Bisulfite-free, base-resolution analysis of 5-formylcytosine at the genome scale

Nat Methods. 2015 Nov;12(11):1047-50. doi: 10.1038/nmeth.3569. Epub 2015 Sep 7.

Abstract

Active DNA demethylation in mammals involves oxidation of 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC). However, genome-wide detection of 5fC at single-base resolution remains challenging. Here we present fC-CET, a bisulfite-free method for whole-genome analysis of 5fC based on selective chemical labeling of 5fC and subsequent C-to-T transition during PCR. Base-resolution 5fC maps showed limited overlap with 5hmC, with 5fC-marked regions more active than 5hmC-marked ones.

Publication types

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

MeSH terms

  • 5-Methylcytosine / chemistry
  • Animals
  • Cell Line
  • CpG Islands
  • Cytosine / analogs & derivatives*
  • Cytosine / chemistry
  • DNA Methylation*
  • DNA Primers / chemistry
  • Epigenomics
  • Gene Expression Regulation
  • Genome
  • Mice
  • Mice, Transgenic
  • Oligonucleotides / genetics
  • Oxygen / chemistry
  • Polymerase Chain Reaction
  • Sequence Analysis, DNA / methods*
  • Stem Cells / cytology
  • Sulfites / chemistry

Substances

  • 5-carboxylcytosine
  • 5-formylcytosine
  • DNA Primers
  • Oligonucleotides
  • Sulfites
  • 5-hydroxymethylcytosine
  • 5-Methylcytosine
  • Cytosine
  • hydrogen sulfite
  • Oxygen

Associated data

  • GEO/GSE66144