Abstract
Recent developments have for the first time allowed the determination of three-dimensional structures of individual chromosomes and genomes in nuclei of single haploid mouse embryonic stem (ES) cells based on Hi–C chromosome conformation contact data. Although these first structures have a relatively low resolution, they provide the first experimental data that can be used to study chromosome and intact genome folding. Here we further analyze these structures and provide the first evidence that G1 phase chromosomes are knotted, consistent with the fact that plots of contact probability vs sequence separation show a power law dependence that is intermediate between that of a fractal globule and an equilibrium structure.
Highlights
Very significant advances have been made in the last decades, understanding how chromosomes are organized in the cell nucleus remains a grand challenge in molecular biology [1,2,3,4,5,6,7,8,9,10,11,12]
All the models for each individual cell showed very similar structures that only differ in a few regions in the vicinity of the nuclear envelope even though they emerge from completely independent starting conformations
The similarity of the different models to each other is shown in Figure 4 for chromosome 14 of cell 2 which is the example that will be illustrated throughout this manuscript
Summary
Very significant advances have been made in the last decades, understanding how chromosomes are organized in the cell nucleus remains a grand challenge in molecular biology [1,2,3,4,5,6,7,8,9,10,11,12]. The segregation of daughter chromosomes requires the extensive reorganization of chromatin fibers from an unfolded state to a compact cylindrical shape. After cell division chromosomes subsequently unfold again during early G1 phase to form chromosome territories [13], where each chromosome occupies a localized, largely non-overlapping region within the nucleus (see Figure 1). Current models suggest that chromosome compaction during mitosis involves Condensin complexes, which are thought to form rings that encircle two chromatin fibers. These Condensin mediated rings replace and extend links formed by the structurally similar Cohesin complexes, in a process that is assisted by Topoisomerase II (for a recent review see [14]). During mitotic chromosome condensation Topoisomerase II catalyzes double strand breaks in one DNA helix allowing the passage of a second helix through the break site, and plays a critical role in altering
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