Figure 1.

5fC and 5caC as TDG-mediated DNA demethylation intermediates. (a) The proposed cycle of DNA methylation (red arrow) and active demethylation (blue arrows). Enzymes are shown for each step along with required co-factors. (b) Visualization of the datasets derived by the two studies over the Hoxa1 and Hoxa2 genes (i) and the Igf2 gene (ii), both in wild-type (WT) and thymine DNA glycosylase (TDG) depleted/knockout mouse embryonic stem cells. 5fC data are plotted as both blue (He and colleagues [7]) and gold (Zhang and colleagues [6]) tracks, while 5caC, as reported by Zhang and colleagues [6], is displayed in red. Although both techniques profile the 5fC mark in WT and TDG depleted cells with a large degree of overlap (i), there are some regions that show technique-dependent enrichment (ii). Data have been filtered to remove background noise (reads <1 and <3 in the He and Zhang studies, respectively). Percentage GC plots (GC%) are shown in black, with Refseq predicted gene structures underneath. abs, antibodies; shTDG, TDG-depleting short hairpin RNA; TET, ten-eleven translocation.