Circadian circuits control plasticity of group 3 innate lymphoid cells by sustaining epigenetic configuration of RORgammat

The gut undergoes daily fluctuations in microbial composition and nutrient availability, synchronized with circadian rhythms governing physiological processes like nutrient absorption and immune response. Group 3 innate lymphoid cells (ILC3s), which depend on RORgammat, maintain gut homeostasis and immune surveillance by secreting IL-22, but can switch to IFNgamma-producing ILC1s, which depend on TBET. Circadian proteins crucially regulate ILC3 development and function, but the underlying mechanisms are incompletely understood. Here we show that clock genes REV-ERBalpha and REV-ERBbeta govern ILC3 homeostasis. Combined REV-ERBalphabeta deficiency skews ILC3s conversion towards ILC1s, reducing ILC3 energy metabolism and IL-22, enhancing IFNgamma, ultimately increasing susceptibility to C. rodentium infection. Single-cell multimomics shows that REV-ERBalphabeta deficiency elevates expression of the clock protein NFIL3, which suppresses RORgammat, tipping the balance away from RORgammat-driven programs and toward TBET-driven identity. We conclude that REV-ERBalphabeta maintain ILC3 traits vital for gut homeostasis and defense against enterocolitis by transcriptional and epigenetic control of clock genes that influence RORgammat.