Related papers: Chromosome Compaction and Chromatin Stiffness Enha…
We propose a model for the formation of chromatin loops based on the diffusive sliding of a DNA-bound factor which can dimerise to form a molecular slip-link. Our slip-links mimic the behaviour of cohesin-like molecules, which, along with…
Active loop extrusion - the process of formation of dynamically growing chromatin loops due to the motor activity of DNA-binding protein complexes - is firmly established mechanism responsible for chromatin spatial organization at different…
Chromatin loop extrusion is a popular model for the formation of CTCF loops and topological domains. Recent HiC data have revealed a strong bias in favour of a particular arrangement of the CTCF binding motifs that stabilize loops, and…
Chromatin loop extrusion by Structural Maintenance of Chromosome (SMC) complexes is thought to underlie intermediate-scale chromatin organization inside cells. Motivated by a number of experiments suggesting that nucleosomes may block loop…
This paper focuses on mechanical aspects of chromatin biological functioning. Within a basic geometric modeling of the chromatin assembly, we give for the first time the complete set of elastic constants (twist and bend persistence lengths,…
Transcriptional noise, or heterogeneity, is important in cellular development and in disease. The molecular mechanisms driving it are, however, elusive and ill-understood. Here, we use computer simulations to explore the role of 3D…
Chromatin fibers composed of DNA and proteins fold into consecutive loops to form rod-shaped chromosome in mitosis. Although the loop growth dynamics is investigated in several studies, its detailed processes are unclear. Here, we describe…
Recent high resolution experiments have provided a quantitative description of the statistical properties of interphase chromatin at large scales. These findings have stimulated a search for generic physical interactions that give rise to…
Nucleosomes are the fundamental building blocks of chromatin that not only help in the folding of chromatin but also in carrying epigenetic information. It is known that nucleosome sliding is responsible for dynamically organizing chromatin…
Chromatin and associated proteins constitute the highly folded structure of chromosomes. We consider a self-avoiding polymer model of the chromatin, segments of which may get cross-linked via protein binders that repel each other. The…
We present Monte-Carlo (MC) simulations of the stretching of a single 30 nm chromatin fiber. The model approximates the DNA by a flexible polymer chain with Debye-H\"uckel electrostatics and uses a two-angle zig-zag model for the geometry…
Loop extrusion by motor proteins mediates the attractive interactions in chromatin on the length scale of megabases, providing the polymer with a well-defined structure and at the same time determining its dynamics. The mean square…
An active loop-extrusion mechanism is regarded as the main out--of--equilibrium mechanism responsible for the structuring of megabase-sized domains in chromosomes. We developed a model to study the dynamics of the chromosome fibre by…
Cell crawling requires the generation of intracellular forces by the cytoskeleton and their transmission to an extracellular substrate through specific adhesion molecules. Crawling cells show many features of excitable systems, such as…
Many researchers have been encouraged to describe the dynamics of chromosomal loci in chromatin using the classical Rouse model of polymer dynamics by the agreement between the measured mean square displacement (MSD) versus time of…
Live-cell imaging experiments have shown that the distal dynamics between enhancers and promoters are unexpectedly rapid and incompatible with standard polymer models. The discordance between the compact static chromatin organization and…
The classic model of eukaryotic gene expression requires direct spatial contact between a distal enhancer and a proximal promoter. Recent Chromosome Conformation Capture (3C) studies show that enhancers and promoters are embedded in a…
A prominent organizational feature of bacterial chromosomes was revealed by Hi-C experiments, indicating anomalously high contacts between the left and right chromosomal arms. These long-range contacts have been attributed to various…
Condensation of hundreds of mega-base-pair-long human chromosomes in a small nuclear volume is a spectacular phenomenon. This process is driven by the formation of chromosome loops. ATP consuming motor, condensin, interacts with chromatin…
Loop extrusion is one of the main processes shaping chromosome organisation across the cell cycle, yet its role in regulating DNA entanglement and nucleoplasm viscoelasticity remains overlooked. We simulate entangled solutions of linear…