The conserved noncoding sequence CNS11 is a master control region for Rorc transcription in type 17 immune cells

Retinoic acid receptor-related orphan receptor γt (RORγt) is the master transcription factor for type 17 immune cells, including T helper 17 (T_H17) cells, group 3 innate lymphoid cells (ILC3s), RORγt⁺ regulatory T (T_reg) cells, and RORγt⁺ γδT cells. While trans-regulatory mechanisms governing Rorc expression are well characterized, cis-regulatory mechanisms, particularly in innate lymphocytes, remain partially understood. Here, we identify CNS11 as an essential cis-regulatory element of Rorc. In T_H17 cells, CNS11 was dispensable for induction but critical for maintaining RORγt expression. In contrast, CNS11 deletion blocked ILC3 progenitor induction, abolishing secondary lymphoid organ formation. CNS11 deletion also abolished the development of RORγt⁺ T_reg, RORγt⁺ γδT, and RORγt⁺ antigen-presenting cells. Mechanistically, CNS11 functioned through a RORγt-dependent feed-forward loop with cell type-specific cofactors: cooperating with RORγt and runt-related transcription factor 3 to direct ILC3 development and with RORγt and/or c-MAF to sustain RORγt expression in T_H17, RORγt⁺ T_reg, and RORγt⁺ γδT cells. Our study reveals CNS11 as a key transcription factor binding hub and master control region for Rorc transcription in distinct lymphocytes.