Dissection of a super-enhancer in vivo (Capture-C)

Many genes determining cell identity are regulated by a set of enhancer elements collectively referred to as super-enhancers. It has been suggested that super-enhancers represent a new class of cis-element, in which the assembly of enhancers confers an emergent property from the extended regulatory domain. To investigate this, we used published criteria to define one of the strongest super-enhancers in mouse erythroid cells – a 24kb region regulating α-globin expression, which comprises five enhancer-like components. Using homologous recombination, we deleted each component of this super-enhancer, singly and in informative combinations, and examined hematologic phenotype, gene expression, chromatin structure and chromosome conformation. Each component behaves independently, in an additive rather than synergistic manner. We conclude that the sub-classification of enhancers is unjustified beyond a description of their strength, which is defined by the number of lineage-specific transcription factors they bind. These findings ask afresh why enhancer-like elements cluster at key genes. NG Capture-C combines 3C library preparation with oligonucleotide capture for the desired viewpoint restriction fragments, in this case the promoters of genes were exclusively used. The method was applied to Wlidtype erythroid cells and to in vivo models where the globin R1 and R2 regulatory elements and the R2 and R3 regulatory elements were deleted in combination.