Fig. 5. Characterization of interactions and chromatin features of loop anchors.
a, The number of loops versus the number of loop anchors in HFFc6 cells, and the expected relationship between anchors engaged in one loop: y = 2x. b,c, Subtraction of FA–DpnII loops from FA + DSG–DpnII loops (b) or from FA + DSG–MNase loops (c) detected at the same anchors. Union loops of the plotted protocols were used. d, Chromatin interaction maps (linear scale) flanked by tracks for ATAC-seq and CUT&RUN or CUT&Tag signals for CTCF, SMC1, H3K4me3 and H3K27ac. Squares in the interaction maps indicate loop anchors detected with all three protocols (cyan squares) or only with the FA + DSG–MNase protocol (black squares)32. e, CTCF, SMC1, H3K4me3 and H3K27ac enrichments at loop anchors detected by all protocols (intersection) or by FA + DSG–MNase alone in HFFc6 cells. Open chromatin regions within anchor coordinates were used to center average enrichments. f, cCREs detected in common and in FA + DSG–MNase-specific loop anchors in e (top) and stratified percentage of promoter–enhancer (P–E) cCREs without CTCF enrichment (bottom). g, Enrichment of CTCF, SMC1, H3K4me3 and H3K27ac at the left (anchor 1) and the right (anchor 2) anchors, for anchors detected in HFFc6 cells using FA–DpnII, FA + DSG–DpnII or FA + DSG–MNase.