Coalescence of liquid or gel-like DNA-encapsulating microdroplets.

Liquid-liquid phase separation plays a prominent role in the physics of life, providing the cells with various membrane-less compartments. These structures exhibit a range of material properties that, in many cases, change over time. Inspired by this, we investigate here an aqueous two-phase system formed by mixing polyethylene glycol with dextran.

Chromatin remodelers: a concise introduction for biophysicists.

Chromatin remodelers are molecular motors that act on nucleosomes: they move them along DNA or (dis-)assemble them. Despite the fact that they perform essential regulatory functions in cells-their deregulation can contribute to the development of cancers and lead to cell death-chromatin remodelers have only received meager attention in the biophysics community so far. In this short text, we attempt to present the key features of this interesting class of enzymes obtained with different experimental and theoretical methods, thereby providing a concise introduction for biophysicists to further stimulate interest in their properties.

The role of transcript regions and amino acid choice in nucleosome positioning.

Eukaryotic DNA is organized and compacted in a string of nucleosomes, DNA-wrapped protein cylinders. The positions of nucleosomes along DNA are not random but show well-known base pair sequence preferences that result from the sequence-dependent elastic and geometric properties of the DNA double helix. Here, we focus on DNA around transcription start sites, which are known to typically attract nucleosomes in multicellular life forms through their high GC content.

The Anticancer Drug Daunomycin Directly Affects Gene Expression and DNA Structure.

Daunomycin (DM), an anthracycline antibiotic, is frequently used to treat various cancers, but the direct effects of DM on gene expression and DNA structure are unclear. We used an in vitro cell-free system, optimized with spermine (SP), to study the effect of DM on gene expression. A bimodal effect of DM on gene expression, weak promotion followed by inhibition, was observed with increasing concentration of DM.

Markedly Different Effects of Monovalent Cations on the Efficiency of Gene Expression.

The effect of monovalent cations on a cell-free transcription-translation (TX-TL) system is examined using a luciferase assay. It is found that the potency for all ions analyzed here is in the order Rb  > K  > Cs  > Na  ≈ Li  > (CH ) N , where Rb is most efficient at promoting TX-TL and the ions of Li , Na , and (CH ) N exhibit an inhibitory effect. Similar promotion/inhibition effects are observed for cell-free TL alone with an mRNA template.

Computer simulations of chromatin phase separation.

Several simulation studies have recently appeared in Biophysical Journal that investigate the formation of biomolecular condensates in the nucleus. These structures explain a large variety of biological phenomena, from epigenetic inheritance, to enhancer-promoter interactions, to the spatial organization of the entire cell nucleus.

Multiplexing mechanical and translational cues on genes.

The genetic code gives precise instructions on how to translate codons into amino acids. Due to the degeneracy of the genetic code-18 out of 20 amino acids are encoded for by more than one codon-more information can be stored in a basepair sequence. Indeed, various types of additional information have been discussed in the literature, e.

Loop extrusion driven volume phase transition of entangled chromosomes.

Experiments on reconstituted chromosomes have revealed that mitotic chromosomes are assembled even without nucleosomes. When topoisomerase II (topo II) is depleted from such reconstituted chromosomes, these chromosomes are not disentangled and form "sparklers," where DNA and linker histone are condensed in the core and condensin is localized at the periphery. To understand the mechanism of the assembly of sparklers, we here take into account the loop extrusion by condensin in an extension of the theory of entangled polymer gels.

Circuit topology analysis of cellular genome reveals signature motifs, conformational heterogeneity, and scaling.

Reciprocal regulation of genome topology and function is a fundamental and enduring puzzle in biology. The wealth of data provided by Hi-C libraries offers the opportunity to unravel this relationship. However, there is a need for a comprehensive theoretical framework in order to extract topological information for genome characterization and comparison.

Slow chromatin dynamics enhances promoter accessibility to transcriptional condensates.

Enhancers are DNA sequences at a long genomic distance from target genes. Recent experiments suggest that enhancers are anchored to the surfaces of condensates of transcription machinery and that the loop extrusion process enhances the transcription level of their target genes. Here, we theoretically study the polymer dynamics driven by the loop extrusion of the linker DNA between an enhancer and the promoter of its target gene to calculate the contact probability of the promoter to the transcription machinery in the condensate.

Circuit Topology Analysis of Polymer Folding Reactions.

Circuit topology is emerging as a versatile measure to classify the internal structures of folded linear polymers such as proteins and nucleic acids. The topology framework can be applied to a wide range of problems, most notably molecular folding reactions that are central to biology and molecular engineering. In this Outlook, we discuss the state-of-the art of the technology and elaborate on the opportunities and challenges that lie ahead.

Pioneer transcription factors in chromatin remodeling: The kinetic proofreading view.

Pioneer transcription factors are a recently defined class of transcription factors which can bind directly to nucleosomal DNA; they play a key role in gene activation in certain pathways. Here we quantify their role in the initiation of nucleosome displacement within the kinetic proofreading scenario of chromatin remodeling. The model allows one to perform remodeling efficiency comparisons for scenarios involving different types of transcription factors and remodelers as a function of their binding and unbinding rates and concentrations.

Translational nucleosome positioning: A computational study.

About three-quarters of eukaryotic DNA is wrapped into nucleosomes; DNA spools with a protein core. The affinity of a given DNA stretch to be incorporated into a nucleosome is known to depend on the base-pair sequence-dependent geometry and elasticity of the DNA double helix. This causes the rotational and translational positioning of nucleosomes.

Ensembles of Breathing Nucleosomes: A Computational Study.

About three-fourths of the human DNA molecules are wrapped into nucleosomes, protein spools with DNA. Nucleosomes are highly dynamic, transiently exposing their DNA through spontaneous unspooling. Recent experiments allowed to observe the DNA of an ensemble of such breathing nucleosomes through x-ray diffraction with contrast matching between the solvent and the protein core.

Dilution of contact frequency between superenhancers by loop extrusion at interfaces.

The loop extrusion theory predicts that cohesin acts as a molecular motor that extrudes chromatin fibers to produce loops. Hi-C experiments have detected relatively high contact frequencies between superenhancers. These probably result from the fact that superenhancers are localized at condensates of transcriptional activators and coactivators.

Histone mark recognition controls nucleosome translocation via a kinetic proofreading mechanism: Confronting theory and high-throughput experiments.

Chromatin remodelers are multidomain enzymatic motor complexes that displace nucleosomes along DNA and hence "remodel chromatin structure," i.e., they dynamically reorganize nucleosome positions in both gene activation and gene repression.

Shortest paths through synonymous genomes.

The elasticity of the DNA double helix varies with the underlying base pair sequence. This allows one to put mechanical cues into sequences that in turn influence the packaging of DNA into nucleosomes, DNA-wrapped protein cylinders. Nucleosomes dictate a broad range of biological processes, ranging from gene regulation, recombination, and replication to chromosome condensation.

The nucleosome: from structure to function through physics.

Eukaryotic cells must fit meters of DNA into micron-sized cell nuclei and, at the same time, control and modulate the access to the genetic material. The necessary amount of DNA compaction is achieved via multiple levels of structural organization, the first being the nucleosome-a unique complex of histone proteins with ∼150 base pairs of DNA. Here we use specific examples to demonstrate that many aspects of the structure and function of nucleosomes can be understood using principles of basic physics, physics-based tools and models.

Physics behind the mechanical nucleosome positioning code.

The positions along DNA molecules of nucleosomes, the most abundant DNA-protein complexes in cells, are influenced by the sequence-dependent DNA mechanics and geometry. This leads to the "nucleosome positioning code", a preference of nucleosomes for certain sequence motives. Here we introduce a simplified model of the nucleosome where a coarse-grained DNA molecule is frozen into an idealized superhelical shape.

Osmotic mechanism of the loop extrusion process.

The loop extrusion theory assumes that protein factors, such as cohesin rings, act as molecular motors that extrude chromatin loops. However, recent single molecule experiments have shown that cohesin does not show motor activity. To predict the physical mechanism involved in loop extrusion, we here theoretically analyze the dynamics of cohesin rings on a loop, where a cohesin loader is in the middle and unloaders at the ends.

The Latest Twists in Chromatin Remodeling.

In its most restrictive interpretation, the notion of chromatin remodeling refers to the action of chromatin-remodeling enzymes on nucleosomes with the aim of displacing and removing them from the chromatin fiber (the effective polymer formed by a DNA molecule and proteins). This local modification of the fiber structure can have consequences for the initiation and repression of the transcription process, and when the remodeling process spreads along the fiber, it also results in long-range effects essential for fiber condensation. There are three regulatory levels of relevance that can be distinguished for this process: the intrinsic sequence preference of the histone octamer, which rules the positioning of the nucleosome along the DNA, notably in relation to the genetic information coded in DNA; the recognition or selection of nucleosomal substrates by remodeling complexes; and, finally, the motor action on the nucleosome exerted by the chromatin remodeler.

The role of DNA sequence in nucleosome breathing.

Roughly 3/4 of human genomes are sequestered by nucleosomes, DNA spools with a protein core, dictating a broad range of biological processes, ranging from gene regulation, recombination, and replication, to chromosome condensation. Nucleosomes are dynamical structures and temporarily expose wrapped DNA through spontaneous unspooling from either end, a process called site exposure or nucleosome breathing. Here we ask how this process is influenced by the mechanical properties of the wrapped DNA, which is known to depend on the underlying base pair sequence.

Performing SELEX experiments in silico.

Due to the sequence-dependent nature of the elasticity of DNA, many protein-DNA complexes and other systems in which DNA molecules must be deformed have preferences for the type of DNA sequence they interact with. SELEX (Systematic Evolution of Ligands by EXponential enrichment) experiments and similar sequence selection experiments have been used extensively to examine the (indirect readout) sequence preferences of, e.g.