reconstruction microscopy (STORM) and Hi-C techniques, we studied the effects of 1,6-hexanediol (1,6-HD)-mediated LLPS disruption/modulation on higher-order chromatin organization in living cells.

Two contributions to the dielectric response of polar liquids.

In this Note, we study the total conservative force {instead of pure electrostatic force as it was carried out in the work by Gavrilov [J. Chem. Phys.

LASCA: loop and significant contact annotation pipeline.

Chromatin loops represent one of the major levels of hierarchical folding of the genome. Although the situation is evolving, current methods have various difficulties with the accurate mapping of loops even in mammalian Hi-C data, and most of them fail to identify chromatin loops in animal species with substantially different genome architecture. This paper presents the loop and significant contact annotation (LASCA) pipeline, which uses Weibull distribution-based modeling to effectively identify loops and enhancer-promoter interactions in Hi-C data from evolutionarily distant species: from yeast and worms to mammals.

Order and stochasticity in the folding of individual Drosophila genomes.

Mammalian and Drosophila genomes are partitioned into topologically associating domains (TADs). Although this partitioning has been reported to be functionally relevant, it is unclear whether TADs represent true physical units located at the same genomic positions in each cell nucleus or emerge as an average of numerous alternative chromatin folding patterns in a cell population. Here, we use a single-nucleus Hi-C technique to construct high-resolution Hi-C maps in individual Drosophila genomes.

Mechanisms mediating suppression of globin gene transcription in Danio rerio nonerythroid cells.

We studied the repression of adult and embryo-larval genes of the major globin gene locus in D. rerio fibroblasts. The results obtained suggest that at least some of the globin genes are repressed by Polycomb, similarly to human α-globin genes.