Distinct super-enhancer elements differentially control Il2ra gene expression in a cell-type specific fashion

Abstract Expression of the IL-2 receptor a-chain (IL-2Ra, also known as CD25) is tightly regulated during T cell development and in mature lymphoid populations. IL-2Ra is constitutively expressed on double negative DN2/DN3 thymocytes and regulatory T cells, but its expression is inducible on mature T and natural killer (NK) cells. The Il2ra gene is regulated in part by a super-enhancer that is extensively bound by STAT5, but whether the super-enhancer elements are differentially used to control the cell-specific expression of Il2ra in distinct cell populations is unknown. Here, we generated a comprehensive series of mutant mice harboring deletion of individual or multiple elements within this super-enhancer. Strikingly, deletions in the upstream super-enhancer region dominantly affected CD25 expression on DN2/DN3 thymocytes and Treg cells, whereas deleting an intronic region primarily decreased IL-2-induced CD25 expression on peripheral CD4+ and CD8+ T and NK cells. Thus, distinct elements control constitutive versus inducible expression of the Il2ra gene in a cell-type-specific manner rather than behaving as simple enhancers whose activity is additive/cooperative, as has been observed for the a-globin and Wap super-enhancers. Moreover, the intronic super-enhancer region was critical for chromatin looping, and deletion of this region altered super-enhancer structure throughout the locus. These results demonstrate differential functions for distinct super-enhancer elements, thereby indicating ways to manipulate CD25 expression in a cell-type specific fashion, an area of importance in autoimmune and other disease states.