Figure 6. Enrichment of 5-hmC at specific enhancers in human H1 ES cells.

A. 5-hmC reads were summed in 100-bp windows in the immediate 4-kb region, as well as 4 kb upstream and downstream of the immediate 4-kb region, centered on each of 12 predicted H1 hES cell enhancers defined on the basis of their chromatin signature [15], [27], [28]. Counts were normalized to the total number of aligned reads in millions and input reads counted and normalized in the same manner were subtracted [15], [27], [28]. B. Heatmap representations of read distributions for 5-hmC and 11 histone modifications at 5 predicted enhancer subtypes found to have significant enrichment in H1 hES cells. Heatmap scale is constant for all marks and indicated in the lower left-hand corner. C. Genomic view of an E8-type enhancer overlapping a region identified as significantly enriched for 5-hmC by peak identification upstream of the PRDM14 gene.