Bisulfite-Free, Nanoscale Analysis of 5-Hydroxymethylcytosine at Single Base Resolution

J Am Chem Soc. 2018 Oct 17;140(41):13190-13194. doi: 10.1021/jacs.8b08297. Epub 2018 Oct 4.


High-resolution detection of genome-wide 5-hydroxymethylcytosine (5hmC) sites of small-scale samples remains challenging. Here, we present hmC-CATCH, a bisulfite-free, base-resolution method for the genome-wide detection of 5hmC. hmC-CATCH is based on selective 5hmC oxidation, chemical labeling and subsequent C-to-T transition during PCR. Requiring only nanoscale input genomic DNA samples, hmC-CATCH enabled us to detect genome-wide hydroxymethylome of human embryonic stem cells in a cost-effective manner. Further application of hmC-CATCH to cell-free DNA (cfDNA) of healthy donors and cancer patients revealed base-resolution hydroxymethylome in the human cfDNA for the first time. We anticipate that our chemical biology approach will find broad applications in hydroxymethylome analysis of limited biological and clinical samples.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • 5-Methylcytosine / analogs & derivatives*
  • 5-Methylcytosine / analysis
  • 5-Methylcytosine / chemistry
  • Cell-Free Nucleic Acids / chemistry*
  • Cell-Free Nucleic Acids / genetics
  • Embryonic Stem Cells / chemistry
  • Genome
  • Genomics / methods*
  • Humans
  • Nucleic Acid Amplification Techniques
  • Oxidation-Reduction
  • Sequence Analysis, DNA


  • Cell-Free Nucleic Acids
  • 5-hydroxymethylcytosine
  • 5-Methylcytosine