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. 2021 May 13;4:571. doi: 10.1038/s42003-021-02089-y

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© The Author(s) 2021

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. 1 — a Comparison between compartment score and H3K9me2 enrichment in 80-kb bin. RPKM of H3K9me2 from WT mESCs is negatively correlated with compartment score. Darker blue represents higher dot density. b, c Comparison between compartment score in WT mESCs and changes in H3K9me2 in Setdb1 KO (b) or Suv39h1/2 DKO (c) mESCs in 80-kb bins. Decreased H3K9me2 is observed in the A and B compartments in Setdb1 KO and Suv39h1/2 DKO mESCs, respectively. d A representative view of H3K9me2 domains in WT mESCs identified by Hiddendomains. Top panel, H3K9me2 ChIP-seq data from WT mESCs; middle panel, H3K9me2 domains; bottom panel, compartment score in 80-kb bins. e Fractions of H3K9me2 domains in the A or B compartments. Although H3K9me2 domains are more enriched in the B compartments than in the A compartments, H3K9me2 also occupies about half of the A compartments. f Length of H3K9me2 domains in each KO mESCs to WT mESCs. The length of H3K9me2 domains in the A compartments is slightly decreased in Setdb1 KO mESCs, whereas that is increased in Suv39h1/2 DKO mESCs. g A correlation matrix of H3K9me2 ChIP-seq data in mESCs. UNC0642-treated mESCs form a cluster distinct from untreated mESCs. Among UNC0642-treated mESCs, Setdb1 KO mESCs show a different H3K9me2 profile. h, i A comparison between compartment score in WT mESCs and changes in H3K9me2 in Setdb1 KO (h) or Suv39h1/2 DKO (i) mESCs treated with UNC0642. j A representative view of H3K9me2 ChIP-seq from G9a/GLP DKO and UNC0642-treated mESCs (chr6:73,266,079-91,207,724). G9a/GLP DKO mESCs show an H3K9me2 profile similar to UNC0642-treated mESCs. A drastic loss of H3K9me2 domains in UNC0642-treated Setdb1 KO mESCs in the A compartments (circled in red). k Heatmaps of H3K9me2 enrichment around G9a/GLP-independent H3K9me2 regions. The A compartment-specific H3K9me2 loss is observed in UNC0642-treated Setdb1 KO mESCs. l Fractions of conserved or lost G9a/GLP-independent H3K9me2 in Setdb1 KO or Suv39h1/2 DKO mESCs treated with UNC0642. m H3K9me2 ChIP-qPCR analysis in regions shown in Fig. S1o. ChIP was performed 5 days after 4-OHT treatment in Setdb1 KO mESCs and 7 days after 4-OHT treatment in Setdb1/Suv39h1/2 TKO mESCs. H3K9me2 in the region 1 and 2 is completely lost in UNC0642-treated TKO mESCs. Data are mean ± SEM; n = 3.