Fig. 3

Visualization of chromosome structures. (a) Frequency distribution of the number of dots (probes) detected in 466 (n) miFISH dot clusters in G1 cells (Dataset 1²³ and Methods). (b) Distributions of the full width half maximum (FWHM) values of the dots identified in 6 different channels for the miFISH chr2 Replicate 1 experiment (Dataset 1²³). n, number of dots. The channels are ordered from left to right by increasing wavelength. In all the violin plots, the horizontal lines indicate the first, second (median) and third quartile (from bottom to top), and the whiskers extend from the minimum to the maximum value. (c) Examples of interpolated structures for 9 out of 466 miFISH dot clusters summarized in (a). Colored dots represent individual probes whereas the connecting lines were drawn by interpolation using the cubic splines curve method (see Methods). Color gradient, from yellow to blue, follows the genomic path of the DNA segment probed (see Fig. 1c). Each dot is colored based on the A/B compartment assignment of the corresponding probe. (d) Normalized curvature peaks in 37 interpolated structures such as those shown in (a), in which all the 16 miFISH probes were identified. (e) Normalized curvature peaks pooled from all 37 structures shown in (d) for the genomic coordinates 55–95 Mb where equal inter-probe spacing (every 3 Mb) was applied. Probes are colored following the scheme shown in Fig. 1c. The Cytobands corresponding to this segment of chr2 are shown above the plot. The grey shading depicts a region depleted of curvatures.