Figure 4. Correlation of level changes in H3 K4/K9/K27me3 changes and mRNA.

(a) Density plot of all genes in the mouse genome that show signal by either microarray or ChIP-seq (N=24,778 genes and N=10,345 genes plotted for H3K4me3/H3K9me3 and H3K27me3, respectively, out of total N=34,497 genes. Genes that showed the absence of microarray or ChIP signals in comparing populations were excluded). Genes changed ≥1.5-fold are marked outside the black lines flanking the origin; genes with <1.5-fold variations are considered ‘unchanged'. (b) % of genes that are decreased (blue), unchanged (green) and increased (red) in their histone marks from EA-HFSCs to LC-HFSCs. Each functional category was defined based on changes in mRNA levels in HFSCs at distinct stages of differentiation and self-renewal (GDB: genes downregulated in the bulge). See the Methods for description of arrays used and Supplementary Data 2 for the lists of genes. Note atypical behaviour of genes upregulated in the bulge (GUB) and tumour suppressors. (c) Dot plot of cyclin-dependent kinase inhibitors (CDKis) and known tumour suppressors that play a role in skin and hair follicle biology (Supplementary Data 2). Expression of CDKis was adopted from our previous qRT–PCR data⁴⁶, whereas mRNA values for the other genes were from microarrays (Supplementary Data 1).