Fig. 2

WHG-STARR-seq enhancers are associated with both open and closed chromatin environments. a Heat maps of various chromatin signal around WHG-STARR-seq enhancers. As generating high-resolution heat maps for all active open or active closed enhancers is too computationally intensive, we randomly sampled 5000 WHG-STARR-seq enhancers from open chromatin regions and from closed chromatin regions, respectively, and plotted signal of WHG-STARR-seq, DNase-seq, H3K4M1, H3K3M2, H3K27Ac, and H3K27M3 around these enhancers. We used all enhancers to make the density plots and boxplots. To make the density plots, we first extended the centers of enhancers to ± 10 kb, and then for each 100-bp tiling window in the extended regions, we calculated the fold enrichment of ChIP signal (normalized by library size) to INPUT signal (normalized by library size) across all windows. We plotted the average of the fold enrichment in the density plots (red: WHG-STARR-seq enhancers; blue: 10,000 random genomic regions). b Boxplots of fold enrichment of signal of various histone marks on WHG-STARR-seq enhancers (±200 bp around enhancer centers) and random genomic regions (±200 bp around random genomic region centers). c Association between gene expression level and nearby WHG-STARR-seq enhancers in open and closed chromatin regions. Enhancers were assigned to their nearest gene. All enhancers were binned into five separate groups according to the rank of enhancer signal (red: active/open enhancers; blue: active/closed enhancers)