Open Access Highly Accessed Methodology article

Array-based assay detects genome-wide 5-mC and 5-hmC in the brains of humans, non-human primates, and mice

Pankaj Chopra2, Ligia A Papale1, Andrew T J White1, Andrea Hatch1, Ryan M Brown1, Mark A Garthwaite6, Patrick H Roseboom1, Thaddeus G Golos567, Stephen T Warren234 and Reid S Alisch1*

Author Affiliations

1 Department of Psychiatry, University of Wisconsin–Madison, 6001 Research Park Blvd., Madison, Wisconsin 53719, USA

2 Departments of Human Genetics, Emory University School of Medicine, 615 Michael Street, Atlanta, Georgia 30322, USA

3 Departments of Biochemistry, Emory University School of Medicine, 615 Michael Street, Atlanta, Georgia 30322, USA

4 Departments of Pediatrics, Emory University School of Medicine, 615 Michael Street, Atlanta, Georgia 30322, USA

5 Departments of Comparative Biosciences, University of Wisconsin – Madison, 1223 Capitol Court, Madison, Wisconsin 53715, USA

6 Obstetrics & Gynecology, University of Wisconsin – Madison, 1223 Capitol Court, Madison, Wisconsin 53715, USA

7 Departments of Wisconsin National Primate Research Center, University of Wisconsin – Madison, 1223 Capitol Court, Madison, Wisconsin 53715, USA

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BMC Genomics 2014, 15:131  doi:10.1186/1471-2164-15-131

Published: 13 February 2014

Abstract

Background

Methylation on the fifth position of cytosine (5-mC) is an essential epigenetic mark that is linked to both normal neurodevelopment and neurological diseases. The recent identification of another modified form of cytosine, 5-hydroxymethylcytosine (5-hmC), in both stem cells and post-mitotic neurons, raises new questions as to the role of this base in mediating epigenetic effects. Genomic studies of these marks using model systems are limited, particularly with array-based tools, because the standard method of detecting DNA methylation cannot distinguish between 5-mC and 5-hmC and most methods have been developed to only survey the human genome.

Results

We show that non-human data generated using the optimization of a widely used human DNA methylation array, designed only to detect 5-mC, reproducibly distinguishes tissue types within and between chimpanzee, rhesus, and mouse, with correlations near the human DNA level (R2 > 0.99). Genome-wide methylation analysis, using this approach, reveals 6,102 differentially methylated loci between rhesus placental and fetal tissues with pathways analysis significantly overrepresented for developmental processes. Restricting the analysis to oncogenes and tumor suppressor genes finds 76 differentially methylated loci, suggesting that rhesus placental tissue carries a cancer epigenetic signature. Similarly, adapting the assay to detect 5-hmC finds highly reproducible 5-hmC levels within human, rhesus, and mouse brain tissue that is species-specific with a hierarchical abundance among the three species (human > rhesus >> mouse). Annotation of 5-hmC with respect to gene structure reveals a significant prevalence in the 3'UTR and an association with chromatin-related ontological terms, suggesting an epigenetic feedback loop mechanism for 5-hmC.

Conclusions

Together, these data show that this array-based methylation assay is generalizable to all mammals for the detection of both 5-mC and 5-hmC, greatly improving the utility of mammalian model systems to study the role of epigenetics in human health, disease, and evolution.

Keywords:
Epigenetics; DNA methylation; 5-hydroxymethylcytosine (5-hmC); Evolution