Fig. 3

Gene expression changes with age and DNA methylation in the colon. a PCA plot constructed using all expressed genes in the intestinal epithelium of the upper small intestine (USI), lower small intestine (LSI), and colon (COL) at ages 4, 12, and 24 months. b Volcano plot showing differential gene expression between young (4 months) and old (24 months) colon samples. c, d Bar plots showing the relationship between DNA methylation (x-axis) and gene expression (average log2rpkm) on the y-axis in the nonCpG island (c) and promoter- CpG island (d) compartments. e, f Scatterplots showing the correlation between DNA methylation change and gene expression change for promoter CpG sites selected based on significance in the permutation analysis. Sites were further divided into those genes that are expressed in young mice (left) and those that are silenced at baseline (right). The plots show a weak but significant negative correlation between methylation change and expression change, for those genes that are expressed at baseline