Figure 2

Depletion of TET1, TET2, or TET3 causes genome-wide loss of 5hmC and both DNA hypomethylation and hypermethylation. (A) Tag density plots of 5mC (dashed line plots) and 5hmC (solid line plots) from -5 to +5 kb across gene promoters, across gene bodies (25 to 75%), and from -5 to +5 kb across the transcription termination site (TTS) (left panels). Tag density plots were also drawn for exons across HCP, intermediate CpG density promoter (ICP), and LCP genes (right panels). (B) Pie charts for genes with decreased (top) and increased (bottom) 5hmC. Pie pieces represent total number of genes with two-fold or greater 5hmC change in the specified gene region. (C) Area proportional Venn diagrams illustrating overlap of promoters that lose 5hmC and gain or lose 5mC in each TET knockdown. P < 0.0001 except for overlap of TET3 hypohydroxymethylation with siTET3 hypermethylation for which P = 0.0009. (D) Tag density of 5mC (left) and 5hmC (right) for only promoters with (i) more than two-fold reduction of 5hmC in siTET1, (ii) more than two-fold reduction of 5mC in all siTET depletion conditions, and (iii) more than two-fold increase of 5mC in all siTET depletions. The region shown is -3 kb upstream and +3 kb downstream relative to TSS. Line colors are as in (A). Colored arrows indicate approximately -1 kb and +250 bp positions relative to the TSS. (E) Tag density of 5mC (top) and 5hmC (bottom) across intronic sequences for only genes showing increased 5hmC within introns of siTET2-treated cells.