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. 2021 Aug 27;12:5157. doi: 10.1038/s41467-021-25418-5

Fig. 3. CTCF loops constrain CRE contacts after mitosis.

Fig. 3

a Schematic showing the stratification of loops (“structural loops”, “dual-function loops”, and “CRE loops”) based on the presence at their anchors of CTCF/cohesin co-occupied sites and CREs. CRE denotes cis-regulatory element. b APA plots showing the signals of loop categories before and after CTCF depletion across cell cycle stages. Bin size: 10 kb. c KR balanced Hi-C contact matrices of representative regions containing structural loops. Bin size: 10 kb. Tracks of CTCF and Rad21 with or without auxin treatment as well as H3K27ac, H3K4me3, and H3K4me1 were from asynchronous G1E-ER4 cells. d Similar to (c), KR balanced Hi-C contact matrices of representative regions containing dual-function loops. Bin size: 10 kb. e Venn diagram of CRE loops. f Heatmap displaying intensities of the 1410 newly gained loops after CTCF depletion. g Heatmap showing the result of k-means clustering on the 3232 CRE loops detected in untreated control samples. h Similar to c, d, KR balanced Hi-C contact matrices of a representative region containing a cluster1-P transient CRE loop. Additional tracks of CTCF and Rad21 from parental cells across designated cell cycle stages are shown1.