biostudies-literatureKassouf MTChinese Academy of Medical Sciences (CAMS)RCUK | MRC | Medical Research FoundationMedical Research CouncilWellcome TrustBiotechnology and Biological Sciences Research Council1033https://www.ebi.ac.uk/biostudies/studies/S-EPMC11762767biostudies-literatureUnknown16(1)Individual enhancers are defined as short genomic regulatory elements, bound by transcription factors, and able to activate cell-specific gene expression at a distance, in an orientation-independent manner. Within mammalian genomes, enhancer-like elements may be found individually or within clusters referred to as locus control regions or super-enhancers (SEs). While these behave similarly to individual enhancers with respect to cell specificity, distribution and distance, their orientation-dependence has not been formally tested. Here, using the α-globin locus as a model, we show that while an individual enhancer works in an orientation-independent manner, the direction of activity of a SE changes with its orientation. When the SE is inverted within its normal chromosomal context, expressNature communicationsThe α-globin super-enhancer acts in an orientation-dependent manner.PMC11762767BB/Y008898/1MR/N00969X/1109097/Z/15/Z2018-I2M-2-002222843/Z/21/ZMR/T014067/1219979/Z/19/ZCornell LBabbs CSousos NHughes JRFrancis HSTelenius JSuciu MCOudelaar MKassouf MTBlayney JXella BDownes DJGosden MHiggs DRSharpe JASmith AJHLarke MShen YSloane-Stanley JHarrold CfalseThe α-globin super-enhancer acts in an orientation-dependent manner.Individual enhancers are defined as short genomic regulatory elements, bound by transcription factors, and able to activate cell-specific gene expression at a distance, in an orientation-independent manner. Within mammalian genomes, enhancer-like elements may be found individually or within clusters referred to as locus control regions or super-enhancers (SEs). While these behave similarly to individual enhancers with respect to cell specificity, distribution and distance, their orientation-dependence has not been formally tested. Here, using the α-globin locus as a model, we show that while an individual enhancer works in an orientation-independent manner, the direction of activity of a SE changes with its orientation. When the SE is inverted within its normal chromosomal context, express2025-01-01T00:00:00Z2025 Jan2025-04-21T23:52:32.505Z2025-04-05T19:19:58.54ZS-EPMC117627673986359510.1038/s41467-025-56380-1