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Gene-Environment Interplay and Epigenetic Processes

Marla B. Sokolowski, PhD, F.R.S.C., W. Thomas Boyce, MD

Co directors of the Child and Brain Development Program, Canadian Institute for Advanced Research (CIFAR), Canada

November 2017


By uncovering how genes and the environment affect each other at the molecular level, epigenetics promises to unveil how individual susceptibility and social conditions work together to affect individual differences in development, behaviour and child well-being. There is increasing evidence demonstrating that interactions between genetic predispositions and early life adversity are related to the emergence of neurodevelopmental health issues.  

This report describes different domains of gene-environment interplay and reviews recent research findings from observational and population studies in humans, and experimental studies in monkeys.


There are at least three categories of processes where interactions between genes/gene expression and the environment lead to differences in development trajectories that affect mental health and well-being. First, there is a correlation between genes and the environment, where a child has a genetic predisposition (an increased chance) of selecting, altering or generating categories of experience, for example, a child with behavioural inhibitions has a tendency to choose less challenging or less intensive social environments. Second, genes and the environment can affect each other bidirectionally. For example, there are cases where genetic variations only become apparent in the presence of specific environmental conditions, and alternatively, there are examples where environmental influences are revealed only among individuals carrying a particular genetic variant (genotype). The third category of interaction involves epigenetic processes where environmental signals mark or tag DNA and in some cases this can alter gene transcription and expression. These processes are discussed in greater detail in the first article of this chapter.2 

The exploration of these three domains of gene-environment interplay has become a prolific and engaging area of biomedical and social science research that promises to illuminate one of the deepest mysteries of human experience — how individual susceptibility and social conditions work together at the behavioural, physiologic, neural, cellular and molecular levels to initiate and sustain individual differences in development, behaviour and health, in some cases lead to disorders.


Many molecular mechanisms control gene expression. Groundbreaking research seeks to reveal how epigenetics is involved in the interplay between genes/gene expression and the environment and the consequences for brain development, behaviour and well-being. 

Research Context

Though suspected for a long time, it was only about a decade ago that reports appeared showing that epigenetic processes are associated with long-term human developmental and health outcomes. Studies in 2002 and 2003 revealed statistical links between early environmental conditions such as child maltreatment and stressful life events and the genetic variant one carries to predict antisocial behaviour and depression and the risk of suicide.3,4  

As the body of research has grown in size and data from a number of studies have been reviewed together in meta-analyses, researchers have found strong evidence for these interactions. For example, a 2010 review of more than 40 studies about gene-environment interactions involving the serotonin transporter gene revealed strong links to sensitivity towards negative and stressful environments,5 and a 2011 review of 54 studies found strong evidence that the serotonin transporter gene 5HTTLPR is involved in moderating the association between stress and depression.6

Recent Research Results

New evidence continues to build, demonstrating that environmental interactions with genes have an impact on early human neurodevelopment. 

Observational Research

One group of researchers recently reported an interaction between mothers’ dopamine receptor gene, DRD4, and reports of prenatal stress with predicting their children’s risk for developing antisocial outcomes such as conduct disorder or oppositional defiant disorder in early adolescence.7 In another study, researchers with the Bucharest Early Intervention Project ( identified a gene-environment interaction in children who remained institutionalized and were carriers of gene variants responsible for maintaining appropriate levels of two brain transmitters, dopamine and norepinephrine. Depletion of these neurotransmitters has been implicated in the risk for major depression. In another study, the early adversity of mothers as measured using a childhood trauma questionnaire interacted with the genetic variant they carried in the PRKG1 gene to affect maternal sensitivity to her infant. One variant buffered these mothers from earlier adversity while the other did not. This gene by environment interaction was replicated in two cohorts.8 Finally, researchers examined data from twins in the Early Childhood Longitudinal Study ( and found that genetic variation contributed in cognitive ability but was dependent on reciprocal, developmentally moderated interactions between children and their environment, and that children who were being raised in higher socioeconomic status homes were showing significantly higher scores by the age of 2 years. 

In studies involving rhesus macaques, researchers demonstrated that early rearing conditions with either mother or peer-related groups interacted with the serotonin transporter gene. That interaction had an observable, predictable impact on the manufacture of stress hormones during times of separation stress.9 Further, the interaction appeared to apply even among normal monkeys, where social dominance status during development worked together with the serotonin transporter gene and could predict the timing of sexual maturation: subordinate female monkeys who carried at least one copy of the altered promoter gene had significant delays in sexual maturation.10

Epigenetic processes at the population level  

One of the most intriguing recent discoveries is that epigenetic processes can influence the development of specific populations of people. For example, the maltreatment of children has been linked to faulty regulation of the hypothalamic-pituitary-adrenal (HPA) axis,11 a complex set of interactions between endocrine glands that produce hormones to regulate many body processes including stress, mood, sexuality, digestion, the immune system and energy storage, to increased inflammatory signaling12 and long-term changes in stress-responsive neural structures.13  

A study of over 200 newborns in Singapore found that there were over 1,400 genomic regions with wide variation in the state of epigenetic tagging across individuals, and that 75% of the measured variability in DNA methylation arose from genetic variants in interaction with environmental factor which included for example, maternal smoking, maternal depression, maternal BMI, infant birth weight and gestational age. Genetic variation alone accounted for 25% of the variation in methylation. Thus, there is a complex relationship between variation in methylation, the DNA sequence and environmental exposures.14 

Finally, researchers have recently demonstrated that epigenetic profiles in human populations are highly divergent, involving differences in frequencies of underlying genetic codes and complex gene-environment interactions. One series of studies examined over 14,000 genes in 180 different cell lines from European and African samples. Researchers found population-level differences in DNA methylation in over one-third of the genes and that most of these differences were attributable to differences in underlying numbers of gene variants.15 Other researchers have found similar epigenetic differences between populations.16,17,18 

Research Gaps 

To date, causal evidence about the relationship between genes and the environment is lacking in human populations. The sheer number of genes and environmental variables and their interactions poses a significant challenge for experimental research design in humans. Causal relationships between candidate DNA variants and their interactions with epigenetic modifications under adverse environmental conditions can be tested using animal models.   

In the future, the use of computers to perform higher-level mathematical modeling techniques to search for gene-environment interactions is expected to overcome this challenge and advance the field. Risk scores associated with developmental phenotypes,19 the observable characteristics and traits in development, and mathematical models of genome-wide association studies could one-day offer more answers than single searches can provide today.20 The way forward will examine how many genes work together as a network to add or multiply the effects that lead to developmental disorders.21 


Gene-environment interplay has emerged as a promising point of origin in studies of divergent developmental trajectories and the emergence of maladaptive outcomes including mental disorders. While there are many molecular mechanisms that control gene expression, research examining epigenetic processes is providing a groundbreaking look at how and under what conditions the intersection of genes/gene expression and the environment arise. 


Early life adversity or enrichment has far reaching effects across the lifespan. Gene-environment interactions between specific gene variants and risk-engendering early social environments may be linked to differences in epigenetic processes, explaining variation among individuals in the expression of genes linked to neurodevelopmental disorders. In the future, changes in epigenetic marks in response to an intervention could also provide useful biomarkers for evaluation of the effectiveness of the intervention.


  1. Boyce WT, Kobor MS. Development and the epigenome: the ‘synapse’ of gene-environment interplay. Developmental Science 2014;18:1:1-23.
  2. Sokolowski MB, Boyce WT. Biology of the Epigenome. In: Tremblay RE, Boivin M, Peters RDeV, eds. Sokolowski MB, Boyce WT, topic eds. Encyclopedia on Early Childhood Development [online]. Published October 2017. Accessed November 17, 2017.
  3. Caspi A, McClay J, Moffitt TE, Mill J, Martin J, Craig IW, Taylor A, Poulton R. Role of genotype in the cycle of violence in maltreated children. Science 2002;297(5582):851-854.
  4. Caspi A, Sugden K, Moffitt TE, Taylor A, Craig IW, Harrington H, McClay J, Mill J, Martin J, Braithwaite A, Poulton R. Influence of life stress on depression: moderation by a polymorphism in the 5-HTT gene. Science 2003;301(5631):386-389.
  5. Caspi A, Hariri AR, Holmes A, Uher R, Moffitt TE. Genetic sensitivity to the environment: the case of the serotonin transporter gene and its implications for studying complex diseases and traits. American Journal of Psychiatry 2010;167:509-527.
  6. Karg K, Burmeister M, Shedden K, Sen S. The serotonin transporter promoter variant (5-HTTLPR), stress, and depression meta-analysis revisited: evidence of genetic moderation. Archives in General Psychiatry 2011;68(5):444-454.
  7. Zohsel K, Buchmann AF, Blomeyer D, Hohm E, Schmidt MH, Esser G, Brandeis D, Banaschewski T, Laucht M. Mothers’ prenatal stress and their children’s antisocial outcomes – a moderating role for the Dopamine D4 Receptor (DRD4) gene. Journal of Child Psychology and Psychiatry 2014;55(1):69-76.
  8. Sokolowski HM, Vasquez OE, Unternaehrer E, Sokolowski DJ, Biergans SD, Atkinson L, Gonzalez A, Silveira PP, Levitan R, O'Donnell KJ, Steiner M, Kennedy J, Meaney MJ, Fleming AS, Sokolowski MB, On behalf of the MAVAN and Toronto Longitudinal Cohort research teams. The Drosophila foraging gene human orthologue PRKG1 predicts individual differences in the effects of early adversity on maternal sensitivity. Cognitive Development 2017;42:62-73.
  9. Barr CS, Newman TK, Shannon C, Parker C, Dvoskin RL, Becker ML, Schwandt M, Champoux M, Lesch KP, Goldman D, Suomi SJ, Higley JD. Rearing condition and rh5-HTTLPR interact to influence limbic-hypothalamic-pituitary-adrenal axis response to stress in infant macaques. Biological Psychiatry 2004;55(7):733-738.
  10. Wilson ME, Kinkead B. Gene–environment interactions, not neonatal growth hormone deficiency, time puberty in female rhesus monkeys. Biology of Reproduction 2008;78(4):736-743.
  11. Tarullo AR, Gunnar MR. Child maltreatment and the developing HPA axis. Hormones and Behavior 2006;50(4):632-639.
  12. Danese A, Pariante CM, Caspi A, Taylor A, Poulton R. Childhood maltreatment predicts adult inflammation in a life-course study. Proceedings of the National Academy of Sciences, USA 2007;104(4):1319-1324.
  13. McGowan PO, Sasaki A, D'Alessio AC, Dymov S, Labonté B, Szyf M, Turecki G, Meaney MJ. Epigenetic regulation of the glucocorticoid receptor in human brain associates with childhood abuse. Nature Neuroscience 2009;12(3):342-348. 
  14. Teh AL, Pan H, Chen L, Ong ML, Dogra S, et al. The effect of genotype and in utero environment on inter-individual variation in neonate DNA methylomes. Genome Research 2014;24(7):1064-1074. 
  15. Fraser HB, Lam LL, Neumann SM, Kobor MS. Population-specificity of human DNA methylation. Genome Biology 2012;13(2):R8.
  16. Adkins RM, Krushkal J, Tylavsky FA, Thomas F. Racial differences in gene-specific DNA methylation levels are present at birth. Birth Defects Research: Part A, Clinical and Molecular Teratology 2011;91(8):728-736.
  17. Heyn H, Moran S, Hernando-Herraez I, Sayols S, Gomez A, Sandoval J, Monk D, Hata K, Marques-Bonet T, Wang L, Esteller M. DNA methylation contributes to natural human variation. Genome Research 2013;23(9):1363-1372.
  18. Moen EL, Zhang X, Mu W, Delaney SM, Wing C, McQuade J, Myers J, Godley LA, Dolan ME, Zhang W. Genome-wide variation of cytosine modifications between European and African populations and the implications for complex traits. Genetics 2013;194(4):987-996. 
  19. Rietveld CA, Medland SE, Derringer J, Yang J, Esko T, et al. GWAS of 126,559 individuals identifies genetic variants associated with educational attainment. Science 2013;340(6139):1467-1471.
  20. Marigorta UM, Gibson G. A simulation study of gene-by-environment interactions in GWAS implies ample hidden effects. Frontiers in Genetics 2014;5:225.
  21. Gratten J, Wray NR, Keller MC, Visscher PM. Large-scale genomics unveils the genetic architecture of psychiatric disorders. Nature Neuroscience 2014;17(6):782-790.

How to cite this article:

Sokolowski MB, Boyce WT. Gene-Environment Interplay and Epigenetic Processes. In: Tremblay RE, Boivin M, Peters RDeV, eds. Sokolowski MB, Boyce WT, topic eds. Encyclopedia on Early Childhood Development [online]. Published November 2017. Accessed December 13, 2017.