Fig. 3: Compartmentalized architecture with an interchromatin (IC) channel network pervading chromatin domain clusters (CDC) with zonal compaction differences both in controls and cohesin depleted, pre- and post-endomitotic nuclei.

a–c DAPI-stained mid-sections of representative nuclei acquired by 3D-SIM from a control nucleus; b cohesin depleted nucleus (6 h auxin); c cohesin depleted multilobulated nucleus (MLN) (30 h auxin) are displayed by seven DAPI intensity classes in false colors, used as proxies for chromatin compaction. The color code on the right indicates the assignment of DAPI signals into seven classes with equal intensity variance. This approach allows threshold-independent signal intensity classification based on the intensity of an individual voxel. Class 1 (blue) pixels close to background intensity, largely reflecting the interchromatin compartment (IC) with only sparse DNA, class 7 (white) pixels with the highest intensities. All nuclei in a-c reveal a network of chromatin domain clusters (CDCs) comprising a compacted core and a surrounding low-density zone co-aligned with class 1 regions that meander between CDCs as part of the IC (see insets). Likewise, all nuclei display a rim of compacted (hetero)chromatin at the nuclear periphery. N = nucleolus; IC = interchromatin channels/lacunae. Images in a–c show representative nuclei from two independent experiments. Scale bars: 5 µm, insets: 0.5 µm. d Relative 3D signal distributions of DAPI intensity classes in control nuclei and cohesin depleted nuclei show an overall similar profile. (control: n = 38, 6 h: n = 39, 30 h: n = 33 cells from two independent experiments). 6 and 30 h, respectively denote incubation time in auxin. Data are represented as mean ± SEM. e Average nuclear volumes (µm³) from the same series of nuclei. The ~2-fold increase of nuclear volumes in (post-endomitotic) MLN after 30 h auxin likely reflects their further increase of a 2n DNA content immediately after endomitosis to a 4n DNA content after another round of DNA replication (Supplementary Fig. 5), for statistical tests see Source Data file. Data in e are represented as boxplot where the middle line indicates the median, the lower and upper hinges correspond to the 25 and 75% quartiles, the upper whisker extends to the largest value no further than 1.5 × IQR (inter-quartile range) from the hinge and the lower whisker extends to the smallest value from the hinge at most 1.5 × IQR. In addition, all data points are plotted individually. Source data are provided as a Source Data file.