Figure 4.

Enrichment of WGBS DMRs according to specific TFs, histone marks or motifs. (A and B) Positional enrichment of de novo DMRs and de-DMRs of HD-ALL against 148 ENCODE TF-binding sites. Two transcription factors, SUZ12 and CTBP2, are highly enriched around de novo DMRs while no specific TFs are enriched around de-DMRs. (C) Enrichment of DMRs of HD-ALL according to H3K4me3 (active) and H3K27me3 (repressive) histone marks of H1 embryonic stem cell (ESC) shows remarkable enrichment of de novo DMRs in bivalent domain characterized by co-occupancy of both histone marks (parallel analysis for ETV6-ALL is presented in Supplementary Figure S5A–C). (D) Positional analysis for histone and TF sites in ESC shows enrichment of H3K4me3 at the center of CTBP2-binding site and dual peak of H3K27me3 around the ±1 kb region from the center, suggesting CTBP2 constitute H3K4me3 part of the bivalent domain. (E) Methylation changes in an exemplary gene, ALX4. In human ESC (H1-hESC), the promoter is poised bivalently with H3K4me3 (active) and H3K27me3 (repressive) histones marks. At differentiation, the gene is activated by H3K4me3 in normal skeletal muscle (HSMM) and suppressed by H3K27me3 in normal lung fibroblasts (NHLF). In ALLs, promoters are mostly methylated (red bars) while gene body is demethylated (blue bars). De novo DMRs frequently coincide with the bivalent regions, CGIs and SUZ12- and CTBP2-binding sites. Note that H3K4me3 marks mostly peak around the CTBP2 sites. (F) Novel and known motifs significantly enriched around DMRs. Regions around de novo DMRs are enriched for REST/NRSF, PU.1 and GATA motifs and others, while those around de-DMRs are so for proto-oncogenes, ERG and MYC and a developmental gene, EBF.