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Fig. 5 | Journal of Translational Medicine

Fig. 5

From: Age-associated hydroxymethylation in human bone-marrow mesenchymal stem cells

Fig. 5

Chromatin signatures associated with DNA hydroxymethylation in MSCs of two different human age groups. a Heatmap showing the relative enrichment of the hyper5hmC (upper) and hypo5hmC (lower) sites for a given set of combinations between ENCODE Broad Histone project cell lines and histone marks. A red tile is drawn only if the 5hmC sites are significantly enriched for the corresponding combination (Fisher’s exact test; p < 0.05). A white to red scale is used to represent the strength of the enrichment, using the base-2 logarithm of the odds ratio (OR) as a measure of shift size. b Upper: Circular layout of chromosomes 1, 4, and 12. Outermost track: Tile chart describing the location of the hyper5hmC and hypo5hmC sites. CpG locations were enlarged to 200 kbp regions centered on the site of interest in order to enhance visualization. Middle and innermost tracks: Histogram charts showing the peak scores obtained from the Broad Histone UCSC data for H3k4me1 (blue), H3k27me3 (brown) and H4k20me1 (red) modifications on the HSMM cell line, averaged over 200 kbp regions. Lower: Genome diagrams showing the relative enrichment of H3k4me1, H3k27me3 and H4k20me1 marks on three specific regions of chromosomes 17 (left) and 6 (right) with hyper5hmCs sites. c Heatmap showing the relative enrichment of the hyper5hmCs (left) and hypo5hmC (right) sites for a given set of combinations between ENCODE Broad ChromHMM project cell lines and chromatin states. A tile is drawn only if the 5hmC sites are significantly enriched for the corresponding combination (Fisher’s exact test; p < 0.05). Tile colors are chosen to resemble those used in the UCSC representation of the ChromHMM dataset. Intensity of color is used to represent the strength of the enrichment, using the base-2 logarithm of the OR as a measure of shift size

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