A methylome-wide study of aging using massively parallel sequencing of the methyl-CpG-enriched genomic fraction from blood in over 700 subjects

Abstract

The central importance of epigenetics to the aging process is increasingly being recognized. Here we perform a methylome-wide association study (MWAS) of aging in whole blood DNA from 718 individuals, aged 25 -92 years (mean 5 55). We sequenced the methyl-CpG-enriched genomic DNA fraction, averaging 67.3 million reads per subject, to obtain methylation measurements for the ∼27 million autosomal CpGs in the human genome. Following extensive quality control, we adaptively combined methylation measures for neighboring, highly-correlated CpGs into 4 344 016 CpG blocks with which we performed association testing. Eleven age-associated differentially methylated regions (DMRs) passed Bonferroni correction (P-value < 1.15 3 10 28 ). Top findings replicated in an independent sample set of 558 subjects using pyrosequencing of bisulfite-converted DNA (min P-value < 10 230 ). To examine biological themes, we selected 70 DMRs with false discovery rate of <0.1. Of these, 42 showed hypomethylation and 28 showed hypermethylation with age. Hypermethylated DMRs were more likely to overlap with CpG islands and shores. Hypomethylated DMRs were more likely to be in regions associated with polycomb/regulatory proteins (e.g. EZH2) or histone modifications H3K27ac, H3K4m1, H3K4m2, H3K4m3 and H3K9ac. Among genes implicated by the top DMRs were protocadherins, homeobox genes, MAPKs and ryanodine receptors. Several of our DMRs are at genes with potential relevance for age-related disease. This study successfully demonstrates the application of next-generation sequencing to MWAS, by interrogating a large proportion of the methylome and returning potentially novel age DMRs, in addition to replicating several loci implicated in previous studies using microarrays.

Identification of differentially methylated markers among cytogenetic risk groups of acute myeloid leukemia

“…Recent studies targeting the whole genome demonstrated overall hypomethylation in association with aging as well as increased methylation in specific promoter CGIs. [26][27][28] In this study, we also observed decreased methylation in older patients. However, the methylation difference between "younger" and "older" AML patients was less prominent than the difference between cytogenetic risk groups.…”

Global remodeling of the mouse DNA methylome during aging and in response to calorie restriction

“…In contrast, loss of methylation occurred at the 3′UTRs and noncoding (introns) and intergenic regions. These findings in mice agree with previous human studies (McClay et al., 2014; Johansson et al., 2013), indicating conservation of age‐related changes in DNA methylation across species. We also observed increasing DNA methylation in other regulatory regions, such as microRNAs and long noncoding RNAs.…”

“…Several earlier studies investigated DNA methylation changes during aging in humans (Horvath et al., 2012; Johansson, Enroth, & Gyllensten, 2013; Jones, Goodman, & Kobor, 2015; McClay et al., 2014; Rakyan et al., 2010; Sun et al., 2010). Changes in DNA methylation with age are less clearly understood in mice; yet, mouse studies offer an opportunity to develop a deeper understanding of methylome remodeling due to the availability of genetic and dietary models and amenability for whole‐organism experiments.…”

DNA methylation and healthy human aging

“…After birth, average DNA methylation levels increase in blood throughout the first year of life (Martino et al ., 2011; Herbstman et al ., 2013). These changes occur preferentially at CpG island shores and shelves, enhancers, and promoters lacking CpG islands (McClay et al ., 2014). In both blood and buccal epithelial cells, DNA methylation between monozygotic twins has been shown to become more variable in the first year of life (Martino et al ., 2011, 2013).…”

“…They differ in two major ways: (i) the rate of change is much higher in early life than later life, and (ii) the genomic locations of the changes are quite different. In early life, DNA methylation is gained globally, but more at island shores and intergenic regions, while in later life, DNA methylation is lost globally, but still gained at islands and shores (Alisch et al ., 2012; Gentilini et al ., 2013; McClay et al ., 2014). …”