Fig. 2: Differential chromatin-level response to IL-4 in BL/6 and BALB/c mice. | Nature Communications

Fig. 2: Differential chromatin-level response to IL-4 in BL/6 and BALB/c mice.

From: Genetic variation in IL-4 activated tissue resident macrophages determines strain-specific synergistic responses to LPS epigenetically

Fig. 2

a Constitutive ATAC-seq peaks (FDR > 0.001) are identified by DiffBind when comparing control (Ctrl) and IL-4 treatment conditions in both strains. The Venn diagram visually represents the overlap of these constitutive ATAC-seq peaks between BL/6 and BALB/c mice. b ATAC-seq induced peaks (FDR ≤ 0.001) are identified by DiffBind between Ctrl and IL-4 treatment in BL/6 and BALB/c mice. Venn diagram shows the overlap of the induced ATAC-seq peaks from BL/6 and BALB/c mice. c Genomic locations of ATAC-seq peaks, both constitutive and induced by IL-4 treatment, display binding sites across multiple genomic regions as annotated by HOMER. The strain names are labeled above the bars. d Using HOMER, we identified the top 4 transcription factors enriched in induced peaks in BL/6 (left panels) and BALB/c (right panels). Only de novo motifs are showed here. Significance was calculated using default statistical setting provided by HOMER. e Box and whiskers plot shows transcription factor motif enrichment scores in ATAC-seq data for select motifs that exhibit differential enrichment between BL/6 and BALB/c, assessed using ChromVAR. PU.1 (n = 17 relevant motifs); NF-κB (n = 4 relevant motifs); AP.1 (n = 30 relevant motifs); STATs (n = 3 relevant motifs); IRFs (n = 5 relevant motifs). Each motif value represents the average of motif enrichment scores of the two replicates. Data are presented as mean value of motif enrichment scores from all motifs +/− SEM. f A heatmap displaying induced enhancers derived from induced ATAC-seq peak data. g Overlap of significantly induced enhancers after IL-4 treatment in peritoneal TRMs from two strains. The top two de novo motifs identified by HOMER are enriched at strain-specific induced enhancers, with an observed gain in the IRF motifs in BL/6 mice. Significance was calculated using default statistical setting provided by HOMER. h The top 3 (BL/6) and top 2 (BALB/c) de novo motifs identified by HOMER enriched in enhancers near strain-specific induced genes (FDR ≤ 0.05 and ≥ 2-foldchange compared with Ctrl). Significance was calculated using default statistical setting provided by HOMER. i The count of induced enhancers or super enhancers near strain-specific induced genes.

Back to article page