Fig. 3
Cell-type-specific frequency of long-range contacts defines chromosome folding in 3D space. a Left, schematic representation of 69 domain borders labeled by a single Oligopaint library (Lib-69) in Chr. 3R. Each probe was spanned at ~ 20 kb, and probes were separated by 320 kb on average (Supplementary Fig. 3a, b). Right, representative two-color 3D-SIM images for all studied cell types. DAPI signal (white) and Lib-69 (pink) are shown. Scale bar = 200 nm. b Left panel, single-cell probability distance distribution p(r) between all pairs of foci imaged by 3D-SIM. The white line represents the population-averaged p(r) frequency. Detailed R g and D max values are shown in Supplementary Fig. 3. D max is defined as the distance that comprises <97% of the area under the p(r) function. Right panel, number of foci per cell for each condition with mean population values shown as solid vertical lines and indicated above. N = 180, from more than three biological replicates. c Schematic representation of the chromosome structure for each cell type. The solid gray line represents the chromatin fiber and pink circles represent domain borders with sizes proportional to the number of regrouped borders. d Hi-C contact frequencies of S2 vs. late embryo cells for all the pairwise combinations of the 69 borders. The solid red line represents the relation expected if frequencies of interactions between the 69 borders were equal between cell types. Insets depict chromosome 3R and different combinations of genomic distances and frequencies of interaction between borders. Matrix resolution = 50 kb. N = 4, from at least three biological replicates
