SATB1 lowers the T cell receptor signaling threshold for thymocyte positive selection via super-enhancer reprogramming.

In early T cell development, thymocytes undergoing positive selection receive relatively weak T cell receptor (TCR) signals. However, the mechanisms by which thymocytes translate weak and transient TCR signals into lineage-defining transcriptional programs remain unclear. Here, we show that SATB1 plays a key role in enhancer activation during positive selection, as it promotes the expression of positive selection-associated genes by enhancing super-enhancer (SE) activation. Notably, SATB1 deficiency disrupts SE topological organization, weakens promoter-enhancer interactions, blunts TCR-induced Ca2+ signaling, and impairs the activation of positive selection genes such as Cd2 and Cd5, leading to defective CD4/CD8 lineage differentiation and abnormal premature thymocyte egress. Furthermore, SATB1 forms liquid-like nuclear condensates that act as scaffolds to build super-enhancer structures, stabilizing enhancer accessibility and enhancing enhancer-promoter interactions. Altogether, our findings suggest that SATB1 plays a crucial role in promoting positive selection by driving super-enhancer reprogramming and establishing enhancer-promotor interactions.