Panel A shows a volcano plot of ATAC-seq peaks comparing cKO and control ILC2s, highlighting differentially accessible chromatin regions. Panel B presents GO Biological Process enrichment analysis of genes associated with differential ATAC-seq peaks, identifying pathways related to cell adhesion, membrane signaling, receptor complexes, and transcriptional regulation. Panel C displays genome browser tracks (ATAC-seq signal) at the Irf4 locus, showing reduced chromatin accessibility in Blimp-1–deficient ILC2s. Panel D compares ATAC-seq accessibility and bulk RNA expression changes, demonstrating coordinated reduction of chromatin accessibility and gene expression at key loci including Irf4. Panel E shows principal component analysis of bulk RNA-seq data from Irf4 minus slash minus versus WT ILC2s, indicating distinct transcriptional separation between genotypes. Panel F presents GO enrichment analysis of differentially expressed genes in Irf4 minus slash minus ILC2s, highlighting altered immune activation, signaling, and migration pathways. Panel G displays a heatmap of cytokine-related genes, showing altered expression patterns in Irf4-/- compared with WT ILC2s. Panel H shows a heatmap of shared Blimp-1/IRF4 target genes, illustrating overlapping transcriptional regulation. Panel I presents relative expression of Prdm1, Il1rl1, and Il9r in Irf4 minus slash minus versus WT small intestinal ILC2s, demonstrating reduced expression of key effector-associated genes in the absence of IRF4.
The IL-33–Blimp-1–IRF4–ST2 axis regulates ILC2 effector functions. (A) Volcano plot of ATAC-seq peaks showing differentially accessible chromatin regions in sort-purified small intestinal ILC2s from naive cKO (Nmur1CrePrdm1fl/fl) vs. Ctrl (Prdm1fl/fl) mice. (B) GO pathway analysis of differentially accessible chromatin regions identified by ATAC-seq in small intestinal ILC2s from naive cKO vs. Ctrl mice. (C) IGV genome browser tracks showing ATAC-seq signal at the Irf4 locus in sort-purified small intestinal ILC2s from Ctrl and cKO mice. (D) Bar plot comparing DESeq2 results from ATAC and bulk RNA-seq from small intestinal ILC2s in cKO vs. Ctrl mice. (E) PCA of bulk RNA-seq of small intestinal ILC2s from Irf4−/− vs. WT mice. (F) GO pathway analysis of differentially regulated genes from bulk RNA-seq of small intestinal ILC2s comparing naive Irf4−/− and WT mice. (G and H) Heatmap showing cytokine-related genes (G) and Blimp-1/IRF4 targets from literature (Cretney et al., 2011; Kwon et al., 2009; Man et al., 2017; Minnich et al., 2016; Ochiai et al., 2013; Tellier et al., 2016; Vasanthakumar et al., 2015) (H) from bulk RNA-seq of small intestinal ILC2s comparing naive Irf4−/− and WT mice. (I) Relative expression of Prdm1, Il1rl1, and Il9r from small intestinal ILC2s from Irf4−/− and WT mice (n = 4–5 mice per group). Mean ± SD; Student’s t test; *P < 0.05; **P < 0.01; ***P < 0.001.