5-hmC Detection & Analysis

In mammalian genomes, 5-mC can be enzymatically oxidized to 5-hmC (5-hydroxymethylcytosine). There is intense scientific curiosity on identifying the epigenetic mechanisms and functions of the 5-hmC. This modification is suggested to be an intermediate between methylation and demethylation of the genome. Occupancy of 5-hmC correlates with inactive or non-productive promoters (1). 5-hmC pattern is different from 5-methylcytosine (5-mC) in many instances (2). Recently, a few analytical methods like chromatography coupled to mass spectroscopy and 5-hmC DNA immunoprecipitation have been developed to quantitate and analyze 5-hmC. However, all the methods fall short of acheiving quantitative site specific resolution.


  1. Bhutani N et al. (2011) Cell 146(6):866-72. PMID: 21925312
  2. Kinney SM et al. (2011) J Biol Chem. 286(28):24685-93. PMID: 21610077
  1. Restriction Enzymes in Chromatin Conformation Capture

    Chromatin conformation capture (3C) techniques allow study of the spatial organization of eukaryotic chromosomes in a 3D context. Learn more about this and other applications of restriction enzymes.

FAQs for 5-hmC Detection & Analysis

Protocols for 5-hmC Detection & Analysis

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EpiMark® 5-hmC and 5-mC Analysis Kit Overview

Balb/C mouse tissue samples using the EpiMark 5-hmC and 5-mC Analysis Kit.
  1. Endpoint PCR of the 6 different reactions needed for methylation analysis. The boxed lanes indicate the presence of 5-hmC.
  2. Real time PCR data was used to determine amounts of 5-hmC and 5-mC present. The results demonstrate a variation in 5-hmC levels in the tissue sources indicated.