Fig. 1

Identification of P300 dense super-enhancers. a Ranked distribution plot of P300, Med1, or H3K27ac binding density identifies a small subset of SEs (above the inflection point) in mouse ESCs. Venn diagram (inset) shows the overlap between P300, Med1, and H3K27ac marked SEs. ChIP-seq data are from [71, 72]. b Genome browser screenshot depicting mESC RNA-seq and ChIP-seq data as labeled. (Top panel) The Myc gene is adjacent to Pvt1, a lncRNA overlapping with a SE identified by P300, Med1 and H3K27ac. (Bottom panel) Oct4 is encoded by the Pou5f1 locus which harbors a SE marked by P300, Med1, and H3K27ac. In addition, P300 co-localizes with the core pluripotency factors Oct4, Sox2, and Nanog in both cases. c Expression of genes near P300 SEs and CEs. Genes that are located within 100 kb of a SE are expressed at higher levels than those near a CE, and all expressed genes. d (Top) ChIA-PET reveals that a P300 SE loops ~100 kb to physically associate with the promoter (marked by H3K4me3) of the ESC-specific L1td1 gene. (Bottom) Chromatin interaction between a SE and a gene highly expressed in mESCs, Epha2. ChIA-PET data are from [20] and depicted as grey lines with blue ends. e In mESCs, 315 additional SEs were identified from P300 density than from Med1 density. Igf2bp1 is shown as an example of a P300-specific SE (upper panel). In contrast, there are only 29 SEs identified by Med1 in mESCs but not by P300. For example, a Med1-specific SE near the gene Macf1 is shown (bottom panel). There are two SEs in close vicinity to Macf1; both were identified as SEs by Med1, while only one qualified as a SE by P300