Targeted and genome-scale strategies reveal gene-body methylation signatures in human cells

Nat Biotechnol. 2009 Apr;27(4):361-8. doi: 10.1038/nbt.1533. Epub 2009 Mar 29.


Studies of epigenetic modifications would benefit from improved methods for high-throughput methylation profiling. We introduce two complementary approaches that use next-generation sequencing technology to detect cytosine methylation. In the first method, we designed approximately 10,000 bisulfite padlock probes to profile approximately 7,000 CpG locations distributed over the ENCODE pilot project regions and applied them to human B-lymphocytes, fibroblasts and induced pluripotent stem cells. This unbiased choice of targets takes advantage of existing expression and chromatin immunoprecipitation data and enabled us to observe a pattern of low promoter methylation and high gene-body methylation in highly expressed genes. The second method, methyl-sensitive cut counting, generated nontargeted genome-scale data for approximately 1.4 million HpaII sites in the DNA of B-lymphocytes and confirmed that gene-body methylation in highly expressed genes is a consistent phenomenon throughout the human genome. Our observations highlight the usefulness of techniques that are not inherently or intentionally biased towards particular subsets like CpG islands or promoter regions.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Base Sequence
  • Cell Nucleus / genetics
  • Chromosome Mapping / methods*
  • DNA / chemistry*
  • DNA / genetics*
  • DNA Methylation / genetics*
  • Gene Targeting / methods*
  • Humans
  • Metabolome / genetics*
  • Molecular Sequence Data
  • Sequence Analysis, DNA / methods*
  • Sulfites


  • Sulfites
  • DNA
  • hydrogen sulfite

Associated data

  • GENBANK/SR008183