CpG Methylation Differences Between Neurons and Glia are Highly Conserved from Mouse to Human

Abstract

Understanding epigenetic differences that distinguish neurons and glia is of fundamental importance to the nascent field of neuroepigenetics. A recent study (Lister & Mukamel, et al., Science 2013) used genome‐wide bisulfite sequencing to survey differences in DNA methylation between these two cell types, in both humans and mice. That study minimized the importance of cell type‐specific differences in CpG methylation, claiming these are restricted to localized genomic regions, and instead emphasized that widespread and highly conserved differences in non‐CpG methylation distinguish neurons and glia. We reanalyzed the data from that study and came to markedly different conclusions. In particular, we found widespread cell type‐specific differences in CpG methylation, with a genome‐wide tendency for neuronal CpG‐hypermethylation punctuated by regions of glia‐specific hypermethylation. Alarmingly, our analysis indicated that the majority of genes identified by the primary study as exhibiting cell type‐specific CpG methylation differences were misclassified. To verify the accuracy of our analysis, we isolated neuronal and glial DNA from mouse cortex and performed quantitative bisulfite pyrosequencing at nine loci. The pyrosequencing results corroborated our analysis, without exception. Most interestingly, we found that gene‐associated neuron vs. glia CpG methylation differences are highly conserved across human and mouse, and are very likely to be functional. In addition to underscoring the importance of independent verification to confirm the conclusions of genome‐wide epigenetic analyses, our data indicate that CpG methylation plays a major role in neuroepigenetics, and that the mouse is likely an excellent model in which to study the role of DNA methylation in human neurodevelopment and disease, and effects of nutrition on these processes.Support or Funding InformationThis work was supported by grants from the National Institutes of Health Roadmap Epigenomics Program [grant number U01DA025956] and the U.S. Department of Agriculture (USDA) [grant numbers CRIS 6250‐51000‐055 and CRIS 3092‐5‐001‐059].