Enhancers and super-enhancers have an equivalent regulatory role in embryonic stem cells through regulation of single or multiple genes

Transcriptional control of Dppa5a and Ooep by multiple enhancers. (A) Schematic representation of the Dppa5a/Ooep locus. Transcription factor-bound regions (red bars), MED1 and H3K27ac ChIP-seq and RNA-seq data obtained from the CODEX database are shown. Predicted enhancers (prEnh) and called super-enhancers (SEs) are shown in black. The deleted enhancer clusters, ΔEC(DppUp) and ΔEC(DppDn), are shown with a line that links the 5′ and 3′ gRNA targets. All data are displayed on the mm10 assembly of the UCSC Genome Browser. (B) Deletion of EC(DppDn) in clones carrying a homozygous deletion of EC(DppUp) greatly affects expression of the linked Dppa5a and Ooep alleles. Allele-specific primers detect 129 or Cast RNA in RT-qPCR from F1 ES, Δ^129/+, Δ^+/Cast, and Δ^129/Cast clones. Expression is shown relative to the F1 ES 129 value. Error bars represent SEM. Significant differences from the F1 ES values are indicated: (*) P < 0.05, (**) P < 0.01, (***) P < 0.001. Significant differences from the parent ΔEC-Up^129/Cast clone are indicated: (ΟΟ) P < 0.01, (ΟΟΟ) P < 0.001.