REVIEW Open Access
Epigenetic regulation of caloric restriction in
aging
Yuanyuan Li
1,3*
, Michael Daniel
1
and Trygve O Tollefsbol
1,2,3,4,5
Abstract
The molecular mechanisms of aging are the subject
of much research and have facilitated potential
interventions to delay aging and aging-related
degenerative diseases in humans. The aging process
is frequently affected by environmental factors, and
caloric restriction is by far the most effective and
established environmental manipulation for extending
lifespan in various animal models. However, the
precise mechanisms by which caloric restriction
affects lifespan are still not clear. Epigenetic
mechanisms have recently been recognized as major
contributors to nutrition-related longevity and aging
control. Two primary epigenetic codes, DNA
methylation and histone modification, are believed to
dynamically influence chromatin structure, resulting in
expression changes of relevant genes. In this review,
we assess the current advances in epigenetic
regulation in response to caloric restriction and how
this affects cellular senescence, aging and potential
extension of a healthy lifespan in humans. Enhanced
understanding of the important role of epigenetics in
the control of the aging process through caloric
restriction may lead to clinical advances in the
prevention and therapy of human aging-associated
diseases.
Keywords: caloric restriction, epigenetic, aging
Introduction
Aging and its direct consequences, such as degenerative
diseases and even death, are inevitable; however, scienti-
fic advances in understanding basic aging mechanisms
have made it much more feasible to postpone aging pro-
cesses and to increase the human lifespan using clinical
approaches. Current studies using model organisms
indicate that aging processes can be manipulated by
many interacting factors which include, but are not lim-
ited to, geneticnutritional and pharmacological interven-
tions [1-3]. Studies of monozygotic twins, who share the
same genotype and often present many phenotypic dif-
ferences [4-7], indicate that external environmental fac-
tors contribute to interindividual differences such as
susceptibility to disease and the potential to live longer.
Dietary control, as a major environmental factor, has a
profound effect on many aspects of health, including
aging, and caloric restriction (CR) is by far the most
effective environmental manipulation that can extend
maximum lifespan in many different species [8,9]. In
fact, the remarkable effect of CR on aging was first
defined in experimental animal models in which McCay
et al. [10] discovered that rats fed a calorie-restricted
diet lived longer than control rats fed a regular diet.
Since then, numerous research findings have revealed
effects of CR on lifespan interference among diverse,
but not all eukaryotes, including yeast, worms, flies, fish
and even mammals [11-13]. In most rodent CR studies,
the limitation of total calories derived from carbohy-
drates, fats or proteins to a level 25% to 60% below that
of control animals fed ad libitum, while containing all
essential nutrients [14-16], can result in a significant
lifespan extension in 50% of rodents [17-21]. In addition
to increasing lifespan in rodents, CR has also been
shown to delay a wide range of aging-associated dis-
eases, such as cancer, diabetes, atherosclerosis, cardio-
vascular diseases and neurodegenerative diseases in
higher mammals, such as nonhuman primates and
humans [13,22-24] (Table 1). The incidence of disease
increases with age and is a fundamental contributor to
mortality. Thus, CR may affect aging processes by favor-
ably influencing broad aspects of human health.
Numerous studies suggest that the effects of CR in the
prevention of the onset of many aging-related degenera-
tive diseases occur through various molecular mechan-
isms, including reduction of oxidative stress or
* Correspondence: lyy@uab.edu
1
Department of Biology, University of Alabama at Birmingham, 1300
University Boulevard, Birmingham, AL 35294, USA
Full list of author information is available at the end of the article
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© 2011 Li et al; licensee BioMed Central Ltd . This is an Open Access arti cle distributed under the terms of the Creative Commons
Attribution License (http://creative commons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in
any medium, pro vided the original work is properly cited.
regulation of metabolic pathways during the progression
of aging [14,25,26]. However, the precise mechanisms of
CR-induced longevity are not very well understood.
Recently, epigenetic mechanisms have received consider-
able attention due to the unique role of interactions
with multiple nutritional factors and the aging pro-
cesses. Epigenetic control is believed to dynamically reg-
ulate gene expression by mechanisms other than
changes in the DNA sequence. This primarily affects
two epigenetic codes: DNA methylation and histone
modification [27-29]. Recent evidence suggests that
DNA methylation status changes in specific gene loci
may play an essential role in CR-dependent aging post-
ponement and longevity [30,31]. More concrete evidence
has emerged, most notably the discovery of silent mat-
ing type information regulation 2 homolog 1 (Sirtuin 1),
a nicotinamide adenine dinucleotide (NAD
+
)-dependent
histone deacetylase (HDAC), since Sirtuin 1 activity has
been linked to the control of lifespan in response to CR
both in vivo and in vitro [32-36]. Although studies of
the characterization and function of epigenetic modifica-
tions in CR-associated longevity are just emerging, a
better understanding of this complex interaction pro-
vides promising clinical opportunities for the prevention
of human aging and degenerative diseases that often
accompany the aging process.
DNA methylation affects aging during caloric restriction
DNA methylation is one of the most important epige-
netic modifications. It provides a stable and heritable
component of epigenetic regulation. DNA methylation
primarily occurs on cytosine residues of CpG dinucleo-
tides, which are frequently clustered into CpG islands
at the regulatory sites of gene promoter regions. The
amount of DNA methylation in a gene control region
generally inversely correlates with gene activation
[37,38]. The methyl groups on CpG dinucleotides can
recruit multiple transcriptional complex proteins,
including methylation-sensitive transcription factors
and methyl-binding proteins that are often associated
with gene silencing [39]. Therefore, DNA methylation
plays an important role in the regulation of gene
expression, maintenance of DNA integrity and stability
in many biological processes, such as genomic imprint-
ing, normal development, cell proliferation and aging
[40-42]. The patterns of DNA methylation are dynami-
cally mediated by at least three independent DNA
methyltransferases (DNMTs): DNMT1, DNMT3a and
DNMT3b. DNMT1 performs a maintenance function
during cell division, while DNMT3a and DNMT3b act
as de novo methyltransferases after DNA replication by
adding a methyl moiety to the cytosine of CpG dinu-
cleotides that have not previously been methylated
[43-47].
During aging processes, there is a progressively
reduced capability for homeostasis and loss of chroma-
tin integrity, predominantly due to aberrant gene
expression [48]. DNA methylation regulation plays a
crucial role during aging processes. Age causes a dra-
matic change in the distribution of 5-methylcytosine
(the product of DNA methylation) across the genome.
This leads to a decrease in global DNA methylation
[49-54]. Although genome-wide levels of methylation
decrease with aging, the promoter regions of many spe-
cific genes tend to switch from unmethylated to methy-
lated status, resulting in gene silencing, which may
include promoters of several tumor- and/or aging-
related genes, such as RUNX3 and TIG1 [53,55] (Table
2). These findings suggest an essential role of aging-
associated DNA methylation changes in the regulation
of aging-related diseases such as cancer.
The evidence suggests that the biological effects of CR
are closely related to chromatin function [56]. In fact,
acting as an important environmental intervention, CR
is speculated to exert its aging-delaying effect through
its capacity to increase genomic stability. Reversal of
aberrant DNA methylation during aging is believed to
be the most effective mechanism for CR to maintain
Table 1 Summary of aging-related diseases affected by caloric restriction in experimental animal models and clinical
trials
a
Diseases Findings Rodents Nonhuman
primates
Humans References
Cancer CR prevents a broad range of cancer incidences, including breast and
gastrointestinal cancer.
Y Y Y/? [17,13,23]
Diabetes CR improves glucose homeostasis and prevents diabetes. Y Y Y [18,13,23,24]
Cardiovascular
diseases
CR lowers blood pressure and favorably alters lipid profile, resulting in
significantly reducing the risk of cardiovascular disease and related
complications.
Y Y Y [19,13,22-24]
Neurodegenerative
diseases
CR reduces aging-associated neuronal loss and neurodegenerative disorders
such as Parkinson’s disease and Alzheimer’s disease.
Y Y Y/? [20,13,23]
Immune
deficiencies
CR delays the onset of T-lymphocyte-dependent autoimmune diseases. Y Y/? Y/? [21]
a
CR, caloric restriction; Y, CR has effects on relevant physiological changes; Y/?, not resolved or not reported.
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chromatin function and subsequently influence aging
processes.
As discussed previously, two major changes in DNA
methylation occur during aging progression. These
changes involve globally decreased but locally increased
DNA methylation status. Interestingly, CR is likely to
recover these aging-induced aberrant DNA methylation
patterns, but by specific loci control rather than globally
[57] (Figure 1). Studies of the comparison of DNA
methylation levels in pancreatic acinar cells between
CR-fed rats and control rats fed ad libitum suggest that
CR increased the methylation level of proto-oncogenes
such as Ras [30] (Table 2). A hypermethylated gene pro-
moter will often be recognized by transcriptional repres-
sor complexes, leading to silencing the expression of
these oncogenes, which contributes to the effects of CR
on cancer prevention. Although the majority of CR
research has been based on experimental animal studies,
we have established an in vitro mammalian cellular sys-
tem to mimic CR-controlled longevity by the reduction
of glucose, the main caloric resource in cell culture
medium [31]. In our current studies of human cells,
DNA hypermethylation of an E2F-1 binding site was
found in the promoter of the p16
INK4a
gene, an impor-
tant tumor suppressor and aging-associated gene. This
DNA hypermethylation of the E2F-1 binding site blocks
access of E2F-1 (an active transcription factor of
p16
INK4a
)tothep16
INK4a
promoter, resulting in
p16
INK4a
downregulation, which contributes to CR-
induced lifespan extension (Table 2 and Figure 1). In
thisregard,thereisastrongtendencyfortheDNA
methylation pathway to predominately control key can-
cer-related genes during CR, suggesting a close connec-
tion between aging and cancer.
On the basis of the preceding discussion, we confirm
that DNMTs play a crucial role in maintaining or
rewriting DNA methylation profiles. Consistently,
DNMT1 activity is significantly elevated in response to
CR to correct the decreased methylation level during
aging [31]. Further studies have also indicated that CR-
caused Dnmt3a level changes in the mouse hippocam-
pus may benefit mouse brain function during aging [58].
Both DNMT1 and DNMT3b play a critical role in regu-
lating cellular senescence in human stem cells [59].
Therefore, it is highly possible that CR modulates DNA
methylation, depending on expression levels and/or
enzymatic activities of individual DNMTs (Figure 1).
Because of the critical roles of DNMTs in the control
of aging and aging-associated diseases such as cancer
and DNMT inhibitors such as azacitidine (5-azacytidine)
and decitabine (5-aza-2’-deoxycytidine) have been widely
used for cancer treatment in both experimental studies
and clinical trials [60] (Table 3). Moreover, some bioac-
tive food components with DNMT inhibition properties,
such as green tea polyphenols and soybean genistein,
have shown cancer prevention and inhibition activities
by reducing DNA hypermethylation of key cancer-caus-
ing genes [61-63] (Table 3). These are important and
encouraging findings that imply the potential translation
of these bioactive dietary compounds into intervention
targets and strategies for the prevention and treatment
of human cancer.
Since restricted caloric intake induces a series of
metabolic responses to nutrition deficiency, effective
regulation of metabolic processes to adapt to this
change could be another important mechanism underly-
ing the effect of CR on longevity. One approach to
interpreting CR in the regulation of metabolic pathways
Table 2 Selected genes regulated by epigenetic factors during caloric restriction
a
Genes Gene functions in aging Epigenetic regulation CR effects References
p16
INK4a
Tumor suppressor gene that inhibits cell cycle and
accumulates during aging
DNA methylation, histone acetylation
(mediated by SIRT1 and HDAC1) and histone
methylation
Downregulation [31,84]
p53 Tumor suppressor gene that induces cell cycle arrest,
apoptosis and senescence; increased p53 promotes aging
Histone acetylation (mediated by SIRT1) Downregulation [88-90]
H-ras Oncogene that accelerates aging DNA methylation Downregulation [30]
RUNX3 Transcription factor that plays important roles in
development; increases methylation with aging
DNA methylation Up regulation [53,55]
Foxo Forkhead transcription factors that control various biological
functions and involve SIRT1-related longevity
Histone acetylation (mediated by SIRT1) Downregulation [91,92]
Ku70 A component of the NHEJ pathway for DSB repair that
regulates apoptosis and DNA repair during aging
Histone acetylation (mediated by SIRT1) Downregulation [99,100]
PGC-1aRegulates mitochondrial function and glucose homeostasis
and interacts with SIRT1 to regulate glucose metabolism
during CR
Histone acetylation (mediated by SIRT1) Upregulation [34,83,93,94]
hTERT Tumor promoting gene; increased hTERT expression is
correlated with telomerase activation and aging delay
Histone acetylation (mediated by HDAC1)
and histone methylation
Upregulation [31]
a
CR, caloric restriction; hTERT, human telomerase reverse transcriptase; HDAC1, histone deacetylase 1; SIRT1, Sirtuin (silent mating type information regulation 2
homolog) 1; NHEJ, non-homologous end joining; DSB, DNA double-strand break.
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is through interventions to treat human obesity, which
has become an important public health issue in recent
years. Obesity is a common metabolic disorder charac-
terized by excessively accumulated body fat and is clo-
sely related to a series of human diseases, including
diabetes, hypertension, dyslipidemia, cardiovascular
complications and even cancer, which are recognized
causes of accelerated aging [64]. Therefore, obesity pre-
vention could be a key underlying factor in the anti-
aging effects of CR. Because of its substantial and pro-
mising effects in promoting weight loss, CR is widely
used in clinical weight control intervention [65]. Current
Figure 1 Caloric restriction regulates epigenetic pathways. Caloric restriction (CR) influences epigenetic processes via two primary
mechanisms: DNA methylation and histone modification. DNA methylation regulation during CR involves DNMT activation, resulting in silencing
the expression of target genes such as p16
INK4a
and Ras due to hypermethylation of these genes. CR-induced histone remodeling primarily
includes histone acetylation and methylation. Deacetylation effects due to activation of SIRT1 and HDAC1 by CR lead to expression changes of
key genes such as p53,Foxo,Ku70,PGC-1aand p16
INK4a
. Histone methylation also plays a role in the regulation of key gene expression, including
hTERT and p16
INK4a
. As a result, epigenetic regulation actively reverses aberrant gene expression during CR, which contributes to CR-associated
aging delay and lifespan extension.
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studies focusing on short-term CR interventions in
obese human subjects revealed that hypocaloric diets
cause DNA methylation changes in specific loci, such as
ATP10A,WT1 and TNF-a, which could be used as early
indicators of a response to the metabolic effects and as
predictors of outcomes in weight-loss programs [66-68].
Although further CR studies have identified a pool of
DNA methylation-controlled candidate genes that may
be closely correlated with metabolic pathways, wide-
spread methylation changes on numerous gene loci that
facilitate CR in reprogramming the DNA methylation
profile may also explain a powerful and universal effect
of CR in influencing different aspects of human health.
Thus, better understanding the functions of these DNA
methylation-sensitive genes may contribute not only to
optimizing personal weight-loss plans, but more impor-
tant, to developing a novel application in slowing down
of aging processes and the prevention of aging-related
diseases.
Surprisingly few studies have investigated genome-
wide alterations in DNA methylation profiles in CR-
induced longevity using in vivo or in vitro models. Thus,
the complete methylation-regulated pathways and target
genes that may be responsible for CR-induced longevity
remain unknown. Further investigations in this particu-
lar area show promising prospects in developing novel
clinical preventative or therapeutic approaches to aging-
related degenerative diseases.
Effects of histone remodeling in control of aging during
caloric restriction
Histone modifications affect the basic structure of the
chromatin unit, the nucleosome. The nucleosome con-
sists of 146 bp of DNA wrapped around an octamer of
histones (two copies of H2A, H2B, H3 and H4 mono-
mers) [69]. In most cases, histone remodeling occurs at
the N-terminal group of lysine (K) residues in histones
by diverse modification patterns such as acetylation,
methylation, ubiquitination and ADP ribosylation,
among which histone acetylation or deacetylation
changes are considered to be the most prevalent
mechanisms of histone modifications [27]. Histone mod-
ifications are associated with both gene activation and
gene repression. The combination of modifications
within histone tails directly changes nucleosome config-
uration and results in the status of chromatin switching
to either a compacted status (tight-close) or a relaxed
status (loose-open) [70]. Therefore, histone modifica-
tions determine the level of openness of chromatin and
thus the degree of gene activity within a certain DNA
region. For example, a deacetylated histone lysine resi-
due has the positive charge, which attracts the negatively
Table 3 Epigenetic clinical trials for aging-related degenerative diseases
a
Drugs Epigenetic
effect
Description Clinical trials References
Azacitidine DNMT inhibitors 5-azacytidine; a chemical analogue of cytidine
that affects DNA methylation as a false
substrate
Phases I, II and III: myelodysplastic syndromes
such as leukemia
[60]
Decitabine DNMT inhibitors 5-aza-2’-deoxycytidine, a chemical analogue of
cytidine that affects DNA methylation as a false
substrate
Phases I, II and III: myelodysplastic syndromes
such as leukemia, cervical, and non-small-cell
lung cancer
[60]
Depsipeptide HDAC inhibitors Cyclic tetrapeptide Phases I and II: hematological tumors such as
leukemia and lymphoma
[78,79]
Phenylbutyrate HDAC inhibitors Aliphatic acid Phases I and II: hematological tumors such as
leukemia and lymphoma and colorectal cancer
[78,79]
Valproic acid HDAC inhibitors Aliphatic acid Phase I: hematological tumors such as
leukemia and lymphoma
[78,79]
Suberoylanilide
hydroxamic
acid
HDAC inhibitors Hydroxamic acid Phases I and II: hematological tumors, such as
leukemia and lymphoma, solid tumors
[78,79]
Resveratrol SIRT1 activator A natural compound enriched in grapes and
red wine
Phase I and II: diabetes, obesity, Alzheimer’s
disease and cancers
[118,119]
Genistein Inhibitor of both
DNMTs and
HDACs
Active epigenetic diet found in soybean
products
Preclinical: diabetes and cancer [61,63,122,123]
EGCG Inhibitor of both
DNMTs and
HDACs
Active epigenetic dietary compound enriched
in green tea
Phase I: diabetes, cardiovascular disease and
cancer
[61,62,124,125]
Sulforaphane HDAC inhibitor Active epigenetic dietary compound enriched
in broccoli sprouts
Preclinical [80,121]
a
DNMT, DNA methyltransferase; HDAC, histone deacetylase; SIRT1, Sirtuin (silent mating type information regulation 2 homolog) 1; EGCG, epigallocatechin gallate.
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charged DNA strand producing a compact chromatin
state that is associated with transcriptional repression.
By contrast, the modification of histone acetylation
removes the positive charge and results in an open
chromatin structure, which leads to active transcription
(Figure 2).
Histone acetylation and deacetylation
Histone acetylation and deacetylation processes are cata-
lyzed by specific enzymes called histone acetyltrans-
ferases (HATs) and HDACs, respectively [71,72] (Figure
2). At least four classes of the HDAC family have been
identified:classIHDACs(HDAC1,HDAC2,HDAC3
and HDAC8) are most closely related to the yeast Rpd3
HDAC; class II HDACs (HDAC4, HDAC5, HDAC6,
HDAC7, HDAC9 and HDAC10) share homology
domains with the yeast enzyme Hda1; class III HDACs
including Sirtuins 1, 2, 3, 4, 5, 6 and 7 are homologues
of the yeast Sir2; and HDAC11 is the only member of
class IV HDACs and closely related to the class I
HDACs.
In addition to their deacetylation function, HDACs are
believed to participate in the regulation of many cellular
functions and gene expression through interactions with
hundreds of different transcription factors [71,73]. It has
also been reported that HDAC activity is increased dur-
ing CR, suggesting that global deacetylation may be a
protective mechanism against nutrition stress and may
influence the aging processes [31].
We have found that altered binding enrichment of
HDAC1, such as on the promoter regions of the
p16
INK4a
and human telomerase reverse transcriptase
(hTERT) genes, the latter of which is a key determinant
of telomerase activity closely associated with aging regu-
lation, leads to beneficial expression changes of these
two genes and contributes to longevity under CR condi-
tions (Figure 1 and Table 2) [31,74,75]. Therefore,
remarkable roles of the HDAC family in regulation of
aging during CR highlight the potential application of
related epigenetic drugs or clinical strategies in aging
and aging-related diseases.
Figure 2 Histone modification pathways. Histone acetylation is mediated by HAT and deacetylation is catalyzed by the HDAC family. The
upper row represents histone acetylation/deacetylation processes mediated by classic HDAC family members, including classes I, II and IV.
Histone acetylation causes an open chromatin structure, leading to active transcription, whereas histone deacetylation is always associated with
transcriptional repression. The middle row indicates a class III HDAC family member, SIRT1, which deacetylates both histone and protein
substrates, resulting in gene silencing in most cases. The lower row represents histone methylation as another important histone modification.
Histone methylation is mediated by HMT, and either gene activation or gene repression by histone methylation is dependent upon the
particular lysine residue that is modified. HAT, histone acetyltransferase; HDAC, histone deacetylase; HMT, histone methyltransferase. SIRT1, Sirtuin
(silent mating type information regulation 2 homolog) 1.
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At this point, HDAC inhibitors have emerged as an
exciting new class of potential anticancer agents despite
little evidence pertaining to other aging-related diseases.
HDAC inhibition causes acetylation of nuclear histones,
leading to transcriptional activation of several key
tumor-related genes, such as the cyclin-dependent
kinase inhibitor p21
WAF1/CIP1
,p53,GATA-1 and estrogen
receptor-a, which contribute to inhibiting cancer prolif-
eration and inducing differentiation both in vitro and in
vivo [76,77]. Several HDAC inhibitors with impressive
antitumor activity and relatively low toxicity, such as
depsipeptide, phenylbutyrate, valproic acid and suberoy-
lanilide hydroxamic acid, are currently undergoing
phases I and II clinical trials (Table 3) [78,79]. These
structurally diverse molecules with properties of HDAC
inhibition support a model in which HDACs are the cri-
tical cellular targets causing chromatin instability and
tumorigenesis. Bioactive dietary ingredients, such as
green tea polyphenols, broccoli sprouts and soybean
genistein, that have natural HDAC inhibition properties
are also considered as potential cancer chemoprevention
compounds which are being studied in preclinical trials
(Table 3) [62,63,80]. This may apply to aging-associated
degenerative diseases that involve similar abnormalities
such as tumorigenesis, and further studies are urgently
needed in this area.
Sirtuin 1 and its substrates
Several HDAC families have been identified, including
class III NAD
+
-dependent HDACs such as Sirtuin 1. Sir-
tuin 1 (SIRT1) in mammals, and its orthologs in other
species (Sirtuin 2 in yeast), deserves special attention
due to its fundamental impact on aging regulation and
CR-related lifespan extension [32-36]. The unusual
enzymatic activity of SIRT1, which largely depends on
NAD/NADH ratio, a key indicator for oxygen consump-
tion, respiratory chain and metabolic rate, suggests that
this protein is tightly connected to the metabolic state
of cells.
The promising effect of SIRT1 in mediating CR and
lifespan extension is supported by a diverse range of
animal models, human subjects and even in vitro CR
cellular systems [31-33,35,36,81-85]. Activation of SIRT1
is frequently seen in different animal organs affected by
CR, whereas inactivation of SIRT1 may lead to abolition
of lifespan extension, suggesting a pivotal role of SIRT1
in lifespan regulation during CR. SIRT1 was initially dis-
covered for its activation in response to CR and its role
in the prolongation of lifespan in yeast [33]. This theory
is solidified by findings in Drosophila,inwhichCR
induces Sir2 activation and subsequent lifespan exten-
sion in wild-type Drosophila rather than in Sir2 mutants
[33]. Further, either the Sir2 activator resveratrol or the
overexpression of Sir2 leads to lifespan extension, and
this longevity is not further induced by CR, suggesting
that Sir2 is an important modulator in the regulation of
aging processes.
In mammals, SIRT1-null mice do not survive longer,
andmostofthemdieduringthepostnatalperiod
[86,87]. They exhibit growth retardation, multiple devel-
opmental defects and sterility, suggesting an important
role of SIRT1 in early development. The role of endo-
genous SIRT1 in mammalian metabolic regulation has
focused mainly on rodents in the context of fasting
under the condition in which SIRT1 overexpression or
its activity is upregulated [33-36]. Extensive studies have
shown that CR induces SIRT1 expression in several tis-
sues of mice or rats [33]. The potential mechanisms by
which SIRT1 mediates CR-induced metabolic alterations
and subsequent aging retardation primarily involve two
aspects: first, SIRT1 activation increases stress resistance
by negative regulation of proapoptotic factors such as
p53 and Foxo (Table 2) [88-92]; second, SIRT1 causes a
series of endocrine responses, including inhibition of
adipogenesis and insulin secretion in pancreatic bcells
by regulation of key metabolism-associated genes such
as peroxisome proliferator-activated receptor gcoactiva-
tor 1a(PGC-1a) (Table 2) [93,94], which facilitates
stress resistance and longevity (Figure 1).
In yeast, Sir2-mediated deacetylation of histones H3
and H4 and concomitant silencing of protein recruit-
ment occurs specifically in heterochromatic regions
located at extrachromosomal ribosomal DNA, telomeres
and silenced mating-type loci, which benefit lifespan
extension in yeast [33,57,83,95]. Human SIRT1 estab-
lishes and maintains chromatin silencing by preferential
deacetylation at histone H4 lysine 16 (H4K16), but it
also has been shown to deacetylate the loci of histone
H3 lysine 9 (H3K9) in vitro [96] (Figure 2). Further,
SIRT1 affects the levels of histone methylation by deace-
tylation of SUV39H1, a mammalian histone methyl-
transferase suppressor, leading to increased levels of the
trimethylated H3K9 (H3K9Me3) modification (a chro-
matin repressor) [97,98].
Although classed as a HDAC, SIRT1 deacetylates a
broad range of substrates, including many nonhistone
substrates [33,83] (Table 2 and Figure 2). These poten-
tial substrates may include several key transcription fac-
tors and regulatory proteins that are involved in
multiple pathways linked to physiological and metabolic
processes that contribute to lifespan extension by CR
(Table 2 and Figure 1). CR is known to exert its effect
by inhibition of apoptosis, which is one of the most
important regulatory mechanisms [14,25,26]. In this
regard, p53 is notable due to its important role in the
regulation of cell death and apoptosis. Downregulated
p53 by SIRT1 deacetylation may affect lifespan by nega-
tively regulating cellular apoptosis and replicative senes-
cence processes [88-90]. Another important protein that
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influences apoptosis is Foxo. Foxo protein can be
directly deacetylated by SIRT1 at lysine residues and its
expression is reduced, thereby repressing Foxo-mediated
apoptosis [91,92]. In addition, the DNA repair protein,
Ku70, can become deacetylated by SIRT1, allowing it to
inactivate the proapoptotic factor Bax, resulting in apop-
tosis inhibition [99,100].
SIRT1 can also regulate the expression of genes that
are involved in metabolic pathways. PGC-1arepresents
the best example of these proteins in CR studies (Table
2). PGC-1ais a key regulator of gluconeogenesis and
fatty acid oxidation [93,94]. It is activated by SIRT1-
mediated deacetylation, which increases its ability to
coactivate HNF4a, a transcription factor that promotes
the expression of gluconeogenic genes and represses
genes involved in glycolysis [34,83]. Therefore, SIRT1-
induced changes in PGC-1aexpression, and its down-
stream metabolic pathways provide a link between
SIRT1 activation and the stimulation and response of
metabolic systems under CR conditions.
Another key gene that can be epigenetically regulated
by SIRT1 is p16
INK4a
, which is a cyclin-dependent kinase
inhibitor linked to cellular senescence regulation [101]
(Table 2). This gene was originally identified as an
importanttumorsuppressorgeneinthatitnegatively
regulates the cell cycle and inhibits tumor growth
[102,103]. Current studies show that p16
INK4a
is signifi-
cantly accumulated during the aging processes, indicat-
ing that p16
INK4a
can serve as a robust aging biomarker
[104,105]. Our recent studies using human cells show
that CR-activated SIRT1 can directly bind to the
p16
INK4a
promoter and decrease its expression through
a deacetylation effect, which contributes to delaying the
aging process and to lifespan extension [84]. Therefore,
SIRT1, acting as a nutrition sensor, decodes the nutri-
tion flux to ensure homeostasis or even a beneficial
state such as increased longevity by reorganizing the
global chromatin structure and dynamically epigeneti-
cally regulating specific genes that may involve apoptosis
regulation, metabolic control and cellular senescence.
Besides its pronounced roles in regulating epigenetic
processes, SIRT1 has been well demonstrated to regulate
genes and interact with signaling other than epigenetic
control during CR, suggesting that SIRT1 may play an
important role in multiaspect cross-talk between epige-
netic and genetic pathways.
Histone methylation
Besides histone acetylation, histone methylation is
another important histone modification that regulates
gene expression [72] (Figure 2). In contrast to histone
acetylation, which is always associated with open chro-
matin status and subsequent gene activation, differen-
tially methylated forms of histones show unique
association patterns with specific proteins that recognize
these markers and thus lead to gene silencing or activat-
ing effects. Lysine residues on histones can be mono-,
di- or trimethylated, and either activation or repression
is dependent upon the particular lysine residue that is
modified [106,107]. Our current studies have shown
that histone methylation modifications such as di- or
trimethylated histone H3 at lysine residue 3 or 4 can
also regulate expression changes of key aging-related
genes, including p16
INK4a
and hTERT, thereby contri-
buting to CR-induced lifespan extension of human cells
(Figure 1 and Table 2) [31,84]. In other studies,
researchers have reported that p16
INK4a
expression can
be regulated by H3K27 trimethylation, which serves as a
recruitment signal for BMI1-containing polycomb-
repressive complexes such as PRC1 during cellular
senescence [108-110]. Therefore, the status of specific
histone methylation can also serve as a transcription
modulator by interacting with different transcription
factors and regulate aging processes under CR
conditions.
Potential epigenetic treatments for aging-related diseases
The promising impact of the chromatin regulators on
aging interference provides an excellent opportunity to
prevent for human aging-related diseases by applying
potential epigenetic drugs. An example of this is resver-
atrol, a natural compound found in grapes and red wine
which has been demonstrated to extend lifespan in Sac-
charomyces cerevisiae,Caenorhabditis elegans and Dro-
sophila through remodeling chromatin structure via
mediation of SIRT1 activity [111-113]. It has been
reported that resveratrol can activate SIRT1 mechanisms
and mimic SIRT1-induced CR cascades, leading to
increased longevity [114]. In addition to its effect on
longevity, this compound is known to positively influ-
ence metabolism and reduce fat and glucose levels,
resulting in increasing glucose tolerance and activation
of several signaling pathways that are relevant to antis-
tress, antioxidation and increased mitochondrial biogen-
esis [115,116]. These effects were illustrated by a
current finding showing that resveratrol opposes the
effects of a high-fat diet in mice [117]. Due to the toxi-
city of the high-fat diet, control animals in this study
had early mortality, whereas resveratrol improved the
health and survival rate of these mice, suggesting the
important role of resveratrol in the aging process. Clini-
cally, a total of 31 human studies involving resveratrol
have been reported in the US national database http://
clinicaltrials.gov/. These studies aimed at investigating
the potential role of resveratrol in diabetes, obesity, Alz-
heimer’s disease and cancer (Table 3). These studies
have revealed promising and universal effects of resvera-
trol by favorably altering cell proliferation, increasing
cellular detoxification, protecting DNA damage,
Li et al.BMC Medicine 2011, 9:98
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Page 8 of 12
modulating metabolic processes and inhibiting tumori-
genesis, which significantly improve human health and
lead to increased human lifespan [118,119].
Epigenetic therapy has shown powerful clinical poten-
tial in delaying aging and preventing aging-related dis-
eases, especially cancer. As we have discussed
previously, DNMT inhibitors, inlcuding azacitidine and
decitabine, as well as HDAC inhibitors, such as depsi-
peptide, phenylbutyrate, valproic acid and suberoylani-
lide hydroxamic acid, have been widely used for cancer
treatment in both experimental studies and clinical trials
(Table 3). Studies have also indicated that resveratrol is
a potent cancer chemopreventative agent. These findings
are extremely encouraging, and future studies focusing
on development of novel epigenetic drugs are urgently
needed to develop effective clinical strategies to treat
human aging-related diseases [120].
“Epigenetic diets”that mimic the effects of caloric
restriction on lifespan
The significant epigenetic impact of CR on delaying
aging and preventing aging-related diseases has moti-
vated efforts to identify natural or synthetic compounds
that mimic the effects of CR. A broad range of diets
have been identified that mediate epigenetic processes,
the so called “epigenetic diets,”providing potential to
reduce aging-associated disease incidence and possibly
extending the quality and length of the human lifespan
by simple consumption of such diets or extracted bioac-
tive dietary compounds [121] (Table 3). As described
previously, resveratrol represents an excellent example
of an “epigenetic diet”and acts as a SIRT1 mimic that
leads to increased longevity in vivo and in vitro
[111-119]. Other important epigenetic diets have
recently been identified, such as green tea, broccoli
sprouts and soybeans, and the bioactive compounds
extracted from these diets have received extensive atten-
tion due to their profound effects on cancer prevention
by altering the aberrant epigenetic profile in cancer cells
[62,63,80,122-125]. In particular, long-term consumption
of these epigenetic diets is highly associated with a low
incidence of various aging-related degenerative diseases
such as cancer and cardiovascular disease, suggesting
that these bioactive diets may affect aging processes by
altering chromatin profiles that also occur in CR [2].
For instance, global gene expression profiling can be
used to identify useful compounds correlated with biolo-
gical age. Dhahbi et al. [126] developed gene expression
profiling methods to discover potential pharmaceuticals
capable of mimicking the effects of CR, which may open
a new avenue in the discovery of promising candidates
that mimic CR and delay aging.
Conclusions
Epigenetically mediated changes in gene expression have
become a major molecular mechanism linking CR with
its potential for improving cell function and health
throughout the life course, leading to delaying the aging
processes and extending longevity. Understanding the
epigenetic mechanisms that influence the nature of
aging by CR might lead to discoveries of new clinical
strategies for controlling longevity in humans. As dis-
cussed in this review, two primary epigenetic codes,
DNA methylation and histone modification, play impor-
tant roles in regulating chromatin structure and expres-
sion of key genes to elicit the global response to CR
(Figure 1). The readily reversible feature of epigenetic
alterations provides great potential for the use of specific
interventions aimed at reversing epigenetic changes dur-
ing aging, which may have a significant impact on delay-
ing aging and preventing human aging-associated
diseases. Although our knowledge of the role of epige-
netic mechanisms in CR and its related health impact is
relatively limited at present, further studies will likely
provide more precise interpretation of this complicated
interaction, thereby facilitating the discovery of novel
approaches linking dietary or pharmaceutical interven-
tions to human longevity. We have learned of the pro-
found effects of SIRT1 and its mimics, such as
resveratrol, in influencing aging processes, and this
exciting example implies that the key to improving the
quality of human life, especially for senior citizens, is in
the not too distant future.
Abbreviations
bp: base pair; CR: caloric restriction; DNMT: DNA methyltransferase; HDAC:
histone deacetylase; HAT: histone acetyltransferase; hTERT: human telomerase
reverse transcriptase.
Acknowledgements
This work was supported by grants from the American Institute for Cancer
Research (AICR), the National Cancer Institute (CA 129415 and CA 13148-31),
Susan G Komen for the Cure and the American Cancer Society Award (IRG-
60-001-47). YL was supported by a Postdoctoral Award (PDA) sponsored by
AICR and American Cancer Society Award.
Author details
1
Department of Biology, University of Alabama at Birmingham, 1300
University Boulevard, Birmingham, AL 35294, USA.
2
Center for Aging,
University of Alabama at Birmingham, 1530 3rdAvenue South Birmingham,
AL 35294, USA.
3
Comprehensive Cancer Center, University of Alabama at
Birmingham, Birmingham, 1802 6th Avenue South, AL 35294, USA.
4
Nutrition
& Obesity Research Center, University of Alabama at Birmingham, 1675
University Boulevard, Birmingham, AL 35294, USA.
5
Diabetes Comprehensive
Center, University of Alabama at Birmingham, 1825 University Boulevard,
Birmingham, AL 35294, USA.
Authors’contributions
YL wrote the first draft of the manuscript. All other authors contributed to
the development of the manuscript. All authors read and approved the final
manuscript.
Li et al.BMC Medicine 2011, 9:98
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Page 9 of 12
Competing interests
The authors declare that they have no competing interests.
Received: 6 May 2011 Accepted: 25 August 2011
Published: 25 August 2011
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Cite this article as: Li et al.: Epigenetic regulation of caloric restriction in
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