Extended Data Fig. 2: Characterization of mitotic cohesin peaks.
From: Extensive mutual influences of SMC complexes shape 3D genome folding
a, Experimental design, showing the strategy of prometaphase arrest in combination with 5-Ph-IAA or/and dTag13 treatment. b, Flow cytometry plot showing the gating strategy to purify WAPL-depleted and WAPL and SMC2 co-depleted mitotic cells. More than three independent experiments were performed. c, Representative images showing FACS purified WAPL-depleted or WAPL and SMC2 co-depleted mitotic cells. Two independent experiments were performed. Scale bar: 10 μm. d, Venn diagram showing the intersection results of RAD21 peaks in the WAPL deficient G1-phase samples and WAPL and SMC2 co-depleted mitotic samples. e, Density heatmap plots showing the ChIP-seq signals of RAD21 peaks that were lost, maintained or gained during mitosis. f, Meta region plots showing the corresponding mitotic CTCF ChIP-seq signals for RAD21 peaks that were lost, maintained or gained. Note that compared to the lost ones, the maintained RAD21 peaks were co-localized by stronger mitotic CTCF binding. CTCF ChIP-seq data was adapted from our previous study24. g, Dot plots showing the average RAD21 ChIP-seq signals for peaks that were lost, maintained or gained during mitosis. Central line denotes mean values (n = 4 and 5 biological replicates for G1-phase and mitotic samples respectively). P values were calculated using two-sided student’s t-test. h, De-novo motif enrichment analysis for the mitotic specific RAD21 peaks. i, Box plot showing that mitotic specific RAD21 peaks (n = 3,642) were significantly larger compared to the interphase Rad21 peaks (n = 29,756). For both box plots, central lines denote medians; box limits denote 25th–75th percentile; whiskers denote 5th–95th percentile. P values were calculated using a two-sided Wilcoxon signed-rank test. j, Meta region plots showing that mitotic specific RAD21 peaks were heavily decorated with active histone marks. k, Pie charts showing that the mitotic specific RAD21 peaks were significantly more likely to co-localize with CREs. P values were calculated using two-sided Fisher’s exact test.
