Extended Data Fig. 6: Analysis of promoter-silencer (P-S) loops.
From: Subtype-specific 3D genome alteration in acute myeloid leukaemia
a, Percentage of P-S loops among all chromatin loops in all samples. b, Size distribution of P-S loops in all samples. c, Percentage of P-S loop anchors overlapping with CTCF binding peaks. d, Normalized EZH2 CUT&Tag signals at H3K27me3 peaks in the P-S loop anchors in THP-1 cells. e, Expression of genes that are located in the P-E vs. P-S loop anchors. P value was calculated by the two-sided Kruskal-Wallis test. P-E loops (n = 31332), P-S loops (n = 7912). Box plot: middle line denotes the median, top/bottom of boxes denotes first/third quartiles and whiskers extend to 1.5 times the interquartile range. f, Expression of genes in different patient samples with different distance to the nearest non-looping H3K27me3-marked silencer. P value calculated by one-sided Wilcoxon rank-sum test. N = 3809, 4403, 3865, 3217, 2490 genes (from left to right each category). Box plot: middle line denotes the median, top/bottom of boxes denotes first/third quartiles and whiskers extend to 1.5 times the interquartile range. g. Distance distribution between the IKZF2 promoter to control or its looped silencers in Kasumi-1 (n = 112 alleles). P value by two-sided Wilcoxon rank-sum test. Box plot: middle line denotes the median, top/bottom of boxes denotes first/third quartiles and whiskers extend to 1.5 times the interquartile range.
