Figure 5.

Speckles pull a subset of A compartments toward nuclear interior, producing their distinct contact patterns with the rest of the genome. (a) Cross sections of two nucleus models with 40 (top) and 10 (bottom) speckles. Speckles in the bottom panel adopt more interior localizations. (b) Radial densities of the A compartment and $A1\mathrm{a}\mathrm{n}\mathrm{d}A2$ subcompartments as a function of the radial position inside the nucleus. The top panel highlights the pulling of the A segments to the interior upon lowering the number of speckles in the system. The lower panel highlights the behavior of the $A1$ and $A2$ segments upon perturbing the number of speckles in the system. (c) Comparison between the two subtypes of A compartments ($AI\mathrm{a}\mathrm{n}\mathrm{d}AII$) and $A1$ and $A2$ subcompartment annotation probabilities for chromosomes 3 and 5. The simulated genome-wide contact matrix between the A loci on chromosome 3 and all even chromosomes is shown on the left. This contact matrix was used for clustering the A loci into two subtypes (see also Figure S11). To see this figure in color, go online.