24-hour rhythms of DNA methylation and their relation with rhythms of RNA expression in the human dorsolateral prefrontal cortex.
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Abstract | Circadian rhythms modulate the biology of many human tissues, including brain tissues, and are driven by a near 24-hour transcriptional feedback loop. These rhythms are paralleled by 24-hour rhythms of large portions of the transcriptome. The role of dynamic DNA methylation in influencing these rhythms is uncertain. While recent work in Neurospora suggests that dynamic site-specific circadian rhythms of DNA methylation may play a role in modulating the fungal molecular clock, such rhythms and their relationship to RNA expression have not, to our knowledge, been elucidated in mammalian tissues, including human brain tissues. We hypothesized that 24-hour rhythms of DNA methylation exist in the human brain, and play a role in driving 24-hour rhythms of RNA expression. We analyzed DNA methylation levels in post-mortem human dorsolateral prefrontal cortex samples from 738 subjects. We assessed for 24-hour rhythmicity of 420,132 DNA methylation sites throughout the genome by considering methylation levels as a function of clock time of death and parameterizing these data using cosine functions. We determined global statistical significance by permutation. We then related rhythms of DNA methylation with rhythms of RNA expression determined by RNA sequencing. We found evidence of significant 24-hour rhythmicity of DNA methylation. Regions near transcription start sites were enriched for high-amplitude rhythmic DNA methylation sites, which were in turn time locked to 24-hour rhythms of RNA expression of nearby genes, with the nadir of methylation preceding peak transcript expression by 1-3 hours. Weak ante-mortem rest-activity rhythms were associated with lower amplitude DNA methylation rhythms as were older age and the presence of Alzheimer's disease. These findings support the hypothesis that 24-hour rhythms of DNA methylation, particularly near transcription start sites, may play a role in driving 24-hour rhythms of gene expression in the human dorsolateral prefrontal cortex, and may be affected by age and Alzheimer's disease. |
Year of Publication | 2014
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Journal | PLoS Genet
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Volume | 10
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Issue | 11
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Pages | e1004792
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Date Published | 2014 Nov
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ISSN | 1553-7404
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URL | |
DOI | 10.1371/journal.pgen.1004792
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PubMed ID | 25375876
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PubMed Central ID | PMC4222754
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Grant list | RF1 AG015819 / AG / NIA NIH HHS / United States
R01AG36836 / AG / NIA NIH HHS / United States
MOP125934 / Canadian Institutes of Health Research / Canada
R01 NS078009 / NS / NINDS NIH HHS / United States
U01AG046152 / AG / NIA NIH HHS / United States
K25 AG041906 / AG / NIA NIH HHS / United States
R01NS078009 / NS / NINDS NIH HHS / United States
R01AG36042 / AG / NIA NIH HHS / United States
R01 AG017917 / AG / NIA NIH HHS / United States
R01AG17917 / AG / NIA NIH HHS / United States
R01AG034504 / AG / NIA NIH HHS / United States
P30 AG010161 / AG / NIA NIH HHS / United States
R0AG04337 / AG / NIA NIH HHS / United States
R01AG15819 / AG / NIA NIH HHS / United States
R01 AG041232 / AG / NIA NIH HHS / United States
R01AG041232 / AG / NIA NIH HHS / United States
P30AG10161 / AG / NIA NIH HHS / United States
MMC112692 / Canadian Institutes of Health Research / Canada
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