(A) Cohesin and condensin are efficiently depleted upon auxin addition. The depletion of Mcd1p and Brn1p tagged with AID upon auxin addition to the media is shown by western-blot analysis. Tubulin is used for loading control. (B) The majority of the positioned loops are cohesin-dependent. Contact maps from mitotically arrested cells were produced with Micro-C XL on wild-type (WT), cohesin Mcd1p-depleted (MCD1-AID), and condensin Brn1p-depleted (BRN1-AID) cells. Contact maps show contacts between the whole genome (first row), followed by contacts from chromosomes VIII to XI at 6.4 kb resolution (second row). The following contact maps show chromosome X and a zoomed-in region (from the full 745 kb to a 250 kb region), with 1.6 kb and 800 bp resolution, respectively. Standard colormap scheme that uses the shades of red from white (no detectable interactions) to black (maximum interactions detected) in log10 scale. (C) Almost no positioned loops are detected upon cohesin depletion, while condensin depletion presents a small reduction in the number of positioned loops. Bar chart shows the loop number called by the HiCCUPS program in wild-type (WT), cohesin Mcd1p-depleted (MCD1-AID), and condensin Brn1p-depleted (BRN1-AID) cells. (D) Genome-wide analysis confirms positioned loop signal is gone in cohesin-depleted cells and slightly reduced upon depletion of condensin. Heatmaps were plotted with 200 bp resolution data for wild-type (WT), cohesin Mcd1p-depleted (MCD1-AID), and condensin Brn1p-depleted (BRN1-AID), and cohesin- and condensin-depleted (MCD1-AID BRN1-AID) cells in ±5 kb regions surrounding the wild-type anchors for positioned loops. Numbers in the corners represent the fold-change of the signal enrichment of the center pixel over the indicated corner pixels (142 pixels). The contact map was normalized by matrix balancing and distance, using a diverging colormap with positive signal enrichment in red and negative signals in blue (gradient of normalized contact enrichment is in log2). (E) Cohesin depletion shows fewer contacts in the size-region corresponding to the size of positioned loops, while condensin depletion does not. Interactions-versus-distance decaying curve shows the normalized contact density (y-axis) against the distance between the pair of crosslinked nucleosomes from 100 bp to 1 Mb (x-axis) for wild-type (WT) in blue, condensin Brn1p-depleted (BRN1-AID) in yellow, and cohesin Mcd1p-depleted (MCD1-AID) in red. (F) Cohesin depletion results in more inter-chromosomes contacts. Bar chart shows the number of inter-chromosomes contacts in wild-type asynchronous (Async), wild-type (WT), cohesin Mcd1p-depleted (MCD1-AID), condensin Brn1p-depleted (BRN1-AID), and cohesin- and condensindepleted (MCD1-AID BRN1-AID) all arrested in mitosis.