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

• Type of Material: Article
• Authors: Pankaj Chopra, Emory University; Ligia A Papale, University of Wisconsin–Madison; Andrew T J White, University of Wisconsin–Madison; Andrea Hatch, University of Wisconsin–Madison; Ryan M Brown, University of Wisconsin–Madison; Mark A Garthwaite, University of Wisconsin–Madison; Patrick H Roseboom, Emory University; Thaddeus G Golos, University of Wisconsin–Madison; Stephen Warren, Emory University; Reid S. Alisch, University of Wisconsin–Madison
• Language: English
• Date: 2014
• Publisher: BioMed Central
• Publication Version: Final Published Version
• Copyright Statement: © 2014 Chopra et al.; licensee BioMed Central Ltd.
• License: Creative Commons Attribution 2.0 Generic
• Final Published Version (URL): http://www.biomedcentral.com/1471-2164/15/131
• Title of Journal or Parent Work: BMC Genomics
• ISSN: 1471-2164
• Volume: 15
• Issue: 131
• Grant/Funding Information: Emory University’s research IT service center and its high performance computer cluster also supported this research.; This research project was supported in part by the Neuropathology core of the Emory Neuroscience NINDS Core Facilities grant, P30NS055077.; This work was supported in part by the University of Wisconsin-Madison department of Psychiatry (RSA), the Alzheimer’s Disease Research Center grant number P50 AG025688 (Emory University human brain tissue), the Conti Center, and National Institutes of Health (NIH) grants MH081884, MH084051, and MH046729, all to Ned H. Kalin and NIH grant MH089606 to S.T.W.
• Keywords: Evolution; Epigenetics; 5-hydroxymethylcytosine (5-hmC); DNA methylation
• Research Categories: Biology, Genetics

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.