A distinct cis-regulatory element is required for ILC3s to maintain intestinal tolerance through amplifying RORγt expression [scRNA-seq]

RORγt is the linage-specific transcription factor for both ILC3 and T-helper 17 (Th17) counterparts, who take an essential place in regulating intestinal homeostasis. While the biological significance of high RORγt expression and its distinct regulatory mechanisms in ILC3s remains investigation. Through comparing ATAC-seq results on ILC3 and Th17 cells, we identified an open chromatin region (OCR369) which specifically regulates ILC3 RORγt expression and development. Mechanistically, OCR369 is bind by the RORγt activator RUNX3, and is also involved in the chromatin-loop formation between OCR369 and RORγt-promoter. OCR369 depletion also impaired the MHCII+ ILC3s, a group of antigen-presenting cells that regulate RORγt+ Treg cells. And disruption of Th/ Treg balance in the OCR369-deficient mice leads to the spontaneous type 2 inflammation in the small intestine, and impaired generation of oral tolerance. Thus, our study revealed a specific RORγt amplifying mechanism in ILC3 and its important role in maintaining intestinal immune environment and food tolerance.