Mapping the semi-nested community structure of 3D chromosome contact networks
Fig 5
Hierarchical and semi-hierarchical models of chromatin folding for human chromosome 10.
(a) Ideal hierarchical folding (Q = 0). Filled circles on the outer rim represent domains; the root symbolizes the entire chromosome. We align the domain aggregates (superstructures) with the inner tree rings, each defining a scale of organization. We select a few domains (red-filled circles) and show their domain-to-root paths with thick edges. These domains assemble into yet larger structures (violet) at every inner ring. As soon as the domains merge into a superstructure labeled ‘453’ (dark violet), they never split apart. (b) Semi-hierarchical folding (Q = 0.30). As in (a), we color the domains in red that merge into a superstructure ‘453’ and highlight their folding paths with thick edges going from the outer rim to the root. Unlike (a), node ‘453’ is scattered across seven tree branches. Thus, ‘453’ only partially nests into larger structures and the domains split and reunite when approaching the root. (c) Nestedness histogram when Q = 0 (ideal hierarchy, red bars) and Q = 1 (random nesting, open bars). When Q = 0, we see two peaks at Nij ± 1, indicating complete segregation and full nestedness. When Q = 1, the domains are fully randomized between the superstructures. While there is still perfect nesting and segregation (as we expect from the random null hypothesis in Methods: Network nestedness), there is also partial overlap for −0.8 < Nij < 0.8. (d) Nestedness histogram with some randomness (Q = 0.30, light-blue bars) overlaying the actual GenLouvain-derived data for chromosome 10 (dark-grey bars). We produced (a) and (b) using RAW Graphs [37].