Related papers: Epigenetic state encodes locus-specific chromatin …
The three-dimensional organization of chromatin is thought to play an important role in controlling gene expression. Specificity in expression is achieved through the interaction of transcription factors and other nuclear proteins with…
A problem of substantial interest is to systematically map variation in chromatin structure to gene expression regulation across conditions, environments, or differentiated cell types. We developed and applied a quantitative framework for…
Spatial organization of chromatin plays a critical role in genome regulation. Various types of affinity mediators and enzymes have been attributed to regulate spatial organization of chromatin from a thermodynamics perspective. However, at…
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 moves dynamically inside the cell nucleus, and its motion is often correlated with gene functions such as DNA recombination and transcription. A recent study has shown that during early embryogenesis of the nematode,…
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…
The 3D folding of a mammalian gene can be studied by a polymer model, where the chromatin fibre is represented by a semiflexible polymer which interacts with multivalent proteins, representing complexes of DNA-binding transcription factors…
We propose the Self Returning Excluded Volume (SR-EV) model for the structure of chromatin based on stochastic rules and physical interactions. The SR-EV rules of return generate conformationally-defined domains observed by single cell…
Epistasis describes the phenomenon that mutations at different loci do not have independent effects with regard to certain phenotypes. Understanding the global epistatic landscape is vital for many genetic and evolutionary theories. Current…
Chromatin looping is a major epigenetic regulatory mechanism in higher eukaryotes. Besides its role in transcriptional regulation, chromatin loops have been proposed to play a pivotal role in the segregation of entire chromosomes. The…
The baseline level of transcription, which is variable and difficult to quantify, seriously complicates the normalization of comparative transcriptomic data, but its biological importance remains unappreciated. We show that this currently…
The population-averaged contact maps generated by the chromosome conformation capture technique provide important information about the average frequency of contact between pairs of chromatin loci as a function of the genetic distance…
We propose that the degree of sweeling of the 30nm chromatin fiber (a "measure" of its transcriptional activity) is mainly determined by the short-ranged electrostatical interaction between different sections of the "folded" DNA chain.…
The contribution to an organism's phenotype from one genetic locus may depend upon the status of other loci. Such epistatic interactions among loci are now recognized as fundamental to shaping the process of adaptation in evolving…
The mechanism and driving forces of chromosome segregation in the bacterial cell cycle of E. coli is one of the least understood events in its life cycle. Using principles of entropic repulsion between polymer loops confined in a cylinder,…
DNA methylation is a primary layer of epigenetic modification that plays a pivotal role in the regulation of development, aging, and cancer. The concurrent activity of opposing enzymes that mediate DNA methylation and demethylation gives…
By observing reconstituted chromatin by fluorescence microscopy (FM) and atomic force microscopy (AFM), we found that the density of nucleosomes exhibits a bimodal profile, i.e., there is a large transition between the dense and dispersed…
The three dimensional structure of DNA in the nucleus (chromatin) plays an important role in many cellular processes. Recent experimental advances have led to high-throughput methods of capturing information about chromatin conformation on…
Increasing evidence suggests that chromosome folding and genetic expression are intimately connected. For example, the co-expression of a large number of genes can benefit from their spatial co-localization in the cellular space.…
Entangled states are ubiquitous amongst fibrous materials, whether naturally occurring (keratin, collagen, DNA) or synthetic (nanotube assemblies, elastane). A key mechanical characteristic of these systems is their ability to reorganise in…