Chromatin conformation, gene transcription, and nucleosome remodeling as an emergent system

Science Advances, Journal Year: 2025, Volume and Issue: 11(2)

Published: Jan. 10, 2025

In single cells, variably sized nanoscale chromatin structures are observed, but it is unknown whether these form a cohesive framework that regulates RNA transcription. Here, we demonstrate the human genome an emergent, self-assembling, reinforcement learning system. Conformationally defined heterogeneous, nanoscopic packing domains by interplay of transcription, nucleosome remodeling, and loop extrusion. We show not topologically associated domains. Instead, exist across structure-function life cycle couples heterochromatin transcription in situ, explaining how enzyme inhibition can produce paradoxical decrease destabilizing domain cores. Applied to development aging, pairing at myogenic genes could be disrupted nuclear swelling. sum, represent foundation explore interactions single-cell level health.

Language: Английский

Heterogeneity induced Block Copolymer Segregation in Confinement

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Nov. 3, 2024

Motivated by the work on block copolymer models that provide insights into epigenetics driven chromosome organization, we investigate segregation behavior of five distinct 2-block co-polymers (BCPs) system with varying sizes, confined within both symmetric and lateral geometries. Using exact enumeration method Langevin dynamics simulation, our simple self-avoiding polymer model reveals robust behaviors (across statics dynamic studies) despite strong finite-size effects. We observe as length increases, compaction intensifies relying non-specific interaction, leading to longer times. The study clearly demonstrates formation globular lamellar phases condensed, stable complex structures in long-range (BCP) systems, providing a simplified analogy lamellar-mediated chromatin compaction, which involves are difficult segregate under physiological conditions. Dominance specific interaction over long range BCP systems leads phase separation self assemblies provides heterochromatin—inactive or domains. In contrast, short-range sequences remain coiled state, exhibiting minimal overlap due short attraction, may corresponds euchromatin regions where diverse epigenetic states coexist, resulting active, non-condensed structures. also asymmetric confinement favors more between BCPs irrespective their underlying sequence.

Language: Английский