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Epigenetics and aging: the targets and the marks
Abstract
'Aging epigenetics' is an emerging field that promises exciting revelations in the near future. Here we focus on the functional and biological significance of the epigenetic alterations that accumulate during aging and are important in tumorigenesis. Paradigmatic examples are provided by the global loss of DNA methylation in aging and cancer and by the promoter hypermethylation of genes with a dual role in tumor suppression and progeria, such as the Werner syndrome (WRN) and lamin A/C genes. Another twist is provided by sirtuins, a family of NAD-dependent deacetylases that act on Lys16 of histone H4, which are emerging as a link between cellular transformation and lifespan.
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“It is recognized that epigenetic stability is proportional related to DNA methylation, as global hypomethylation of DNA may lead to genomic instability [179, 180].”
From Air pollution and children’s health—a review of adverse effects associated with prenatal exposure from fine to ultrafine particulate matter (2021) · cites this paper as [179]
In the citing paper
“Increased histone H4K16 acetylation, H4K20 trimethylation or H3K4 trimethylation, as well as decreased H3K9 methylation or H3K27 trimethylation, constitute age-associated epigenetic marks (Fraga and Esteller, 2007; Han and Brunet, 2012).”
From The Hallmarks of Aging (2013) · cites this paper as Fraga and Esteller, 2007
In the citing paper
“The age-associated repression of TERT is reminiscent of other key longevity-associated genes, where epigenetic alterations altering chromatin structure and accessibility accumulate in the cis-regulatory sequences during aging, leading changes in the transcriptional regulation of genes governing aging.41,42”
From TERT activation targets DNA methylation and multiple aging hallmarks (2024) · cites this paper as [41]
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Epigenetic differences arise during the lifetime of monozygotic twins
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Stem-cell ageing modified by the cyclin-dependent kinase inhibitor p16INK4a
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The Regulation of INK4/ARF in Cancer and Aging
Kim, W. Y., & Sharpless, N. E. (2006) · Cell · doi:10.1016/j.cell.2006.10.003 · Cited by 1,009
Calorie restriction–the SIR2 connection
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Inhibition of SIRT1 Reactivates Silenced Cancer Genes without Loss of Promoter DNA Hypermethylation
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Epigenetic inactivation of the premature aging Werner syndrome gene in human cancer
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Turner, J. D., D’Ambrosio, C., Vögele, C., & Diewald, M. (2020) · International Journal of Molecular Sciences · doi:10.3390/ijms21093142 · Cited by 18
“Furthermore, both longitudinal [44] and cross-sectional studies [45,46] have shown that differences increase significantly as twins age.”
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“Epigenetics in recent years has attracted research awareness and provided an additional level of how gene expression is regulated [37].”
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Combinatorial identification of DNA methylation patterns over age in the human brain
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Epigenetics and the Uremic Phenotype: A Matter of Balance
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“Age-related changes to DNA methylation at cytosine-phos-phate-guanine (CpG) motifs are a conserved hallmark of mammalian aging (Fraga and Esteller, 2007).”
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“Environmental factors, including aging and nutrition, have been associated with aberrant epigenetic modifications [151,152].”
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“With epigenetic silencing on LMNA, which is one of progeroid genes, we could observe a corresponding malignant transformation [18].”
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“Based on the original insights of Fraga and Esteller [20], and the more effective implementation strategies of Hannum and Horvath [21,22], these tools use complex regression algorithms to interpret the results from epigenome wide methylation arrays to infer overall health status using a metric termed “accelerated agin…”
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“Meanwhile, the effect of aging should be considered in the analysis because aging decreases the methylation level of global DNA and increases that of CpG islands in patients [22,23].”
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“Further, independent studies corroborate that methylation of H4K20 increases progressively with age in murine models and the abundance of this mark is positively associated with senescence [38,51].”
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“Today, epigenetics is commonly defined as changes in gene expression that occur without a change in DNA sequence (4, 11).”
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“Epigenetic clocks have emerged as a potential molecular tool for measuring biological aging, offering a deeper perspective on this process and its implications for health [10–12].”
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Gene-environment interaction and Mendelian randomisation
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Epigenetic Analysis in Human Neurons: Considerations for Disease Modeling in PD
de Boni, L., & Wüllner, U. (2019) · Frontiers in Neuroscience · doi:10.3389/fnins.2019.00276 · Cited by 8
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“, DNA methylation and histone modification) and age has been reported [6].”
BackgroundTesting Two Evolutionary Theories of Human Aging with DNA Methylation Data
Robins, C., McRae, A. F., Powell, J. E., Wiener, H. W., Aslibekyan, S. W., Kennedy, E. M., Absher, D., Arnett, D. K., Montgomery, G. W., Visscher, P. M., et al. (2017) · Genetics · doi:10.1534/genetics.117.300217 · Cited by 10
“DNAmethylation is anepigeneticmodification that isdynamic with age (Fraga and Esteller 2007; Bocklandt et al. 2011; Koch and Wagner 2011; Alisch et al. 2012; Hannum et al. 2013; Horvath 2013; Xu and Taylor 2014) and has been shown to be heritable in cross-sectional family studies (McRae et al.…”
BackgroundLian, S.-S., He, Y., Li, X., Zhao, B., Hou, R., Hu, X.-L., Zhang, L.-L., & Bao, Z. (2015) · Journal of Ocean University of China · doi:10.1007/s11802-015-2507-2 · Cited by 10
“cn be the result of the progressive loss of DNMT1 efficacy (Fraga and Esteller, 2007).”
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“Other examples of genes with increased promoter methylation during aging include those encoding Ecadherin, c-fos and collagen α1 (reviewed in Fraga and Esteller 2007 ).”
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Promoter methylation analysis of CDH1 and p14ARF genes in patients with urothelial bladder cancer
Bayramov, B., Gunes, S., Buyukalpelli, R., Aydın, O., & Henkel, R. (2018) · OncoTargets and Therapy · doi:10.2147/ott.s158259 · Cited by 9
“26,37 These findings might indicate that aging may be a risk factor for bladder cancer.”
The influence of aging on the methylation status of brain‐derived neurotrophic factor gene in blood
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“in [31]).”
Histone Modification Changes During Aging
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Long-term exposure to traffic-related air pollution is associated with epigenetic age acceleration
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“11 The first-generation clocks were developed by Hannum and Horvath, and both were able to accurately predict an individual's actual age.”
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“Increased H4K20me3 and H3K4me3 and decreased H3K9me1 and H3K27me3 histone modification levels have been described as common age-associated epigenetic marks [108–110].”
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“As parents get older, environmental exposures may influence post-transcriptional histone modifications and methylation patterns [33].”
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Relationship of nutrigenomics and aging: Involvement of DNA methylation
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“stages [27].”
Novel Therapeutic Targets in Neuropsychiatric Disorders: The Neuroepigenome
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“[70] Fraga MF, Esteller M.”
BackgroundMoindrot, B., Bouvet, P., & Mongélard, F. (2012) · Sub-cellular biochemistry/Subcellular biochemistry · doi:10.1007/978-94-007-4525-4_16 · Cited by 11
“Similarly to what happens during tumorigenesis, DNA-methylation pattern changes in an age-related manner: aged cells exhibit lower DNA-methylation level except on some speci fi c genes exhibiting a local hypermethylation (reviewed in Fraga and Esteller 2007 ; Gonzalo 2010 ) .”
BackgroundBioinformatics for Diagnosis, Prognosis and Treatment of Complex Diseases
Shen, B. (2013) · Translational Bioinformatics · doi:10.1007/978-94-007-7975-4 · Cited by 8
Abudahab, S., Slattum, P. W., Price, E. T., & McClay, J. L. (2023) · Pharmacogenomics · doi:10.2217/pgs-2023-0199 · Cited by 11
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An epigenetic proxy of chronic inflammation outperforms serum levels as a biomarker of brain ageingPreprint
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iPSCs as a major opportunity to understand and cure age-related diseases
Lemey, C., Milhavet, O., & Lemaı̂tre, J.-M. (2015) · Biogerontology · doi:10.1007/s10522-015-9579-7 · Cited by 10
“Histone marks, such as H4K16 acetylation, and H4K20 and H3K4 trimethylation increase, while, H3K9 methylation and H3K27 trimethylation decrease during aging (Fraga and Esteller 2007; Shuo and Brunet 2013).”
Is Programmed Aging a Cause for Optimism?
Mitteldorf, J. (2015) · Current Aging Science · doi:10.2174/1874609808666150422112826 · Cited by 5
PTK2 rs7460 and rs7843014 Polymorphisms and Exceptional Longevity: A Functional Replication Study
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Epigenetic epidemiology in psychiatry: A translational neuroscience perspective
Pishva, E., Kenis, G., Lesch, K., Prickaerts, J., Steinbusch, H. W. M., van den Hove, D., van Os, J., & Rutten, B. P. F. (2012) · Translational Neuroscience · doi:10.2478/s13380-012-0024-y · Cited by 4
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“Increased histone H4K16 acetylation, H4K20 tri-methylation, or H3K4 tri-methylation, as well as decreased H3K9 methylation or H3K27 tri-methylation, constitute age-associated epigenetic marks [27, 38].”
BackgroundAssociation of blood cadmium levels with epigenetic age acceleration in U.S. adults aged > 50 years
Mi, P., Cao, X., Feng, H., & Wang, H. (2025) · Frontiers in Public Health · doi:10.3389/fpubh.2025.1504830 · Cited by 7
“Increasing evidence suggests that several manifestations of aging are epigenetic (5–7).”
The rosetta stone of successful ageing: does oral health have a role?
Poser, M., Sing, K. E. A., Ebert, T., Ziebolz, D., & Schmalz, G. (2023) · Biogerontology · doi:10.1007/s10522-023-10047-w · Cited by 7
“Epigenetic alterations are associated with ageing (Armanios and Blackburn 2013; Fraga and Esteller 2007) Histone modification and the resulting expression of certain genes has been linked to prolonged lifespan.”
BackgroundBasic Epigenetic Mechanisms of Aging
Strazhesko, I. D., Yesakova, A. P., Akopyan, A. A., & Tkacheva, O. N. (2023) · Advances in Gerontology · doi:10.1134/s2079057024600241
“DNA Methylation The degree of DNA methylation, including both hypo-and hypermethylation of DNA, undergoes changes as the body grows older [6].”
Genome-Wide Integrative Transcriptional Profiling Identifies Age-Associated Signatures in Dogs
Kim, H. S., Jang, S., & Kim, J. (2023) · Genes · doi:10.3390/genes14061131 · Cited by 8
“Methylation is thought to hinder the plasticity of cell differ ntiation mechanisms, a d likely contributes to the development of tumors [74].”
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“…including metabolites, blood cell count and other routine lab tests (Earls et al., 2019; Momoshina, Kochetov et al. 2018), DNA methylation (Fraga & Esteller, 2007; Horvath & Raj 2018; Bell et al. 2019), gene expression in tissue (Momoshina, Volosnikova et al. 2018) or blood (Harries et…”
BackgroundThe concept of ageing in evolutionary algorithms: Discussion and inspirations for human ageing
Dimopoulos, C., Papageorgis, P., Boustras, G., & Efstathiades, C. (2017) · Mechanisms of Ageing and Development · doi:10.1016/j.mad.2017.02.002 · Cited by 6
Park, C. S., Valomon, A., & Welzl, H. (2015) · PLoS ONE · doi:10.1371/journal.pone.0130891 · Cited by 5
Genetic and epigenetic markers of gliomas
Semenova, E., & Filatov, M. V. (2013) · Cell and Tissue Biology · doi:10.1134/s1990519x13040123 · Cited by 6
“Moreover, it has been sug gested that disturbed epigenetic mechanisms is the main defect of gliomagenesis (Nagarajan and Cos tello, 2009).”
BackgroundCardelli, M., & Marchegiani, F. (2013) · Current Pharmaceutical Design · doi:10.2174/1381612811319090021 · Cited by 7
Epigenetics and Lifestyle: The Impact of Stress, Diet, and Social Habits on Tissue Homeostasis
Pérez, R. F., Santamarina‐Ojeda, P., Fernández, A. F., & Fraga, M. F. (2019) · Elsevier eBooks · doi:10.1016/b978-0-12-814879-2.00020-0 · Cited by 3
Self-citationComputational Methods for Developing Novel Antiaging Interventions
Chand, A., Chettiyankandy, P., Moharana, M., Sahu, S. N., Pradhan, S. K., Pattanayak, S. K., Mahapatra, S. P., Bissoyi, A., Singh, A. K., & Chowdhuri, S. (2018) · Springer eBooks · doi:10.1007/978-981-13-1699-9_12 · Cited by 9
Small Changes, Big Effects: Chromatin Goes Aging
Lazarus, A., Banerjee, K. K., & Kolthur‐Seetharam, U. (2012) · Sub-cellular biochemistry/Subcellular biochemistry · doi:10.1007/978-94-007-4525-4_8 · Cited by 6
Chapter 25 – Aging Epigenetics
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Dragoumani, K., Kletsas, D., Chrousos, G. P., Vlachakis, D., & Balatsos, N. A. A. (2025) · Genes · doi:10.3390/genes16070796 · Cited by 5
Quantitative sensory testing in elderly: longitudinal study
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Epigenetic epidemiology of age-related diseases
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“…that is determined after fertilization and can be modified only by mutations, the epigenetic labels are quite dynamic and extremely sensitive to a number of stimuli, thus being modifiable throughout a lifetime (Fraga et al., 2005a, b, 2007; Fraga and Esteller, 2007; Bjornsson et al., 2008;).”
BackgroundGene Expression, Epigenetics and Ageing
Maniyadath, B., Shukla, N., & Kolthur‐Seetharam, U. (2018) · Sub-cellular biochemistry/Subcellular biochemistry · doi:10.1007/978-981-13-2835-0_16 · Cited by 6
Application of Theranostics to Measure and Treat Cell Heterogeneity in Cancer
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First Nations, Métis and Inuit Health and the Law: A Framework for the Future
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Nutrition, Epigenomics and the Development of Obesity
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From the lab to lifestyle: epigenetic clocks in personalized aging and health
Ibáñez-Cabellos, J. S., García‐Giménez, J. L., Escobar, J., Pallardó, F. V., & Mena-Mollá, S. (2026) · Biogerontology · doi:10.1007/s10522-026-10447-8 · Cited by 5
Dai, Q., Zhao, S., Li, J., Li, N., Wang, A., Gao, Z., & Fan, Y.-C. (2025) · Experimental Eye Research · doi:10.1016/j.exer.2025.110272 · Cited by 4
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“44,45 In a study conducted by Wan et al., genome-wide DNA methylation microarray analysis of POAG and normal human trabecular meshwork samples showed that localized accumulation of GDF7 protein (a member of the TGF-β super-family) promotes trabecular meshwork fibrosis, which in turn causes reduced…”
Downstream Assays for Variant Resolution
Shayota, B. J. (2023) · Pediatric Clinics of North America · doi:10.1016/j.pcl.2023.05.006 · Cited by 3
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Maldonato, B., Vergara, A. G., Yadav, J., Glass, S. M., Paragas, E. M., Li, D.-Y., Lazarus, P., McClay, J., Ning, B., Daly, A., et al. (2022) · Drug metabolism reviews (Softcover ed.) · doi:10.1080/03602532.2022.2101662 · Cited by 4
“However, more recently and particularly in the last decade, it has become apparent that sweeping changes occur to the epigenome through adulthood and into old age (Fraga and Esteller 2007; Horvath 2013; McClay et al. 2014; Benayoun et al. 2015).”
BackgroundA simple, rapid, interpretable, actionable and implementable digital PCR based mortality index
Philibert, R. A., Long, J. D., Mills, J. A., Beach, S. R. H., Gibbons, F. X., Gerrard, M., Simons, R., Pinho, P., Ingle, D., Dawes, K., et al. (2020) · Epigenetics · doi:10.1080/15592294.2020.1841874 · Cited by 4
“Beginning with the work of Fraga and Esteller in 2007, and Bocklandt and associates in 2011, a number of investigators have attempted to use epigenetic approaches to assess age or risk for mortality [3,4].”
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“This instability is referred to as ‘aging epigenetics’, and associations between age and DNA modifications other than sequence mutations have been investigated (Fraga and Esteller 2007).”
BackgroundCollin, L., McCullough, L. E., Conway, K., White, A. J., Xu, X., Cho, Y., Shantakumar, S., Teitelbaum, S., Neugut, A., Santella, R., et al. (2019) · PLoS ONE · doi:10.1371/journal.pone.0210884 · Cited by 4
“The divergence of the epigenome as a function of age due to stochastic changes in methylation (a phenomena termed “epigenetic drift”[41, 42]) may contribute to tumorigenic transformation [42] including chromosomal instability, mutations, genetic recombination, large deletions, or translocations [43].”
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Inflammation in Aging and Age-related Diseases
Reale, M. (2014) · Journal of Gerontology & Geriatric Research · doi:10.4172/2167-7182.1000e126 · Cited by 4
“During aging, the DNA methylation pattern can change, and many studies have characterized the genes or genomic regions that either get hypermethylated or hypomethylated with age [13,14].”
BackgroundJiang, L.-J. (2014) · Journal of the History of Biology · doi:10.1007/s10739-014-9382-3 · Cited by 4
Aging: Reading, Reasoning, and Resolving Using Drosophila as a Model System
Nisha, N., Raj, K., Pragati, Tandon, S., Chanu, S. I., & Sarkar, S. (2020) · Springer eBooks · doi:10.1007/978-981-32-9005-1_14 · Cited by 3
Bibikova, M. V. (2015) · Elsevier eBooks · doi:10.1016/b978-0-12-800140-0.00002-9 · Cited by 6
Chromosomal Position Effect and Aging
Gilson, É., & Magdinier, F. (2009) · Springer eBooks · doi:10.1007/978-1-4419-0639-7_9 · Cited by 4
Milano, M., Cinaglia, P., Guzzi, P., & Cannataro, M. (2025) · Comput. Biol. Medicine · doi:10.1016/j.compbiomed.2025.110765 · Cited by 3
Metadata
- Authors
- Fraga, M. F., & Esteller, M.
- Affiliations
- Spanish National Cancer Research Centre (ES)
- Corresponding author
- Esteller, Manel
- Venue
- Trends in Genetics
- Publisher
- Elsevier BV
- Published
- 2007-08
- Volume
- 23
- Issue
- 8
- Pages
- 413-418
- ISSN
- 0168-9525 (ISSN-L)
- OpenAlex
- W1990916340
- Cited by
- 690
- References
- 75
- Citations by year
- 2026: 11 · 2025: 23 · 2024: 19 · 2023: 31 · 2022: 29 · 2021: 30 · 2020: 49 · 2019: 52 · 2018: 43 · 2017: 30 · 2016: 32 · 2015: 46 · 2014: 43 · 2013: 48 · 2012: 47
- FWCI
- 3.14
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- Trends in Genetics (publishedVersion)
- PubMed (publishedVersion)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Epigenetics and DNA Methylation
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Cell Biology › Telomeres, Telomerase, and Senescence
- Keywords
- DNA methylation loss, promoter hypermethylation, tumor suppression genes, Hutchinson-Gilford progeria syndrome, Werner syndrome, lamin A/C, sirtuins, cell transformation, lifespan, carcinogenesis
- MeSH terms
- Animals, Histones, Humans, Models, Biological, Cellular Senescence, DNA Methylation, Gene Silencing, Epigenesis, Genetic
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