Fig. 3: Classification of genomic regions based on their differential interactions connectivity patterns. | Nature Communications

Fig. 3: Classification of genomic regions based on their differential interactions connectivity patterns.

From: HMGA1 orchestrates chromatin compartmentalization and sequesters genes into 3D networks coordinating senescence heterogeneity

Fig. 3

a Differential interactions network of OIS compared to Grow on chromosome 1 with nodes coloured by their overlap with H3K9me 3 and HMGA1-dense regions. b Model representation of the k-core decomposition of an example network with k-max equal to 3. c The k-core decomposition of the network of increased interactions in OIS compared to Grow on chromosome 1, with the size of each node (200 kb bins) reflecting the degree (number of interactions) of the node and the k-core value as the node colour; edge colour reflects the minimum k-core of its nodes; arrow indicates the nodes with the maximum k-core value (k-max). d Normalised ChIP-seq signal tracks of HMGA1, Lamin B1, and H3K9me3 in Grow and OIS around the regions which form the degeneracy core (k-max) of chromosome 1 shown in c. e The k-core decomposition (left) of the chromosome 3 network (200 kb bins) of increased contacts in OIS compared to Grow, with the node colour corresponding to its k-core and the node size to its degree; the full network of differential interactions highlighting the HMGA1 (middle) and H3K9me3 (right) normalised ChIP-seq signal of each node; arrow indicates the cluster of regions with low k-core and HMGA1, but high H3K9me3 ChIP-seq signal. f Heatmap of the k-core values, classification, and epigenetic properties, represented by the ChIP-seq (or ATAC-seq) scaled normalised signal of H3K9me3, HMGA1, LaminB1 in Grow and OIS, H3K27me3, ATAC-seq (accessibility), and H3K27ac, of all the bins with k-core of at least 1. g The network of (all) differential interactions of OIS compared to Grow on chromosome 2 with nodes classified as: Core (yellow), Peri (peri-core, magenta), AltCore (alternative core, cyan), ExCore (excluded from cores, navy blue) and other (grey). h The A/B compartment score and H3K9me3 ChIP-seq signal of the genomic bins in each of the classes. i The distributions of the HMGA1 signal, the AT%, H3K27ac and H3K27me3 signal of the bins in each class. j Lamin B1 signal in Grow (left) and OIS (right) of all the bins in each of the classes. h–j Compared regions: n = 2900 Core, n = 915 Peri, n = 2892 AltCore, n = 2368 ExCore, and 5235 Other. Box plot centre line represents the median, the bounds correspond to the 0.25 and 0.75 quantiles, the whiskers represent the 0.1 and 0.9 quantiles. P-values derived from two-sided Wilcoxon testing.

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