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. Author manuscript; available in PMC: 2013 Oct 25.
Published in final edited form as: Cell. 2013 Apr 18;153(3):692–706. doi: 10.1016/j.cell.2013.04.002

Figure 4. Tdg-depletion induced ectopic 5fC and 5caC accumulate at distal regulatory regions.

Figure 4

(A) Average conservation (phastCons) scores within regions flanking the center of 5mC/5hmC/5fC/5caC peaks (non-overlapping with exons or promoters) in Tdg-deficient mouse ESCs. The number of peaks that are located outside exons and proximal promoters (+/− 1kb flanking TSSs) for each cytosine modification is also shown.

(B) Heat maps of 5mC/5hmC/5fC/5caC levels (normalized read density) at centers of LMRs previously identified in mouse ESCs. The heat maps are ranked by the mean of 5caC signals in Tdg-deficient cells (top: highest, bottom: lowest).

(C) Heat maps of 5hmC and 5caC levels (normalized read density) in control and Tdg-deficient cells at centers of annotated genomic features or enriched regions for transcriptional regulators, histone modifications, pluripotency transcription factors (TFs) and distal regulatory regions (derived from published datasets in mouse ESCs). The difference in 5hmC and 5caC levels between control and Tdg-deficient cells (shTdg minus shCtrl) is also shown for all, proximal (overlapping with +/−1kb flanking TSSs) and distal features.

See also Figure S4.