Figure 4

Relationships between gene expression and DNA epigenetic marks. (A) Quantity of upregulated and downregulated genes in siTET1, siTET2, and siTET3 conditions. (B) NCCIT cell gene expression changes that occur with siTET depletions were compared to gene expression changes that occur during RA-induced differentiation from UD to DF. Downregulated genes in siTET1, siTET2, and siTET3 depleted cells were significantly enriched for genes upregulated during differentiation. Shown are the percentages of genes downregulated in siTET conditions that overlap with genes that become upregulated in DF cells and the percentage of total upregulated genes in DF cells. (C) Hypo- or hyper-5hmC introns of siTET depletions were compared to basal gene expression levels in UD NCCIT cells. Shown is the percentage of genes with 5hmC changes in introns in siTET-treated cells that occur in highly, moderately, or lowly expressed genes. These percentages of overlapping genes are compared to the total percentage of highly (red bar), moderately (gold bar), or lowly (green bar) expressed genes. (D) Area proportional Venn diagrams showing the number of repressed genes that are in proximity to H3K27ac-marked enhancers that lose 5hmC upon TET depletion (*P < 0.0001; ^‡P = 0.0060). (E) Ontology analysis of repressed genes that lose 5hmC in nearby enhancers in siTET1-, siTET2-, and siTET3-treated cells.