TSS methylation dynamics. (a) Fluorescent image of the Lgr5 GFP knock-in SI and a typical FACS profile. Boxes indicate GFP_High and GFP_Low populations. (b) All TSSs (+/- 1 kb) of which we had at least 80 CpG data-points in each methylome were analysed and their methylation status in the hair bulge (X-axis) was plotted against their methylation status in the SI (y-axis). (c-e) Expression of genes associated with TSSs with at least 50% DNA methylation difference between hair bulge and SI Lgr5_high population. (c) and (d) show the expression of genes with higher DNA methylation levels in the SI and hair bulge, respectively. (e) Displays a subset of genes from (d) that shows low to no expression in Lgr5_High, but are expressed in the Villus. In all cases only the values inside the 1.5 interquartile range are plotted. (f) Amount of differentially expressed genes (two-fold; 2log) between different cell types as indicated. (g) Genome browser view of the DNA methylation status of Lgr5 upon differentiation. Arrow indicates direction of transcription. (h-j) Correlation of TSS methylation between the methylomes as indicated. All TSSs (+/- 1 kb) of which we had at least 50 CpG data-points in each methylome were analysed. The one gene with a DMR on the TSS methylation is indicated with an arrow.
Kaaij et al. Genome Biology 2013 14:R50 doi:10.1186/gb-2013-14-5-r50