Lattice simulation-based diffusion modelling of 3D chromatin structure.

ABSTRACT: Eukaryotic nuclear genome is extensively folded in the nuclei, and the chromatin structure experiences dramatic changes, i.e., condensation and decondensation, during the cell cycle. However, a model to persuasively explain the preserved chromatin interactions during cell cycle remains lacking. In this paper, we developed two simple, lattice-based models that mimic polymer fiber decondensation from initial fractal or anisotropic condensed status, using Markov Chain Monte Carlo (MCMC) methods. By simulating the dynamic decondensation process, we observed about 8.17% and 2.03% of the interactions preserved in the condensation to decondensation transition, in the fractal diffusion and anisotropic diffusion models, respectively. Intriguingly, although interaction hubs, as a physical locus wher

SUBMITTER: Yang Q 

PROVIDER: S-EPMC9260290 | biostudies-literature | 2022

REPOSITORIES: biostudies-literature