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Reversing DNA methylation: mechanisms, genomics, and biological functions.

ABSTRACT: Methylation of cytosines in the mammalian genome represents a key epigenetic modification and is dynamically regulated during development. Compelling evidence now suggests that dynamic regulation of DNA methylation is mainly achieved through a cyclic enzymatic cascade comprised of cytosine methylation, iterative oxidation of methyl group by TET dioxygenases, and restoration of unmodified cytosines by either replication-dependent dilution or DNA glycosylase-initiated base excision repair. In this review, we discuss the mechanism and function of DNA demethylation in mammalian genomes, focusing particularly on how developmental modulation of the cytosine-modifying pathway is coupled to active reversal of DNA methylation in diverse biological processes.

SUBMITTER: Wu H

PROVIDER: S-EPMC3938284 | biostudies-literature | 2014 Jan

REPOSITORIES: biostudies-literature

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Reversing DNA methylation: mechanisms, genomics, and biological functions.

Wu Hao H Zhang Yi Y

Cell 20140101 1-2

Methylation of cytosines in the mammalian genome represents a key epigenetic modification and is dynamically regulated during development. Compelling evidence now suggests that dynamic regulation of DNA methylation is mainly achieved through a cyclic enzymatic cascade comprised of cytosine methylation, iterative oxidation of methyl group by TET dioxygenases, and restoration of unmodified cytosines by either replication-dependent dilution or DNA glycosylase-initiated base excision repair. In this ...[more]

PMID: 24439369

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Project description:Study questionAre reproductive characteristics associated with genome-wide DNA methylation and epigenetic age?Summary answerOur data suggest that increasing parity is associated with differences in blood DNA methylation and small increases in epigenetic age.What is known alreadyA study of 397 young Filipino women (ages 20-22) observed increasing epigenetic age with an increasing number of pregnancies.Study design, size, durationWe used data from 2356 non-Hispanic white women (ages 35-74) enrolled in the Sister Study cohort.Participants/materials, setting, methodsData on reproductive history were ascertained via questionnaire. Of the 2356 women, 1897 (81%) reported at least one live birth. Among parous women, 487 (26%) women reported ever experiencing a pregnancy complication. Three epigenetic clocks (i.e. Hannum, Horvath and Levine) and genome-wide methylation were measured in DNA from whole blood using Illumina's HumanMethylation450 BeadChip. We estimated association β-values and 95% CIs using linear regression.Main results and the role of chanceAll three epigenetic clocks showed weak associations between number of births and epigenetic age (per live birth; Hannum: β = 0.16, 95% CI = 0.02, 0.29, P = 0.03; Horvath: β = 0.12, 95% CI = -0.04, 0.27, P = 0.14; Levine: β = 0.27, 95% CI = 0.08, 0.45, P = 0.01); however, additional adjustment for current BMI attenuated the associations. Among parous women, a history of abnormal glucose tolerance during pregnancy was associated with increased epigenetic age by the Hannum clock (β = 0.96; 95% CI = 0.10, 1.81; P = 0.03) and Levine clocks (β = 1.69; 95% CI = 0.54, 2.84; P < 0.01). In epigenome-wide analysis, increasing parity was associated with methylation differences at 17 CpG sites (Bonferroni corrected P≤ 1.0 × 10-7).Limitations, reasons for cautionWe relied on retrospective recall to ascertain reproductive history and pregnancy complications.Wider implications of the findingsOur findings suggest that parity is associated with small increases in epigenetic age and with DNA methylation at multiple sites in the genome.Study funding/competing interest(s)This research was supported by the Intramural Research program of the NIH, National Institute of Environmental Health Sciences (Z01-ES049033, Z01-ES049032 and Z01-ES044055). None of the authors have a conflict of interest.Trial registration numberNot applicable.

Dataset Information

Reversing DNA methylation: mechanisms, genomics, and biological functions.

Publications

Reversing DNA methylation: mechanisms, genomics, and biological functions.

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