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. Author manuscript; available in PMC: 2021 Nov 16.
Published in final edited form as: Nat Methods. 2021 Sep 3;18(9):1046–1055. doi: 10.1038/s41592-021-01248-7

Figure 5: Characterization of interactions and chromatin features of loop anchors.

Figure 5:

a. Number of loops versus number of loop anchors in HFFc6. Expected relationship between anchor engaged in one loop: y=2x

b,c.FA-DpnII loops subtracted from FA+DSG-DpnII (b) or FA+DSG-MNase (c) loops detected at the same anchors. Union loops of the plotted protocols were used.

d. Interactions (linear scale) and Cut&Run/Cut&Tag signals for CTCF, SMC1, H3K4me3 and H3K27ac Loop anchors detected with all three protocols (Cyan squares) or only with FA+DSG-MNase (Black squares) (37).

e. CTCF, SMC1, H3K4me3 and H3K27ac enrichments at loop anchors detected by all protocols (intersection) or FA+DSG-MNase alone in HFFc6. Open chromatin regions within anchor coordinates were used to center average enrichments.

f. cCREs detected in common and FA+DSG-MNase specific loop anchors from Figure 5e (top) and stratified percentage of Promoter-Enhancer cCREs without CTCF enrichment (bottom).

g. Enrichment of CTCF, SMC1, H3K4me3 and H3K27ac separated between left (Anchor1) and right (Anchor 2) anchor for anchors detected in HFFc6 using FA-DpnII, FA+DSG-DpnII or FA+DSG-MNase.