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

Enhancer clusters are required for transcription of their target genes. (A,D) Schematic representation of the Sall1 (A) and Tet1 (D) loci. 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. Each deleted enhancer cluster (ΔEC) is designated by a line that links the 5′ and 3′ gRNA targets. All data are displayed on the mm10 assembly of the University of California at Santa Cruz (UCSC) Genome Browser. (B,E) Allele-specific RNA-seq analysis reveals EC specificity for cis-regulation of Sall1 (B) and Tet1 (E). Scatter plots indicate differences in 129 transcript abundance between F1 ES cells and the ΔEC^129/+ clones. Transcript levels are log₂-transformed reads per million. In each scatter plot, the EC target gene is highlighted in red. (C,F) Deletion of the EC dramatically reduces expression of the linked Sall1 (C) or Tet1 (F) allele. Allele-specific primers detect 129 or Cast RNA in RT-qPCR from F1 ES, ΔEC^129/+, and ΔEC^+/Cast clones. Expression for each allele is shown relative to the total. Error bars represent SEM. Significant differences from the F1 ES values are indicated: (**) P < 0.01, (***) P < 0.001.