Figure 4.

Dpf2 Depletion Modulates Levels of H3K27ac and OCT4

(A) Heatmap of expression levels (log₂RPKM+1) in Dpf2^fl/fl and Dpf2^−/− ESCs for differentially expressed genes between Dpf2^fl/fl and Dpf2^−/− ESCs and their DPF2 binding based on a DPF2 peak within 10 kb of the TSS (red, bound; black, unbound genes).

(B) Number of genomic sites with a significant change in H3K27ac (>2-fold difference) between Dpf2^fl/fl and Dpf2^−/− ESCs, divided into those with a reduction (top) and increase (bottom) in Dpf2^−/− ESCs, and their association with DPF2 in WT ESCs.

(C) Heatmap of normalized tag density profiles of H3K27ac experiments in Dpf2^fl/fland Dpf2^−/− cells at sites with significant H3K27ac changes from (B).

(D) Metaplots of average signal intensities for H4tetrac, H3K9ac, H3K4me1, H3K27me3, OCT4, SOX2, and P300 at DPF2-bound sites in ESCs with reduced (top) or increased (bottom) H3K27ac, as defined in (B), for Dpf2^fl/fl (blue) and Dpf2^−/− ESCs (red).

(E) As in (B), but for sites with significant differences in OCT4 instead of H3K27ac.

(F) Metaplots of average signal intensities for OCT4 in Dpf2^fl/fl and Dpf2^−/− ESCs at sites with significant OCT4 changes that are also occupied by DPF as defined in (E).

(G) Heatmap of normalized tag density profiles of H3K27ac e in Dpf2^fl/fl and Dpf2^−/− ESCs at sites with significant OCT4 binding changes and occupied by DPF2 (E) and corresponding metaplots of signal intensities.

(H) Genome browser view of ChIP-seq tracks of DPF2, BRG1, EED, and OCT4 binding as well as H3K27ac and H3K27me3 for the Bmp4 locus. DPF2 data are from WT ESCs and the others from Dpf2^fl/fl and Dpf2^−/− ESCs, indicated as fl/fl and −/−. Regions highlighted in blue signify ESC enhancer regions as defined by ChromHMM in Chronis et al. (2017). The values on the y axis represent fold enrichment over control.

(I) Heatmap of normalized tag density profiles of DPF2, EED, H3K27ac, and P300, at sites exhibiting a reduction in BRG1 in Dpf2^−/− ESCs compared with Dpf2^fl/fl ESCs. DPF2 data are from WT ESCs and all others from Dpf2^fl/fl and Dpf2^−/− ESCs, indicated as fl/fl and −/−.

(J) Metaplots of average signal intensities for DPF2 and BRG1, H3K27ac, p300 and Oct4 at sites defined in (I).