Abstract
BackgroundSeveral studies have reported age-associated changes in DNA methylation in the first few years of life and in adult populations, but the extent of such changes during childhood is less well studied. The goals of this study were to investigate to what degree intra-individual changes in DNA methylation are associated with aging during childhood and dissect the methylation changes directly associated with aging from the effect mediated through variation in cell-type composition (CTC).ResultsWe performed reduced representation bisulfite sequencing (RRBS) in peripheral whole-blood samples collected at 2, 10, and 16 years of age. We identified age-associated longitudinal changes in DNA methylation at 346 CpGs in 178 genes. Analyses separating the effect mediated by CTC variability across age identified 26 CpGs located in 12 genes that associated directly with age. Hence, the CTC changes across age appear to act as a mediator of the observed DNA methylation associated with age. The results were replicated using EpiTYPER in a second sample set selected from the same cohort. Gene ontology analyses revealed enrichment of transcriptional regulation and developmental processes. Further, comparisons of the mean DNA methylation differences between the time points reveal greater differences between 2 to 10 years and 10 to 16 years, suggesting that the identified age-associated DNA methylation patterns manifests in early childhood.ConclusionsThis study reveals insights into the epigenetic dynamics associated with aging early in life. Such information could ultimately provide clues and point towards molecular pathways that are susceptible to aging-related disease-associated epigenetic dysregulation.Electronic supplementary materialThe online version of this article (doi:10.1186/s13148-016-0277-3) contains supplementary material, which is available to authorized users.
Highlights
Several studies have reported age-associated changes in DNA methylation in the first few years of life and in adult populations, but the extent of such changes during childhood is less well studied
To assess whether differences in cell-type proportions (CTP) in peripheral whole-blood have an impact on the observed age-associated changes in DNA methylation, we investigated whether cell-type composition (CTC) acts as a mediator
In line with the results presented above indicating that the study is underpowered, we chose an exploratory approach and based the gene ontology (GO) analyses on genes associated with CpGs with a Benjamini and Hochberg (BH) false discovery rate (FDR) < 25 % (n = 78 genes out of 15 339 genes included in the background list)
Summary
Several studies have reported age-associated changes in DNA methylation in the first few years of life and in adult populations, but the extent of such changes during childhood is less well studied. The goals of this study were to investigate to what degree intra-individual changes in DNA methylation are associated with aging during childhood and dissect the methylation changes directly associated with aging from the effect mediated through variation in cell-type composition (CTC). DNA methylation has diverse roles in many aspects of human biology (e.g., cell differentiation [1], genomic imprinting [2], and gene expression [3]). DNA methylation is highly variable between individuals and between cell types and tissues [4]. Age-associated changes in DNA methylation involve two distinct phenomena: epigenetic drift and the epigenetic clock [9], both involving intra-individual changes over time. While epigenetic drift [8] involves changes that are different between individuals, the epigenetic clock characterizes
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