Figure 4

Regulatory factor occupancy at UC DMRs. (A) Ninety RF cell type combinations are clustered based on the occupancy of the RF in the respective cell type at UC DMRs. Binary overlaps between UC DMRs and 18 different RFs across the five cell types are shown in red. The top color bars indicate different cell types, and highlight CTCF/RAD21 binding (pink), POLR2A (olive), TAF1/TBP (turquoise), REST (light blue), and EZH2 (purple) binding, respectively. Characteristics of DMRs are shown in five panels to the right of the heatmap: CpG Island (CGI; green); H1ESC, GM12878, HEPG2, K562, chromatin states for four cell types (see color bar). The clustering highlights the cell type independent binding patterns at UC DMRs of RFs such as CTCF, RAD21 and POLR2A, as well as the similar but cell-type specific binding patterns of TBP and TAF1 across all cell lines. (B) The frequency of UC DMRs with RF binding is shown for selected RFs and combinations of RFs for each methylation pattern (1 to 3). Strong depletion (*D) or enrichment (*E) of RF binding is indicated (all P <4 × 10^-6, Fisher’s exact test), the regulatory factor frequency bars are color coded as the factors in (A).