Extended Data Fig. 13: Impact of 5-AZA treatment on chromatin structure.
From: Subtype-specific 3D genome alteration in acute myeloid leukaemia
a, Global CG methylation levels of U937 under DMSO or 5-AZA treatment. b, A snapshot of DNA methylation levels across a genomic region. c-d, DNA methylation levels at CpGi, CpG shores (<2Kb), CpG shelves (2Kb-4Kb), open sea (rest of genome), and CTCF binding sites under 12-day DMSO or 0.5μM 5-AZA treatment. DMSO: n = 2,691,094 CpG types, 5-AZA n = 2,669,959 CpG types. CTCF binding sites were defined from HSPC cells. N = 10,960 CTCF sites. P value by two-sided Wilcoxon rank-sum test. Violin plot: middle line denotes the median, top/bottom of boxes denotes first/third quartiles and boundary extend to 1.5 times the interquartile range. e, Enrichment of CpGi and open sea at each type of switching compartment. P value by two-sided Wilcoxon rank-sum test. From left to right for both CpGi and Open sea: n = 808, n = 372, n = 636, n = 338; 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. Methylation levels for each type of switching compartment at CpGi (upper) and open sea (lower). From left to right: CpGi panel: n = 20,566, n = 450, n = 4,651, n = 910; Open sea panel: n = 591, n = 731, n = 4,531, n = 1,398. P value by two-sided Wilcoxon rank-sum test. AB: A in DMSO group and B in 5-AZA group. Violin plot: middle line denotes the median, top/bottom of boxes denotes first/third quartiles and boundary extend to 1.5 times the interquartile range. g, CpGi at one or both anchors of two types of loops under 5-Aza treatment. h, Methylation levels for two types of loops at CpGi and open sea. From left to right: CpGi panel: n = 2,871, n = 596; Open sea panel: n = 117,177, n = 20,499. P value by two-sided Wilcoxon rank-sum test. Violin plot: middle line denotes the median, top/bottom of boxes denotes first/third quartiles and boundary extend to 1.5 times the interquartile range.
