Figure 2. RNA Polymerase II, co-factors and chromatin regulators at super-enhancers.

A) ChIP-Seq binding profiles for RNA Polymerase II (RNAPII) and the indicated transcriptional co-factors and chromatin regulators at the POLE4 and miR-290-295 loci in ESCs. OSN denotes the merged ChIP-Seq binding profiles of the transcription factors Oct4, Sox2 and Nanog, and serves as a reference. Red dots indicate the median enrichment of all bound regions in the respective ChIP-Seq datasets, and are positioned at maximum 20% of the axis height. (rpm/bp: reads per million per base pair)

B) Metagene representations of the mean ChIP-Seq signal for RNAPII and the indicated transcriptional co-factors and chromatin regulators across typical enhancers and super-enhancer domains. Metagenes are centered on the enhancer region, and the length of the enhancer reflects the difference in median lengths (703bp for typical enhancers, 8667bp for super-enhancers). Additional 3kb surrounding each enhancer region is also shown.

C) Fold difference values of ChIP-Seq signal between typical enhancers and super-enhancers for RNAPII and the indicated transcriptional co-factors and chromatin regulators, and RNA-Seq. Total signal indicates the mean ChIP-Seq signal (total reads) at typical enhancers and super-enhancers normalized to the mean value at typical enhancers. Density indicates the mean ChIP-Seq density at constituent enhancers (rpm/bp) of typical enhancers and super-enhancers normalized to the mean value at typical enhancers. Enhancer read % indicates the percentage of all reads mapped to enhancer regions that fall in the constituents of typical enhancer or super-enhancer regions. Reads mapped to exons were removed for the RNA-Seq analysis.

D) Metagene representations of the mean ChIP-Seq density for RNAPII and the indicated transcriptional co-factors and chromatin regulators across the constituent enhancers within typical enhancers and super-enhancers. Each metagene is centered on enhancer constituents. Additional 2.5kb surrounding the constituent enhancer regions is also shown.

E) Model showing RNAPII, transcriptional co-factors and chromatin regulators that are found in ESC super-enhancers. The indicated proteins are responsible for diverse enhancer-related functions, such as enhancer looping, gene activation, nucleosome remodeling and histone modification.

See also Figure S2.