Multipartite super-enhancers function in an orientation-dependent manner
Kassouf MT., Francis HS., Gosden M., Suciu MC., Downes DJ., Harrold C., Larke M., Oudelaar M., Cornell L., Blayney J., Telenius J., Xella B., Shen Y., Sousos N., Sharpe JA., Sloane-Stanley J., Smith A., Babbs C., Hughes JR., Higgs DR.
Transcriptional enhancers regulate gene expression in a developmental-stage and cell-specific manner. They were originally defined as individual regulatory elements that activate expression regardless of distance and orientation to their cognate genes. Genome-wide studies have shown that the mammalian enhancer landscape is much more complex, with different classes of individual enhancers and clusters of enhancer-like elements combining in additive, synergistic and redundant manners, possibly acting as single, integrated regulatory elements. These so-called super-enhancers are largely defined as clusters of enhancer-like elements which recruit particularly high levels of Mediator and often drive high levels of expression of key lineage-specific genes. Here, we analysed 78 erythroid-specific super-enhancers and showed that, as units, they preferentially interact in a directional manner, to drive expression of their cognate genes. Using the well characterised α-globin super-enhancer, we show that inverting this entire structure severely downregulates α-globin expression and activates flanking genes 5’ of the super-enhancer. Our detailed genetic dissection of the α-globin locus clearly attributes the cluster’s functional directionality to its sequence orientation, demonstrating that, unlike regular enhancers, super-enhancers act in an orientation-dependent manner. Together, these findings identify a novel emergent property of super-enhancers and revise current models by which enhancers are thought to contact and activate their cognate genes.Competing Interest StatementJ.R.H. is a founder and shareholder of Nucleome Therapeutics; J.R.H., and D.J.D. are paid consultants for Nucleome Therapeutics. J.R.H. holds patents for Capture-C (nos. WO2017068379A1, EP3365464B1 and US10934578B2). These authors declare no other financial or non-financial interests. The remaining authors declare no competing interests.