Psychological and social–contextual factors are recognized for their ability to produce profound effects on brain development and plasticity and, in turn, for their influence on the development of behavior. Mechanisms underlying these environmentally driven phenomena are not fully understood, but over the past decade the birth of epigenetics research has caused a paradigm shift to occur with respect to our understanding of gene–environment interactions in this capacity. It has become clear that epigenetic processes such as DNA methylation (Figure 1) actively regulate human genomes in response to environmental input and are poised to do so not only during early-life development but also as we develop throughout the life span. One alluring aspect of epigenetic regulation of gene expression that has emerged is its capability to drive long-term and even multigenerational trajectories in behavioral development. The birth of epigenetics research has thus provided an exciting new level of analysis for understanding tenets central to the discipline of developmental psychopathology.
(Color online) DNA compaction and methylation. (a) DNA in the nucleus is wrapped around histone proteins, forming what is referred to as chromatin. This provides a highly ordered packaging state of DNA to serve as a building block of chromosomes. (b) DNA methylation occurs at cytosine residues of cytosine–guanine (CG) dinucleotides that are often clustered within gene regulatory regions. DNA methylation is an epigenetic mechanism typically associated with gene suppression, as methyl groups can interfere with the binding of transcription factors necessary to promote gene transcription and/or recruit repressor proteins that promote a compact chromatin state not permissive to gene transcription. However, there are reports of DNA methylation being associated with active gene transcription (Chahrour et al., Reference Chahrour, Jung, Shaw, Zhou, Wong and Qin2008; Uchida et al., Reference Uchida, Hara, Kobayashi, Otsuki, Yamagata and Hobara2011).
Central to a developmental psychopathology perspective is the examination of the biological, psychological, and social–contextual factors that facilitate adaptation and maladaptation across the life span (Cicchetti, Reference Cicchetti1993; Cicchetti, Reference Cicchetti, Cicchetti and Cohen2006; Sroufe & Rutter, Reference Sroufe and Rutter1984). As will be reviewed here, studies have demonstrated that DNA methylation alterations are biological responses to psychological and social–contextual factors. This has afforded a new framework with which to understand how psychological and social–contextual factors can interact with our biology and, in turn, a route through which behavior could arise. The dynamic nature of DNA methylation renders it an ideal substrate that is responsive to environmental factors, whereas its stable nature renders it capable of maintaining sustained changes in brain function and behavior that are a consequence of environmentally driven changes in gene regulation and activity. The examination of risk and protective processes and mechanisms in typical and atypical development is also central to a developmental psychopathology perspective (Cicchetti, Reference Cicchetti1993, Reference Cicchetti, Cicchetti and Cohen2006; Sroufe & Rutter, Reference Sroufe and Rutter1984). To this end, evidence is emerging that DNA methylation alterations could serve as mechanisms through which risk and protective factors may operate to yield a phenotype. DNA methylation is also increasingly being recognized as a biological process that can influence our psychological functioning from infancy to senescence. Finally, because a focus on the boundary between normal and abnormal development is central to a developmental psychopathology perspective (Cicchetti, Reference Cicchetti1993, Reference Cicchetti, Cicchetti and Cohen2006; Sroufe & Rutter, Reference Sroufe and Rutter1984), DNA methylation is highlighted as a valuable measure informative of norms and aberrations present at the molecular level.
Changes in DNA Methylation as a Function of Caregiving Environments
Although it has become clear over the past decade that epigenetic processes operate throughout the life span, the evidence available at present indicates that environmentally driven DNA methylation changes are especially robust and long lived when they occur during sensitive periods (i.e., prenatal or early postnatal development). Cross-disciplinary studies have long indicated that sensitive periods during development are heightened epochs of brain plasticity where environmental factors are able to shape (i.e., program) neural circuits to direct structural and functional aspects of brain and behavior for the life span. Although it has been appreciated for some time that the long-term consequences of early-life experiences represent so-called epigenetic influences, it has only been within the past decade that empirical evidence that directly supports this notion has been presented. Such paradigm-shifting studies have forced us to recognize the sensitivity of DNA methylation at specific gene loci within the brain to the quality of early-life experiences. Furthermore, these studies have illustrated the ability of parental care (including the lack thereof) to canalize DNA methylation patterns with multigenerational consequences for the genome and behavior. The following discussion examines developmental studies with rodent models that have made it clear that DNA methylation is a molecular process sensitive to early-life environmental input. These studies have also illustrated that experience-induced changes in DNA methylation occur in brain circuitry with functional relevance to behavioral trajectories and psychopathology.
Evidence from rodent studies
In 2004, investigators brought forth evidence that challenged the previously held view that epigenetic mechanisms are static and unresponsive to the environment outside of embryonic development and periods of cellular differentiation. Data they presented indicated that methylation of DNA associated with the glucocorticoid receptor (GR) gene, a gene underlying stress responsivity through its regulation of hypothalamic–pituitary–adrenal (HPA) activity, was directly associated with the type of caregiving experienced during the first postnatal week (Weaver et al., Reference Weaver, Cervoni, Champagne, D'Alessio, Sharma and Seckl2004). Specifically, they showed that adult male rats that had been reared by nurturing mothers that exhibited high levels of pup licking and grooming (LG) had low levels of methylation of DNA associated with the GR gene within their hippocampus, whereas adults who had been raised by low-LG mothers exhibited hypermethylation of GR DNA. These observations were consistent with GR gene expression patterns and anxiety-related behavior of the animals. Animals with low methylation had higher expression of the GR gene and exhibited stress resilience, whereas animals with higher methylation had lower gene expression and increased anxiety-like behavior. Through a series of cross-fostering studies, they were able to demonstrate that the levels of GR promoter methylation were determined by the mother's behavior during the postnatal period and were not a product of the biological mother's behavioral predilection. These data were key in providing an association between the levels of caregiving behavior and DNA methylation of the GR gene promoter. Finally, in an effort to help establish a causal link between the observed epigenetic modifications, gene expression patterns, and adult behavior, they demonstrated that pharmacologically manipulating methylation patterns removed group differences in DNA methylation, histone acetylation (another epigenetic mark), gene expression, and behavior.
Since this landmark study, laboratories have continued to link caregiver experiences with DNA methylation patterns. We have also learned that the effects of the caregiving environment on DNA methylation are not exclusive to the GR gene, as other genes within the hippocampus (and other brain regions, as discussed below) show similar sensitivity to the quality of the caregiving environment. For example, maternal LG behavior affects γ-aminobutyric acid (GABA) inhibitory circuits, as males reared by low-LG mothers show reduced hippocampal levels of the rate-limiting enzyme in GABA synthesis (glutamic acid decarboxylase [GAD1]), an effect shown to be associated with increased methylation of GAD1 promoter DNA (Zhang et al., Reference Zhang, Hellstrom, Bagot, Wen, Diorio and Meaney2010). Other studies have shown that infant male rats experiencing repeated separation from their mother and nest environment show altered methylation and expression of estrogen receptor (ERβ) DNA (a gene that encodes a receptor responsive to estrogen; Wang, Meyer, & Korz, Reference Wang, Meyer and Korz2012) and increased methylation (and therefore reduced expression) of the synaptic plasticity gene reelin within the hippocampus (Qin et al., Reference Qin, Tu, Sun, Zhang, Chen and Zhao2011). Furthermore, it has been demonstrated that epigenetic changes can occur on a much broader genomewide scale within the hippocampus in response to maternal LG behaviors (McGowan et al., Reference McGowan, Suderman, Sasaki, Huang, Hallett and Meaney2011).
Experience-induced changes in DNA methylation are a mechanism by which early-life caregiving experiences can also produce long-lasting alterations in function of the HPA axis, particularly at the level of the hypothalamus. Increased LG behavior of male infant rats, which improves learning and memory capacity in adulthood, has been shown to reduce expression of and methylation of the corticotropin releasing hormone (Crh) gene in the paraventricular nucleus (PVN) of the hypothalamus (Korosi et al., Reference Korosi, Shanabrough, McClelland, Liu, Borok and Gao2010; McClelland, Korosi, Cope, Ivy, & Baram, Reference McClelland, Korosi, Cope, Ivy and Baram2011). The impact of infant (male and female) separation on depressive-like behaviors and Crh and GR gene expression in the hypothalamus have been linked to DNA methylation profiles (Chen, Evans, et al., Reference Chen, Evans, Liu, Honda, Saavedra and Aguilera2012; Franklin et al., Reference Franklin, Russig, Weiss, Gräff, Linder and Michalon2010). Furthermore, male mice show hypomethylation of arginine vasopressin (AVP) DNA and increased AVP gene expression in the PVN, effects that coincide with increased corticosterone secretion, both at basal conditions and in response to stress, as well as an attenuated memory capacity a year after experiencing repeated separations from their mother (Murgatroyd et al., Reference Murgatroyd, Patchev, Wu, Micale, Bockmuhl and Fischer2009).
Maternal care also promotes epigenetic changes of additional genes and epicenters of stress regulation, cognitive control, addiction, and maternal behavior. For example, some of our work has shown that infant rats repeatedly exposed to an adverse caregiving environment exhibit significant methylation of brain-derived neurotrophic factor (Bdnf) DNA in their prefrontal cortex that either persists throughout (DNA associated with exon IX) or evolves (exon IV) during development (Roth, Lubin, Funk, & Sweatt, Reference Roth, Lubin, Funk and Sweatt2009). Aberrant caregiving behaviors were elicited by the combination of environmental novelty and resource deprivation (lack of nesting material), factors in our hands and those of others capable of producing abnormal caregiving behaviors that include a high proportion of rough handling, pup stepping on and dragging, active avoidance (neglect), and decreased LG of pups (Ivy, Brunson, Sandman, & Baram, Reference Ivy, Brunson, Sandman and Baram2008; Raineki, Cortés, Belnoue, & Sullivan, Reference Raineki, Cortés, Belnoue and Sullivan2012; Roth et al., Reference Roth, Lubin, Funk and Sweatt2009; Roth & Sullivan, Reference Roth and Sullivan2005). Adult DNA methylation profiles in our study were also found to coincide with reduced Bdnf gene expression and aberrant maternal behavior. Helping to establish a link between the methylation and gene changes, we also demonstrated that the gene deficits could be reversed through pharmacological manipulation of the methylation patterns.
In the hippocampus and nucleus accumbens of adolescent rats (age 35 days), methylation of mu-opioid receptor (Oprm1) DNA has been linked to the quantity of pup LG behavior (Hao, Huang, Nielsen, & Kosten, Reference Hao, Huang, Nielsen and Kosten2011). In addition, low-LG mothers are known to yield female offspring that exhibit decreased ER-α expression and a corresponding increase in methylation associated with the ER-α promoter in the medial preoptic area (MPOA) of the hypothalamus, whereas the opposite is true of high-LG mothers (Champagne et al., Reference Champagne, Weaver, Diorio, Dymov, Szyf and Meaney2006). Finally, work has shown that increased maternal care of male rats increases adulthood expression of anti-inflammatory cytokine interleukin 10 gene mRNA within microglia of the nucleus accumbens, an effect established during the first postnatal week and maintained via decreased methylation of DNA associated with the interleukin 10 gene (Schwarz, Hutchinson, & Bilbo, Reference Schwarz, Hutchinson and Bilbo2011). Increased maternal care in this study also produced animals that were more resilient to reinstatement of morphine-conditioned place preference.
Evidence from human studies
In human epigenetic studies (which have primarily focused on adults), it is difficult to distinguish methylation patterns that may have developed as a response to the caregiving environment from those that occurred as a consequence of additional experiences throughout life. Functional polymorphisms are predicted to add an extra layer of complexity to understanding how behavioral outcome is moderated by early-life experiences. Furthermore, there is the question of the validity of peripheral measures of DNA methylation (obtained from blood samples or cheek swabs) in accurately reflecting the complexity of DNA methylation patterns within the brain (i.e., gene-specific and region-specific responses). Nevertheless, studies have reported associations between DNA methylation changes and early-life caregiving experiences.
Akin to the rodent literature, the human GR gene (Nr3c1) appears equally susceptible to experience-induced and long-lasting changes in DNA methylation. For example, increased DNA methylation of Nr3c1 and ribosomal RNA genes (and a corresponding decrease in transcript levels) were found in hippocampal samples derived from adult males with a history of childhood abuse (Labonté, Yerko, et al., Reference Labonté, Yerko, Gross, Mechawar, Meaney and Szyf2012; McGowan et al., Reference McGowan, Sasaki, Huang, Unterberger, Suderman and Ernst2008, Reference McGowan, Sasaki, D'Alessio, Dymov, Labonte and Szyf2009). In another study linking the effects of early-life adversity with epigenetic modification of the human GR gene, parental loss, childhood maltreatment, and disruptions in parental care were found to be associated with increased Nr3c1 promoter DNA methylation (as determined from leukocyte DNA) and attenuated cortisol responses to a stress challenge (Tyrka, Price, Marsit, Walters, & Carpenter, Reference Tyrka, Price, Marsit, Walters and Carpenter2012). Epigenetic changes in response to early-life experiences also appear to occur on a much broader, genomewide scale within the hippocampus. Male individuals with histories of severe abuse during childhood have been shown to exhibit genomewide changes in hippocampal DNA methylation, including hypermethylation of over 200 gene promoters and hypomethylation of around 100 gene promoters, many of which are involved in neural plasticity (Labonté, Suderman, et al., Reference Labonté, Suderman, Maussion, Navaro, Yerko and Mahar2012).
Epigenetic regulation of other gene loci has been linked to childhood experiences. For example, antisocial behavior in females with a history of childhood sexual abuse coincides with both genotype and hypermethylation of DNA associated with the promoter region of the gene encoding the serotonin transporter (Beach, Brody, Todorov, Gunter, & Philibert, Reference Beach, Brody, Todorov, Gunter and Philibert2011; Vijayendran, Beach, Plume, Brody, & Philibert, Reference Vijayendran, Beach, Plume, Brody and Philibert2012). Increased stress responsivity in maternally and socially isolated infant macaques has likewise been linked to genotype and hypermethylation of the gene encoding the serotonin transporter (Kinnally et al., Reference Kinnally, Capitanio, Leibel, Deng, LeDuc and Haghighi2010, Reference Kinnally, Feinberg, Kim, Ferguson, Leibel and Coplan2011). Children (male and female) aged 7 to 10 years and raised in institutional care show greater methylation of DNA associated with a number of genes involved in controlling serotonin and glucocorticoid biosynthesis, immune responses, and cell-signaling pathways involved in memory formation than do children of the same age who were raised by their biological parents (Naumova et al., Reference Naumova, Lee, Koposov, Szyf, Dozier and Grigorenko2012). Finally, adolescent and adult DNA methylation levels, including those of genes known to play an important role in cell-signaling pathways within the brain, have been linked to maternal and paternal stress levels during early childhood years (Borghol et al., Reference Borghol, Suderman, McArdle, Racine, Hallett and Pembrey2012; Essex et al., Reference Essex, Thomas Boyce, Hertzman, Lam, Armstrong and Neumann2011).
Changes in DNA Methylation as a Function of the Prenatal Environment
The intrauterine environment is also recognized as a major contributor to normal growth and development of an individual, and disturbances at this critical time are recognized for their ability to adversely affect behavioral development and the long-term mental health of offspring. Across-species studies have shown that one way prenatal stress and environmental factors can alter developmental trajectories is through changes in DNA methylation.
Evidence from rodent studies
In one of the earliest studies of gestational stress (using a regimen that included restraint stress and exposure to predator odor or loud noises), prenatally stressed male (but not female) offspring when adult were found to exhibit marked changes in expression of the Crh and GR genes, reduced methylation of Crh DNA in both the hypothalamus and amygdala, and increased HPA-axis responsivity and a depressive-like phenotype (Mueller & Bale, Reference Mueller and Bale2008). Data since have been consistent in showing the ability of stress experienced directly by the mother to render epigenetic consequences in offspring. Restraint stress has been shown to produce high levels of Dnmt1 and 3a (genes encoding enzymes that are responsible for adding methyl groups to DNA) mRNA in the frontal cortex and hippocampus of male offspring (Matrisciano et al., Reference Matrisciano, Tueting, Dalal, Kadriu, Grayson and Davis2012). This same study showed that prenatally stressed mice also displayed increased methylation of DNA associated with synaptic plasticity genes (including reelin) and several schizophrenic-like behaviors, including hyperactivity, deficits in social interaction, altered prepulse inhibition, and memory capacity. Restraint stress of pregnant rats has also recently been associated with changes in placental and fetal HSD11B2 mRNA and methylation, a gene whose product helps protect the fetus against the damaging effects of stress hormones (Jensen Peña, Monk, & Champagne, Reference Jensen Peña, Monk and Champagne2012).
In utero experiences also affect epigenetic regulation of genes and circuitry associated with addiction and motivation. Altered DNA methylation of the dopamine receptor 2 gene has been found in the nucleus accumbens of adult rats that were exposed to in utero glucocorticoids (Rodrigues et al., Reference Rodrigues, Leao, Pego, Cardona, Carvalho and Oliveira2011). Consumption of a high-fat diet during pregnancy has been shown to produce offspring that prefer sucrose and fat in adulthood, a phenotype that is accompanied by DNA hypomethylation and increased expression of several reward-related genes (including the Oprm1 and dopamine reuptake transporter) within the nucleus accumbens or prefrontal cortex (Vucetic, Kimmel, Totoki, Hollenbeck, & Reyes, Reference Vucetic, Kimmel, Totoki, Hollenbeck and Reyes2010). Studies are beginning to indicate that the epigenetic consequences of prenatal stress likely occur on a broad genomewide scale (Mychasiuk, Ilnytskyy, Kovalchuk, Kolb, & Gibb, Reference Mychasiuk, Ilnytskyy, Kovalchuk, Kolb and Gibb2011) and that stress does not have to be experienced directly by the mother in order for it to affect her offspring. One report has shown global DNA methylation (frontal cortex and hippocampus), gene expression, and behavioral alterations in offspring of pregnant rats that were simply housed with another female who was repeatedly subjected to stress outside of the home cage (Mychasiuk, Schmold, et al., Reference Mychasiuk, Schmold, Ilnytskyy, Kovalchuk, Kolb and Gibb2011).
Evidence from human studies
Methylation status of the human genome appears equally sensitive to a variant of prenatal factors. For example, infants born to mothers who reported high levels of depression and anxiety during their third trimester of pregnancy exhibit increased methylation of the Nr3c1 promoter in cord blood cells (Oberlander et al., Reference Oberlander, Weinberg, Papsdorf, Grunau, Misri and Devlin2008). Methylation status of the gene encoding the serotonin transporter (SLC6A4) is likewise affected by maternal depression, as increased maternal depressed mood scores have been associated with decreased maternal (peripheral leukocytes) and infant (umbilical cord) SLC6A4 promoter methylation (Devlin, Brain, Austin, & Oberlander, Reference Devlin, Brain, Austin and Oberlander2010). An unbalanced diet consumed during pregnancy (one that is linked to elevated blood pressure and cortisol in adult offspring) produces methylation of the GR gene (Drake et al., Reference Drake, McPherson, Godfrey, Cooper, Lillycrop and Hanson2012). In addition, maternal alcohol and tobacco use are factors known to alter methylation of DNA associated with genes important in placental growth and development (Suter et al., Reference Suter, Ma, Harris, Patterson, Brown and Shope2011; Wilhelm-Benartzi et al., Reference Wilhelm-Benartzi, Houseman, Maccani, Poage, Koestler and Langevin2011).
Changes in DNA Methylation as a Function of Later-Life Events
The studies highlighted in the previous sections are consistent with the notion that epigenetic alterations caused by adversity within the intrauterine or caregiving environments may provide a basis for the concept of developmental origins of health and disease. Adversity experienced later in life is likewise recognized for its ability to render lasting psychological and health costs, and emerging evidence suggests that changes in gene expression mediated by DNA methylation have significance in these outcomes as well.
Evidence from rodent studies
In parallel to developmental studies, research efforts aimed at understanding molecular mechanisms underlying memory processes and stress outcomes have illustrated the sensitivity of the adult rodent brain to environmentally driven epigenetic alterations. It is interesting that these experience-driven changes appear to occur with similar selectivity for gene networks and circuitry as that affected by early-life adversity. Much of the pioneering work in regard to DNA methylation alterations in memory formation has utilized contextual fear conditioning, a behavioral paradigm that produces robust and long-lasting fear memories in rodents. Data illustrate that hours following fear conditioning when the fear memory is being formed (consolidated) there are changes in hippocampal DNA methylation that include demethylation and transcriptional activation of the memory enhancing gene reelin (Miller & Sweatt, Reference Miller and Sweatt2007) and both DNA methylation and demethylation of DNA associated with the Bdnf gene within the hippocampus (Lubin, Roth & Sweatt, Reference Lubin, Roth and Sweatt2008). There are also changes in methylation of DNA associated with calcineurin within the prefrontal cortex, an effect that is sustained for at least several weeks (Miller et al., Reference Miller, Gavin, White, Parrish, Honasoge and Yancey2010).
Alterations in hippocampal DNA methylation appear to serve as markers not only of memory but also of exposure to chronic stress (Chertkow-Deutsher, Cohen, Klein, & Ben-Shachar, Reference Chertkow-Deutsher, Cohen, Klein and Ben-Shachar2010; Roth, Zoladz, Sweatt, & Diamond, Reference Roth, Zoladz, Sweatt and Diamond2011). For example, repeated exposure to predatory and social instability stress produces rodents that show learning and memory deficits, increased anxiety-like behavior, and glucocorticoid abnormalities weeks to months following the initiation of the stress regimen (Zoladz, Conrad, Fleshner, & Diamond, Reference Zoladz, Conrad, Fleshner and Diamond2008; Zoladz, Fleshner, & Diamond, Reference Zoladz, Fleshner and Diamond2012). We have recently shown that these behavioral abnormalities coincide with robust alterations in hippocampal Bdnf DNA methylation (that vary by subregion) and gene expression (Roth et al., Reference Roth, Zoladz, Sweatt and Diamond2011).
Other types of stress exposure have been shown to engage DNA methylation as determined from central (Elliott, Ezra-Nevo, Regev, Neufeld-Cohen, & Chen, Reference Elliott, Ezra-Nevo, Regev, Neufeld-Cohen and Chen2010; LaPlant et al., Reference LaPlant, Vialou, Covington, Dumitriu, Feng and Warren2010; Sterrenburg et al., Reference Sterrenburg, Gaszner, Boerrigter, Santbergen, Bramini and Elliott2011; Uchida et al., Reference Uchida, Hara, Kobayashi, Otsuki, Yamagata and Hobara2011) or peripheral (Tung et al., Reference Tung, Barreiro, Johnson, Hansen, Michopoulos and Toufexis2012) measures. Social defeat stress is associated with a lasting decrease in methylation of Crh DNA in the hypothalamus of animals that develop social avoidance behavior (Elliott et al., Reference Elliott, Ezra-Nevo, Regev, Neufeld-Cohen and Chen2010). It is interesting that mice in this study that did not show these epigenetic modifications also did not develop social avoidance behavior following defeat stress. Stress-susceptible (inbred BALB/c) and stress-resilient (C57BL/6) male mice are known to show behavioral differences following chronic exposure to mild stressors, and a study recently attributed these phenotypes to differential epigenetic marking of glial cell derived neurotrophic factor (Gdnf) DNA within the nucleus accumbens (Uchida et al., Reference Uchida, Hara, Kobayashi, Otsuki, Yamagata and Hobara2011). Although both strains of mice were shown to display increased methylation of the Gdnf promoter following chronic stress, stress-susceptible mice (BALB) showed additional epigenetic changes that lead to repression of Gdnf transcription, including gene promoter interactions with histone deactylases (HDACs). In contrast, mice that adapted to chronic stress (B6) showed additional epigenetic changes permissive for Gdnf transcription. These studies are beginning to provide a glimpse of the epigenetic attributes of stress resilience versus stress susceptibility.
Evidence from human studies
To date, there has only been one study that investigated changes in DNA methylation immediately following a specific stressful event in humans (Unternaehrer et al., Reference Unternaehrer, Luers, Mill, Dempster, Meyer and Staehli2012). Study participants were adults who had been exposed to war adversities in early childhood and subjected to the Trier Social Stress Test (TSST). Each participant had blood samples drawn at a time point prior to the TSST, 10 min following completion of the TSST, and 90 min after the TSST. Examination of DNA methylation patterns of two stress-related genes, oxytocin receptor and Bdnf, revealed stress-evoked DNA methylation changes across targeted sequences of the oxytocin receptor gene, with very little change detected in Bdnf DNA (though change was detected at one Bdnf CG site). Although their study population was based on individuals who might have increased susceptibility to DNA methylation changes (due to early-life stress and/or aging), their within-subject design provides seminal evidence regarding the ability of acute psychosocial stress in humans to have immediate epigenetic consequences. Work highlighted in the next section demonstrates DNA methylation alterations with reference to experiencing a number of lifetime stressful events or trauma exposure in posttraumatic stress disorder (PTSD).
Psychiatric Disorders With Aberrant DNA Methylation
Studies in the previous sections were chosen to demonstrate the remarkable ability of environmental input, both during and outside of periods of early-life development, to alter DNA methylation. These studies make it clear that DNA methylation alterations (both short- and long-lived) are biological responses to psychological and social–contextual factors. Furthermore, these observations are consistent with the hypothesis that epigenetic marking of genes could underlie aspects of psychopathology, especially in regard to neuropsychiatric disorders that can be associated with early-life stress and abnormal brain development and function. To this end, in this section I summarize evidence linking the presence of DNA methylation alterations with schizophrenia (SZ), PTSD, and mood disorders.
SZ
Increased Dnmt1 expression and decreased expression of reelin and GAD1 are common findings in the cortex of individuals with SZ (Guidotti et al., Reference Guidotti, Ruzicka, Grayson, Veldic, Pinna and Davis2007; Ruzicka et al., Reference Ruzicka, Zhubi, Veldic, Grayson, Costa and Guidotti2007; Veldic et al., Reference Veldic, Caruncho, Liu, Davis, Satta and Grayson2004, Reference Veldic, Kadriu, Maloku, Agis-Balboa, Guidotti and Davis2007; Veldic, Guidotti, Maloku, Davis, & Costa, Reference Veldic, Guidotti, Maloku, Davis and Costa2005). Deficits in reelin and GAD1 levels have been linked to altered methylation levels (Abdolmaleky et al., Reference Abdolmaleky, Cheng, Russo, Smith, Faraone and Wilcox2005; Connor & Akbarian, Reference Connor and Akbarian2008; Grayson et al., Reference Grayson, Jia, Chen, Sharma, Mitchell and Guidotti2005; Huang & Akbarian, Reference Huang and Akbarian2007), and genomewide epigenetic approaches on cortical tissue suggest there are many additional gene loci with altered DNA methylation in SZ, including other gene families related to GABAergic and neurotrophic (Bdnf) function (Connor & Akbarian, Reference Connor and Akbarian2008; Mill et al., Reference Mill, Tang, Kaminsky, Khare, Yazdanpanah and Bouchard2008). Peripheral measures of DNA methylation implicate epigenetic marking of the monoamine oxidase A gene promoter (Chen, Zhang, Zhang, Shen, & Xu, Reference Chen, Zhang, Zhang, Shen and Xu2012), DNA associated with several serotonin receptors (Abdolmaleky et al., Reference Abdolmaleky, Yaqubi, Papageorgis, Lambert, Ozturk and Sivaraman2011; Carrard, Salzmann, Malafosse, & Karege, Reference Carrard, Salzmann, Malafosse and Karege2011; Ghadirivasfi et al., Reference Ghadirivasfi, Nohesara, Ahmadkhaniha, Eskandari, Mostafavi and Thiagalingam2011), and the catechol-O-methyltransferase gene (Abdolmaleky et al., Reference Abdolmaleky, Cheng, Faraone, Wilcox, Glatt and Gao2006; Lott et al., Reference Lott, Burghardt, Burghardt, Bly, Grove and Ellingrod2012; Melas et al., Reference Melas, Rogdaki, Ösby, Schalling, Lavebratt and Ekström2012; Nohesara et al., Reference Nohesara, Ghadirivasfi, Mostafavi, Eskandari, Ahmadkhaniha and Thiagalingam2011). Finally, a genomewide analysis of DNA methylation on peripheral blood DNA samples obtained from monozygotic twin pairs discordant for major psychosis showed numerous loci with DNA methylation differences between twins discordant for SZ and bipolar disorder (Dempster et al., Reference Dempster, Pidsley, Schalkwyk, Owens, Georgiades and Kane2011).
PTSD
Peripheral measures of methylation show strong associations between child abuse, total life stress, methylation of DNA associated with genes related to immune function and inflammation, and the diagnosis of PTSD (Smith et al., Reference Smith, Conneely, Kilaru, Mercer, Weiss and Bradley2011; Uddin et al., Reference Uddin, Aiello, Wildman, Koenen, Pawelec and de los Santos2010). An interaction between methylation status of the SLC6A4 (Koenen et al., Reference Koenen, Uddin, Chang, Aiello, Wildman and Goldmann2011) or MAN2C1 (Uddin, Galea, et al., Reference Uddin, Galea, Chang, Aiello, Wildman and de los Santos2011) genes and the number of traumatic events experienced has been reported in PTSD. Assessment of serum DNA methylation patterns in genomic repetitive elements (LINE-1 and Alu) of US military service members pre- and postdeployment and with or without PTSD diagnosis suggest DNA methylation operative as a resilience or vulnerability factor (Rusiecki et al., Reference Rusiecki, Chen, Srikantan, Zhang, Yan and Polin2012).
There is also emerging evidence of a “double hit” model, in which having a risk allele and promoter DNA methylation may more accurately capture molecular risk of PTSD. For example, 9-repeat allele carriers of the dopamine transporter (SLC6A3) gene show an increased risk of lifetime PTSD when in conjunction with high methylation present in the SLC6A3 promoter (Chang et al., Reference Chang, Koenen, Galea, Aiello, Soliven and Wildman2012). Methylation of genes within the pituitary adenylate cyclase-activating polypeptide (PACAP) system, a system responsive to cellular stress and implicated in neurotrophic function, also appears to predict PTSD diagnosis. Females with high plasma PACAP levels and greater methylation of the PACAP receptor gene (ADCYAP1R1) containing a polymorphism show strongest PTSD symptoms and physiological fear responses (Ressler et al., Reference Ressler, Mercer, Bradley, Jovanovic, Mahan and Kerley2011).
Suicide and mood disorders
Epigenetic phenomena have similarly been associated with suicide and depression. Dnmt mRNA alterations (Poulter et al., Reference Poulter, Du, Weaver, Palkovits, Faludi and Merali2008), increased Bdnf DNA methylation (Keller et al., Reference Keller, Sarchiapone, Zarrilli, Videtic, Ferraro and Carli2010), and altered methylation patterns of numerous genes that play a role in neuronal growth, development, and cholinergic transmission (Sabunciyan et al., Reference Sabunciyan, Aryee, Irizarry, Rongione, Webster and Kaufman2012) have been found in the brains (within the frontal cortex, amygdala, and PVN) of individuals who committed suicide and/or had been diagnosed with major depression. Altered levels of Dnmt mRNA (Higuchi et al., Reference Higuchi, Uchida, Yamagata, Otsuki, Hobara and Abe2011) and Bdnf DNA methylation (Fuchikami et al., Reference Fuchikami, Morinobu, Segawa, Okamoto, Yamawaki and Ozaki2011) have likewise been found in peripheral measures in patients with major depression. Other findings in depressed patients include increased methylation of genes involved in brain development and metabolic processes (Uddin, Koenen, et al., Reference Uddin, Koenen, Aiello, Wildman, de los Santos and Galea2011), decreased methylation of genes, such as the inflammatory gene interleukin 6 (Uddin, Koenen, et al., Reference Uddin, Koenen, Aiello, Wildman, de los Santos and Galea2011), and high methylation of the angiotensin converting enzyme gene (Zill et al., Reference Zill, Baghai, Schüle, Born, Früstück and Büttner2012).
Evidence for the Heritable Nature of Acquired DNA Methylation Changes
Data from the previous sections are also consistent with the notion that if DNA methylation is an operational mechanism subserving an organism the ability to adapt to environmental factors, then the heritable nature of epigenetic changes could allow information acquired during one's lifetime to be passed on to offspring. Intriguing data from animal studies provide support that this does occur. As pointed out in an earlier section, infant experiences with nurturing mothers (high-LG behavior) decreases methylation of DNA associated with ER-α gene in the MPOA, producing increased gene expression and responsivity to hormonally primed maternal behavior (Champagne et al., Reference Champagne, Weaver, Diorio, Dymov, Szyf and Meaney2006). As a consequence of these epigenetic modifications, offspring and grand-offspring from high-LG mothers become high-LG mothers themselves (Champagne, Reference Champagne2008; Champagne & Meaney, Reference Champagne and Meaney2007). In this model, transmission of behavior and DNA methylation patterns represent experience-dependent inheritance mediated by maternal care itself.
As evidence of the ability of early-life adversity to produce multigenerational effects on DNA methylation, we have shown that offspring born to females that were maltreated (in their infancy) likewise showed altered Bdnf DNA methylation patterns (Roth et al., Reference Roth, Lubin, Funk and Sweatt2009). We used cross-fostering studies to address whether the appearance of DNA methylation alterations in this generation of infants was due to the mother's caregiving behaviors. Our results revealed that the changes in DNA methylation were not simply a product of the postnatal experience, as they were not easily reversed by altering the caregiving environment. One intriguing explanation for our results is the phenomenon of germ-line inheritance, and though we have yet to address this notion in our model, other studies have directly demonstrated heritable epigenetic and behavior changes via the germ-line that are independent of maternal care.
In an earlier section, the ability of infant separation to produce lasting changes in depressive-like behaviors and methylation of the Crh gene (Franklin et al., Reference Franklin, Russig, Weiss, Gräff, Linder and Michalon2010) was discussed. From this same study, anxiety and depression-related behaviors, as well as methylation changes, were also found to be present in offspring and grand-offspring derived from males that had experienced the initial separation (Franklin et al., Reference Franklin, Russig, Weiss, Gräff, Linder and Michalon2010; Weiss et al., Reference Smith, Conneely, Kilaru, Mercer, Weiss and Bradley2011). This is an important observation because in rodents the males do not provide infant care and are typically removed from a cage once successful mating has occurred. Subsequent studies from this line of work have revealed deficits in cognition and social interaction transmitted through the F3 generation but also stress resiliency, suggesting both positive and negative long-term and transgenerational effects of early-life stress (Franklin et al., 2011). Paternal transmission of stress-related behaviors induced by social defeat have also recently been demonstrated (Dietz et al., Reference Dietz, LaPlant, Watts, Hodes, Russo and Feng2011).
Another line of evidence supporting epigenetic transmission of acquired information comes from that manipulating the prenatal environment. Fetal-alcohol-exposed rats exhibit deficits in expression of the proopiomelanocortin (POMC), an effect that coincides with increased methylation of the POMC promoter and persists in F2 and F3 generation males (Govorko, Bekdash, Zhang, & Sarkar, Reference Govorko, Bekdash, Zhang and Sarkar2012). Offspring of pregnant guinea pigs treated with synthetic glucocorticoids show sustained alterations in central nervous system DNA methylation and gene expression (within the cerebellum), an effect likewise present in the next generation (Crudo et al., Reference Crudo, Petropoulos, Moisiadis, Iqbal, Kostaki and Machnes2012). Providing some of the strongest evidence of the phenomenon of germ-line epigenetic inheritance, including altered stress responses for three to four generations removed from the initial environmental insult, are studies exposing pregnant dams to endocrine disruptors (Crews et al., Reference Crews, Gillette, Scarpino, Manikkam, Savenkova and Skinner2012; Skinner, Anway, Savenkova, Gore, & Crews, Reference Skinner, Anway, Savenkova, Gore and Crews2008) or high-fat diets during gestation (Dunn & Bale, Reference Dunn and Bale2011).
Questions and Challenges in the Field
Animal studies over the past decade have provided fascinating insight into the relationship between environmental factors, experience-driven DNA methylation patterns, and behavioral outcomes. Discoveries as summarized in Figure 2 are consistent with the notion that epigenetic mechanisms underlie cause–effect relations in regard to neurobehavioral development and later stress-driven abnormalities. As applied to human development and psychopathology, epigenetic studies in humans also provide compelling evidence for DNA methylation alterations as a biological substrate through which a variety of factors can alter individuals for the long haul (Figure 2). Although studies are being published at a rapid pace, behavioral epigenetics is still considered an emerging scientific field, and there are many unresolved issues and challenges that are certain to attract additional research. This final section serves as a forum to propose a handful of questions (arranged in no order of importance) that might drive future research (both with animal models and humans) to more clearly elucidate the role of epigenetics in development and psychopathology.
What are the natural pathways by which environmental stimuli preferentially alter DNA methylation in brain regions, and how are these changes then translated into altered gene networks, circuitry, and behavior?
(Color online) Summary of psychological and social–contextual factors known to produce DNA methylation alterations. (Top) Experiences known to produce behavioral change in both developing and adult rodents that have been linked to altered DNA methylation and gene expression profiles. These epigenetic changes occur in many brain regions with known relevance to psychopathology, several of which are depicted here. (Bottom) Many of these animal findings have translated to similar observations in humans. A growing number of psychiatric disorders, several of which are listed here, have also been associated with DNA methylation alterations.
Although it is clear that environmental factors have direct effects on gene expression and behavior via alterations in DNA methylation that appear to have some brain region specificity, we do not at present understand how this may be the case. We do know that postmitotic neurons express the enzymatic machinery necessary for modifying chromatin and DNA methylation states (Brown, Weaver, Meaney, & Szyf, Reference Brown, Weaver, Meaney and Szyf2008; Feng, Chang, Li, & Fan, Reference Feng, Chang, Li and Fan2005; Ma et al., Reference Ma, Jang, Guo, Kitabatake, Chang and Pow-Anpongkul2009), providing a susceptible basis for environmentally driven epigenetic modifications. Brain region, and cell-type specificity for that matter, would require qualitative, quantitative, and spatial arrangement of mechanisms capable of orchestrating responses to similar stimuli, which appears to be in place. In the hippocampus for example, isoforms of Dnmt are known to vary by subregion (Brown et al., Reference Brown, Weaver, Meaney and Szyf2008) and cell type (Feng et al., Reference Feng, Chang, Li and Fan2005; Siegmund & Connor, Reference Siegmund and Connor2007). Although most studies have utilized a candidate gene approach to identify specific sites of DNA methylation changes (and rightly so, because this is a more sensitive approach for detecting methylation changes), an increasing number of studies that have utilized genomewide approaches indicate changes are occurring at numerous gene loci. This would suggest changes in gene networks, with functional implications for disruptions at the circuit and behavioral levels. How DNA methylation changes orchestrate these downstream effects is not known, and it is certainly an opportunity for future focus.
Do experiences within early-life developmental windows produce the greatest effects on DNA methylation?
Studies exposing either developing or adult animals to a variety of stressors demonstrate the remarkable ability of the central nervous system to alter its epigenetic status in response to environmental factors. At the same time, this shows that experiences do not have to be confined to early-life developmental periods in order to evoke DNA methylation changes. Whether sensitive periods early in life truly represent heightened periods of vulnerability to these types of changes is an issue that has not been systematically addressed. Expression profiles of Dnmt1, 3a, and 3b genes are detectable in neurons throughout the life span, though Dnmt3a is known to peak during the early postnatal period (Brooks, Marietta, & Goldman, Reference Brooks, Marietta and Goldman1996; Feng et al., Reference Feng, Chang, Li and Fan2005; Goto et al., Reference Goto, Numata, Komura, Ono, Bestor and Kondo1994). To directly answer this question, studies would need to incorporate a life span approach to provide information regarding when epigenetic modifications are more likely to occur, or perhaps be attenuated, in response to a specific stimulus or experience. Worth considering in this context is that it is possible that a much broader gene pool could be at play during sensitive periods (such as in early postnatal development or adolescence), whereas a more restricted gene pool is responsive to later-life factors.
With relevance to the importance of utilizing a life span approach, evidence has emerged that experiences do not always translate into immediate changes in DNA methylation but that changes can evolve after an appreciable delay. For example, separation of infant mice produces changes in AVP DNA methylation that are not detectable during infancy, but rather, seem to evolve over the course of development only to be present within adult tissue (Murgatroyd et al., Reference Murgatroyd, Patchev, Wu, Micale, Bockmuhl and Fischer2009). Adding further complexity, we also know that DNA methylation patterns naturally change with maturation and aging processes (Numata et al., Reference Numata, Ye, Hyde, Guitart-Navarro and Tao2012; Penner et al., Reference Penner, Roth, Chawla, Hoang, Roth and Lubin2010; Siegmund & Connor, Reference Siegmund and Connor2007). Both of these phenomena likely have significance in terms of “stress incubation” and direct versus indirect trajectories leading to later behavior change or the onset of psychiatric disorder.
Are better animal models needed to fully realize the translational implications of DNA methylation?
Our knowledge regarding the role of epigenetic modifications in mediating behavioral effects has been mostly derived from rodent models that exclude any confounds of genetic variability and where the behavior outcome is fairly uniform. It is important to consider that in humans, however, genetic polymorphisms exist, and it is often the case that experiences that produce a particular outcome in some people do not in others. Thus, functional polymorphisms are predicted to add an extra layer of complexity to understanding how behavioral outcome is moderated by life experiences, and it may be the case that polymorphisms serve as predispositions that make individuals more susceptible to subsequent epigenetic alterations and disease. The flip side of this is that certain polymorphisms could also serve as protective factors against epigenetic alterations.
Although keeping animals in constant conditions to understand the association between an early-life experience and later outcome has obvious value, this experimental design excludes the reality of complex social environments and the summing effects of total life experiences that we know profoundly influence human behavior. One way that animal research could address this issue is to incorporate both early-life and later-life stress exposures in various models to determine outcomes associated with cumulative stress and epigenetic loads. Furthermore, it should be evident from the developmental animal studies reviewed here that rodent models have focused on mother–pup interactions and how the dynamics within this context can influence DNA methylation and subsequent development. In humans it is not the case that only mothers interact with their children, and a broader social context (fathers, grandparents, childcare facilities, etc.) has an ability to leave its imprint on DNA methylation and gene expression patterns. Animal models with communal nesting and environmental complexity may be a way to capture this.
Does DNA methylation play an important role in why males and females often have different outcomes from the same experience?
Some of the evidence reviewed in earlier sections suggests that epigenetic activity plays an important role in sex specificity and susceptibility to stress. This may be due to developmental windows in which some genes have the potential to be differentially marked between male and females. For example, DNA methylation of the ER-α gene is higher in female rodents than in males at postnatal day 1 (Schwarz, Nugent, & McCarthy, Reference Schwarz, Nugent and McCarthy2010). mRNA and protein levels of Dnmt3a (Kolodkin & Auger, Reference Kolodkin and Auger2011) and MeCP2 (Kurian, Forbes-Lorman, & Auger, Reference Kurian, Forbes-Lorman and Auger2007) within the infant amygdala are higher in females than in males, but by postnatal day 10 these sex differences have disappeared. Dnmt3a is highest in the female and male cortex at postnatal day 10, whereas Dnmt1 is highest after weaning (Westberry, Trout, & Wilson, Reference Westberry, Trout and Wilson2010). Within the MPOA, gene promoters involved in sexual differentiation of the brain show differential epigenetic patterns between males and females at both an embryonic and early postnatal stage (Matsuda et al., Reference Matsuda, Mori, Nugent, Pfaff, McCarthy and Kawata2011). It stands to reason that developmental epigenetic studies that incorporate both sexes will reveal substantial etiological information regarding sex-specific development of behavior.
Can we target the epigenome for behavioral benefits?
A new type of therapy aimed at correcting epigenetic “defects” has received considerable attention. In so-called epigenetic therapy, investigators aim to use drugs like 5-azacytidine, zebularine, sodium butyrate, and trichostatin A to relax chromatin structure in order to provide gene transcription accessibility. The ability of these drugs to correct epigenetic patterns was first recognized in cancer treatment, but the scope of their application has continued to be broadened to include enhancing cognition and treating specific symptoms of various psychiatric disorders. HDAC inhibitors, for example, have been successfully used to reverse deficits in synaptic plasticity, learning and memory, and stress-related behaviors in rodents (for a review, see Abel & Zukin, Reference Abel and Zukin2008).
In several of the aforementioned developmental studies, investigators have successfully modified patterns of DNA methylation in the adult brain that were associated with early-life experiences (Roth et al., Reference Roth, Lubin, Funk and Sweatt2009; Weaver et al., Reference Weaver, Cervoni, Champagne, D'Alessio, Sharma and Seckl2004). The ability of epigenetic therapy to reverse gene deficits (and behavior) that were either set up in infancy or in cognitively impaired animals is a remarkable finding in its own right. Since these studies have only examined the effects of epigenetic therapy on gene patterns or behavior on a rather short-time scale (hours to days later), whether this strategy would be successful as a standalone treatment to stably (i.e., life-long) reverse aberrant DNA methylation and behavior patterns is not known. Animals would need to be followed for long periods of time (another point arguing for a life-span design in studies) and, perhaps, through multiple generations. This approach is not only necessary to help us understand trajectories of psychiatric disorders, but to understand when, where, and how to successfully intervene. Whether behavioral therapies, such as environmental or social enrichment, would be better suited for such a long-term application, or in combination with drugs targeted at epigenetically modifying programs of genes, is also a question open for investigation.
Can peripheral measures really tell us anything about the brain?
DNA methylation alterations continue to be linked to psychiatric disorders, and this has led to the idea that peripheral measures of DNA methylation (including from blood samples or cheek swabs) can serve as a proxy for brain changes that have already occurred or even as a predictive biomarker for the probability of some outcome or individual responsivity to clinical treatment. As highlighted in an earlier section, a growing body of work has noticeably demonstrated a link between blood-DNA methylation profiles and the risk for and diagnosis of psychiatric disorders. Since there is accumulating evidence that epigenetic modifications occur with specificity across tissue and cell types (Davies et al., Reference Davies, Volta, Pidsley, Lunnon, Dixit and Lovestone2012; Iwamoto et al., Reference Iwamoto, Bundo, Ueda, Oldham, Ukai and Hashimoto2011; Ladd-Acosta et al., Reference Ladd-Acosta, Pevsner, Sabunciyan, Yolken, Webster and Dinkins2007), however, questions arise regarding the ability of peripheral measures of DNA methylation to serve as an accurate and reliable proxy for changes occurring the brain and, thus, the viability of using DNA methylation as a biomarker.
Although the link between peripheral and central measures has not been unequivocally established, evidence we do have at present suggests blood-DNA methylation profiles do show promise of serving as valuable diagnostic biomarkers. For example, it was shown in one study that methylation patterns of the rodent catechol-O-methyltransferase gene were directly correlated in peripheral blood mononuclear cells and the prefrontal cortex (Ursini et al., Reference Ursini, Bollati, Fazio, Porcelli, Iacovelli and Catalani2011). However, methylation in the peripheral blood mononuclear cells did not correlate with patterns in the hippocampus (although they were in the same direction) or striatum. In the largest cross-tissue and interindividual comparison of blood and brain methylation patterns in humans, investigators found that though DNA methylation at specific gene loci were found to differ between tissue types (blood, cortex, cerebellum, etc.), strong correlations between DNA methylation for blood and brain tissue were present (Davies et al., Reference Davies, Volta, Pidsley, Lunnon, Dixit and Lovestone2012).
Conclusions
Paradigm-shifting research in the past decade has provided evidence that epigenetics serve as candidate pathways by which experiences can leave their mark on genes to drive sustained changes in behavior. Although we still lack a complete understanding of the cause-and-effect role of epigenetic mechanisms in health outcomes and disease, evidence is clear that epigenetic alterations are biological consequences of early-life and later-life environmental input. Furthermore, the evidence at hand suggests these alterations likely play a role in the development and enduring nature of psychopathology. Although a complete picture has yet to emerge, our charge now is to incorporate the insights we have gained from these studies into programs and policies, an action point increasingly making its way into the literature (Birnbaum & Jung, Reference Birnbaum and Jung2011; Hackman, Farah, & Meaney, Reference Hackman, Farah and Meaney2010; Rothstein, Cai, & Marchant, Reference Rothstein, Cai and Marchant2009). These include those of the public health sector, such as programs designed to help alleviate socioeconomic disparities and child advocacy programs aimed at helping infants and young children cope with early-life adversity. What we have learned regarding epigenetics and health outcomes has previously under-appreciated legal and ethical implications, which could include litigations regarding multigenerational, environmentally driven health effects. Finally, in the realm of medical policy this should include policy decisions regarding diets (including infant formula) and chemical exposure, medical experiences such as in vitro fertilization, and funding of research aimed at early detection and interventions to restore normal brain function and health.
In conclusion, epigenetic studies over the past decade have contributed fascinating insight into the role of DNA methylation (and chromatin for that matter) as a rich source for interactions between our environment and static genome. The birth of epigenetics research has provided an exciting new level of analysis for understanding tenets central to the discipline of developmental psychopathology. Further research using human study populations and animal models, especially those with clinical relevance, promises a greater understanding of the regulatory role of epigenetic processes in aspects of brain development relevant to the etiology of and resilience to psychiatric disorders. The current momentum in the field also points toward the applicability of using epigenetics, along with genetic polymorphisms, in providing individualized medicine and predicting more effective responses to treatments.
