Epigenetics and well-being: optimal adaptation to the environment

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Chapter 13
Epigenetics and well-being: optimal
adaptation to the environment
Moshe Szyf and Michael Pluess
Epigenetics and well-being: optimal adaptation
to the environment: an introduction
Whether PWB is predetermined by our genes—the legacy of inherited sequence differences
between humans—or whether it is past experiences and physical and social environments that
impact on our long-term well-being represents a fundamental question (see Chapter 15). The
genes that we inherit from our parents certainly define to a large extent our physical and mental
characteristics. However, the naive belief that all differences between humans could be explained
by differences in the DNA sequence is inconsistent with our current understanding of gene func-
tion (see Chapter 2). Genes are “programmed” (i.e., switched on or off) by epigenetic mechanisms
and this programming shapes the way genes function in different organs of the body at different
times in life and in different contexts. The main focus of the emerging field of epigenetics so far
has been on unraveling how aberrant epigenetic programming of genes could lead to disease.
This has been well developed in the field of cancer research and more recently became the focus
of metabolic and neurological/psychiatric disease research. As a consequence, epigenetics is start-
ing to impact both diagnosis and treatment of cancer and it is anticipated that this will spread to
other medical disciplines. However, there has been very little discussion or research regarding the
potential role of epigenetic mechanisms in relation to PWB. In this chapter we will review basic
epigenetic mechanisms and point to the potential impact of these mechanisms on PWB. Given
the rather biological focus of this chapter, we will define well-being as optimal adaptation to the
environment, associated with good physical and psychological health, reflecting optimal function-
ing within a specific environment and not just the absence of maladaptive development.
The first challenge to genetic determinism or the idea that genotype exclusively defines pheno-
type came from the field of embryology. Multicellular organisms like ourselves have essentially
the same DNA in all our tissues and organs, but it is clear that different genes are expressed in
different organs, creating the startling phenotypic diversity seen in complex organisms. In add-
ition to tissue specific gene expression of genetically identical cells, the roles of these different
cells in the body are context dependent. For example, particular cells in the immune system like
T-cells must express proteins on their surface for the recognition of specific foreign proteins or
cells. However, cells that recognize particular invaders need to be activated only when the body is
challenged. Consequently, each of these functions requires the expression of specific genes (e.g.,
those encoding the required proteins that distinguish the cells as T-cells) but also regulation of
such gene expression dependent on particular contexts and particular times. How could one DNA
template define such a diversity of gene expression? Almost seven decades ago this exact question
was raised by Waddington (1959), who coined the term epigenetics as a synthesis of two concepts
AQ1
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in embryology: genetics and epigenesis. Although no concrete mechanisms were proposed back
then, the idea was that DNA undergoes transformations during embryonal development that do
not involve changes in the genetic structure (i.e., DNA sequence), but instead define different tra-
jectories for DNA in differently developing tissues and organs. In the last half-century, research in
biochemistry has focused on investigating such epigenetic processes involved in marking where
and when genes are to be expressed during development.
One fundamental question has been whether epigenetic programming of genes is defined
exclusively by innate evolutionary conserved factors—including genetic make-up—or whether
these processes could be modulated in response to external environmental influences. A related
question is whether epigenetic processes are limited to early developmental periods or whether
they are amenable to changes throughout life. Although the main focus in the epigenetic literature
has been on aberration of epigenetic marks in human disease, this chapter argues that the same
processes play an important role regarding the development of well-being by adapting genome
function to external environments and experiences. Importantly, while a misfit between epigen-
etic adaptation and environmental conditions is likely to result in maladaptation and potential
pathology, it is conceivable that a good fit between adaptive epigenetic programming and the
environment will result in optimal functioning, including PWB.
Epigenetic mechanisms
Genes contain the information required to make RNA, which in turn contains the information
to make proteins (see Chapter 2). Proteins are required for both building anatomical structures
as well as performing physiological functions throughout the life-course. Epigenetic mechanisms,
on the other hand, determine when and where the genes will produce mRNA which encode the
proteins. Epigenetic mechanisms include several biochemical processes that act at different levels
(this chapter will cover mainly chromatin modification and DNA methylation, see Figure 13.1).
The DNA molecule is packaged in chromatin, which allows the large DNA molecule to be con-
tained in the small nuclear space. The basic building block of chromatin is the nucleosome, which
is composed of eight histone proteins (Finch et al., 1977); 140 base pairs of DNA are wrapped
around a single unit of a nucleosome, which is then packaged in the nucleus in higher-order
structures. Chromatin states define the accessibility of different genes to a machinery of proteins
that activate genes to transcribe RNA as well as other proteins that maintain genome integrity,
repair defective DNA, and trigger DNA synthesis. Importantly, chemical modifications of the
tails of these histone proteins determine whether the DNA will be accessible for transcription
(Strahl and Allis, 2000). In addition to chemical histone modification, there are other important
epigenetic modifications such as noncoding RNA (Flanagan and Wild, 2007; Mohammad et al.,
2012). Noncoding RNA has important regulatory functions, but in contrast to mRNA it does not
get translated (i.e., coded) into proteins (see Chapter 2). Finally, the spatial positioning of nucleo-
somes on DNA also plays a critical role in defining where and when genes are transcribed.
The most proximal epigenetic modification is the chemical coating of the DNA molecule itself
by a small chemical group, a methyl moiety in a process termed DNA methylation (Hotchkiss,
1948). Recent studies suggest that the methyl coating could be further modified chemically by
hydroxylation (Kriaucionis and Heintz, 2009) and carboxylation (Ito et al., 2011). Thus, the DNA
chemical entity itself contains two layers of information: genetic and epigenetic. By having this
dual identity, the genetic identity, which is common in all tissues, and the DNA methylation pat-
tern, which is cell-type specific (Razin and Szyf, 1984), the DNA can exhibit genetic uniformity
concurrent with phenotypic diversity.
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Figure 13.1 Graphical illustration of two important epigenetic mechanisms: DNA methylation and
histone modification.
Reprinted by permission from Macmillan Publishers Ltd: Nature, 441 (7090), pp. 143–145, doi:10.1038/441143a, Jane
Qiu, Unfinished Symphony, Copyright © 2006, Nature Publishing Group.
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The lesson from embryology is that remarkable phenotypic diversity can be achieved with the
same genetic sequence. It is easy to see how stochastic drifts in the way the epigenetic patterns
are generated during embryology might cause disease later in life by altering the programming
of genes. It is also easy to accept that exposure to chemicals during gestation that would interfere
with the biochemical processes and the enzymes that lay down these patterns could result in long-
term changes in gene function. Indeed, studies using the Agouti mouse model have shown how
maternal diet affects coat color of its offspring as well as other metabolic phenotypes: a methyl-
rich diet of the mother during gestation resulted in changes in DNA methylation that altered the
regulation of the Agouti gene that defines coat color in these mice (Dolinoy, Huang, and Jirtle,
2007; Waterland and Jirtle, 2003). It is conceivable that maternal diet during pregnancy and other
gestational experiences are also important for the development of PWB in humans. In other
words, the provision of a balanced source of methyl moieties may enable the innate epigenetic
processes to operate at optimal levels. However, although interventions such as folic acid supple-
mentation are commonly used to provide an adequate supply of methyl supply during gestation,
the proper balance of methyl dietary supplementation is still unclear (Kim, 2004).
A critical question for our discussion is whether there are—in addition to the innate and gen-
etically predetermined epigenetic processes occurring during early development—similar organ-
ized processes that adapt the epigenetic profile to signals from experience and external exposures
to create an “experience-dependent” epigenome that could confer multiple different phenotypes
to identical genotypes based on their specific early life experience. Recently, it has been proposed
that epigenetic mechanisms could serve as genome adaptation mechanisms that adapt the func-
tioning of the genome to signals derived from experience (Szyf, 2012). This might be particularly
important during early life when signals from the caregiving environment alter the epigenome to
adapt to anticipated environments in adulthood. The potential mismatch between these envir-
onmentally programmed epigenomic states with the actual environment later in life has been
hypothesized to be causing both physical disease and behavioral and mental disorders (Gluckman
and Hanson, 2005; Szyf, 2012). However, a good match between epigenetic adaptations in early
life and adult environments would result in optimal adaptation to the specific environmental
conditions (Pluess and Belsky, 2011). As mentioned earlier, it remains to be determined whether
these proposed adaptive epigenetic mechanisms are limited to early life only or whether they con-
tinue to adapt the genome throughout life, and whether these epigenetic alterations are reversible
later in life by environmental and behavioral interventions. In any case, it is clear that if such an
environmental-responsive genome-adaptation mechanism exists, it did not evolve to cause dis-
ease but rather to ensure life-long optimal functioning within a specific environment, ultimately
aimed at increasing fitness (see Chapter 4). While such optimal functioning is likely to include
PWB it is important to clarify that it is reproductive fitness rather than individual emotional well-
being that is the focus of processes related to natural selection (and reproductive fitness is not
necessarily contingent on PWB).
Chromatin modification
Out of all the observed possible chemical modifications of the N-terminal tails of histone pro-
teins, Histone acetylation is the most studied one since it is almost ubiquitously associated with
gene activation by opening accessibility of DNA to proteins that turn on gene transcription (Lee
et al., 1993; Perry and Chalkley, 1982). Histone methylation, on the other hand, could either turn
genes on or turn them off. These different states of chromatin modifications are important for
the proper programming of genes during development and through life (see also Chapter 2). The
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main difference between genetic alterations and epigenetic alterations is potential reversibility.
Germ line changes in sequence cannot be changed short-term in a feasible way (except through
rare de novo mutations) and are thus transferred from generation to generation. Given that epi-
genetic marks are laid down and removed by enzymatic reactions, and the state of histone modi-
fication needs to be maintained by the balance of different chromatin modification enzymes (i.e.,
acetyltransferase and histone deacetylase), it should be possible to alter the state of chromatin
modification by altering the activity of one of these enzymes with the help of pharmacological
agents. In fact, pharmacological treatments targeting histone acetylation are now tested as pos-
sible treatment of neurobehavioral disease (Abel and Zukin, 2008; Fass et al., 2013; Fischer et al.,
2010).
An important facet of chromatin modification is that histone modification occurs in a highly
targeted manner in response to signaling pathways in the cell. These enzymes are targeted to par-
ticular sites in the genome by trans-acting factors that are activated in response to developmental
and experiential signals (for a review and detailed discussion, see Szyf, 2009). Given that neuronal
processes target histone modification enzymes by activation of signaling pathways (Guan et al.,
2002) it is potentially possible to alter chromatin states not only by blocking the histone- modifying
enzymes, but also by tapping into the signaling pathways that guide and target these enzymes in
the first place. These signaling pathways are activated by experience, providing a potential mech-
anism for how behavioral interventions such as exercise and diet might contribute to optimal
functioning through epigenetic reprogramming. This obviously has important implications for
reversal and correction of adverse epigenetic marks and promotion of adaptive epigenetic marks
that contribute to optimal functioning. Consequently, it may be possible to improve and prevent
challenges to well-being-related outcomes by altering epigenetic states through specific actions
and exposures to supportive environments.
DNA methylation
DNA methylation is a remarkable epigenetic modification given that it is part of the chemical
entity of DNA (Hotchkiss, 1948). That is, the same chemical structure contains both ancestral
information in the genetic sequence as well as epigenetic information in the form of distribution
of methyl groups. DNA derived from different cell types has an identical sequence but different
distribution of DNA methyl moieties (Razin and Szyf, 1984). Thus, DNA methylation provides
a basic molecular explanation for the idea proposed by Waddington (1959) that DNA undergoes
transformation during embryogenesis to gain particular epigenetic forms in different tissues.
Although DNA methylation was already described more than sixty years ago (Hotchkiss, 1948), it
is only recently that studies using genome-wide mapping of DNA methylation were able to con-
firm these early observations of tissue-specific DNA methylation patterns and their formation
during cellular differentiation (Lister et al., 2009) and embryonal development (Lister et al., 2013).
Early studies on the role of DNA methylation in regulating genome function suggested that
methyl marks in critical command posts of genes (5’ regulatory regions) can silence gene expres-
sion (Razin and Riggs, 1980). In other words, DNA methylation can mark which segments of
the genome are expressed in particular cell types during cellular differentiation. Later studies
provided mechanisms for such silencing of gene function by DNA methylation. A methyl group
at a critical position of a gene can directly interfere with binding of protein factors that normally
interact with this position in order to turn the gene on (transcription factors). By disrupting such
interaction, DNA methylation silences the gene (Comb and Goodman, 1990). An alternative
mechanism was proposed a decade later, which involves recruitment of proteins that recognize
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methylated DNA in regulatory regions of gene-termed methylated DNA binding proteins (MBD)
(Nan et al., 1998). These proteins recruit chromatin-modifying complexes that modify chromatin
and silence gene function (Nan et al., 1998), illustrating the tight relationship between the two
epigenetic levels of regulation of genes: DNA methylation and chromatin (histone) modification
(D’Alessio and Szyf, 2006).
The reversible DNA methylation reaction
DNA methylation—as well as chromatin modification—is defined by reversible enzymatic reac-
tions and is thus potentially manipulatable throughout life by social experience. The main interest
in DNA methylation has been in explaining the process of cellular differentiation during develop-
ment and addressing the enigma of how one genome could express a diverse set of phenotypes in
a multicellular organism like humans. The idea that DNA methylation is responsible for cellular
identity seemingly implies that DNA methylation patterns must remain fixed after completion of
cellular differentiation, since any change in DNA methylation might threaten the cellular identity
of adult tissues. The concept of maintenance DNA methylation in palindromic CG dinucleotide
sequences through cell division was consistent with this idea (Razin and Riggs, 1980). The trans-
fer of methyl groups to DNA is catalyzed by enzymes DNA methyltransferases (DNMT) that use
the ubiquitous methyl donor S-adenosyl-methionine (Adams et al., 1975; Drahovsky and Morris,
1971; Gold et al., 1966). DNMT1 is a DNA methyltransferase enzyme that is proficient in methy-
lating the daughter strand across a methyl group in the parental strand, thus allowing the faithful
copying of a DNA methylation pattern during cell division ensuring the maintenance of the DNA
methylation pattern (Gruenbaum et al., 1982). This mechanism is extremely important in cell
division and implies that once a change in DNA methylation is introduced into the DNA it will
be maintained through subsequent cell divisions of the cell lineage. However, in postmitotic cells
that do not divide, such as neurons in the brain, this feature (not mechanism) is irrelevant, sug-
gesting that DNA methylation could play an important role in further modifying the phenotype
in adult tissue in response to experiential signals. Support for the proposed ability to form new
DNA methylation states in the adult brain, well after completion of brain maturation, is provided
by the fact that reduction in DNMT3A in the aging brain is implicated in reduced cognition and
that cognition could be augmented in an aging mouse by reintroduction of DNMT3A (Oliveira,
Hemstedt, and Bading, 2012). If DNA methylation were static in adult brains, these manipulations
of an enzyme involved in DNA methylation would not be effective.
If indeed DNA methylation is dynamic in response to signals in mature cells that do not divide
any further (i.e., postmitotic), then the DNA methylation reaction has to be reversible. In other
words, there must be mechanisms that can remove methyl groups from DNA in the absence of
cell division. Two principal reasons account for the initial resistance to accept the idea that DNA
methylation is a reversible biochemical reaction. First, if DNA methylation is indeed guarding
the differentiated phenotype of a cell, it has to be persistently and strictly maintained. Second, the
bond between a methyl group and a carbon ring is considered an extremely strong chemical bond.
Notwithstanding these objections, more than a decade ago we proposed that DNA methylation
is a reversible signal like other physiological signals (Ramchandani et al., 1999) and reported the
existence of a protein with an activity that could directly remove methyl moieties from cytosine
(Bhattacharya et al., 1999). Although the activity of this specific protein was contested (Ng et al.,
1999), other activities that reverse DNA methylation were proposed and demonstrated (Barreto
et al., 2007; Guo et al., 2013; Jost, 1993; Rai et al., 2008; Razin et al., 1986). Thus, although the
biochemical mechanism responsible for DNA methylation is still being explored, it is nevertheless
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clear that DNA methylation is a reversible reaction. Therefore, DNA methylation is a candidate
mechanism to dynamically alter and adapt gene programs in response to experiential signals, as
will be discussed in Figure 13.2.
Epigenetic adaptation to the environment
Adaptation of genome function to changing, life-long environmental conditions is critical for
optimal functioning of the organism. Natural selection, which acts through genetic sequence
selection, is a slow and inefficient mechanism and cannot account for the dynamic changes in the
environment that occur through a single life-course or a few generations. Optimal functioning—
reflected to some extent in PWB—will obviously be compromised without adjustment of genome
functions to changing environments. Thus, predetermined genetic and conserved epigenetic
signals generated during development cannot by themselves delineate successful adaptation
across life. It stands to reason that maintenance of optimal functioning will require genome
adaptation at multiple timescales from a transgenerational timescale where critical experiential
information is passed from one generation to the other, a life-long timescale that ensures a stable
phenotype is well adapted to anticipated environments, up to proximal timescales that require
Transcription
factor
X
CH3
X
Transcription
factor
X
Ac
Ac Ac
Transcription
machinery
Transcription
machinery
DNMT
Demethylases
Protein A Protein A
X
Phenotype A Phenotype B
CH3
Figure 13.2 DNA methylation reactions. DNA methylation and other chromatin modifications
provide different functional states to identical genes. An active gene (on the left) is characterized
by an open chromatin and acetylated histones with no methylation in transcription start sites and
critical transcription factor binding sites. The gene is transcribed as indicated by the dark grey
horizontal arrow encoding a protein that contributes to a phenotype a. If the gene is methylated
(CH3) (right) either in response to developmental innate triggers or exogenous environmental
triggers, DNA methylation prevents binding of either transcription factors or the transcription
machinery or both. The histones are modified as well by lack of acetylation (Ac) or methylation
(CH3) in particular residues, such as lysine 9 on histone 3. The gene is not transcribed (X) and
a protein is not produced contributing to a different phenotype B. The state of methylation is
defined by a balance of enzymatic reactions, methylation by DNA methyltransferases (DNMT), and
demethylation by demethylases.
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further adjustment in response to fast-changing environments (Szyf, 2012). First, evidence for the
hypothesis that the biochemical epigenetic mechanisms discussed embed environmental infor-
mation in the genome came with experiments that examined the impact of experiences in early
life on behavioral outcomes in rats.
First evidence: epigenetic changes in response to maternal care
It has been suggested that the developing child receives cues from the immediate environment
regarding the quality of future environments and that adaptation of the phenotype in response
to these cues would prepare the developing child for the anticipated world that she/he is going
to live in (Barker, 1998; Gluckman and Hanson, 2005). Most of the epidemiological and animal
research that examines the impact of early experiences focuses on how adversity early in life is
associated with mental and physical disorders later in life. However, it stands to reason that the
same processes that operate in early developmental periods to translate early life experience into
life-long phenotypes are fundamentally adaptive processes that prepare the organism for optimal
functioning in a specific context and that adult disease represents a maladaptation of this inherent-
ly adaptive response (Gluckman and Hanson, 2005; Szyf, 2012). Understanding these processes
is therefore critical in order to elucidate how early experiences can shape adult well-being (see
Figure 13.3).
The first evidence for epigenetic processes mediating the impact of early experience on life-
long behavioral phenotypes came from studies in rats. A long line of work has demonstrated that
the natural variation in maternal care is associated with phenotypic differences in their adult
offspring, particularly in behaviors related to stress responsivity (Francis et al., 1999; Liu et al.,
Signaling pathways
System wide
Social
Physical
Well-being
Bio
Developmental
CH3
CH3CH3CH3
CH3CH3
CH3CH3
CH3CH3
CH3
Bio
Physical
Social
Phenotype
Figure 13.3 Epigenetic adaptation to the environment. Epigenetic adaptation of genome function
to innate developmental signals and exogenous environmental signals from three spheres: the
biosphere, the physical sphere, and the social sphere. These act on signaling pathways that sculpt
the DNA methylation to adjust genome function to developmental and environmental signals and
define a phenotype that promotes optimal functioning.
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1997). Adult offspring of rat mothers that provided low-quality parenting (i.e., low licking and
grooming) showed heightened stress responsivity in comparison with offspring of mothers that
provided high-quality parenting (i.e., high licking and grooming). Cross-fostering experiments
revealed that these differences in offspring behavior were neither genetic nor germ-line mediated
(Francis et al., 1999).
The first line of studies demonstrating epigenetic programming by early life experience focused
on candidate genes. The glucocorticoid receptor (GR) in the hippocampus acts in a negative
feedback of the hypothalamic-pituitary-adrenal axis (HPA) by glucocorticoid (GC). Weaver
etal. (2004) showed that differences in maternal licking and grooming resulted in differences in
DNA methylation, histone acetylation, and expression of the NR3C1 GR exon 17 promoter in the
hippocampus. These differences emerged in the pups soon after birth in response to maternal care
and remained stable into adulthood, suggesting that reduced expression of GR in the hippocam-
pus in offspring of low licking and grooming mothers—programmed by epigenetic silencing—
leads to heightened stress responsivity.
What is the mechanism that translates maternal care into epigenetic changes in a particular
address in the genome? First, empirical work suggests that the release of neurotransmitters in
response to behavioral signals activates particular neuronal receptors in specific anatomic posi-
tions and circuitries in the brain, which in turn trigger a cascade of intracellular signaling pro-
teins that activate transcription factors that target chromatin-modifying enzymes to the genome
(Weaver et al., 2007). Neuronal activation was shown to alter DNA methylation in the brain,
most probably through a pathway that involves signaling and targeting by chromatin and DNA
sequence specific factors (Chen et al., 2003; Zhou et al., 2006). For example, changes in the state
of phosphorylation of MeCP2—a protein that recognizes methylated DNA in response to neur-
onal activation—were shown to target demethylation to the BDNF sequence in neuronal cultures.
MeCP2 was proposed to mediate demethylation of the Arginine Vasopressin (AVP) gene in neuro-
ns of the hypothalamic paraventricular nucleus in response to early life stress (Murgatroyd et al.,
2009). These results provide biochemical plausibility for the notion that social exposures can alter
DNA methylation in the brain. Importantly, in non-neuronal tissues, activation of hormones such
as glucocorticoids in response to stress as well as other candidate cytokines might be operating
through similar mechanisms.
The fact that these DNA methylation changes occur through organized physiological path-
ways rather than chaotic responses to adversity suggests that the underlying mechanisms are
adaptive and evolved to promote optimal functioning by altering genome programming to cope
with anticipated challenges. In other words, the main implication of a dynamic epigenome is the
potential to adapt to the environment by shaping the phenotype to the anticipated environmental
conditions in order to secure optimal functioning through successful adaptation.
An important question is whether these adaptive dynamic epigenetic responses in early child-
hood are fixed thereafter or whether they are reversible in later life in order to adapt to potential
environmental changes. To test the plausibility of reversing early life epigenetic programming
in adulthood we used pharmacological epigenetic modifiers that were injected into the brain of
adult rats who were either reared by high- or low-licking and grooming mothers. We used either
trichostatin A—an inhibitor of histone deacetylase—to increase histone acetylation and reduce
DNA methylation and activate the NR3C1 gene in the offspring of low-licking and groom-
ing mothers, or methionine—a donor of methyl groups—to increase DNA methylation and
silence the NR3C1 gene in offspring of high-licking and grooming mothers (Weaver et al., 2004;
Weaver et al., 2005). We showed that we could reverse the hyper-activated stress responsivity in
the offspring of low-licking and grooming rats and enhance stress responsivity in offspring of
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high-licking and grooming rats, demonstrating that in spite of the long-term stability of early
life epigenetic programming it could be reversed in adulthood using epigenetic pharmacological
modifiers (Weaver et al., 2004; Weaver et al., 2005).
The immediate follow-up question is whether reversal of epigenetic programming is limited
to pharmacological agents or whether behavioral interventions later in life could act through the
same pathways, and reverse early life epigenetic programming and readjust the epigenome to the
current adult environment. The observation that social environments and other experiences acti-
vate signaling pathways that could trigger changes in DNA methylation certainly suggests that
this might be a possibility (Weaver et al., 2004). Importantly, the basic concepts revealed in the
Weaver et al. (2004) study were supported by several other studies examining candidate genes in
models of early life social adversity. For example, DNA methylation of the BDNF gene promoter
in the adult prefrontal cortex in rat pups was altered in response to exposure to stressed abusive
fostering mothers (Roth et al., 2009), and the AVP gene was shown to be hypo-methylated in
the hypothalamus paraventricular nucleus in mice exposed to early life stress (Murgatroyd et al.,
2009). Furthermore, maternal separation resulted in altered DNA methylation in the hippocam-
pus in the promoters of the NR3C1, AVP, and Nuclear Receptor Subfamily 4, Group A, (Nr4a1)
genes (Kember et al., 2012). An interesting experiment in mice provides support for the idea
presented here that the DNA methylation alterations seen in response to social stress mediate
phenotypic adaptation, and that this mechanism persists even in adults and is not limited to
early life exclusively: Elliott et al. (2010) showed that chronic social stress in adult mice triggered
demethylation of the regulatory region of the CRH gene, but only in a subset of mice that dis-
played social avoidance.
Early life adversity and DNA methylation changes in humans
The effects of early life adversity on changes in DNA methylation of the NR3C1 gene in the hippo-
campus have been replicated in a sample of human brains of people that committed suicide and
control subjects. Consistent with animal studies, the NR3C1 promoter (1f) was hyper-methylated
at particular sites in the hippocampus of those who were exposed to child abuse as compared with
those who were not (McGowan et al., 2009). In addition, NR3C1 was examined in several studies
regarding the impact of early life adversity and stress on children. For example, Nr3c1(1f) exon
was found to be slightly differentially methylated in genomic DNA from cord blood mononuclear
cells from neonates who were exposed to maternal depression in utero (Oberlander et al., 2008).
Similarly, a correlation was observed between stress in pregnant women, their newborn birth
weight, and hyper-methylation of the NR3C1 promoter in cord blood (Mulligan et al., 2012).
Other studies have shown increased NR3C1 methylation in people who experienced early paren-
tal death (Melas et al., 2013) and in relation to severity and the number of type of maltreatments
during childhood (Perroud et al., 2011). Although these studies are intriguing, we are not aware
of any published study that investigated whether positive supportive environmental influences
have similar effects on DNA methylation. However, given that epigenetic mechanisms aim at
adaptation to the environment, it can be expected that the epigenome would be shaped equally
by positive exposures.
Broad response of the epigenome to early life adversity
DNA methylation and other epigenetic processes are highly tissue specific and this has been
known for three decades (Razin and Szyf, 1984). Recent studies recapitulated these conclusions
that many differentially methylated regions exist between different tissues, although consistency
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in inter-individual DNA methylation between tissues has been shown (Slieker et al., 2013). It is
therefore plausible that any change in DNA methylation that is relevant for behavior will only be
detected in the brain. If this were true, it would make the study of epigenetics almost impossible
in living humans. However, the assumption behind such an argument is that the brain and body
and the different physiological systems are independent entities. We will argue here on the basis
of accumulating data that the changes in DNA methylation that are detected in response to envir-
onmental influences are not limited to the brain and involve other tissues as well in an integrated
body-wide response. In other words, the changes in DNA methylation in the periphery (e.g.,
blood, saliva) are not a “surrogate” marker of changes in the brain, but instead reflect the cross-
talk between the brain and the periphery that is normally needed to integrate physiological and
mental processes required for maintaining optimal functioning.
Another related issue is the focus on candidate genes. A narrow interpretation of early life
adversity would focus on stress, and therefore, most work to date has focused on the glucocortic-
oid receptors and other stress-related genes, as described in previous sections. However, genes act
in networks (Tuch, Li, and Johnson, 2008), and it is therefore plausible that early life environment
will reorganize the epigenetic states of complex networks of genes rather than a few genes asso-
ciated with the immediate stress response. There is now emerging evidence that the changes in
DNA methylation in response to early life stress involve many genes and that they are not limited
to the brain, as we will discuss.
DNA methylation in blood. Changes in DNA methylation associated with early life social adver-
sity are not limited to the brain. When we examined adult rhesus monkeys that were exposed to
differential rearing during early life with their biological mother or in a nursery, differences in
methylation were observed in hundreds of genes in both prefrontal cortex and T cells from blood
samples (Provencal et al., 2012). Although there was a small overlap between blood and brain,
most of the differences were tissue specific, supporting the hypothesis that T cells are not mere-
ly surrogates to the brain, but rather play a particular role in the response to early life maternal
deprivation. The question whether DNA methylation changes relevant to behavior are detectable
in blood cells has important practical implications for the study of behavioral epigenetics in living
humans, but also for the future development of DNA methylation probes as tools for risk predic-
tion and follow-up of response to interventions or therapeutics. Several studies have provided
preliminary evidence for DNA methylation differences in blood cells that are reflective of social
exposures. For example, Uddin et al. (2010) reported DNA methylation of immune-related genes
in blood samples of people suffering from PTSD. Similar differences in blood DNA methylation
of individuals with PTSD have been associated with child maltreatment (Mehta et al., 2013).
Furthermore, changes in blood DNA methylation of the FKBP5 gene were detected as a function
of early life maltreatment (Klengel et al., 2013) and in the NR3C1 gene of adults with history of
child maltreatment (Perroud et al., 2011). Finally, genome-wide changes in blood DNA methyla-
tion in adults were found to be associated with early life poverty (Borghol et al., 2012). These stud-
ies point to the prospect that it might be possible to use noninvasive DNA methylation markers of
both health and disease and to utilize them for following up interventions that aim at increasing
physical well-being and PWB.
Gene-specificity of DNA methylation. Examination of the differences in the maternal transcrip-
tome between offspring of high- and low-licking and grooming rat mothers revealed differences
in hundreds of genes. For example, the changes in DNA methylation, transcription, and histone
acetylation in response to maternal care in the rat hippocampus were not limited to the NR3C1
gene, but involved large spans of the genome (Kohlmann et al., 2011). Furthermore, epigenetic
modulations with trichostatin A and methionine that reversed the impact of maternal care on
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stress responsivity also impacted hundreds of genes (Weaver, Meaney, and Szyf, 2006). Similar
findings emerged in brains of human suicide victims who were exposed to child abuse as chil-
dren: differences in DNA methylation were found not only in the NR3C1 gene, but also in the
promoters of rRNA genes which are involved in the ubiquitous protein synthesis machinery and
are unrelated to the stress response (McGowan et al., 2008). Hence, as in rats, there is a broad
DNA methylation response to child adversity in the human hippocampus (Labonte et al., 2013;
Suderman et al., 2012).
In summary, although data are still sparse and most studies suffer from limitations, they never-
theless all point to the fact that changes in DNA methylation associated with the social envir-
onment are not limited to the brain and are not limited to a small subset of candidate genes.
Together, these data support the idea that changes in DNA methylation in response to the early
environment do not just reflect stochastic noise like random genetic differences. On the contrary,
DNA methylation changes are highly organized, affecting multiple gene pathways and multiple
body systems. They point to the possibility that there is a physiological system that senses early life
physical and social environments and programs the genome in response. If indeed such a system
exists, it stands to reason that it was selected in evolution not to cause adult disease, but to prepare
the individual for a biologically optimal life by coordinating genome function with anticipated
environments.
Epigenetic change as mediator of gene–environment interaction
Extreme genetic determinism argues that genetic variation explains both vulnerabilities of humans
as well as well-being outcomes. Examples supporting this view are found in rare Mendelian muta-
tions with extremely high penetrance, such as genes associated with Alzheimer’s disease (Piaceri,
Nacmias, and Sorbi, 2013; Tanzi, 2013) or breast cancer (Bowcock, 1993). However, in most other
cases the relationship is more complex and single genetic changes in common alleles are associ-
ated with only a small effect, whereas the combination of multiple genetic differences explains
larger proportions of the variance (see Chapter 15).
In contrast to this extreme view of genetic determinism the dominant idea in the field to date
is that, although genetic variation plays a critical role, genetic effects can be influenced by envir-
onmental exposure including both chemical–physical and social environments (see Chapters11
and 12). For a long time such gene–environment interactions have been a predominately statis-
tical construct describing situations where the statistical probability for a genetic variant to confer
either risk or protection from a disease was influenced by environmental conditions. However,
in absence of a biological mechanism for gene–environment interaction it is difficult to either
understand or take full advantage of this concept for intervention and prevention. One of the
most cited documents of such a statistical interaction is the report that the short allele of the
serotonin transporter gene (5-HTTLPR) is associated with high risk of depression when the car-
riers of this allele were exposed to stressful environments early in life (Caspi et al., 2003). Since
this pioneering study, many other reports have described gene–environment interactions (see
Chapter11).
The epigenetic studies described here are beginning to provide a general mechanism for the way
in which exposures and experiences can stably program genes and alter their long-term function.
The studies on the pathways leading from maternal care to NR3C1 epigenetic programming in the
rat (Weaver et al., 2004, 2007)—discussed earlier—provide a physiological route for how early life
social conditions alter the epigenetic programming of the gene. Changes in NR3C1 DNA methy-
lation in response to child abuse that are detected during adulthood probably involve similar
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EPIGENETICS AND WELL-BEING
223
interactions. Thus, it is suggested here that gene–environment interactions are the normal process
by which external environments modulate the genome to ensure adequate adaptation of genome
function to these environments, and that genetic variation tweaks these adaptations further.
There is empirical evidence that well-defined gene–environment interactions involve alter-
ations in DNA methylation which are triggered by the early environment and modulated by
genetic differences. For example, in rhesus macaques the short allele of the 5-HTTLPR is targeted
for DNA methylation when the monkeys experience early life maternal deprivation leading to
enhanced risk of depression (Barr et al., 2004). Similarly, the 5-HTTLPR short allele was more
methylated in Rhesus monkeys that were maternally deprived, and such higher methylation was
associated with behavioral stress reactivity in infants (Kinnally et al., 2010).
An allele of the FKBP5 gene, encoding a proximal negative regulator of response to glucocortic-
oids, has been found to confer risk for PTSD upon individuals if they experienced early life adver-
sity (Zimmermann et al., 2011). Recent studies are consistent with the idea that the mechanisms
that mediate this environmental effect on this gene are epigenetic, suggesting that the genetic
sequence alters the probability of a site becoming methylated in response to adverse early life con-
ditions. For example, Klengel et al. (2013) demonstrated that a distant sequence at intron 7, which
also contains a glucocorticoid response element (GRE), is differentially demethylated in carriers
of the FKBP5 risk allele who were exposed to adversity early in life in comparison with either risk
allele carriers not exposed to early life adversity or those exposed to adversity but not carriers
of the risk allele. Thus, activation of GR by glucocorticoids—which are elevated in response to
early life distress—may recruit demethylases to a GRE in intron 7 of the FKBP5 gene, resulting in
demethylation of this polymorphic sequence (Klengel et al., 2013).
In summary, we propose that gene–environment interactions evolved to guarantee successful
adaptation to the environment (i.e., optimal functioning) so that changes in the environment as
interpreted at critical points in life, particularly early life, are registered as changes in gene function.
Implications of epigenetics for understanding and enhancing
psychological well-being
Although we are very early on in our understanding of how epigenetic processes respond to envir-
onmental cues, it is important to consider the impact that the concepts emerging from epigenetic
research might have on our understanding of PWB and the promotion thereof. The main focus
of most genetic and epigenetic research has been on the identification of genetic and epigenetic
factors that can either predict or associate with disease. The underlying hypothesis in such work
has been that genetic and epigenetic variation occurs randomly. If indeed DNA methylation and
other epigenetic changes that are associated with disease are stochastically generated, then the
implications for well-being promotion are limited. However, the hypothesis proposed here sug-
gests that this might not be the case. DNA methylation changes that occur during early life are
proposed to be a mechanism for promoting optimal functioning through successful adaptation by
adjusting the genome to environmental signals, thus preparing the organism to function well in
anticipated environments. If the data indeed point to an organized process that responds to envir-
onmental signals, it is highly unlikely that it evolved exclusively in relation to adverse experiences.
Understanding how these epigenetic processes function in response to supportive environmental
influences and in the prediction of positive outcomes might provide new insights into strategies
that will promote epigenomic-driven well-being.
One of the fundamental properties of epigenetic processes is that they are reversible. This
bears the optimistic message that it might be possible to alter the course of an epigenetic
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224
trajectory aimed toward vulnerability, unhealthy growth, and aging through pharmacological
treatment. For example, it was possible to reverse a cancer state by inhibiting the DNA methy-
lation enzyme DNMT1 (Ramchandani et al., 1997), and the anxious and stressful behavior
of adult offspring of a low-licking and grooming rat could be reversed by treatment with the
histone deacetylase inhibitor trichostatin A (Weaver et al., 2004). Such epigenetic interven-
tions with drugs or nutritional supplements that either promote or inhibit DNA methylation
such as the methyl donor SAM might be used to promote well-being. However, even more
interesting are the possibilities that certain behavioral interventions might alter trajectories of
DNA methylation and reverse adverse DNA methylation signatures and promoter healthier
programs. One example is the role of physical exercise beyond its immediate proximal effects
on metabolism and muscle function: recent evidence suggests that exercise in both animals
(Tajerian et al., 2013) and humans could alter DNA methylation profiles (Barres et al., 2012;
Nitert et al., 2012; Ronn and Ling, 2013) and, thus, account for the long-term and broad posi-
tive effect that exercise has on health and well-being. It stands to reason that exercise is an
example of an intervention that can tap into the physiological processes that control DNA
methylation states associated with the regulation of gene networks involved in metabolism.
Hence, it seems likely that pharmacological, nutritional, and behavioral interventions that tap
into the DNA methylation and epigenetic regulatory mechanisms might be able to protect and
promote physical well-being and PWB.
Although we have almost no information on DNA methylation alterations at later points in
life, it stands to reason that DNA methylation continues to evolve and respond to environmental
signals throughout the life-course. Given that DNA methylation change has been associated with
aging (Issa, 2014), it is tempting to speculate that healthy aging involves proper progression of
the DNA methylation profile and that unhealthy aging will involve disruption of this process. It
will be important to understand how the evolving DNA methylation profiles during aging pre-
dict healthy aging, what the processes are that might disrupt the physiological trajectory of DNA
methylation, how they are influenced by environments and exposure to create resilience, and
under what conditions this process becomes maladaptive. Such knowledge might open up possi-
bilities to utilize DNA methylation markers in order to differentiate healthy and unhealthy aging
and design interventions that will reverse the DNA methylation profiles of unhealthy aging to
profiles associated with healthy aging.
In summary, we propose that epigenetic processes are fundamental for understanding PWB,
particularly regarding how environmental and genetic factors interact in the development of posi-
tive outcomes. In order to advance knowledge pertaining to epigenetics and well-being, future
research efforts should move the focus from identifying markers for disease toward how epigen-
etic processes coordinate and respond to environmental signals throughout life in the prediction
of well-being. Delineating healthy trajectories of DNA methylation and understanding how they
relate to specific environmental exposures and experiences will provide important tools and strat-
egies to understand, monitor, and promote the development of PWB.
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Chapter 13
Q. No. Query
AQ1 Please check the level of headings “DNA methylation in blood.”
and “Gene-specicity of DNA methylation.”
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