show Abstracthide AbstractRecent studies have highlighted super-enhancers (SEs) as important regulatory elements for gene expression, but their intrinsic properties remain incompletely characterized. Through an integrative analysis of Hi-C and ChIP-seq data, we find that a significant fraction of SEs are hierarchically organized, containing both hub and non-hub enhancers. Hub enhancers share similar histone marks with non-hub enhancers, but are distinctly associated with cohesin and CTCF binding sites and disease-associated genetic variants. Genetic ablation of hub enhancers results in profound defects in gene activation and local chromatin landscape. As such, hub enhancers are the major constituents responsible for SE functional and structural organization. Overall design: ChIP-seq was performed to determine the chromatin occupancy of H3K27ac, GATA1 and TAL1 in MYO1D hub or non-hub enhancer knockout K562 cells. MYO1D Non-hub enhancer deletion: chr17:31220757+31222033 (1277 bp) MYO1D Hub enhancer deletion: chr17:31236528+31240709 (4182 bp)