DNA methylation and differentiation: HOX genes in muscle cells

Table 1 Quantification of 5mC and 5hmC at five tested CCGG sites in the four HOX clusters

^a5hmC and 5mC were quantified by an enzymatic assay (Epimark; New England Biolabs) coupled with real-time PCR as described in Methods. Two biological replicates each were tested for myoblasts, skeletal muscle biopsy samples, heart and brain autopsy samples, and leukocytes. One sample of foreskin fibroblasts was assayed. The tested positions of CpG sites (in CCGG sequences) were as follows (hg19): HOXB5 intron 1, chr17:46670028; HOXA5 exon 1, chr7:27183175; HOXA7 upstream, chr7: 27197926; HOXC6 upstream, chr12:54423458; and HOXD4 intron 1, chr2:177017078. These positions are also indicated in Figures 1, 2, 4 and 6.
^bSamples with ratios of (5mC + 5hmC)/total C greater than 0.4 are shown in in boldface.
^cSamples with more than 40% of modified C as 5hmC are shown in boldface.

ISSN: 1756-8935