High-performance Computational Modeling of Chromosome Structure

Abstract

We present a polymer modeling approach to generate the ensemble of 3D chromosome conformations at different time points of mitosis-interphase transition. Dynamics of structure during mitosis-G1 transition indicates quick and slow stages of chromosome shape alterations. At intermediate and late time scale the changes in chromosome compaction are small. To assess time dependence of contact map establishment during G1 we calculate contact maps at different times after mitotic decondensation. We demonstrate that the patterns of contacts observed soon after mitotic decondensation remain similar during G1. Whole contact map for mouse chromosome 18 at late G1 time correlates with the experimental chromosome conformation capture data. The simulations reproduce the main experimental findings, contact map persistence during G1 as well as specific pattern of long-range interactions in interphase chromosome. Our results suggest that spatial compartmentalization of an interphase chromosome is driven by interactions between different types of megabase sized chromatin domains during the formation of globular chromosome state at the end of mitotis to G1 transition.