Fig. 3

Visualizing and quantifying cohesin-dependent chromatin structures. a,b Auxin-dependent degradation of cohesin. HCT-116-RAD21-mAC cells [52], in which the cohesin subunit RAD21 is auxin-degradable and fused to the fluorescent protein gene mClover, were treated with 500 μM of auxin for 6 h (a) or left untreated (b). c Comparison of mean fluorescence in auxin-treated vs untreated cells confirms that auxin leads to efficient degradation of RAD21-mClover (p < 10^− 5). d,e Example 3D super-resolution images of individual chromosome regions in HCT-116-RAD21-mAC cells left untreated (d) or treated with auxin (e). The arrows in e point at isolated stretches that likely correspond to single chromatin fibers, with approximate lengths of 1.6 μm, 3.2 μm, and 0.5 μm, from left to right. Color indicates axial coordinates. For animated 3D views, see Additional file 4: Video S3. f,g Violin plots compare the distributions of gyration radii (f) and smoothness (g) in cells with (n = 43) or without (n = 50) cohesin depletion by auxin treatment. Median gyration radii differ significantly (p = 0.013), as do smoothness values (p = 5 × 10^− 4) (two-sided rank sum tests). See also cumulative distribution functions and bootstrap analyses in Additional file 1: Fig. S7 and S8d