Figure 5.

DNA methylation and chromatin changes during erythroid differentiation in CpG-rich promoters. (A) Circos plots illustrating the changes in DNA methylation status of newly silenced (left) and newly expressed (right) CpG-rich promoters during differentiation from HSPCs (top half of the circle) to BasoEs (bottom half) as a function of expression levels. The bands connecting the half-circles indicate the redistribution of genes from HSPCs into the indicated categories in BasoEs. The outer circle represents the expression levels (Q1 [silent], dark blue; Q2, blue; Q3 orange; Q4, [highly expressed], red). The inner circle segments represent the methylation status of the promoters (gray: unmethylated [UMR-containing]; purple: methylated [no-UMR]). The numbers on the outside indicate the number of promoters according to their methylation status split by expression quartile. In the plot on the left, promoters (active in HSPC [quartiles Q2-Q4] but silent in BasoE [quartile Q1]) were almost all unmethylated and remained so after differentiation. In the plot on the right, the newly expressed promoters (silent in HSPCs but active in BasoEs) were almost all already unmethylated in HSPCs. (B) Circos plots illustrating the change in chromatin status of promoters as a function of their location in HMDs or PMDs and as a function of their change in expression during differentiation from HSPCs to BasoEs (clockwise): newly silenced in BasoEs, newly expressed in BasoEs, expressed in both HSPCs and BasoEs, and not expressed in either HSPCs or BasoEs. The bands connecting the half-circles indicate the redistribution of genes from HSPCs into the indicated categories in BasoEs. The outer circles represent the location of the promoters in HMDs (H, brown), short PMDs (S, light green), or long PMDs (L, dark green). The outer circle was omitted from the HSPC side of the graph, because almost the entire genome of HSPC is located in HMDs. The inner circle represents the chromatin states. For clarity, the 15 ChromHMM classes were summarized into 5 larger categories: active (TssA, TssAFlnk, TxFlnk, Tx, TxWk, EnhG, Enh, ZNF/Rpts; red), bivalent (TssBiv, BivFlnk, EnhBiv; purple), repressed (ReprPC, ReprPCWk, green), heterochromatin (blue), and quiescent (gray). The circle segments above the dotted line represent the methylation and chromatin status of promoters in HSPCs, those below the dotted line the methylation and chromatin status of promoters in BasoEs. The numbers on the outside indicate the number of promoters in each category. The graph illustrates the observation that the promoters newly expressed in BasoEs and promoters expressed in both cell types exhibits few chromatin changes during differentiation and that the promoters newly silenced in BasoEs and promoters silent in both cell types exhibit much more dramatic chromatin structure changes.