Fig. 2: Model 3D structures are a bona fide representation of chromatin conformations in single cells.

a, Illustration of the method employed to associate single-molecule model 3D structures (top) with a corresponding chromatin 3D structure from imaging data (bottom) via RMSD^28,54 (Main Text and Methods). b, In the 2.5-Mb human HCT116 locus considered, where imaged single-cell chromatin conformations are available²², the distribution of RMSD between the 3D structures of the SBS model and their best-matching experimental structure (brown), and that of RMSD between SAW structures (control) and their best-matching experimental conformation (orange), are shown. The two distributions are statistically different (two-sided Mann–Whitney U-test P = 0); the pie chart highlights that 93% of the former is below the first tertile of the latter. c, Distributions of RMSD between the experimental (exp.) structures and best-matching conformation from the SBS model (brown) and the SAW model (orange) are statistically different (P = 0), and 70% of the former is below the first tertile of the latter. d, In the HCT116 locus, experimental and in silico Hi-C contact matrices (two heatmaps on the left), in silico SPRITE and GAM matrices (two heatmaps in the middle) and model and experimental average distance matrices (two heatmaps on the right) are shown.