Extended Data Fig. 8: Bioinformatic analysis showing that IRF6 target genes are involved in lipid metabolism and tight-junction formation, which are essential for epidermal barrier function.
From: The RIPK4–IRF6 signalling axis safeguards epidermal differentiation and barrier function
a, Schematic of the analysis pipeline that was used to identify putative and high-confidence IRF6 targets. The histone ChIP–seq dataset that yielded an IRF6 motif (the ISRE) is marked in red. b, Heat map showing clustering of 35,176 genes into four clusters: active, repressed, bivalent and low-signal promoter groups (top to bottom) (n = 11,942, n = 2,580, n = 3,154 and n = 17,500, respectively). Each row reports log2-transformed reads per million (RPM) in a 5,000-bp window around the start of the gene for H3K4me3 (left two columns) and H3K27me3 (right two columns) in the wild-type background. c, Distribution of log2-transformed read counts in a 5,000-bp window (binned at 50 bp) around 815 putative IRF6 targets (54 out of 869 targets were filtered out owing to low signal) for H3K4me3, H3K27me3, H3K27ac and ATAC-seq signal in the wild-type background, sorted in the same way as b. The number of putative IRF6 targets in active, repressed, bivalent and low-signal groups are 412, 64, 129 and 210, respectively. Genes that are significantly up- or downregulated in Irf6−/− versus wild-type E16.5 skin (n = 3 each, from the RNA-seq dataset) are shown in red and blue to the right. P values were obtained using a moderated t-test (two-sided) with the Benjamini–Hochberg method for multiple comparisons. d, Toluidine blue staining of wild-type and Irf6−/− E18.5 embryos (n = 3 each). Scale bar, 1 cm. e, Graph showing weight loss of wild-type control (n = 4) and Irf6−/− (n = 4) newborn mice over time. Data are mean ± s.d. Unpaired, two-tailed Fisher’s exact test with 95% confidence interval. f–h, Screenshots showing normalized read coverage for ATAC-seq, H3K4me3, H3K27ac and H3K27me3 in wild-type and Irf6−/− skin for occludin (Ocln) (e), Pnpla1 (f) and Grhl3 (g). Genes are indicated in blue in the top panel; red boxes highlight the signal at the start of the gene. Representative of n = 2 for wild type and Irf6−/−.
