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 where a certain number of monomers inter-connected, were observed in diffused polymer models in both simulations, they were not associated with the preserved interactions. Our simulation demonstrated that there might exist a small portion of chromatin interactions that preserved during the diffusion process of polymers, while the interacted hubs were more dynamically formed and additional regulatory factors were needed for their preservation.