From genes to enhancers and everything in between: The role of enhancer distance in transcriptional regulation

This study investigates the impact of linear genomic distance between enhancers and gene promoters on transcriptional regulation. Utilizing a novel genome engineering strategy termed Delete-to-Recruitment (Del2Rec), we systematically excised intervening DNA to juxtapose distal regulatory elements with target promoters. This approach revealed that reducing enhancer–promoter distance is sufficient to reactivate genes that were developmentally silenced.
Within the human β-globin (HBB) locus, Del2Rec-mediated recruitment of the locus control region (LCR), a super-enhancer, to the promoters of fetal HBG genes resulted in robust transcriptional reactivation in adult erythroid cells. These findings underscore enhancer–promoter proximity as a critical determinant of developmental gene silencing. Notably, the embryonic HBE gene, typically transcriptionally inert in adult erythropoiesis, was also reactivated via Del2Rec, further validating the strategy’s scope.
To assess the generalizability of Del2Rec beyond the HBB locus, we applied the method to the α-globin (HBA) locus and the utrophin (UTRN) gene. In the HBA locus, juxtaposition of the R2 enhancer led to stable reactivation of the embryonic HBZ gene in adult blood cells, indicating a reproducible and positive regulatory effect. In contrast, application of Del2Rec to UTRN—a gene of clinical relevance in Duchenne muscular dystrophy—yielded inconclusive results in human myoblasts. While enhancer repositioning did not yet elicit clear transcriptional activation, further functional analyses are warranted to delineate regulatory potential and contextual constraints.
Collectively, our findings position enhancer–promoter distance as a fundamental and tunable axis of gene regulation. Del2Rec provides a powerful framework to dissect enhancer logic and offers new avenues for therapeutic genome reconfiguration.