Brownian dynamics simulations reveal regulatory properties of higher-order chromatin structures

A present model of the higher-order chromosome organization suggests the organization of chromosome built up by loops. Here we focus on a single rosette-like part of the fiber and analyse the diffusion behaviour of small particles (corresponding to single proteins/protein complexes) and the accessibility of such particles in relation to the dynamic rosette structure. Surprisingly, although the diffusion pattern of the diffusing particles revealed free diffusion, an area of about 6-12 kbp in the innermost part of these domains becomes visible which is inaccessible even for small particles (corresponding to single proteins/protein complexes). A localisation of a promotor sequence in this area might silence the respective gene by the physical inaccessibility of this area for transcription factors. We conclude that the compartmentalisation of chromatin in domains of a specific dynamical three-dimensional (3D) structure might be of high functional importance.