Fig. 5

DNA hypomethylation is followed by H3K4me3 enrichment and activates transcription. (a) Venn diagrams of number of H3K4me3 (left) and H3K27me3 (right) peaks in WT and Dnmt1 KO MEF cells, in blue and red, respectively. (b) Scatter plot of DNA methylation profiles in Dnmt1 KO versus WT cells. (c) Scatter plot of RNA-Seq transcription profiles of Dnmt1 KO versus WT. The scattering density is shown in green. (d) Scatter plot of DNA methylation profiles in Dnmt1 KO versus WT cells for H3K4me peaks over promoters of WT cells. (e) Scatter plot of DNA methylation profiles in Dnmt1 KO versus WT cells for H3K4me peaks over promoters of Dnmt1 KO cells. (f) Scatter plot of DNA methylation profiles in Dnmt1 KO versus WT cells for H3K4me peaks over enhancers of WT cells. (g) Scatter plot of DNA methylation profiles in Dnmt1 KO versus WT cells for H3K4me peaks over enhancers of Dnmt1 KO cells. (h) Scatter plot of transcriptomics profiles in Dnmt1 KO versus WT cells for H3K4me peaks over promoters of WT cells. (i) Scatter plot of transcriptomics profiles in Dnmt1 KO versus WT cells for H3K4me peaks over promoters of Dnmt1 KO cells. (j) Scatter plot of transcriptomics profiles in Dnmt1 KO versus WT cells for H3K4me peaks over enhancers of WT cells. (k) Scatter plot of transcriptomics profiles in Dnmt1 KO versus WT cells for H3K4me peaks over enhancers of Dnmt1 KO cells. (l) DNA methylation, H3K4me3 and transcription in several loci of WT (blue tracks) and Dnmt1 KO (red tracks) MEF cells. Green bars above the gene map locate the CpG islands. The y-axis represents the DNA methylation measured as the percentage of reads that support the methylated state of each CpG (estimated methylation level). For each histone mark track, the y-axis represents the normalized level of ChIP-seq signal over the genomic regions. (m ) Pie charts of the genomic structural composition of the H3K4me3 peaks loci specific to WT and Dnmt1 KO cells. (n) Number of specific RNA-seq peaks in WT and Dnmt1 KO cells