Fig. 4: Epigenetic regulation of YAP is involved in the VPA-and-EPZ6438-driven regenerative response in vitro. | Cell Research

Fig. 4: Epigenetic regulation of YAP is involved in the VPA-and-EPZ6438-driven regenerative response in vitro.

From: Establishment of intestinal organoid cultures modeling injury-associated epithelial regeneration

Fig. 4

a Expression of the YAP gene signature was overlaid on the regenerative trajectory from Hyper-organoids with and without VPA/EPZ6438 treatment shown in Fig. 3f. b The expression dynamics of YAP signature was cataloged in a pseudotime manner shown as a red line (successful reprogramming), a green line (failed reprogramming) and a blue line (pre-branch before bifurcation). Thick lines indicate the average gene expression patterns in each branch. c Volcano plot displaying the results of differential gene expression analysis performed between successful branch and failed branch. The dots representing YAP target genes are indicated as red. d Expression of the YAP gene signature was overlaid on the UMAPs shown in Fig. 3b and d, respectively. Hyper- and –VE/ENR-organoids are separated by the orange and blue dotted line. e Violin plots showing the entire range of metagene expression levels per single cell per cluster for the transcriptional programs of all clusters (left) and stem cell clusters (right) in different organoids. f Heatmap displaying H3K27me3 signals at promoter regions of YAP target genes in different organoids. g ChIP-seq (H3K27me3) and RNA-seq tracks of YAP target genes in different organoids.

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