Age-related epigenetic changes at base excision repair genes and their modulation by dietary restriction in mice

Abstract

Accumulation of damage in DNA is a characteristic feature of ageing which may result from a decline in DNA repair efficiency. Base excision repair (BER) is the primary mechanism used to repair small-scale DNA damage such as that caused by oxidation. I hypothesised that epigenetic events contribute to the ageing process through deregulation of BER gene expression and that these adverse effects of ageing may be modulated by dietary restriction (DR). To test these hypotheses, I quantified DNA methylation and histone post-translational modifications at BER-gene (Ogg1 and Apex) promoters, together with expression of these genes, in tissues from ageing mice and from mice exposed to DR. Phenotypic changes in DNA incision activity and oxidative damage were also quantified. Cytosine methylation was measured by pyrosequencing at the Ogg1 promoter in brain and livers from ad libitum (AL) and 40% DR mice at 3, 12, 24 and 30 months of age (n=5/group). Ogg1 promoter methylation decreased with age in the liver (p=0.018) and brain (p=0.016) and DR significantly reduced Ogg1 promoter methylation (p=0.014) in the brain. Additionally, in the brain there was a 2 fold enrichment in histone 4 acetylation (H4Ac) and histone 3 lysine 27 tri-methylation (H3K27Me3) as measured by the ChIP assay at Ogg1 and Apex promoters in 30 month old AL animals compared with 3 month old animals (p<0.05). H4Ac was 2.5-fold higher in the Ogg1 promoter in liver in 30 month old DR versus 30 month old AL animals (p=0.004). Furthermore H4K27Me3 was significantly (p=0.023) lower at the liver Ogg1 promoter in 30 month old compared with 3 month old animals. Ogg1 gene expression decreased with age in the brain (n.s.) and liver (p=0.005). Perhaps surprisingly, Ogg1 and Apex expression levels were higher in the brain (p=0.034) but lower in the liver (p=0.003) of DR compared with AL animals. I used a comet-based in vitro assay to quantify BER-related incision activity but did not observe any significant changes in the liver or in whole brain in response to ageing or to DR. However DNA incision activity varied considerably between different brain regions and DR enhanced incision 2 fold in the cortex (p=0.031) and subcortical regions (p=0.019). 8-oxoguanine lesions measured by HPLC-ECD decreased with age (AL and DR) (p<0.001) in the liver but no effect of age was detected in the brain. ii This study revealed for the first time that tissue-specific epigenetic changes at BER genes occur during ageing and the data presented here suggest that epigenetic changes at BER-related gene promoters may affect BER activity in some tissues. Furthermore, I have shown that DR influences the epigenetic and transcription changes in BER-related genes observed during ageing.