Figure 4. The organization of cohesin-dependent loops.

(A) Features of chromatin loops organization from the contact map. Contact map showing the interaction in the 40–160 kb region of chromosome I overlay with the tracks for Mcd1p ChIP-seq signal and peaks. Squares indicate loops from adjacent CARs. Circles indicate loops from distal CARs. Dashed lines indicate the position of barriers that insulate from loop expansion. (B) Model for loops organization. Each CAR (Mcd1p peak) forms a loop with the CAR that follows and a loop with the CAR that precedes (Bidirectional loops from adjacent CARs). Some CAR can form loops with distal peaks (CAR0 with CAR+2, and CAR0 with CAR-2) (loop expansion). The high-residency CAR (peaks with the highest Mcd1p signal) are barriers to loop expansion. (C) The distribution of the size of positioned loops is correlated to the cohesin peak interval. The histogram shows the probability of the length distribution for positioned loop size and Mcd1p peak interval in the range from 0 to 40 kb. The inset table highlights the median length. (D) The positioned loop signal is detected till the +5 CARs interval genome-wide. Heatmaps were plotted with 200 bp resolution data for WT. A ±5 kb region surrounding each loop anchor and the corresponding CARs interval from +1 to +10. (E) The levels of cohesin binding in a loop anchor influence the strength of the corresponding loop and the ability to function as a barrier. Heatmaps were plotted with 200 bp resolution data for WT. We plotted a ±5 kb region either surrounding the high-residency CARs and the corresponding two-interval CARs (first panel); or surrounding the low-intensity CARs and the corresponding two-interval CARs (second panel); or surrounding a CAR and the corresponding two-interval CAR with a high-residency CAR in the middle (third panel).

Figure 4—figure supplement 1. Cohesin-dependent organization of loops.

(A) Genome-wide analysis confirms loop expansion in wild-type. Bar chart shows the percentage of the number of positioned loops per anchor in wild-type (WT) arrested in mitosis. (B) Around half of the visibly positioned loops are missed by HiCCUPS loop calling program. Contact map showing the interaction in the 40–160 kb region of chromosome I overlay with the tracks for Mcd1p ChIP-seq signal and peaks. Squares indicate loops called by HiCCUPS. Circles indicate visibly distinct positioned loops missed by HiCCUPS. Dashed lines indicate the position of barriers that insulate from loop expansion. (C) The positioned loop signal is detected till the +5 loop anchors interval genome-wide. Quantification of the heatmap analysis in Figure 3D. The chart shows the loop enrichment (Log2 of the ration of the loop signal in the center of the heatmap divided for the background signal in the corner) on the y-axis present at each CAR interval (x-axis) in wild-type (WT) cells in mitosis. (D) The positioned loop intensity correlates with the intensity of the Mcd1p ChIP-seq signal at the corresponding loop anchors. Loop intensity was sorted into quartiles from high to low. Mcd1p ChIP-seq signal was plotted against the loop anchors at the center. (E) Scatter plot showing a positive correlation of positioned loop intensity and Mcd1p ChIP-seq signal. Averaged ChIP-seq peak signals at the positioned loop anchors and the contact enrichment of loops (quantified by HiCCUPS or Chromosight) were normalized with z-score, and then plotted with Mcd1p signal at y-axis and loop intensity at x-axis. The scatter plot shows a positive correlation between two measurements with a Spearman coefficient at 0.63.