The expression of BATF is regulated by cytokines which maintains the chromatin landscape in ILC3s. (A) Linear correlation between Batf expression in ILC3s of scRNA-seq and a Seurat module score calculated using genes pooled from a gene list for TGF-β and IL-6 signaling. (B) Flow cytometry plot showing expression of BATF in ILC3s under different cytokines stimulation in vitro. Media include IL-2, IL-7, and SCF only. Isotype, isotype control. (C) Quantification of MFI of BATF in ILC3s as cultured in A. *P < 0.05, **P < 0.01 (one-way ANOVA analysis). (D) Scatter plot (MA plot) showing M value (log₂[read density in Rag1^−/− ÷ read density in Rag1^−/−Batf^−/−]) vs. A value (0.5 × log₂[read density in Rag1^−/− × read density in Rag1^−/−Batf^−/−]) of the merged set of Rag1^−/− and Rag1^−/−Batf^−/− promoter ATAC-seq peaks after normalization. The top 3,000 peaks are highlighted for Rag1^−/− (dark green) and Rag1^−/−Batf^−/− (dark red) ILC3s. Selected genes are labeled. (E) Selected Th1-associated TF binding motifs significantly enriched in the top 3,000 specific promoters of Rag1^−/−Batf^−/− ILC3s. (F) GO analysis of gene sets with differential chromatin accessibility between WT (dark green) and cKO (dark red) for the top six Molecular Signature Database pathways enriched in WT or cKO-specific promoters was performed using GREAT. Pathways of interest are highlighted in color. (G) Heatmap for genome-wide distribution of anti-BATF and control rabbit IgG binding signals at peak centers in ILC3s sorted from the SI of Rag1^−/− mice using CUT&Tag sequencing. (H) Distribution of BATF binding peaks across the genome of ILC3s as assessed in G.