Figure 4.
Common changes in chromatin induced by stress signaling and Mi-2β depletion.(A) Heatmap of K-means clustering of ATAC-seq datasets from 0 h (before TS), 6 h, or 24 h after TS and from Mi2Δ keratinocytes centered on dATACi peaks identified after 6 h of TS. C1, 2,311 peaks; C2, 1,545 peaks; C3, 2,365 peaks; C4, 1,389 peaks; C5, 1,568 peaks. (B) Histograms of read densities (read count per million mapped reads) plotted at ±5 kb from the dATACi peaks identified at 6 h after TS for the five clusters (C1–C5) shown in the heatmap in A and color-coded for the four ATAC-seq datasets (0 h, 6 h, 24 h, and Mi2Δ keratinocytes). (C) Heatmap of K-means clustering of ATAC-seq datasets from 0, 6, or 24 h after TS and Mi2Δ keratinocytes centered on dATACi peaks identified at 24 h in TS keratinocytes. C1, 2,190 peaks; C2, 1,490 peaks; C3, 639 peaks; C4, 974 peaks; C5, 974 peaks. (D) Histograms of read densities (read count per million mapped reads) plotted at ±5 kb from the dATACi peaks identified at 24 h after TS for the five clusters (C1–C5) shown in the heatmap in C and color-coded for four ATAC-seq datasets (0 h, 6 h, 24 h, and Mi2Δ keratinocytes). (E) Percentage of dATACi peaks with AP1 motifs and promoter association is shown for each of the five clusters (C1–C5) identified at 6 h after TS together with P values for motif discovery. (F) Venn diagram depicting the overlap of genes associated with dATACi peaks identified after TS (6 or 24 h) or after Mi2Δ depletion in keratinocytes. (G) Expression of genes associated with dATACi peaks is shown as a box-whisker plot of log2 normalized read counts from RNA-seq data from 6 or 24 h after TS. The whiskers extend from the smallest to the largest expression value within each group. Significance in difference in expression was obtained by a two-tailed unpaired t test; *, P < 0.005; **, P < 0.0005. (H) Bar graph depicting the frequency and number of all significantly up-regulated genes (|log2 fold change| ≥1, FDR <0.05) after 6 h of TS that were also associated with dATACi peaks at the same time point and/or with dATACi peaks in Mi2Δ keratinocytes. Genes with dATACi peak association under one (Mi2Δ: green; 6 h: red), both (yellow), or neither (gray) condition are color coded. A similar presentation is provided for genes that were commonly up-regulated at 6 h after TS and in Mi2Δ keratinocytes. Commonly up-regulated genes had a higher significant association with dATACi peaks compared with all up-regulated genes (*, P < 0.0001 determined by Fisher’s exact test). (I) Genome browser tracks on Il24, showing increased chromatin accessibility (ATAC-seq) after TS (6 or 24 h) or in Mi2Δ keratinocytes. Mi-2β ChIP-seq in mouse primary cultured keratinocytes is also shown. Mi-2β peaks associated with dATACi peaks are depicted as blue rectangles. Analysis was performed with ATAC-seq and RNA-seq datasets described in Figs. 3 and 1. ChIP-seq for Mi-2β was performed from primary mouse keratinocytes generated from newborn mice after brief expansion in culture.

Common changes in chromatin induced by stress signaling and Mi-2 β depletion. (A) Heatmap of K-means clustering of ATAC-seq datasets from 0 h (before TS), 6 h, or 24 h after TS and from Mi2Δ keratinocytes centered on dATACi peaks identified after 6 h of TS. C1, 2,311 peaks; C2, 1,545 peaks; C3, 2,365 peaks; C4, 1,389 peaks; C5, 1,568 peaks. (B) Histograms of read densities (read count per million mapped reads) plotted at ±5 kb from the dATACi peaks identified at 6 h after TS for the five clusters (C1–C5) shown in the heatmap in A and color-coded for the four ATAC-seq datasets (0 h, 6 h, 24 h, and Mi2Δ keratinocytes). (C) Heatmap of K-means clustering of ATAC-seq datasets from 0, 6, or 24 h after TS and Mi2Δ keratinocytes centered on dATACi peaks identified at 24 h in TS keratinocytes. C1, 2,190 peaks; C2, 1,490 peaks; C3, 639 peaks; C4, 974 peaks; C5, 974 peaks. (D) Histograms of read densities (read count per million mapped reads) plotted at ±5 kb from the dATACi peaks identified at 24 h after TS for the five clusters (C1–C5) shown in the heatmap in C and color-coded for four ATAC-seq datasets (0 h, 6 h, 24 h, and Mi2Δ keratinocytes). (E) Percentage of dATACi peaks with AP1 motifs and promoter association is shown for each of the five clusters (C1–C5) identified at 6 h after TS together with P values for motif discovery. (F) Venn diagram depicting the overlap of genes associated with dATACi peaks identified after TS (6 or 24 h) or after Mi2Δ depletion in keratinocytes. (G) Expression of genes associated with dATACi peaks is shown as a box-whisker plot of log2 normalized read counts from RNA-seq data from 6 or 24 h after TS. The whiskers extend from the smallest to the largest expression value within each group. Significance in difference in expression was obtained by a two-tailed unpaired t test; *, P < 0.005; **, P < 0.0005. (H) Bar graph depicting the frequency and number of all significantly up-regulated genes (|log2 fold change| ≥1, FDR <0.05) after 6 h of TS that were also associated with dATACi peaks at the same time point and/or with dATACi peaks in Mi2Δ keratinocytes. Genes with dATACi peak association under one (Mi2Δ: green; 6 h: red), both (yellow), or neither (gray) condition are color coded. A similar presentation is provided for genes that were commonly up-regulated at 6 h after TS and in Mi2Δ keratinocytes. Commonly up-regulated genes had a higher significant association with dATACi peaks compared with all up-regulated genes (*, P < 0.0001 determined by Fisher’s exact test). (I) Genome browser tracks on Il24, showing increased chromatin accessibility (ATAC-seq) after TS (6 or 24 h) or in Mi2Δ keratinocytes. Mi-2β ChIP-seq in mouse primary cultured keratinocytes is also shown. Mi-2β peaks associated with dATACi peaks are depicted as blue rectangles. Analysis was performed with ATAC-seq and RNA-seq datasets described in Figs. 3 and 1. ChIP-seq for Mi-2β was performed from primary mouse keratinocytes generated from newborn mice after brief expansion in culture.

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