Differences in DNA methylation between human neuronal and glial cells are concentrated in enhancers and non-CpG sites.
We applied Illumina Human Methylation450K array to perform a genomic-scale single-site resolution DNA methylation analysis in neuronal and nonneuronal (primarily glial) nuclei separated from the orbitofrontal cortex of postmortem human brain. The findings were validated using enhanced reduced representation bisulfite sequencing. We identified thousands of sites differentially methylated (DM) between neuronal and nonneuronal cells. The DM sites were depleted within CpG-island-containing promoters but enriched in predicted enhancers. Classification of the DM sites into those undermethylated in neurons (neuronal type) and those undermethylated in nonneuronal cells (glial type), combined with findings of others that methylation within control elements typically negatively correlates with gene expression, yielded large sets of predicted neuron-specific and non-neuron-specific genes. These sets of predicted genes were in excellent agreement with the available direct measurements of gene expression in human and mouse. We also found a distinct set of DNA methylation patterns that were unique for neuronal cells. In particular, neuronal-type differential methylation was overrepresented in CpG island shores, enriched within gene bodies but not in intergenic regions, and preferentially harbored binding motifs for a distinct set of transcription factors, including neuron-specific activity-dependent factors. Finally, non-CpG methylation was substantially more prevalent in neurons than in nonneuronal cells.
VISN 3 Mental Illness Research, Education and Clinical Center (MIRECC), James J. Peters VA Medical Center, Bronx, NY, USA, The Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA, Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA, Research Division, Hospital for Special Surgery, New York, NY, USA, Illumina, Inc., San Diego, CA, USA and National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA.
Alexey
A
Kozlenkov
Panos
P
Roussos
Alisa
A
Timashpolsky
Mihaela
M
Barbu
Sergei
S
Rudchenko
Marina
M
Bibikova
Brandy
B
Klotzle
William
W
Byne
Rebecca
R
Lyddon
Antonio Fabio
AF
Di Narzo
Yasmin L
YL
Hurd
Eugene V
EV
Koonin
Stella
S
Dracheva
D000328:Adult; D000818:Animals; D001665:Binding Sites; D001921:Brain / Q000378:metabolism*; D002467:Cell Nucleus / Q000235:genetics; D018899:CpG Islands; D019175:DNA Methylation; D004742:Enhancer Elements, Genetic; D019143:Evolution, Molecular; D015870:Gene Expression; D015894:Genome, Human; D006801:Humans; D008297:Male; D051379:Mice; D009457:Neuroglia / Q000378:metabolism*; D009474:Neurons / Q000378:metabolism*; D059372:Nucleotide Motifs; D014157:Transcription Factors / Q000378:metabolism; D024363:Transcription Initiation Site; D055815:Young Adult
D014157:Transcription Factors