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. 2022 Dec 22;30(1):38–51. doi: 10.1038/s41594-022-00892-7

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© The Author(s) 2022

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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Fig. 5 — a, Schematic of the DNA methylation perturbation system used in this study. b, LC–MS quantification of 5-methylcytosine/total cytosine for HCT116 (left, n = 5 biological replicates), HCT116 cells treated with 5Aza (48 h) (middle, n = 10) and DNMT1/DNMT3b knockout (DKO) (right, n = 2) cells. Data are presented as mean values with ±s.d. error bars. c, Stacked heatmaps of H3K9me3 ChIP–seq signal in HCT116 (left), 5Aza 48 h (middle) and DKO (right) centered at uniformly rescaled B₄ domains, sorted vertically by the intradomain H3K9me3 ratio between DKO and HCT116, and partitioned into two categories: persistent domains (top) and disrupted domains (bottom) in DKO. d, Scatter plots of 50-kb bins along E1 versus E2 (HCT116 eigenvectors), colored by Protect-seq signal for HCT116 (left), 5Aza 48 h (middle) and DKO (right). e, Box plots quantifying the distribution of log₂ ratios of mean domain signal between HCT116 and 5Aza in persistent (left, n = 185) and disrupted (right, n = 116) B₄ domains. Signals shown are Protect-seq, HP1a, H3K9me3 and H3K9me2. Box extents give the interquartile range with whiskers extending by a factor of 1.5 and the notch representing the confidence interval around the median. Points represent outliers. f, Same as e but between HCT116 and DKO. g, Contact frequency maps of a 40-Mb genomic region (chr9:0–40 Mb) in HCT116 (left), 5Aza 48 h (middle) and DKO (right) containing representative examples of persistent and disrupted domains. Below, ChIP–seq tracks for H3K27me3, H3K9me2, H3K9me3, HP1α and H2A.Z. h, Heatmap displaying the pairwise mean observed/expected contact frequency between active, H3K27me3 and H3K9me3 domains split into either disrupted or persistent labels in DKO based on ChromHMM states learned at 50 kb. i, Sankey plot of disrupted domains illustrating the chromatin transition from H3K9me3-HP1α/β in HCT116 cells to H3K9me2 and/or other repressive states based on ChromHMM in DKO cells.