Fig. 1: Epigenetic regulation of mesenchymal niches in GI development.
From: Epigenetic control of cellular crosstalk defines gastrointestinal organ fate and function
a Diagram of GFP + mesenchymal cell isolation from E13.5 Bapx1Cre/+;Rosa26mTmG mice. b Differentially expressed genes (DEGs) in RNA-seq data from E13.5 intestinal (Int, blue) versus stomach (St, red) mesenchyme (n = 2 biological replicates per tissue). Dashed red lines show thresholds for FDR adjusted p-value = 0.05 and log2(fold-change) = ±1. The top 15 genes per tissue, ranked by p-value, are labeled. c RNA-seq and ATAC-seq signals at example genes with tissue-specific expression and accessibility in the intestine (left) and stomach (right). Tracks depict merged signals from n = 2 biological replicates. Negative values indicate reverse-strand signal. Gene models from the WashU browser refGene track are shown. d E13.5 mesenchymal ATAC-seq signals for Int and St. Top: aggregate profiles for differentially accessible regions (DARs) in St (blue), Int (red), and non-significantly (N.S.) differential regions are shown for Int (left) and St (right). Bottom: Heatmap of ATAC signals for Int (top) and St (bottom) DARs. Viewing range shows peak center ±4 kb. e Comparison of DE and DA gene promoters in St versus Int. Pearson’s R is reported. f Aggregate profiles show signals from ENCODE E14.5 histone ChIP-seq and E13.5 ATAC signals from Int (left) and St (right) at expressed gene promoters. DEGs are categorized and color-coded as above. Simplified ENCODE ChromHMM chromatin state annotations are centered on promoters of DEGs, as described in panel. Top enriched GO terms are listed beside their corresponding cluster. Box and whisker plots show median (center), 1st and 3rd quartiles (limits of box). Whiskers extended to largest value within 1.5* the interquartile range (defined by box). (n = number of peak regions in each corresponding cluster (left of heatmap)).
