1 Hoffmann, A. & Spengler, D. DNA memories of early social life. Neuroscience 264, 64-75, doi:10.1016/j.neuroscience.2012.04.003 (2014).
2 Enoch, M. A. The role of early life stress as a predictor for alcohol and drug dependence. Psychopharmacology 214, 17-31, doi:10.1007/s00213-010-1916-6 (2011).
3 Kirsch, D., Nemeroff, C. M. & Lippard, E. T. C. Early Life Stress and Substance Use Disorders: Underlying Neurobiology and Pathways to Adverse Outcomes. Adversity and Resilience Science, doi:10.1007/s42844-020-00005-7 (2020).
4 Szyf, M., Tang, Y. Y., Hill, K. G. & Musci, R. The dynamic epigenome and its implications for behavioral interventions: a role for epigenetics to inform disorder prevention and health promotion. Transl Behav Med 6, 55-62, doi:10.1007/s13142-016-0387-7 (2016).
5 Nylander, I. & Roman, E. Is the rodent maternal separation model a valid and effective model for studies on the early-life impact on ethanol consumption? Psychopharmacology 229, 555-569, doi:10.1007/s00213-013-3217-3 (2013).
6 Meaney, M. J. Maternal care, gene expression, and the transmission of individual differences in stress reactivity across generations. Annu Rev Neurosci 24, 1161-1192, doi:10.1146/annurev.neuro.24.1.1161 (2001).
7 Weaver, I. C. et al. Epigenetic programming by maternal behavior. Nat Neurosci 7, 847-854, doi:10.1038/nn1276 (2004).
8 McGowan, P. O. et al. Epigenetic regulation of the glucocorticoid receptor in human brain associates with childhood abuse. Nat Neurosci 12, 342-348, doi:10.1038/nn.2270 (2009).
9 Berkel, T. D. M. & Pandey, S. C. Emerging Role of Epigenetic Mechanisms in Alcohol Addiction. 41, 666-680, doi:10.1111/acer.13338 (2017).
10 Warnault, V., Darcq, E., Levine, A., Barak, S. & Ron, D. Chromatin remodeling--a novel strategy to control excessive alcohol drinking. Transl Psychiatry 3, e231, doi:10.1038/tp.2013.4 (2013).
11 Barbier, E. et al. DNA methylation in the medial prefrontal cortex regulates alcohol-induced behavior and plasticity. J Neurosci 35, 6153-6164, doi:10.1523/jneurosci.4571-14.2015 (2015).
12 Dugué, P. A. et al. Alcohol consumption is associated with widespread changes in blood DNA methylation: Analysis of cross-sectional and longitudinal data. Addict Biol, e12855, doi:10.1111/adb.12855 (2019).
13 Holmes, A., Spanagel, R. & Krystal, J. H. Glutamatergic targets for new alcohol medications. Psychopharmacology 229, 539-554, doi:10.1007/s00213-013-3226-2 (2013).
14 Kalivas, P. W., Lalumiere, R. T., Knackstedt, L. & Shen, H. Glutamate transmission in addiction. Neuropharmacology 56 Suppl 1, 169-173, doi:10.1016/j.neuropharm.2008.07.011 (2009).
15 Tsai, G. & Coyle, J. T. The role of glutamatergic neurotransmission in the pathophysiology of alcoholism. Annu Rev Med 49, 173-184, doi:10.1146/annurev.med.49.1.173 (1998).
16 Bell, R. L. et al. Ethanol-Associated Changes in Glutamate Reward Neurocircuitry: A Minireview of Clinical and Preclinical Genetic Findings. Prog Mol Biol Transl Sci 137, 41-85, doi:10.1016/bs.pmbts.2015.10.018 (2016).
17 Kalivas, P. W. The glutamate homeostasis hypothesis of addiction. Nat Rev Neurosci 10, 561-572, doi:10.1038/nrn2515 (2009).
18 Yuan, T. F. & Hou, G. The effects of stress on glutamatergic transmission in the brain. Mol Neurobiol 51, 1139-1143, doi:10.1007/s12035-014-8783-9 (2015).
19 Gunn, B. G. et al. Dysfunctional astrocytic and synaptic regulation of hypothalamic glutamatergic transmission in a mouse model of early-life adversity: relevance to neurosteroids and programming of the stress response. The Journal of neuroscience : the official journal of the Society for Neuroscience 33, 19534-19554, doi:10.1523/jneurosci.1337-13.2013 (2013).
20 Toya, S. et al. Early-life-stress affects the homeostasis of glutamatergic synapses. Eur J Neurosci 40, 3627-3634, doi:10.1111/ejn.12728 (2014).
21 Watt, M. J., Weber, M. A., Davies, S. R. & Forster, G. L. Impact of juvenile chronic stress on adult cortico-accumbal function: Implications for cognition and addiction. Progress in neuro-psychopharmacology & biological psychiatry 79, 136-154, doi:10.1016/j.pnpbp.2017.06.015 (2017).
22 Takamori, S., Rhee, J. S., Rosenmund, C. & Jahn, R. Identification of a vesicular glutamate transporter that defines a glutamatergic phenotype in neurons. Nature 407, 189-194, doi:10.1038/35025070 (2000).
23 Takamori, S., Rhee, J. S., Rosenmund, C. & Jahn, R. Identification of differentiation-associated brain-specific phosphate transporter as a second vesicular glutamate transporter (VGLUT2). The Journal of neuroscience : the official journal of the Society for Neuroscience 21, Rc182 (2001).
24 Anne, C. & Gasnier, B. Vesicular neurotransmitter transporters: mechanistic aspects. Current topics in membranes 73, 149-174, doi:10.1016/B978-0-12-800223-0.00003-7 (2014).
25 Comasco, E., Hallman, J. & Wallén-Mackenzie, A. Haplotype-tag single nucleotide polymorphism analysis of the vesicular glutamate transporter (VGLUT) genes in severely alcoholic women. Psychiatry Res 219, 403-405, doi:10.1016/j.psychres.2014.05.052 (2014).
26 Sakae, D. Y. et al. The absence of VGLUT3 predisposes to cocaine abuse by increasing dopamine and glutamate signaling in the nucleus accumbens. Mol Psychiatry 20, 1448-1459, doi:10.1038/mp.2015.104 (2015).
27 Flatscher-Bader, T., Zuvela, N., Landis, N. & Wilce, P. A. Smoking and alcoholism target genes associated with plasticity and glutamate transmission in the human ventral tegmental area. Hum Mol Genet 17, 38-51, doi:10.1093/hmg/ddm283 (2008).
28 Vrettou, M. et al. VGLUT2 rs2290045 genotype moderates environmental sensitivity to alcohol-related problems in three samples of youths. European child & adolescent psychiatry, doi:10.1007/s00787-019-01293-w (2019).
29 Alsiö, J. et al. Enhanced sucrose and cocaine self-administration and cue-induced drug seeking after loss of VGLUT2 in midbrain dopamine neurons in mice. The Journal of neuroscience : the official journal of the Society for Neuroscience 31, 12593-12603, doi:10.1523/JNEUROSCI.2397-11.2011 (2011).
30 Vrettou, M. et al. Ethanol affects limbic and striatal presynaptic glutamatergic and DNA methylation gene expression in outbred rats exposed to early-life stress. Addict Biol 22, 369-380, doi:10.1111/adb.12331 (2017).
31 Birgner, C. et al. VGLUT2 in dopamine neurons is required for psychostimulant-induced behavioral activation. Proceedings of the National Academy of Sciences of the United States of America 107, 389-394, doi:10.1073/pnas.0910986107 (2010).
32 Hnasko, T. S. et al. Vesicular glutamate transport promotes dopamine storage and glutamate corelease in vivo. Neuron 65, 643-656, doi:10.1016/j.neuron.2010.02.012 (2010).
33 Truitt, W. A. et al. Ethanol and nicotine interaction within the posterior ventral tegmental area in male and female alcohol-preferring rats: evidence of synergy and differential gene activation in the nucleus accumbens shell. Psychopharmacology, doi:10.1007/s00213-014-3702-3 (2014).
34 Zhou, F. C., Sahr, R. N., Sari, Y. & Behbahani, K. Glutamate and dopamine synaptic terminals in extended amygdala after 14-week chronic alcohol drinking in inbred alcohol-preferring rats. Alcohol 39, 39-49, doi:10.1016/j.alcohol.2006.06.013 (2006).
35 McClintick, J. N. et al. Gene expression changes in serotonin, GABA-A receptors, neuropeptides and ion channels in the dorsal raphe nucleus of adolescent alcohol-preferring (P) rats following binge-like alcohol drinking. Pharmacology, biochemistry, and behavior 129, 87-96, doi:10.1016/j.pbb.2014.12.007 (2015).
36 McBride, W. J. et al. Gene expression within the extended amygdala of 5 pairs of rat lines selectively bred for high or low ethanol consumption. Alcohol 47, 517-529, doi:https://doi.org/10.1016/j.alcohol.2013.08.004 (2013).
37 Zhang, C. R., Ho, M. F., Vega, M. C., Burne, T. H. & Chong, S. Prenatal ethanol exposure alters adult hippocampal VGLUT2 expression with concomitant changes in promoter DNA methylation, H3K4 trimethylation and miR-467b-5p levels. Epigenetics & chromatin 8, 40, doi:10.1186/s13072-015-0032-6 (2015).
38 Bendre, M., Comasco, E., Nylander, I. & Nilsson, K. W. Effect of voluntary alcohol consumption on Maoa expression in the mesocorticolimbic brain of adult male rats previously exposed to prolonged maternal separation. Transl Psychiatry 5, e690, doi:10.1038/tp.2015.186 (2015).
39 Krueger, F. & Andrews, S. R. Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications. Bioinformatics 27, 1571-1572, doi:10.1093/bioinformatics/btr167 (2011).
40 Hayes, A. F. & Matthes, J. Computational procedures for probing interactions in OLS and logistic regression: SPSS and SAS implementations. Behavior research methods 41, 924-936, doi:10.3758/BRM.41.3.924 (2009).
41 Farré, D. et al. Identification of patterns in biological sequences at the ALGGEN server: PROMO and MALGEN. Nucleic acids research 31, 3651-3653, doi:10.1093/nar/gkg605 (2003).
42 Messeguer, X. et al. PROMO: detection of known transcription regulatory elements using species-tailored searches. Bioinformatics 18, 333-334, doi:10.1093/bioinformatics/18.2.333 (2002).
43 Jones, P. A. Functions of DNA methylation: islands, start sites, gene bodies and beyond. Nat Rev Genet 13, 484-492, doi:10.1038/nrg3230 (2012).
44 MacDougald, O. A., Cornelius, P., Lin, F. T., Chen, S. S. & Lane, M. D. Glucocorticoids reciprocally regulate expression of the CCAAT/enhancer-binding protein alpha and delta genes in 3T3-L1 adipocytes and white adipose tissue. The Journal of biological chemistry 269, 19041-19047 (1994).
45 Tsigos, C. & Chrousos, G. P. Hypothalamic-pituitary-adrenal axis, neuroendocrine factors and stress. Journal of psychosomatic research 53, 865-871 (2002).
46 Erickson, E. K., Blednov, Y. A., Harris, R. A. & Mayfield, R. D. Glial gene networks associated with alcohol dependence. Scientific Reports 9, 10949, doi:10.1038/s41598-019-47454-4 (2019).
47 Moore, L. D., Le, T. & Fan, G. DNA methylation and its basic function. Neuropsychopharmacology 38, 23-38, doi:10.1038/npp.2012.112 (2013).
48 Bendre, M. et al. Early life stress and voluntary alcohol consumption in relation to Maoa methylation in male rats. Alcohol 79, 7-16, doi:https://doi.org/10.1016/j.alcohol.2018.11.001 (2019).
49 Shih, J. C., Chen, K. & Ridd, M. J. Monoamine oxidase: from genes to behavior. Annu Rev Neurosci 22, 197-217, doi:10.1146/annurev.neuro.22.1.197 (1999).
50 Zharkovsky, A., Anier, K. & Kalda, A. S-adenosylmethionine modifies cocaine-induced DNA methylation and increases locomotor sensitization in mice. International Journal of Neuropsychopharmacology 16, 2053-2066, doi:10.1017/S1461145713000394 %J International Journal of Neuropsychopharmacology (2013).
51 Todkar, A. et al. HPA Axis Gene Expression and DNA Methylation Profiles in Rats Exposed to Early Life Stress, Adult Voluntary Ethanol Drinking and Single Housing. Front Mol Neurosci 8, 90, doi:10.3389/fnmol.2015.00090 (2015).
52 Koob, G. F. & Volkow, N. D. Neurobiology of addiction: a neurocircuitry analysis. The lancet. Psychiatry 3, 760-773, doi:10.1016/S2215-0366(16)00104-8 (2016).
53 Michels, K. B. et al. Recommendations for the design and analysis of epigenome-wide association studies. Nature Methods 10, 949, doi:10.1038/nmeth.2632
https://www.nature.com/articles/nmeth.2632#supplementary-information (2013).
54 Leenen, F. A., Muller, C. P. & Turner, J. D. DNA methylation: conducting the orchestra from exposure to phenotype? Clinical epigenetics 8, 92, doi:10.1186/s13148-016-0256-8 (2016).
55 Turner, J. D., Kirschner, S. A., Molitor, A. M., Evdokimov, K. & Muller, C. P. in International Encyclopedia of the Social & Behavioral Sciences (Second Edition) (ed James D. Wright) 839-847 (Elsevier, 2015).
56 Kurdyukov, S. & Bullock, M. DNA Methylation Analysis: Choosing the Right Method. Biology 5, 3, doi:10.3390/biology5010003 (2016).