  Three-dimensional interphase organization of metazoan genomes has been linked
to cellular identity. However, the principles governing 3D interphase genome
architecture and its faithful transmission through disruptive events of
cell-cycle, like mitosis, are not fully understood. By using Brownian dynamics
simulations of Drosophila chromosome 3R up to time-scales of minutes, we show
that chromatin binding profile of Polycomb-repressive-complex-1 robustly
predicts a sub-set of topologically associated domains (TADs), and inclusion of
other factors recapitulates the profile of all TADs, as observed
experimentally. Our simulations show that chromosome 3R attains interphase
organization from mitotic state by a two-step process in which formation of
local TADs is followed by long-range interactions. Our model also explains
statistical features and tracks the assembly kinetics of polycomb subnuclear
clusters. In conclusion, our approach can be used to predict structural and
kinetic features of 3D chromosome folding and its associated proteins in
biological relevant genomic and time scales.
