Fig. 2: Dip-C reveals differences between active and inactive GI hubs.

a, Dip-C was performed on 161 FAC-sorted GFP⁺ nuclei from Mor28iGFP and gg8-tTA>tetOP-2iGFP mice. Three-dimensional models of individual nuclei were rendered using haplotype-imputed contact maps (top left) and coloured by chromosome (bottom left). A representative Mor28iGFP nucleus stripped of all genes except inactive ORs (small spheres), the active OR allele (large sphere) and GIs (medium spheres) is shown, coloured by chromosome (top right). The active Mor28 allele was near a cluster of GIs, marking the active hub (bottom left). Further GI clusters were also detected (bottom right). b, Binary arrays were generated for each cell (rows) and depict GIs within less than 2.5 p.r. of the P2 allele (non-Cas, chr7) when it is active (top, gg8-tTA>tetOP-2iGFP Dip-C, n = 87 cells; see Extended Data Fig. 5b for Mor28iGFP Dip-C) or inactive (bottom, OMPiGFP, n = 40 cells from publicly available data). c, Hierarchical clustering of GI spatial relationships in a P2⁺ nucleus. The dendrogram was cut at 2.5 p.r. The active GI hub is shown in green and the inactive hub of the most similar size in black. d, Dip-C model depicting the topology of active and inactive hubs selected for contact analysis. e–h, Heatmaps of interchromosomal contacts made between GIs in the active hub (e; CSS = 0.0117, n = 117 cells with contacts pooled from two independent experiments); GIs in the inactive hub (f; CSS = 0.00891, n = 109 cells with contacts pooled from two independent experiments); GIs and the active OR (g; CSS = 0.0120, n = 70 cells with contacts pooled from two independent experiments); and GIs and the maximally engaged inactive OR in the inactive hub (h; CSS = 0.00621, n = 106 cells with contacts pooled from two independent experiments). CSS was measured by dividing the contacts in any 50 kb bin by the sum of all contacts in the 2 × 2 Mb square, where the CSS at the focus of interaction is noted in the bottom right corner. GIH, GI hub.

Source Data