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Dietary restriction protects from age-associated DNA methylation and induces epigenetic reprogramming of lipid metabolism

ABSTRACT: Dietary restriction (DR), a reduction in food intake without malnutrition, increases most aspects of health during ageing and extends lifespan in diverse species including rodents and rhesus monkeys. However the mechanisms by which DR interacts with the ageing process to improve health at old age are poorly understood. DNA methylation could play an important role in mediating the effects of DR, because it is sensitive to the effects of nutrition and can affect gene expression memory over time. Here we have profiled genome-wide changes in DNA methylation, gene expression and lipidomics in response to DR and ageing in mouse liver. DR strongly retarded age-related changes in DNA methylation. With ageing, DNA methylation became confined to genic elements and was associated with reduced gene expression, particularly of genes involved in lipid metabolism.

ORGANISM(S): Mus musculus

PROVIDER: GSE92486 | GEO | 2017/02/24

SECONDARY ACCESSION(S): PRJNA357680

REPOSITORIES: GEO

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Project description:Beneficial effects of SIRT1 on healthspan are likely to be pleiotropic and may include effects on DNA methylation. We demonstrated recently that manipulating SIRT1 in human cells affected DNA methylation of a panel of test genes, and that genes with expression modified by dietary restriction corresponded with genes that underwent changes in DNA methylation during ageing. Here we tested the hypothesis that genes particularly susceptible to SIRT1-induced effects on DNA methylation across the genome map to genes for which DNA methylation changes during ageing. We increased or reduced SIRT1 expression in human intestinal (Caco-2) and vascular endothelial (HuVEC) cells by transient transfection with an expression construct or with siRNA, respectively. Effects on DNA methylation were measured by enriching for the methylated fraction then either sequencing (HuVEC) or hybridising to a human promoter microarray (Caco-2). Effects using these two different cell lines and techniques for analysis were remarkably consistent. Genes with a DNA methylation status affected by SIRT1 manipulation were enriched for those that undergo age-dependent changes in DNA methylation, thus supporting our hypothesis. Polycomb group protein target genes (PCGTs), which are suppressed by epigenetic mechanisms in stem cells and have been shown previously to correspond with loci particularly susceptible to age-related changes in DNA methylation, were over-represented within the set of genes showing altered DNA methylation in response to SIRT1 manipulation in both cell lines. We thus propose that effects of SIRT1 to extend healthspan include influences on the DNA methylation status of genes affected during ageing, in particular PCGTs. Analysis of methylation profiles of Caco-2 cells meeting the following conditions: SIRT1 overexpressed by transfection with pCMV6-ENTRY-SIRT1 (2 replicates), corresponding vector control (2 replicates), each of the siRNAs that target SIRT1 (1 & 2 replicates, respectively) and control siRNA (2 replicates).

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Dietary restriction protects from age-associated DNA methylation and induces epigenetic reprogramming of lipid metabolism

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