Related papers: Spatio-temporal patterns of active epigenetic turn…
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,…
Recent experiments have been able to visualise chromosome organization in fast-growing E.coli cells. However, the mechanism underlying the spatio-temporal organization remains poorly understood. We propose that the DNA adopts a specific…
Epigenetics plays a key role in cellular differentiation and maintaining cell identity, enabling cells to regulate their genetic activity without altering the DNA sequence. Epigenetic regulation occurs within the context of hierarchically…
Many organisms possess both a cell cycle to control DNA replication and a circadian clock to anticipate changes between day and night. In some cases, these two rhythmic systems are known to be coupled by specific, cross-regulatory…
We discover a new type of nonequilibrium phase transition in a model of chromatin dynamics, which accounts for the coherent motions that have been observed in experiment. The coherent motion is due to the long-range cooperation of molecular…
Topologically Associating Chromatic Domains are spatially distinct chromatin regions that regulate transcription by segregating active and inactive genomic elements. Empirical studies show that their formation correlates with local patterns…
Focusing on the DNA-bridging nucleoid proteins Fis and H-NS, and integrating several independent experimental and bioinformatic data sources, we investigate the links between chromosomal spatial organization and global transcriptional…
The approach for the description of the DNA conformational transformations on the mesoscopic scales in the frame of the double helix is presented. Due to consideration of the joint motions of DNA structural elements along the conformational…
The significant role of epigenetic mechanisms within natural systems has become increasingly clear. This paper uses a recently presented abstract, tunable Boolean genetic regulatory network model to explore aspects of epigenetics. It is…
The spreading and regulation of epigenetic marks on chromosomes is crucial to establish and maintain cellular identity. Nonetheless, the dynamical mechanism leading to the establishment and maintenance of a given, cell-line specific,…
The phase-separation occurring in a system of mutually interacting proteins that can bind on specific sites of a chromatin fiber is here investigated. This is achieved by means of extensive Molecular Dynamics simulations of a simple polymer…
Dynamics of nucleosomes, the building blocks of the chromatin, has crucial effects on expression, replication and repair of genomes in eukaryotes. Beside constant movements of nucleosomes by thermal fluctuations, ATP-dependent chromatin…
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…
Epigenetic landscapes, represented by patterns of chemical modifications on histone tails, are essential for maintaining cell identity and tissue homeostasis. These landscapes are shaped by multiple factors, including local biochemical…
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,…
Essential life processes take place across multiple space and time scales in living organisms but understanding their mechanistic interactions remains an ongoing challenge. Advanced multiscale modeling techniques are providing new…
Spatiotemporal coordination of chromatin and subnuclear compartments is crucial for cells. Numerous enzymes act inside nucleus\textemdash some of those transiently link and pass two chromatin segments. Here we study how such an active…
MicroRNAs are extensively known for post-transcriptional gene regulation and pattern formation in the embryonic developmental stage. We explore the origin of these spatio-temporal patterns mathematically, considering three different motifs…
Understanding the interplay among processes that occur over different timescales is a challenging issue in the physics of systems regulation. In gene regulation, the timescales for changes in chromatin states can differ from those for…
In a quasi-1D thermal convective system consisting of a large array of nonlinearly coupled oscillators, clustering is the way to achieve a regime of mostly antiphase synchronized oscillators. This regime is characterized by a spatiotemporal…