The Conserved Non-Coding Sequence CNS11 Is A Master Control Region for Rorc Transcription in Type 17 Immune Cells [4C-Seq]

As the master transcription factor, ROR?t controls the development and function of all type 17 immune cells. Although the trans-regulatory mechanisms governing Rorc expression have been extensively studied, the cis-regulatory mechanisms that differentially regulate Rorc transcription across distinct lymphocytes, particularly in innate lymphocytes, remain largely unknown. Here, we identified CNS11 at the Rorc gene as essential for the development of all type 17 immune cells. Deletion of CNS11 impaired the maintenance but not induction of Th17 cells, abolished the development of ROR?t+ Treg cells, ROR?t+ ?dT cells and ROR?t+ antigen-presenting cells, and blocked ILC3 induction from early progenitors, leading to a complete absence of secondary lymphoid organs. Mechanistically, CNS11 mediates the Rorc transcription through a ROR?t-dependent feedforward regulatory loop in a cell-type-specific manner. Specifically, the interaction of CNS11 with ROR?t and RUNX3 dictated the development of ILC3s, while its interaction with ROR?t and/or c-MAF was crucial for ROR?t expression in Th17 cells, ROR?t+ Treg cells and ROR?t+ ?dT cells. Our study reveals CNS11 as a key transcription factor binding hub and master control region for Rorc transcription in distinct lymphocytes. Overall design: 4C experiment of CNS11 in ILC3s isolated from the small intestine lamina propria of Rag1-deficient mice.