Fig. 2: Local organization of the genome.

a Incidence matrix visualization of a region in Chromosome 22 from adult fibroblasts (V1-V4). The numbers in the left column represent genomic loci at 100 kb resolution, vertical lines represent multi-way contacts, where nodes indicate the corresponding locus' participation in this contact. The blue and yellow regions represent two TADs, T1 and T2. The six contacts, denoted by the labels i-vi, are used as examples to show intra- and inter-TAD contacts in (b, c, and d). b Hyperedge and read-level visualizations of the multi-way contacts i-vi from the incidence matrix in (a). Blue and yellow shaded areas (bottom) indicate which TAD each locus corresponds to. c A hypergraph is constructed using the hyperedges from (b) (multi-way contacts i-vi from a). The hypergraph is decomposed into its pairwise contacts in order to be represented as a graph. d Contact frequency matrices were constructed by separating all multi-way contacts within this region of Chromosome 22 into their pairwise combinations. TADs were computed from the pairwise contacts using the methods from²⁸. Example multi-way contacts i-vi are superimposed onto the contact frequency matrices. Multi-way contacts in this figure were determined at 100 kb resolution after noise reduction, originally derived from read-level multi-way contacts (see Hypergraph Filtering in Methods).