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Fig. 2 | Genome Biology

Fig. 2

From: Large scale genomic reorganization of topological domains at the HoxD locus

Fig. 2

Tripartite interactions between Hoxd13 and the regulatory islands. a Orthogonal projections from 3D DNA FISH (as in Fig. 1b) performed using either Hoxd13 and two regulatory islands (left) or three islands (GCR, island II, and island I) in E12.5 forelimb autopod cells. Scale bar: 400 nm. b 3D DNA measurements showing variations in the distribution of physical distances between Hoxd13 and island II (purple, bottom), Hoxd13 and island IV (cyan, middle), or island II and island IV (yellow, top). c Heatmap of unique tripartite interactions in the centromeric TAD region generated from 4C-seq data using Hoxd13 as a viewpoint (from white, corresponding to no interaction, to dark blue, indicating more than five unique interactions in the 20-kb bin). For each Hoxd13–X–Y triple interaction, the X and Y regions were assigned to a bin of 20 kb and reported into the matrix with bins of 20 kb. To avoid possible PCR artifacts, identical X–Y pairs were counted only once. Below are represented the positions of the genes and the digit enhancers. The purple line shows the limits of C-DOM as identified in [9]

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