Fig. 5: TAD-like structures in modeled single-cell conformations during Drosophila embryogenesis.

Simulated heat maps of the region (chr2L: 11.0–12.0 Mb) in embryos at pre-MBT cycles 9–13 (a) and S2R+ (d) are shown. The lower left triangles represent the experimental Hi-C propensities, and the upper right triangles represent the simulated contact probabilities. Resolution is 2 kb. Boundary strength profiles of 5,000 conformations in embryos at cycles 9–13 (b) and S2R+ (e) are shown below the combo heat maps. They are ordered by the number of domain boundaries. Three representatives of single-cell spatial-distance heat maps (on the left) and corresponding visualizations of conformations (on the right) in embryos at pre-MBT cycles 9–13 (c) and S2R+ (f) are shown. These single-cell conformations have different numbers of domain boundaries. The number of boundaries from top to bottom is 0, 3, and 5, respectively. Arrows indicate their positions in the boundary strength profiles. Boundary strength curves are drawn under the spatial-distance maps, with red dots representing the local maxima identified as domain boundaries. Bars in different colors under the boundary strength curves represent different domains identified in that conformation, which are also labeled in 3D visualizations. g Correspondence between distance maps of two modeled single-cell conformations (chr3R:12.20–12.90 Mb of Drosophila S2R+ at 2 kb resolution) with two conformations constructed from imaging studies in Mateo et al. (r = 0.75 and 0.79, Fig. 2d of²⁰ reprinted with permission). Proportions of single-cell conformations with different numbers of TADs are shown in h for each cell type. Source data are provided as a Source Data file.