DNA loops and TADs observed in mouse oocytes are largely dependent on Scc1-cohesin. (A) Representative images of in situ fixed Scc1^fl/fl, Scc1^Δ/Δ, Wapl^fl/fl, and Wapl^Δ/Δ GV-oocytes in SN state (mature, SN). A single Z plane is shown to better visualize vermicelli structures in Wapl^Δ/Δ oocytes. DNA is shown in blue, and Smc3 and Scc1 in gray. Scale bar, 10 µm. (B) Average loops, TADs, and compartmentalization in Scc1^fl/fl, Scc1^Δ/Δ, Wapl^fl/fl, and Wapl^Δ/Δ GV-oocytes in SN state. The number of oocytes analyzed is indicated in the figure. Three Wapl^fl/fl, four Wapl^fl/fl (Tg)Zp3-Cre, two Scc1^fl/fl, and two Scc1^fl/fl (Tg)Zp3-Cre littermate females were analyzed. (C) P_c(s) for Scc1^fl/fl, Scc1^Δ/Δ, Wapl^fl/fl, and Wapl^Δ/Δ GV-oocytes in SN state. Slopes of the log(P_c(s)) curves for each condition are shown below the P_c(s) plots. Gray lines show the controls Scc1^fl/fl (left panel) and Wapl^fl/fl (right panel), and blue lines show Scc1^Δ/Δ (left panel) and Wapl^Δ/Δ (right panel). (D) Quantification of the number of contacts within loop coordinates. This is calculated by extracting the contacts from the heat maps for each loop and normalizing by the sample size of each condition. The average number of contacts observed per loop is represented. The removal of Scc1-cohesin results in there being, on average, statistically less contacts within the loops, while in the absence of Wapl there are, on average, statistically more contacts per loop (paired Wilcoxon rank-sum test). The sample size is the same as in B.