Fig. 6

DNMT3A and TET1 regulate bivalent gene expression via PRC2-mediated H3K27me3. a Hierarchical clustering analysis of differentially expressed genes in WT, Dnmt3a KO, Tet1 KO, and Dnmt3a-Tet1 DKO ESCs. Genes Smad6 and Bmpr2 belong to Hippo / TGF-beta signaling (over-represented in C1) while Foxo3 and Akt3 in PI3K-Akt signaling pathway (over-represented in C2). Their expression difference between cell lines was confirmed by RT-qPCR (shown in Additional file 1: Figure S9b). b Heatmap representations of H3K27me3 enrichment on the flanking 5 kb surrounding the specific TSSs in each cluster in WT, Dnmt3a KO, Tet1 KO, and DKO ESCs. All TSSs are listed in the same order as Fig. 6a. c Average density profiles for H3K27me3 marks at genes from C1 (top) and C2 (bottom) clusters in indicated cells. d UCSC genome browser tracks depicting DNA methylation (WGBS) in WT ESCs and H3K27me3 in WT, Dnmt3a KO, Tet1 KO, and DKO ESCs at Smad6 (top) and Foxo3 gene (bottom). e Heatmap representations of SUZ12 occupancy on the flanking 5 kb surrounding the TSSs in cluster C1–C7 in WT, Dnmt3a KO, Tet1 KO and DKO ESCs. f Average density profiles for SUZ12 occupancy at genes from C1 (top) and C2 (bottom) clusters in indicated cells