Organization of the Mitotic Chromosome

Mitotic chromosomes are among the most recognizable structures in the cell, yet for over a century their internal organization remains largely unsolved. We applied chromosome conformation capture methods, 5C and Hi-C, across the cell cycle and revealed two distinct three-dimensional folding states of the human genome. We show that the highly compartmentalized and cell type–specific organization described previously for nonsynchronous cells is restricted to interphase. In metaphase, we identified a homogenous folding state that is locus-independent, common to all chromosomes, and consistent among cell types, suggesting a general principle of metaphase chromosome organization. Using polymer simulations, we found that metaphase Hi-C data are inconsistent with classic hierarchical models and are instead best described by a linearly organized longitudinally compressed array of consecutive chromatin loops. The three-dimensional (3D) organization ofgenomes plays critical roles in regulatingchromosomal processes, including gene regulation, DNA replication, and genome sta-bility (1–4). During the cell cycle, chromosomes transition between two distinct folding states: in-terphase and metaphase. Interphase chromosome