Fig. 4

c-Jun represses PNT by maintain the closed naïve enhancers. A. Violin plots for the normalized ATAC-seq tag density for all peaks within the indicated primed (C1 and C2) and naive (C3 and C4) groups in WT EpiSC-like, c-Jun knock out EpiSC-like, PNT-D3 WT EpiSC-like, PNT-D3 c-Jun knock out EpiSC-like and ESC. D = day. Data were converted to a Z score based on the row-wise SD for each peak. B. Selected genome views for the ATAC-seq data and c-Jun ChIP-seq data in EpiSC, WT EpiSC-like, c-Jun knock out EpiSC-like, PNT-D3 WT EpiSC-like, PNT-D3 c-Jun knock out EpiSC-like and ESC. D = day. Genome views: Dppa5a (chr9:78,363,039–78,377,161), Zfp42 (chr8:43,293,267–43,309,209). The RNAseq expression values for the respective genes is shown in the bar plot below the genome view. RNA-seq data are from 2 biological replicates, expression units are in normalized tag counts. C. Violin plots for the normalized ATAC-seq tag count for the ATAC-seq data for C3 peaks, for EpiSC, PNT-JNKi-D3, PNT + JNKi-D3 and ESC. Data were converted to a Z score based on the row-wise SD for each peak. P value was from a Mann–Whitney U test. * means P < 0.0005. D. Scatterplot showing the difference between transcriptional profiles with or without JNKi at day 3 (D3) in PNT. JNKi promotes naive marker genes Nanog, Esrrb, Tfcp2l1 and Klf2 activation during PNT