Fig. 2

Epigenetic profiling identifies the enhancer regions in FGSCs. a Genome browser views of H3K4me1, H3K27ac, H3K4me3, H3K27me3, RNA Pol II, and DNA methylation (DNAme) enrichment profiles in FGSCs for an active (Ifitm3, top red box) or poised (Zp3, bottom red box) enhancer and the flanking regions. b Distribution of active and poised enhancers relative to their closest UCSC gene transcription start site (TSS). c K-means clustering of H3K4me1 and H3K27ac ChIP-Seq signals, the predictors of active enhancers, in ESCs and FGSCs. A window of 10 kb (−5 kb to +5 kb) around the peak center is shown. d Gene expression was measured as fragments per kilobase of exon per million fragments mapped (FPKM) and calculated for all mouse UCSC genes (blue) and for those closest (within 200 kb) to FGSC-specific active enhancers (red) (class 2 in c). Transcription levels in both cell types are presented as box plots (p values were calculated using paired Wilcoxon tests). e Enriched mouse phenotypes for nearest genes within 200 kb of FGSC enhancer signatures (p < 0.05). Loss of genes (e.g., Npr2 and Ptgs2) with FGSC-specific enhancer signatures causes abnormal reproductive system physiology [57, 58]. f Number of bivalent promoters in ESCs and FGSCs