scholarly journals Aging and Caloric Restriction Modulate the DNA Methylation Profile of the Ribosomal RNA Locus in Human and Rat Liver

Nutrients ◽  
2020 ◽  
Vol 12 (2) ◽  
pp. 277 ◽  
Author(s):  
Noémie Gensous ◽  
Francesco Ravaioli ◽  
Chiara Pirazzini ◽  
Roberto Gramignoli ◽  
Ewa Ellis ◽  
...  

A growing amount of evidence suggests that the downregulation of protein synthesis is an adaptive response during physiological aging, which positively contributes to longevity and can be modulated by nutritional interventions like caloric restriction (CR). The expression of ribosomal RNA (rRNA) is one of the main determinants of translational rate, and epigenetic modifications finely contribute to its regulation. Previous reports suggest that hypermethylation of ribosomal DNA (rDNA) locus occurs with aging, although with some species- and tissue- specificity. In the present study, we experimentally measured DNA methylation of three regions (the promoter, the 5′ of the 18S and the 5′ of 28S sequences) in the rDNA locus in liver tissues from rats at two, four, 10, and 18 months. We confirm previous findings, showing age-related hypermethylation, and describe, for the first time, that this gain in methylation also occurs in human hepatocytes. Furthermore, we show that age-related hypermethylation is enhanced in livers of rat upon CR at two and 10 months, and that at two months a trend towards the reduction of rRNA expression occurs. Collectively, our results suggest that CR modulates age-related regulation of methylation at the rDNA locus, thus providing an epigenetic readout of the pro-longevity effects of CR.

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Jack Hearn ◽  
Fiona Plenderleith ◽  
Tom J. Little

Abstract Background Patterns of methylation influence lifespan, but methylation and lifespan may also depend on diet, or differ between genotypes. Prior to this study, interactions between diet and genotype have not been explored together to determine their influence on methylation. The invertebrate Daphnia magna is an excellent choice for testing the epigenetic response to the environment: parthenogenetic offspring are identical to their siblings (making for powerful genetic comparisons), they are relatively short lived and have well-characterised inter-strain life-history trait differences. We performed a survival analysis in response to caloric restriction and then undertook a 47-replicate experiment testing the DNA methylation response to ageing and caloric restriction of two strains of D. magna. Results Methylated cytosines (CpGs) were most prevalent in exons two to five of gene bodies. One strain exhibited a significantly increased lifespan in response to caloric restriction, but there was no effect of food-level CpG methylation status. Inter-strain differences dominated the methylation experiment with over 15,000 differently methylated CpGs. One gene, Me31b, was hypermethylated extensively in one strain and is a key regulator of embryonic expression. Sixty-one CpGs were differentially methylated between young and old individuals, including multiple CpGs within the histone H3 gene, which were hypermethylated in old individuals. Across all age-related CpGs, we identified a set that are highly correlated with chronological age. Conclusions Methylated cytosines are concentrated in early exons of gene sequences indicative of a directed, non-random, process despite the low overall DNA methylation percentage in this species. We identify no effect of caloric restriction on DNA methylation, contrary to our previous results, and established impacts of caloric restriction on phenotype and gene expression. We propose our approach here is more robust in invertebrates given genome-wide CpG distributions. For both strain and ageing, a single gene emerges as differentially methylated that for each factor could have widespread phenotypic effects. Our data showed the potential for an epigenetic clock at a subset of age positions, which is exciting but requires confirmation.


Epigenetics ◽  
2011 ◽  
Vol 6 (9) ◽  
pp. 1085-1094 ◽  
Author(s):  
David J. Martino ◽  
Meri K. Tulic ◽  
Lavinia Gordon ◽  
Megan Hodder ◽  
Tara R. Richman ◽  
...  

2021 ◽  
pp. 1-8
Author(s):  
Concetta Schiano ◽  
Maria D’Armiento ◽  
Monica Franzese ◽  
Rossana Castaldo ◽  
Gabriele Saccone ◽  
...  

Increasing evidence suggests that maternal cholesterol represents an important risk factor for atherosclerotic disease in offspring already during pregnancy, although the underlying mechanisms have not yet been elucidated. Eighteen human fetal aorta samples were collected from the spontaneously aborted fetuses of normal cholesterolemic and hypercholesterolemic mothers. Maternal total cholesterol levels were assessed during hospitalization. DNA methylation profiling of the whole <i>SREBF2</i> gene CpG island was performed (<i>p</i> value &#x3c;0.05). The Mann-Whitney U test was used for comparison between the 2 groups. For the first time, our study revealed that in fetal aortas obtained from hypercholesterolemic mothers, the <i>SREBF2</i> gene shows 4 significant differentially hypermethylated sites in the 5′UTR-CpG island. This finding indicates that more effective long-term primary cardiovascular prevention programs need to be designed for the offspring of mothers with hypercholesterolemia. Further studies should be conducted to clarify the epigenetic mechanisms underlying the association between early atherogenesis and maternal hypercholesterolemia during pregnancy.


2017 ◽  
Author(s):  
Niran Hadad ◽  
Archana Unnikrishnan ◽  
Jordan A. Jackson ◽  
Dustin R. Masser ◽  
Laura Otalora ◽  
...  

AbstractBrain aging is marked by cognitive decline and susceptibility to neurodegeneration. Caloric-restriction (CR) increases neurogenesis, improves memory function, and protects from age-associated neurological disorders. Epigenetic mechanisms, including DNA methylation, are vital to normal CNS cellular and memory functions, and are dysregulated with aging. The beneficial effects of CR have been proposed to work through epigenetic processes, but this is largely unexplored. We therefore tested whether life-long CR prevents age-related DNA methylation changes in the brain. Hippocampal DNA from young (3 months) and old (24 months) male mice fed ad libitum and 24 month old mice fed a 40% calorierestricted diet from 3 months of age were examined by genome-wide bisulfite sequencing to measure methylation with base-specificity. Over 27 million CG and CH (non-CG) sites were examined. Of the ~40,000 differentially methylated CGs (dmCGs) and ~80,000 CHs (dmCHs) with aging, >1/3 were prevented by CR and were found across genomic regulatory regions and gene pathways. CR also caused alterations to CG and CH methylation at sites not differentially methylated with aging, and these CR-specific changes demonstrated a different pattern of regulatory element and gene pathway enrichment than those affected by aging. CR-specific DNMT1 and TET3 promoter hypermethylation corresponded to reduced gene expression. These findings demonstrate that CR attenuates age-related CG and CH hippocampal methylation changes, in combination with CR-specific methylation that may also contribute to the neuroprotective effects of CR. The prevention of age-related methylation alterations is also consistent with the pro-longevity effects of CR working through an epigenetic mechanism.


2018 ◽  
Author(s):  
Jack Hearn ◽  
Marianne Pearson ◽  
Mark Blaxter ◽  
Philip Wilson ◽  
Tom J. Little

AbstractThe degradation of epigenetic control with age is associated with progressive diseases of ageing, including cancers, immunodeficiency and diabetes. Reduced caloric intake slows the effects of aging and age-related diseases, a process likely to be mediated by the impact of caloric restriction on epigenetic factors such as DNA methylation. We used whole genome bisulphite sequencing to study how DNA methylation patterns change with diet in a small invertebrate, the crustaceanDaphnia magna.Daphniashow the classic response of longer life under CR, and they reproduce clonally, which permits the study of epigenetic changes in the absence of genetic variation. Global CpG methylation was 0.7-0.9%, and there was no difference in overall methylation levels between normal and calorie restricted replicates. However, 453 regions were differentially methylated (DMRs) between the normally fed and calorie restricted (CR) replicates. Of these 61% were hypomethylated in the CR group, and 39% were hypermethylated in the CR group. Gene Ontogeny (GO) term enrichment of hyper and hypo-methylated genes showed significant over- and under-representation in three molecular function terms and four biological process GO terms. Notable among these were kinase and phosphorylation activity, which have a well-known functional link to cancers.


Blood ◽  
2010 ◽  
Vol 116 (21) ◽  
pp. 4796-4796
Author(s):  
Dong-Myung Shin ◽  
Wu Wan ◽  
Rui Liu ◽  
Janina Ratajczak ◽  
Andrzej Bartke ◽  
...  

Abstract Abstract 4796 We have previously demonstrated the presence of very small (smaller than erythrocytes) Oct-4+SSEA-1+Sca-1+Lin-CD45- VSELs in bone marrow (BM) and in several murine adult organs (Leukemia 2006;20:857 and Cytometry 2009;73:1116). These small cells i) have large nuclei that contain primitive open chromatin, ii) express Oct-4 gene (as confirmed by our recent promoter methylation and chromatin structure analysis studies), and iii) posses bivalent domain-marked promoter regions of homeodomain-containing developmental master transcription factors, such as Dlx-, Irx-, Lhx-, Pou-, Pax-, and Six-family proteins. Furthermore, the epigenetic changes in selected somatic-imprinted genes (e.g., Igf2-H19 and RasGrf1) involved in insulin-factor signaling (Igf-1, Igf-2, and Insulin) govern their quiescent state, thus preventing them from unleashing proliferation and spontaneous growth of teratomas (Leukemia 2009;23:2042). O other hand it is well known that i) Igf-1 signaling negatively regulates lifespan in worms, flies, and mammals (Cell 2005;120:449) and that ii) Igf-1 and insulin levels in blood are positively regulated by caloric uptake. Indeed, we found that the pool size and pluripotentiality of VSELs decreases during aging. Accordingly, in our studies performed on young (4-week-old) and old (2-year-old) mice we found that i) the number of VSELs and their pluripotentiality decreases with age, ii) VSELs from old mice show lower expression of Oct-4, Nanog, Sox2, Klf4, and cMyc, iii) the Oct-4 promoter becomes hypermethylated with age and has a closed chromatin structure, iv) VSELs from old mice show somatic methylation in both Igf2-H19 and Rasgrf1 loci, and v), as a result, VSELs from these mice have increased sensitivity to insulin/insulin factors signaling. This suggests that chronic insulin receptor/Igf-1 receptor signaling in VSELs may contribute to age-related depletion of these cells. To explain better the role of insulin signaling in VSELs, we measured by FACS the number of VSELs in murine Laron dwarfs, which exhibit chronic Igf-1 deficiency and, as a result, live 30–40% longer than their normal littermates. We report here, for the first time, that the number of VSELs in the BM of Igf-1–deficient Laron dwarfs is 3–4 fold higher and is maintained at a higher level during aging compared to normal wild type (wt) littermates. Molecular analysis studies will confirm whether or not the molecular signature of VSELs in aging Laron dwarfs is somehow protected from age-related changes (e.g., by the methylation status of the Oct-4 promoter and/or genomic imprinted genes). Based on our data, we postulate novel linkages between Igf-1 level, aging, and the stem cell compartment. According to our hypothesis, early in development a population of VSELs would be deposited in developing organs as a backup for tissue-committed stem cells and play a role in rejuvenation of tissues and organ regeneration after damage. These cells would be protected from uncontrolled proliferation and age-related depletion by changes in imprinted genes that regulate insulin signaling. We further hypothesize that in the adult body the pool of VSEL cells is regulated by the circulating Igf-1 level. An increase in Igf-1 level (e.g., resulting from a chronically high calorie diet) would accelerate an age-dependent decrease in VSELs and their potential to rejuvenate tissues. By contrast, a low Igf-1 level (e.g., as seen in Laron dwarf mutants or due to caloric restriction) would have a protective effect on the overall pool of these cells. Thus, we present for the first time a hypothesis that reconciles aging, longevity, Igf-1 signaling, and caloric uptake and negative effect of Igf-1 and high calorie uptake on number/function of pluripotent VSELs deposited in adult tissues. Disclosures: No relevant conflicts of interest to declare.


2020 ◽  
Vol 41 (Supplement_2) ◽  
Author(s):  
G Benincasa ◽  
C Schiano ◽  
T Infante ◽  
M Franzese ◽  
R Casale ◽  
...  

Abstract Aims Immune endothelial inflammation, underlie coronary heart disease (CHD) related phenotypes, could provide new insight into the pathobiology of the disease. We investigated DNA methylation level of the unique CpG island of HLA-G gene in CHD patients and evaluated the correlation with cardiac computed tomography angiography (CCTA) features. Methods Thirty-two patients that underwent CCTA for suspected CHD were enrolled for this study. Obstructive CHD group included fourteen patients, in which there was a stenosis greater than or equal to 50% in one or more of the major coronary arteries detected; whereas subjects with Calcium (Ca) Score=0, uninjured coronaries and with no obstructive CHD were considered as control subjects (Ctrls) (n=18). For both groups, DNA methylation profile of the whole 5'UTR-CpG island of HLA-G was measured. The plasma soluble HLA-G (sHLA-G) levels were detected in all subjects by specific ELISA assay. Statistical analysis was performed using R software. Results For the first time, our study reported that 1) a significant hypomethylation characterized three specific fragments (B, C and F) of the 5'UTR-CpG island (p=0.05) of HLA-G gene in CHD patients compared to Ctrl group; 2) hypomethylation level of one specific fragment positively correlated with coronary Ca score, a relevant parameter of CCTA (p&lt;0.05) between two groups. Conclusions Our results showed that reduced levels of circulating HLA-G molecules could derive from epigenetic marks inducing hypomethylation of specific regions into 5'UTR-CpG island of HLA-G gene in CHD patients with obstructive coronary stenosis vs non critical stenosis group. Funding Acknowledgement Type of funding source: Public grant(s) – National budget only. Main funding source(s): Italian Minister of Health


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