Fig. 4

H3K9me3 changes linked to Smarcad1-KO in the colon. a EdgeR analysis (p < 0.05) of read counts over H3K9me3 peaks reveals regions with significant alterations in this histone mark on deletion of Smarcad1 in the small intestinal epithelium by Vil-cre (KO). Datasets shown as averaged from 3 replicates (for additional data and annotations, see Additional file 8: Table S7). b Examples of H3K9me3 changes over Bach1. The top annotation tracks indicate the gene, exons, and H3K9me3 MACS peaks. Read counts are shown in linear scale, color coded. Chromosomal position and length in kbp are indicated. c Link between changes in gene expression and changes in H3K9me3. Venn diagrams showing the distribution of differentially expressed genes (DEG) in the colon on Smarcad1-KO (93 DEG in either whole crypt or sorted epithelium datasets, see Additional file 1: Fig. S2b, Additional file 4: Table S3) and genes with differential H3K9me3 MACS peaks within ± 5 kbp of the gene (EdgeR p < 0.05, see Additional file 8: Table S7). There is a statistically significant overlap between genes with decreased expression and increased H3K9me3 (p = 0.05, chi-square, number of expressed genes 25,965, Additional file 2: Table S1). The Venn diagrams are not drawn to scale. d Normalized H3K9me3 ChIP-seq read count quantitation over MACS peaks, log2 transformed, adjusted for matching distributions in SeqMonk. Separate quantitations over all annotated genes (32,029 genes) and ± 5 kbp up- and downstream of genes with up- and downregulated expression in the colon on Smarcad1-KO (93 DEG in either whole crypt or sorted epithelium datasets, see Additional file 1: Fig. S2b, Additional file 4: Table S3). p values from an unpaired two-tailed t test with Welch’s correction are indicated (n = 3). Error bars indicate the SEM of read count quantitation of each biological replicate