Single-CpG resolution mapping of 5-hydroxymethylcytosine by chemical labeling and exonuclease digestion identifies evolutionarily unconserved CpGs as TET targets

Genome Biol. 2016 Mar 29;17:56. doi: 10.1186/s13059-016-0919-y.


Conventional techniques for single-base resolution mapping of epigenetic modifications of DNA such as 5-hydroxymethylcytosine (5hmC) rely on the sequencing of bisulfite-modified DNA. Here we present an alternative approach called SCL-exo which combines selective chemical labeling (SCL) of 5hmC in genomic DNA with exonuclease (exo) digestion of the bead-trapped modified DNA molecules. Associated with a straightforward bioinformatic analysis, this new procedure provides an unbiased and fast method for mapping this epigenetic mark at high resolution. Implemented on mouse genomic DNA from in vitro-differentiated neural precursor cells, SCL-exo sheds light on an intrinsic lack of conservation of hydroxymethylated CpGs across vertebrates.

Keywords: 5-hydroxymethylcytosine; 5hmC; Selective chemical labeling; Single-CpG resolution.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • 5-Methylcytosine / analogs & derivatives
  • Animals
  • Cells, Cultured
  • CpG Islands
  • Cytosine / analogs & derivatives*
  • Cytosine / metabolism
  • DNA / chemistry
  • DNA / metabolism*
  • DNA Methylation
  • Embryonic Stem Cells / chemistry
  • Embryonic Stem Cells / cytology
  • Epigenesis, Genetic
  • Epigenomics / methods*
  • Exonucleases / metabolism*
  • Mice
  • Sequence Analysis, DNA / methods
  • Staining and Labeling


  • 5-hydroxymethylcytosine
  • 5-Methylcytosine
  • Cytosine
  • DNA
  • Exonucleases