Fig. 3

c-Jun bind to closed naïve enhancers in EpiSCs. A. ATAC-seq datasets from mouse EpiSC and ESC presented as open or closed state as described [9]. Top scale indicates normalized tag count in color shades. Note: primed for loci open in EpiSC; naive for loci open in ESC; Bothopen as open loci in both ESC and EpiSC. B. TF motifs enriched at least 1.5-fold higher than background and P value less than 0.01 for each category of ATAC-seq peaks defined in panel A. *P value < 10–20 from HOMER. C. Heatmap shows naive and primed loci closed and open during naive to prime transition in vitro at different time points. D indicates day of the differentiation process. Naive and primed ATAC-seq peaks defined in A. And c-Jun ChIP-seq data was performed in EpiSC, which divide naive and primed peaks into four groups. D. Pie chart presenting the number of peaks c-Jun occupied in primed and naive loci. E. Motif analysis showing pluripotent transcription factors that enriched in C3 peaks (peaks defined in C). F. Heatmap of sequence read density for ATAC-seq and H3K27ac, H3K27me3, H3K4me3 data in ESC and EpiSC signal on C3 peaks and pluripotency transcription factors Esrrb, Klf4, Nr5a2, Sox2 and Tfcp2l1 binding profile in C3 peaks. Sequenced reads ranked by mean signal strength. Windows are centered on the ATAC-seq pea summit. Each row of the heatmap is a genomic locus. The ChIP-seq data of H3K27me3 and H3K4me3 in ESCs were taken from GSE80280 [51], the ChIP-seq data of H3K27ac in ESCs was taken from GSE98404 [9] and the ChIP-seq data of H3K27me3, H3K27ac, H3K4me3 were taken from GSE57407 [52]. The ChIP-seq data of Sox2 and Klf4 were taken from GSE90893 [8], the ChIP-seq data of Esrrb and Tfcp2l1 were taken from GSE11431 [53] and the ChIP-seq data of Nr5a2 was taken from GSE1901 [54]. G. Violin plots for the normalized ATAC-seq tag density for all peaks in C3 and C4 groups. Data were converted to a Z score to the emphasis change. Data were converted to a Z score based on the row-wise SD for each peak. P value was calculated by the Mann-Whitney U test. * means P < 0.0005.