Selective Chemical Labeling Reveals the Genome-Wide Distribution of 5-hydroxymethylcytosine

Nat Biotechnol. 2011 Jan;29(1):68-72. doi: 10.1038/nbt.1732. Epub 2010 Dec 12.

Abstract

In contrast to 5-methylcytosine (5-mC), which has been studied extensively, little is known about 5-hydroxymethylcytosine (5-hmC), a recently identified epigenetic modification present in substantial amounts in certain mammalian cell types. Here we present a method for determining the genome-wide distribution of 5-hmC. We use the T4 bacteriophage β-glucosyltransferase to transfer an engineered glucose moiety containing an azide group onto the hydroxyl group of 5-hmC. The azide group can be chemically modified with biotin for detection, affinity enrichment and sequencing of 5-hmC-containing DNA fragments in mammalian genomes. Using this method, we demonstrate that 5-hmC is present in human cell lines beyond those previously recognized. We also find a gene expression level-dependent enrichment of intragenic 5-hmC in mouse cerebellum and an age-dependent acquisition of this modification in specific gene bodies linked to neurodegenerative disorders.

Publication types

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

MeSH terms

  • 5-Methylcytosine / analogs & derivatives
  • Animals
  • Bacteriophage T4 / enzymology
  • Biotin / chemistry*
  • Cerebellum / chemistry
  • Cytosine / analogs & derivatives*
  • Cytosine / analysis
  • DNA / chemistry*
  • DNA / genetics
  • Genome*
  • Genome, Human*
  • Glucosyltransferases / metabolism
  • HEK293 Cells
  • HeLa Cells
  • Humans
  • Mice
  • Models, Molecular
  • Molecular Sequence Data
  • Sequence Analysis, DNA
  • Staining and Labeling / methods*

Substances

  • 5-hydroxymethylcytosine
  • 5-Methylcytosine
  • Biotin
  • Cytosine
  • DNA
  • Glucosyltransferases

Associated data

  • GEO/GSE25398