McGovern PE, Zhang J, Tang J, Zhang Z, Hall GR, Moreau RA, et al. Fermented beverages of pre- and proto-historic China. Proc Natl Acad Sci. 2004;101(51):17593–8.

CAS  PubMed  Google Scholar 

Griswold MG, Fullman N, Hawley C, Arian N, Zimsen SRM, Tymeson HD, et al. Alcohol use and burden for 195 countries and territories, 1990–2016: a systematic analysis for the Global Burden of Disease Study 2016. Lancet. 2018;392(10152):1015–35.

Rehm J, Gmel G, Sempos CT, Trevisan M. Alcohol-related morbidity and mortality. Alcohol Res Health. 2003;27(1):39–51.

PubMed  PubMed Central  Google Scholar 

Harris RA, Trudell JR, Mihic SJ. Ethanol’s molecular targets. Sci Signal. 2008;1(28):re7.

PubMed  PubMed Central  Google Scholar 

Geil CR, Hayes DM, McClain JA, Liput DJ, Marshall SA, Chen KY, et al. Alcohol and adult hippocampal neurogenesis: promiscuous drug, wanton effects. Prog Neuro-Psychopharmacol Biol Psychiatry. 2014;54:103–13.

CAS  Google Scholar 

• Pandey SC, Kyzar EJ, Zhang H. Epigenetic basis of the dark side of alcohol addiction. Neuropharmacology. 2017;122:74–84 This review article integrates the concept of allostasis of epigenetic changes in the amygdala, a framework to understand negative affective state of alcohol use disorder by targeting windows of plasticity. These ideas help to better understand why epigenetic effects of acute and chronic ethanol are crucial for discovering better treatments for alcohol use disorder and related sequelae.

CAS  PubMed  PubMed Central  Google Scholar 

Yoshimura M, Pearson S, Kadota Y, Gonzalez CE. Identification of ethanol responsive domains of adenylyl cyclase. Alcohol Clin Exp Res. 2006;30(11):1824–32.

CAS  PubMed  Google Scholar 

Das R, Esposito V, Abu-Abed M, Anand GS, Taylor SS, Melacini G. cAMP activation of PKA defines an ancient signaling mechanism. Proc Natl Acad Sci U S A. 2007;104(1):93–8.

CAS  PubMed  Google Scholar 

Pandey SC. Neuronal signaling systems and ethanol dependence. Mol Neurobiol. 1998;17(1):1–15.

CAS  PubMed  Google Scholar 

Misra K, Pandey SC. The decreased cyclic-AMP dependent-protein kinase A function in the nucleus accumbens: a role in alcohol drinking but not in anxiety-like behaviors in rats. Neuropsychopharmacology. 2006;31(7):1406–19.

CAS  PubMed  Google Scholar 

Pandey SC, Roy A, Zhang H. The decreased phosphorylation of cyclic adenosine monophosphate (cAMP) response element binding (CREB) protein in the central amygdala acts as a molecular substrate for anxiety related to ethanol withdrawal in rats. Alcohol Clin Exp Res. 2003;27(3):396–409.

CAS  PubMed  Google Scholar 

Pandey SC, Zhang H, Roy A, Xu T. Deficits in amygdaloid cAMP-responsive element–binding protein signaling play a role in genetic predisposition to anxiety and alcoholism. J Clin Invest. 2005;115(10):2762–73.

CAS  PubMed  PubMed Central  Google Scholar 

Kumar S, Porcu P, Werner DF, Matthews DB, Diaz-Granados JL, Helfand RS, et al. The role of GABA(A) receptors in the acute and chronic effects of ethanol: a decade of progress. Psychopharmacology. 2009;205(4):529–64.

Lovinger DM, White G, Weight FF. Ethanol inhibits NMDA-activated ion current in hippocampal neurons. Science. 1989;243(4899):1721–4.

CAS  PubMed  Google Scholar 

Ron D, Messing RO. Signaling pathways mediating alcohol effects. Curr Top Behav Neurosci. 2013;13:87–126.

CAS  PubMed  PubMed Central  Google Scholar 

Tsankova N, Renthal W, Kumar A, Nestler EJ. Epigenetic regulation in psychiatric disorders. Nat Rev Neurosci. 2007;8(5):355–67.

CAS  Google Scholar 

Shukla SD, Lim RW. Epigenetic effects of ethanol on the liver and gastrointestinal system. Alcohol Res Curr Rev. 2013;35(1):47–55.

Google Scholar 

Waddington CH. The strategy of the genes: a discussion of some aspects of theoretical biology. Allen & Unwin; 1957. 280 p.

McEwen BS. Allostasis and the epigenetics of brain and body health over the life course: the brain on stress. JAMA Psychiatry. 2017;74(6):551–2.

PubMed  Google Scholar 

Szutorisz H, Hurd YL. Epigenetic effects of cannabis exposure. Biol Psychiatry. 2016;79(7):586–94.

CAS  PubMed  Google Scholar 

Krishnan HR, Sakharkar AJ, Teppen TL, Berkel TDM, Pandey SC. The epigenetic landscape of alcoholism. Int Rev Neurobiol. 2014;115:75–116.

PubMed  PubMed Central  Google Scholar 

Ponomarev I. Epigenetic control of gene expression in the alcoholic brain. Alcohol Res Curr Rev. 2013;35(1):69–76.

Google Scholar 

Hsu F-M, Gohain M, Chang P, Lu J-H, Chen P-Y. Chapter 4 - bioinformatics of epigenomic data generated from next-generation sequencing. In: Epigenetics in Human Disease. 2nd ed: Academic Press; 2018. p. 65–106. (Translational Epigenetics; vol. 6).

Hamamoto R, Komatsu M, Takasawa K, Asada K, Kaneko S. Epigenetics analysis and integrated analysis of multiomics data, including epigenetic data, using artificial intelligence in the era of precision medicine. Biomolecules. 2019;10(1):Pii: E62.

Google Scholar 

Bagot RC, Labonté B, Peña CJ, Nestler EJ. Epigenetic signaling in psychiatric disorders: stress and depression. Dialogues Clin Neurosci. 2014;16(3):281–95.

PubMed  PubMed Central  Google Scholar 

Feng J, Nestler EJ. Epigenetic mechanisms of drug addiction. Curr Opin Neurobiol. 2013;23(4):521–8.

CAS  PubMed  PubMed Central  Google Scholar 

Esteller M. Epigenetics in cancer. N Engl J Med. 2008;358(11):1148–59.

CAS  PubMed  Google Scholar 

French SW. Epigenetic events in liver cancer resulting from alcoholic liver disease. Alcohol Res Curr Rev. 2013;35(1):57–67.

Google Scholar 

Mahnke AH, Miranda RC, Homanics GE. Epigenetic mediators and consequences of excessive alcohol consumption. Alcohol. 2017;60:1–6.

CAS  PubMed  PubMed Central  Google Scholar 

Toh TB, Lim JJ, Chow EK-H. Epigenetics of hepatocellular carcinoma. Clin Transl Med. 2019;6:8.

Google Scholar 

Uysal F, Ozturk S, Akkoyunlu G. DNMT1, DNMT3A and DNMT3B proteins are differently expressed in mouse oocytes and early embryos. J Mol Histol. 2017;48(5–6):417–26.

CAS  PubMed  Google Scholar 

Mahmoud AM, Ali MM. Methyl donor micronutrients that modify DNA methylation and cancer outcome. Nutrients. 2019;13:11(3).

Google Scholar 

Li E, Zhang Y. DNA methylation in mammals. Cold Spring Harb Perspect Biol. 2014 May;6(5).

Boyes J, Bird A. DNA methylation inhibits transcription indirectly via a methyl-CpG binding protein. Cell. 1991;64(6):1123–34.

CAS  PubMed  Google Scholar 

Watt F, Molloy PL. Cytosine methylation prevents binding to DNA of a HeLa cell transcription factor required for optimal expression of the adenovirus major late promoter. Genes Dev. 1988;2(9):1136–43.

CAS  PubMed  Google Scholar 

Cedar H, Bergman Y. Programming of DNA methylation patterns. Annu Rev Biochem. 2012;81:97–117.

CAS  PubMed  Google Scholar 

Guo JU, Su Y, Zhong C, Ming G, Song H. Hydroxylation of 5-methylcytosine by TET1 promotes active DNA demethylation in the adult brain. Cell. 2011;145(3):423–34.

CAS  PubMed  PubMed Central  Google Scholar 

Bednar J, Horowitz RA, Grigoryev SA, Carruthers LM, Hansen JC, Koster AJ, et al. Nucleosomes, linker DNA, and linker histone form a unique structural motif that directs the higher-order folding and compaction of chromatin. Proc Natl Acad Sci. 1998;95(24):14173–8.

Luger K, Mäder AW, Richmond RK, Sargent DF, Richmond TJ. Crystal structure of the nucleosome core particle at 2.8 Å resolution. Nature. 1997;389(6648):251–60.

CAS  PubMed  Google Scholar 

Hergeth SP, Schneider R. The H1 linker histones: multifunctional proteins beyond the nucleosomal core particle. EMBO Rep. 2015;16(11):1439–53.

CAS  PubMed  PubMed Central  Google Scholar 

Renthal W, Nestler EJ. Chromatin regulation in drug addiction and depression. Dialogues Clin Neurosci. 2009;11(3):257–68.

PubMed  PubMed Central  Google Scholar 

Bannister AJ, Kouzarides T. Regulation of chromatin by histone modifications. Cell Res. 2011;21(3):381–95.

CAS  PubMed  PubMed Central  Google Scholar 

Kouzarides T. Chromatin modifications and their function. Cell. 2007;128(4):693–705.

CAS  PubMed  PubMed Central  Google Scholar 

Jakovcevski M, Akbarian S. Epigenetic mechanisms in neurological disease. Nat Med. 2012;18(8):1194–204.

CAS  PubMed  PubMed Central  Google Scholar 

Arrowsmith CH, Bountra C, Fish PV, Lee K, Schapira M. Epigenetic protein families: a new frontier for drug discovery. Nat Rev Drug Discov. 2012;11(5):384–400.

CAS  PubMed  Google Scholar 

Nightingale KP, O’Neill LP, Turner BM. Histone modifications: signalling receptors and potential elements of a heritable epigenetic code. Curr Opin Genet Dev. 2006;16(2):125–36.

CAS  PubMed  Google Scholar 

Costa FF. Non-coding RNAs, epigenetics and complexity. Gene. 2008;410(1):9–17.

CAS  PubMed  Google Scholar 

Kim T-K, Hemberg M, Gray JM, Costa AM, Bear DM, Wu J, et al. Widespread transcription at neuronal activity-regulated enhancers. Nature. 2010;465(7295):182–7.

Kolovos P, Knoch TA, Grosveld FG, Cook PR, Papantonis A. Enhancers and silencers: an integrated and simple model for their function. Epigenetics Chromatin. 2012;5:1.

CAS  PubMed  PubMed Central  Google Scholar 

Robison AJ, Nestler EJ. Transcriptional and epigenetic mechanisms of addiction. Nat Rev Neurosci. 2011;12(11):623–37.

CAS  PubMed  PubMed Central  Google Scholar 

. Bohnsack JP, Teppen T, Kyzar EJ, Dzitoyeva S, Pandey SC. The lncRNA BDNF-AS is an epigenetic regulator in the human amygdala in early onset alcohol use disorders. Transl Psychiatry. 2019;6:9 This translational study outlines an epigenetic mechanism in the human post-mortem amygdala by which alcohol exposure in adolescence promotes persistent BDNF dysregulation and resultant behavioral dysfunction by a naturally occurring lncRNA and its associated epigenetic regulatory mechanisms.

Google Scholar 

Jiang M-C, Ni J-J, Cui W-Y, Wang B-Y, Zhuo W. Emerging roles of lncRNA in cancer and therapeutic opportunities. Am J Cancer Res. 2019;9(7):1354–66.

CAS  PubMed  PubMed Central