Related papers: Epigenetic Chromatin Silencing: Bistability and Fr…

One of the most important problems in development is how epigenetic domains can be first established, and then maintained, within cells. To address this question, we propose a framework which couples 3D chromatin folding dynamics, to a…

Embryonic stem cells (ESC) have the potential to self-renew indefinitely and to differentiate into any of the three germ layers. The molecular mechanisms for self-renewal, maintenance of pluripotency and lineage specification are poorly…

In population genetics, mutation rate is often treated as a homogeneous parameter across the genome. Empirical evidence, however, shows systematic variation across genomic contexts associated with chromatin organization and epigenomic…

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…

While noise is generally associated with uncertainties and often has a negative connotation in engineering, living organisms have evolved to adapt to (and even exploit) such uncertainty to ensure the survival of a species or implement…

Gene regulatory dynamics is governed by molecular processes and therefore exhibits an inherent stochasticity. However, for the survival of an organism it is a strict necessity that this intrinsic noise does not prevent robust functioning of…

Epigenetic inheritance during cell division is essential for preserving cell identity by stabilizing the overall chromatin organisation. Heterochromatin,the condensed and transcriptionally silent fraction of chromatin,is marked by specific…

Reconciling the stability of epigenetic patterns with the rapid turnover of histone modifications and their adaptability to external stimuli is an outstanding challenge. Here, we propose a new biophysical mechanism that can establish and…

The emergence of and transitions between distinct phenotypes in isogenic cells can be attributed to the intricate interplay of epigenetic marks, external signals, and gene regulatory elements. These elements include chromatin remodelers,…

Recently, a large number of studies have been carried out on the early signatures of sudden regime shifts in systems as diverse as ecosystems, financial markets, population biology and complex diseases. Signatures of regime shifts in gene…

Chromosomal crossovers play a crucial role in meiotic cell division, as they ensure proper chromosome segregation and increase genetic variability. Experiments have consistently revealed two key observations across species: (i) the number…

Multiple phenotypic states often arise in a single cell with different gene-expression states that undergo transcription regulation with positive feedback. Recent experiments have shown that at least in E. coli, the gene state switching can…

Despite the greater functional importance of protein levels, our knowledge of gene expression evolution is based almost entirely on studies of mRNA levels. In contrast, our understanding of how translational regulation evolves has lagged…

Epigenetics is a driving force of important and ubiquitous phenomena in nature such as cell differentiation or even metamorphosis. Oppositely to its widespread role, understanding the biophysical principles that allow epigenetics to control…

Gene expression is a noisy process that leads to regime shift between alternative steady states among individual living cells, inducing phenotypic variability. The effects of white noise on the regime shift in bistable systems have been…

A simple stochastic model of a self regulating gene that displays bistable switching is analyzed. While on, a gene transcribes mRNA at a constant rate. Transcription factors can bind to the DNA and affect the gene's transcription rate.…

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…

The epigenetic pathway of a cell as it differentiates from a stem cell state to a mature lineage-committed one has been historically understood in terms of Waddington's landscape, consisting of hills and valleys. The smooth top and…

Biological evolution of a population is governed by the fitness landscape, which is a map from genotype to fitness. However, a fitness landscape depends on the organisms environment, and evolution in changing environments is still poorly…

Gene expression in cells is stochastic, yet differentiation is robust. We propose a mechanism in which frustrated genes with weakly stable intermediate expression undergo noise-driven switching between basins of attraction, followed by…