Figure 3
Impact of TET depletion at key regulatory elements. (A) Tag density plots of 5mC (top) and 5hmC (bottom) in enhancer elements defined by previously published H9 ESC H3K27ac ChIP-seq profiles [GEO: GSM605307]. Red arrow in the bottom panel denotes a trough of 5hmC at enhancer boundaries that is lost in siTET2/3-treated cells. (B) Box plots of log2 fold-change based on differential SICER analysis of (i) 5hmC and (ii) 5mC peaks. Fold-change is shown for CGIs and CGI shores and is stratified by changes of greater than four-fold (>4×) and changes between two-fold and four-fold (2×). (C) Tag density plots of 5hmC and 5mC for CGIs in promoters, gene bodies, and intergenic regions. (D) Bar graph illustrating the proportion of CGIs and CGI shores in three gene regions that sustain hypermethylation in each TET knockdown. (E) Area proportional Venn diagrams of CGIs with loss of 5hmC, loss of 5mC, and gain of 5mC under siTET1, siTET2, and siTET3 depletion conditions. (F) Area proportional Venn diagrams representing CGI shore hypermethylation coinciding with 5hmC gain in siTET2 and 5hmC loss in siTET1 depletion conditions (P < 0.0001 for both).