Epigenetics and Ageing

Bellizzi, Dina; Guarasci, Francesco; Iannone, Francesca; Passarino, Giuseppe; Rose, Giuseppina

doi:10.1007/978-3-030-20762-5_7

Cited by 5 publications

(2 citation statements)

References 312 publications

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“…Epigenetic modifications of DNA can regulate gene expression, either by modulating chromatin structure, or through interactions during DNA transcription (Gibney & Nolan, 2010). A substantial effort has been directed towards studying epigenetic modifications in the context of ageing in recent years, and a rapidly growing body of studies has uncovered associations between age and the state of the epigenome (Bellizzi et al, 2019). The primary epigenetic process studied is DNA methylation (DNAm), which refers to the addition of a methyl group to a cytosine followed by a guanine separated by the phosphate backbone, usually referred to as a CpG site (Moore et al, 2013).…”

Section: Introductionmentioning

confidence: 99%

DNA methylation markers of age(ing) in non‐model animals

et al. 2023

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Inferring the chronological and biological age of individuals is fundamental to population ecology and our understanding of ageing itself, its evolution, and the biological processes that affect or even cause ageing. Epigenetic clocks based on DNA methylation (DNAm) at specific CpG sites show a strong correlation with chronological age in humans, and discrepancies between inferred and actual chronological age predict morbidity and mortality. Recently, a growing number of epigenetic clocks have been developed in non‐model animals and we here review these studies. We also conduct a meta‐analysis to assess the effects of different aspects of experimental protocol on the performance of epigenetic clocks for non‐model animals. Two measures of performance are usually reported, the R2 of the association between the predicted and chronological age, and the mean/median absolute deviation (MAD) of estimated age from chronological age, and we argue that only the MAD reflects accuracy. R2 for epigenetic clocks based on the HorvathMammalMethylChip4 was higher and the MAD scaled to age range lower, compared with other DNAm quantification approaches. Scaled MAD tended to be lower among individuals in captive populations, and decreased with an increasing number of CpG sites. We conclude that epigenetic clocks can predict chronological age with relatively high accuracy, suggesting great potential in ecological epigenetics. We discuss general aspects of epigenetic clocks in the hope of stimulating further DNAm‐based research on ageing, and perhaps more importantly, other key traits.

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Section: Introductionmentioning

confidence: 99%

DNA methylation markers of age(ing) in non‐model animals

et al. 2023

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“…[38][39] Each are known to be involved in a variety of pathologies, including nonalcoholic fatty liver disease (NAFLD), diabetes, cardiovascular disease, cancer, neurodegeneration, and aging. [11][12]32,[40][41][42][43][44][45] The current model suggests that SIRT3 deacetylates proteins within the tricarboxylic acid (TCA) cycle, the electron transport chain (ETC), fatty acid β-oxidation, ketogenesis, antioxidant defense, and mitochondrial protein synthesis. [46][47][48][49][50][51] SIRT5 is localized in both mitochondria and the cytosol and possesses several enzymatic functions including lysine desuccinylase, demalonylase, and deglutarylase activity.…”

Section: Introductionmentioning

confidence: 99%

Quantifying Competition among Mitochondrial Protein Acylation Events Induced by Ethanol Metabolism

et al. 2019

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Mitochondrial dysfunction is one of many key factors in the etiology of alcoholic liver disease (ALD). Lysine acetylation is known to regulate numerous mitochondrial metabolic pathways and recent reports demonstrate that alcohol-induced protein acylation negatively impacts these processes. To identify regulatory mechanisms attributed to alcohol-induced protein posttranslational modifications, we employed a model of alcohol consumption within the context of wild type (WT), sirtuin 3 knockout (SIRT3 KO), and sirtuin 5 knockout (SIRT5 KO) mice to manipulate hepatic mitochondrial protein acylation. Mitochondrial fractions were examined by label-free quantitative HPLC-MS/MS to reveal competition between lysine acetylation and succinylation. A class of proteins defined as "differential acyl switching proteins" demonstrate select sensitivity to alcohol-induced protein acylation. A number of these proteins reveal saturated lysine-site occupancy, suggesting a significant level of differential stoichiometry in the setting of ethanol consumption. We hypothesize that ethanol downregulates numerous mitochondrial metabolic pathways through differential acyl switching proteins. Data are available via ProteomeXchange with identifier PXD012089.

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Independent avian epigenetic clocks for aging and development

Haller,

Risse,

Sepers

et al. 2024

Preprint

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Information on individual age is a fundamental aspect in many ecological and evolutionary studies. However, accurate and non-lethal methods that can be applied to estimate the age of wild animals are often absent. Furthermore, since the process of ageing is accompanied by a physical decline and the deterioration of biological functions, the biological age often deviates from the chronological age. Epigenetic marks are widely suggested to be associated with this age-related physical decline, and especially changes in DNA methylation are suggested to be reliable age-predictive biomarkers. Here, we developed separate epigenetic clocks for ageing for development in a small passerine bird, the great tit (Parus major). The ageing clock was constructed and evaluated using erythrocyte DNA methylation data of 122 post-fledging individuals, and the developmental clock using 67 pre-fledging individuals from a wild population. Using a leave-one-out cross validation approach, we were able to accurately predict the ages of individuals with mediation absolute deviations of 0.40 years for the ageing and 1.06 days for the development clock. Moreover, using existing data from a brood-size manipulation we show that nestlings from reduced broods are estimated to be biologically older compared to control nestlings, while they are expected to have higher fitness. These epigenetic clocks provide further evidence that, as observed in mammals, changes in DNA methylation of certain CpG sites are highly correlated with chronological age in birds and open up new avenues for broad applications in behavioural and evolutionary ecology.

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Epigenetics and Ageing

Cited by 5 publications

References 312 publications

DNA methylation markers of age(ing) in non‐model animals

DNA methylation markers of age(ing) in non‐model animals

Quantifying Competition among Mitochondrial Protein Acylation Events Induced by Ethanol Metabolism

Independent avian epigenetic clocks for aging and development

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