Supplementary Figure 8: Combined expression of Aiolos and T-bet represses type 3 signature genes.

a, UCSC snapshots of the Rorc locus. Tracks represent cut and run for H3K27ac (green, 0-300 RPKM), IKZF3 (blue, 0 to 100 RPKM) or ATAC-seq (red, 0 to 100 RPKM). Fold change plots below H3K27ac tracks represent differences between H3K27ac in MNK3 expressing T-bet or both Aiolos and T-bet. Conserved IKZF3 motifs between mouse loci (top snapshots) and human loci (bottom snapshots) are indicated in dashed lines. Relative kb scale and gene locations are indicated on top. b, RORγt expression by intracellular staining in control MNK3, MNK3 expressing T-bet and MNK3 expressing Aiolos and T-bet. c, RORγt MFI (n=3). Significance was calculated by ordinary one-way ANOVA multiple comparison test using the Prism7 software. *p≤0.05. One experiment representative of 3 is shown. d, UCSC snapshots of representative ILC1/NK genes (Ifng, Eomes), housekeeping genes (B2m, Suv39h2) and ILC3 genes (Il17a/f, S100a4). Tracks represent cut and run for H3K27ac (green, 0-300 RPKM) or IKZF3 (blue, 0 to 100 RPKM). Relative kb scale and gene locations are indicated on top. e, Specificity of Aiolos binding peaks at the II22 locus. Peaks are not observed on control or Tbet transduced MNK3. f, Mean H3K27ac cut and run values across all H3K27ac peaks that overlap (left) or do not overlap (right) IKZF3 peaks. g, De-novo motif prediction of genome-wide IKZF3 peaks. Left: de novo peak. Middle: closest match in the HOMER database. Right: p-value of motif enrichment. Rep, replicate.