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

From: DNA methylation and differentiation: HOX genes in muscle cells

Location of tested site (5mC + 5hmC)/All C (ratio)a
5hmC/(5mC + 5hmC) (%)
Mb1 Mb2 Skel muscle1 Skel muscle2 Heart1 Heart2 Brain1 Brain2 Leuk1 Leuk2 Fib
HOXB5 in1 0.93 b 0.80 0.43 0.41 0.06 0.01 0.04 0 0.05 0.00 0.03
  0% 15% 63% c 100% 100% 100% 100%   0% 0% 100%
HOXA5 ex1 0.99 0.96 0.19 0.04 0.05 0 0.02 0.01 0.97 0.86 0.02
  0% 1% 17% 0 0   100% 62% 0% 0% 0%
HOXA7 upstr 0.99 0.65 0.55 0.48 0.01 0 0.02 0.01 0.07 0.02 0.02
  0% 1% 15% 0% 0%   78% 62% 71% 0% 4%
HOXC6 ex2 0.98 0.46 0.26 0.01 0.01 0 0.04 0 0.18 0.03 0.02
  0% 2% 31% 0% 0%   100%   0% 0% 1%
HOXD4 in1 0.98 0.92 0.78 0.54 0.08 0.03 0.05 0 0.08 0.01 1.00
  0% 0% 10% 0% 48% 0% 100%   0% 0% 3%
  1. 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.
  2. bSamples with ratios of (5mC + 5hmC)/total C greater than 0.4 are shown in in boldface.
  3. cSamples with more than 40% of modified C as 5hmC are shown in boldface.