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. 2020 Feb 7;9:e51325. doi: 10.7554/eLife.51325

Figure 5. Identification of mouse embryonic palatal epithelium-specific active enhancers.

(A) Workflow of ATAC-seq in epithelium and mesenchyme cells isolated from palate shelves dissected from E14.5 embryos. (B) Heatmap plots of ATAC-seq and E14.5 mouse facial prominence H3K27Ac ChIP-seq (Klein and Andersen, 2015) in tissue-specific NFRs. (C) Plot of average density of H3K27Ac ChIP-seq signal, showing higher signal at cluster 1 elements than cluster 2 elements. (D) GO enrichment (MGI mouse gene expression pattern) of genes associated with cluster 1 elements. (E and F) UCSC Genome browser views of the mouse genome (mm10 build) showing the ATAC-seq and H3K27Ac ChIP-seq signals near the Krt17 and Runx2 genes. Red box, an example of a mouse palate-epithelium active enhancer (mPEAE). Blue boxes, examples of mouse palate mesenchyme active enhancers (mPMAEs). (G) Motifs enriched in cluster 1 of E14.5 palate-epithelium specific NFRs with elements overlying transcription start sites removed (i.e., mPEAEs). Motifs shared with zGPAEs are in bold.

Figure 5—source data 1. Density plot for H3K27Ac ChIP-seq in two clusters, as plotted in Figure 5C.
Figure 5—source data 2. Barchart for GO enrichment, as plotted in Figure 5D.

Figure 5.

Figure 5—figure supplement 1. Concordance of replicates of mouse embryonic palatal epithelium ATAC-seq.

Figure 5—figure supplement 1.

(A) Correlation of three biological replicates of E14.5 mouse palate epithelium and mesenchyme ATAC-seq results. (B) ATAC-seq density plot of different clusters of E14.5 mouse palate epithelium specific NFRs. (C) GO enrichment (MGI mouse gene expression pattern) of genes associated with cluster 2 elements. (D and E) UCSC Genome browser view showing the ATAC-seq and H3K27Ac ChIP-seq signals in Krt14 and Klf4 locus.
Figure 5—figure supplement 2. Summary of ATAC-seq in HIOEC and HEPM cells.

Figure 5—figure supplement 2.

(A) Heatmap plots of ATAC-seq of HIOEC- and HEPM-specific NFRs. (B). GO enrichment for the genes near cluster 1 of HIOEC-specific NFRs. (C). GO enrichment for the genes near cluster 2 of HIOEC-specific NFRs. (D and E) UCSC Genome browser tracks showing the HIOEC and HEPM ATAC-seq and NHEK H3K27Ac ChIP-seq signals in IRF6 (D) and RUNX2 (E) locus.
Figure 5—figure supplement 3. Motifs enriched in hOEAEs and shared among zGPAEs, mPEAEs and hOEAEs.

Figure 5—figure supplement 3.

(A) Motifs enriched in hOEAEs. Bold, shared motifs enriched in all three epithelial tissues. (B) The significance of enrichment of each of the shared motifs among hOEAEs, mPEAEs and zPEAEs.