Fig. 5
Smarcad1-KO changes chromatin accessibility in the small intestine. a The scatter plot of normalized read counts over ATAC-seq MACS peaks shows 84 differentially accessible regions (blue and red dots) as identified by EdgeR (padjust < 0.05, n = 3) on deletion of Smarcad1 in the small intestinal epithelium (KO) compared to control (WT). For additional data and annotations, see Additional file 9: Table S8. b Comparison between genes with differential accessibility and genes with differential H3K9-trimethylation on Smarcad1-KO (ATAC-seq and ChIP-seq MACS peaks, annotation with closest gene ± 5 kbp, n = 3, see Additional file 6: Table S5, Additional file 9: Table S8). Of the genes that show increased accessibility and decreased H3K9me3, Clec2g and Lyz1 are overexpressed on deletion of Smarcad1 in the small intestinal epithelium (KO). There was no overlap between genes with increased accessibility and increased H3K9me3 nor with genes with decreased accessibility and decreased H3K9me3. The Venn diagrams are not drawn to scale