Fig. 5

Epigenetic regulation of gene expression and TEs in naïve and primed cells. A H3K9me2 (left) and H3K9me3 (right) enrichment signal in differential enriched peaks. There are 28,347 and 32,326 enriched H3K9me2 and H3K9me3 peaks in naïve PSCs and 13,701 and 9,832 enriched H3K9me2 and H3K9me3 peaks in primed PSCs, respectively. The ChIP-seq signals are calculated as log2 ratio of normalized reads relative to the input. B H3K9me3, H3K9me2, and Dnmt3b enrichment signal profile plot around the TSS of 2C genes in naïve and primed PSCs, respectively. The ChIP-seq signals are calculated as log2 ratio of normalized reads relative to the input. The Wilcoxon signed-rank test was used to calculate the significance of difference. C Density plot of RNA-seq and ChIP-seq signal of Dux locus. Arrow indicates the direction of transcription. H3K4me3 was used to indicate the promoters of genes and analyzed based on published data from naïve mESCs cultured in serum/Lif [69]. RNA-seq signals are normalized by CPM, ChIP-seq signals are normalized by RPKM. D Differential enriched H3K9me3 peaks distribution in TEs. Peaks located in regions outside of TEs are labeled as Others. E, G Plot of H3K9me3, H3K9me2, and Dnmt3b binding profile and heatmap at all L1Md_T and IAPEz-int loci in naïve and primed PSCs. The ChIP-seq signals are calculated as log2 ratio of normalized reads relative to the input. F, H Density plot of RNA-seq and ChIP-seq signal of representative L1Md_T and IAPEz-int loci in naïve and primed PSCs. Arrow indicates the direction of transcription. H3K4me3 were used to indicate the promoters of genes. RNA-seq signals are normalized by CPM, and ChIP-seq signals are normalized by RPKM