This article is part of a special issue on epigenomics.

Open Access Open Badges Research

Non-genotoxic carcinogen exposure induces defined changes in the 5-hydroxymethylome

John P Thomson16, Harri Lempiäinen26, Jamie A Hackett16, Colm E Nestor13, Arne Müller2, Federico Bolognani2, Edward J Oakeley5, Dirk Schübeler4, Rémi Terranova2, Diana Reinhardt136, Jonathan G Moggs26* and Richard R Meehan16*

Author affiliations

1 MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, UK

2 Investigative Toxicology, Preclinical Safety, Translational Sciences, Novartis Institute for Biomedical Research, Lichtstrasse 35, CH-4057 Basel, Switzerland

3 Breakthrough Breast Cancer Research Unit, University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, UK

4 Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland

5 Biomarker Development, Human Genetics and Genomics, Translational Sciences, Novartis Institutes for Biomedical Research, Maulbeerstrasse 66, 4056 Basel, Switzerland

6 Member of MARCAR consortium

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Citation and License

Genome Biology 2012, 13:R93  doi:10.1186/gb-2012-13-10-r93

Published: 3 October 2012



Induction and promotion of liver cancer by exposure to non-genotoxic carcinogens coincides with epigenetic perturbations, including specific changes in DNA methylation. Here we investigate the genome-wide dynamics of 5-hydroxymethylcytosine (5hmC) as a likely intermediate of 5-methylcytosine (5mC) demethylation in a DNA methylation reprogramming pathway. We use a rodent model of non-genotoxic carcinogen exposure using the drug phenobarbital.


Exposure to phenobarbital results in dynamic and reciprocal changes to the 5mC/5hmC patterns over the promoter regions of a cohort of genes that are transcriptionally upregulated. This reprogramming of 5mC/5hmC coincides with characteristic changes in the histone marks H3K4me2, H3K27me3 and H3K36me3. Quantitative analysis of phenobarbital-induced genes that are involved in xenobiotic metabolism reveals that both DNA modifications are lost at the transcription start site, while there is a reciprocal relationship between increasing levels of 5hmC and loss of 5mC at regions immediately adjacent to core promoters.


Collectively, these experiments support the hypothesis that 5hmC is a potential intermediate in a demethylation pathway and reveal precise perturbations of the mouse liver DNA methylome and hydroxymethylome upon exposure to a rodent hepatocarcinogen.