Fig. 2: Targeting of de novo DNMTs in ExE depends on underlying chromatin landscape. | Nature Communications

Fig. 2: Targeting of de novo DNMTs in ExE depends on underlying chromatin landscape.

From: Mechanisms and function of de novo DNA methylation in placental development reveals an essential role for DNMT3B

Fig. 2: Targeting of de novo DNMTs in ExE depends on underlying chromatin landscape.

a The genome browser shot shows ChIP-seq replicates for H3K4me3, H3K27ac, H3K4me1, H3K27me3 and H3K36me3 in E6.5 extra-embryonic ectoderm (ExE), using 1 kb running windows and enrichment normalised RPKM. Hypomethylated differentially methylated regions (DMRs) identified in the Dnmt3a, Dnmt3l, Dnmt3b and Dnmt3a/b KOs using logistic regression and >20% difference are shown as annotation tracks. b Eight distinct chromatin features were identified using UMAP dimensionality reduction and clustering of 100-CpG windows using histone modification abundance in ExE. c The bean plot shows the ChIP-seq signal for histone modifications in ExE within each defined chromatin feature. The horizontal bars show the median. d The bar plot shows the relative enrichment of the most hypomethylated DMRs (hypoDMRs, identified using binomial statistic) in Dnmt3a, Dnmt3b and Dnmt3l KO ExEs for chromatin features. Statistical comparisons are provided in Supplementary Data 2. e UMAP from b) highlighting the 100 CpG window harbouring the most hypomethylated DMRs for the respective KOs ExEs: Dnmt3a (N = 3,255), Dnmt3b (N = 3,860) and Dnmt3l (N = 1,281) (left to right).

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