Articles Clustered According to Topic (There are Redundancies)

(This List Should be considered a starting point only)


Epigenetics Home | Syllabus | Topics & Weekly Readings | Schedules

Chapter 1: General Introduction (Michael)

Chapter 2: Mechanics of Epigenetics Simplified

Chapter 3: Assessment of Epigenetic States

Chapters 4 and 5: Diet, Acquired and Transgenerational Epigenetic Changes

Dutch Studies
H. Delisle. [Foetal programming of nutrition-related chronic diseases]. Sante 2002; 12: 56-63.
K.B. Michels. Early life predictors of chronic disease. J Womens Health (Larchmt) 2003; 12: 157-161.
R.C. Painter, et al. Maternal nutrition during gestation and carotid arterial compliance in the adult offspring: the Dutch famine birth cohort. J Hypertens 2007; 25: 533-540.
T. Roseboom, et al. The Dutch famine and its long-term consequences for adult health. Early Hum Dev 2006; 82: 485-491.
T.J. Roseboom, et al. Blood pressure in adults after prenatal exposure to famine. J Hypertens 1999; 17: 325-330.
Z. Stein & M. Susser. The Dutch famine, 1944-1945, and the reproductive process. II. Interrelations of caloric rations and six indices at birth. Pediatr Res 1975; 9: 76-83.
A.W. Braam, et al. Religious denomination and depression in older Dutch citizens: patterns and models. J Aging Health 1998; 10: 483-503.

Swedish Overkalix Studies
L.O. Bygren, et al. Longevity determined by paternal ancestors' nutrition during their slow growth period. Acta Biotheor 2001; 49: 53-59.
G. Kaati, et al. Cardiovascular and diabetes mortality determined by nutrition during parents' and grandparents' slow growth period. Eur J Hum Genet 2002; 10: 682-688.
M.E. Pembrey, et al. Sex-specific, male-line transgenerational responses in humans. Eur J Hum Genet 2006; 14: 159-166.
P. Tinghog, et al. Migration and mortality trajectories: a study of individuals born in the rural community of Overkalix, Sweden. Soc Sci Med 2011; 73: 744-751.
G. Kaati, et al. Transgenerational response to nutrition, early life circumstances and longevity. Eur J Hum Genet 2007; 15: 784-790.
M.E. Pembrey. Male-line transgenerational responses in humans. Hum Fertil (Camb) 2010; 13: 268-271.
B.T. Heijmans, et al. The epigenome: archive of the prenatal environment. Epigenetics 2009; 4: 526-531.
B.T. Heijmans, et al. Persistent epigenetic differences associated with prenatal exposure to famine in humans. Proc Natl Acad Sci U S A 2008; 105: 17046-17049.
M.E. Pembrey. Male-line transgenerational responses in humans. Hum Fertil (Camb) 2010; 13: 268-271.

Others
G.C. Burdge, et al. Progressive, transgenerational changes in offspring phenotype and epigenotype following nutritional transition. PLoS One 2011; 6: e28282.
T. Delport & I. Pollard. Changing perspective on obesity: genetic and environmental health consequences in the offspring. Eubios Journal of Asian and International Bioethics 2010; 20: 170-173.
L. Gong, et al. Gestational low protein diet in the rat mediates Igf2 gene expression in male offspring via altered hepatic DNA methylation. Epigenetics 2010; 5: 619-626.
R. Lambrot, et al. Low paternal dietary folate alters the mouse sperm epigenome and is associated with negative pregnancy outcomes. Nat Commun 2013; 4: 2889.
R.A. Waterland, et al. Maternal methyl supplements increase offspring DNA methylation at Axin Fused. Genesis 2006; 44: 401-406.
G.L. Wolff, et al. Maternal epigenetics and methyl supplements affect agouti gene expression in Avy/a mice. FASEB J 1998; 12: 949-957.
R.A. Waterland, et al. Season of conception in rural gambia affects DNA methylation at putative human metastable epialleles. PLoS Genet 2010; 6: e1001252.
J.A. Colacino, et al. Pretreatment dietary intake is associated with tumor suppressor DNA methylation in head and neck squamous cell carcinomas. Epigenetics 2012; 7: 883-891.
T. Delport & I. Pollard. Changing perspective on obesity: genetic and environmental health consequences in the offspring. Eubios Journal of Asian and International Bioethics 2010; 20: 170-173.
R. Lambrot, et al. Low paternal dietary folate alters the mouse sperm epigenome and is associated with negative pregnancy outcomes. Nat Commun 2013; 4: 2889.
G. Arakeri, et al. Cleft lip and palate: an adverse pregnancy outcome due to undiagnosed maternal and paternal coeliac disease. Med Hypotheses 2010; 75: 93-98.

Chapter 6: Social influences Upon Epigenetic States


Rat Nuturing
R.M. Sapolsky. Mothering style and methylation. Nat Neurosci 2004; 7: 791-792.
I.C. Weaver. Epigenetic programming by maternal behavior and pharmacological intervention. Nature versus nurture: let's call the whole thing off. Epigenetics 2007; 2: 22-28.
I.C. Weaver, et al. Epigenetic programming by maternal behavior. Nat Neurosci 2004; 7: 847-854.
I.C. Weaver, et al. Reversal of maternal programming of stress responses in adult offspring through methyl supplementation: altering epigenetic marking later in life. J Neurosci 2005; 25: 11045-11054.
B.S. Wheeler, et al. Uncoupling of genomic and epigenetic signals in the maintenance and inheritance of heterochromatin domains in fission yeast. Genetics 2012; 190: 549-557.

Psychology and Trauma
B. Labonte, et al. Genome-wide epigenetic regulation by early-life trauma. Arch Gen Psychiatry 2012; 69: 722-731.
P.O. McGowan, et al. Epigenetic regulation of the glucocorticoid receptor in human brain associates with childhood abuse. Nat Neurosci 2009; 12: 342-348.
B. Labonte, et al. Genome-wide epigenetic regulation by early-life trauma. Arch Gen Psychiatry 2012; 69: 722-731.
P.G. Roma, et al. Effects of cross-fostering on cocaine-induced conditioned taste aversions in Fischer and Lewis rats. Dev Psychobiol 2007; 49: 172-179.
T.L. Roth, et al. Lasting epigenetic influence of early-life adversity on the BDNF gene. Biol Psychiatry 2009; 65: 760-769.
J.M. Schwarz, et al. Early-life experience decreases drug-induced reinstatement of morphine CPP in adulthood via microglial-specific epigenetic programming of anti-inflammatory IL-10 expression. J Neurosci 2011; 31: 17835-17847.
S. Keller, et al. Increased BDNF promoter methylation in the Wernicke area of suicide subjects. Arch Gen Psychiatry 2010; 67: 258-267.
C. Ernst, et al. Alternative splicing, methylation state, and expression profile of tropomyosin-related kinase B in the frontal cortex of suicide completers. Arch Gen Psychiatry 2009; 66: 22-32.
Z. Kaminsky, et al. Epigenetics of personality traits: an illustrative study of identical twins discordant for risk-taking behavior. Twin Res Hum Genet 2008; 11: 1-11.
M. Pascual, et al. Impact of TLR4 on behavioral and cognitive dysfunctions associated with alcohol-induced neuroinflammatory damage. Brain Behav Immun 2011; 25 Suppl 1: S80-91.
A.W. Braam, et al. Religious denomination and depression in older Dutch citizens: patterns and models. J Aging Health 1998; 10: 483-503.
Y. Liu, et al. Depression in pregnancy, infant birth weight and DNA methylation of imprint regulatory elements. Epigenetics 2012; 7: 735-746.
J. Elia, et al. Attention-deficit/hyperactivity disorder genomics: update for clinicians. Curr Psychiatry Rep 2012; 14: 579-589.
B.G. Dias & K.J. Ressler. Parental olfactory experience influences behavior and neural structure in subsequent generations. Nat Neurosci 2013.

Chapter 7: Epigenetic Risks and Medicine
, Drugs

Addicitive Drugs and Alcohol
J.A. Colacino, et al. Pretreatment dietary intake is associated with tumor suppressor DNA methylation in head and neck squamous cell carcinomas. Epigenetics 2012; 7: 883-891.
S.L. Youngentob & J.I. Glendinning. Fetal ethanol exposure increases ethanol intake by making it smell and taste better. Proc Natl Acad Sci U S A 2009; 106: 5359-5364.
I. Ponomarev, et al. Gene coexpression networks in human brain identify epigenetic modifications in alcohol dependence. J Neurosci 2012; 32: 1884-1897.
S.L. Youngentob & J.I. Glendinning. Fetal ethanol exposure increases ethanol intake by making it smell and taste better. Proc Natl Acad Sci U S A 2009; 106: 5359-5364.
Z. Zhou, et al. Substance-specific and shared transcription and epigenetic changes in the human hippocampus chronically exposed to cocaine and alcohol. Proc Natl Acad Sci U S A 2011; 108: 6626-6631.
W. Renthal, et al. Delta FosB mediates epigenetic desensitization of the c-fos gene after chronic amphetamine exposure. J Neurosci 2008; 28: 7344-7349.
P.G. Roma, et al. Effects of cross-fostering on cocaine-induced conditioned taste aversions in Fischer and Lewis rats. Dev Psychobiol 2007; 49: 172-179.
V. Nieratschker, et al. Epigenetic alteration of the dopamine transporter gene in alcohol-dependent patients is associated with age. Addict Biol 2012.P.G.
Roma, et al. Effects of cross-fostering on cocaine-induced conditioned taste aversions in Fischer and Lewis rats. Dev Psychobiol 2007; 49: 172-179.
J.M. Schwarz, et al. Early-life experience decreases drug-induced reinstatement of morphine CPP in adulthood via microglial-specific epigenetic programming of anti-inflammatory IL-10 expression. J Neurosci 2011; 31: 17835-17847.
V. Pastor, et al. Histone deacetylase inhibition decreases preference without affecting aversion for nicotine. J Neurochem 2011; 116: 636-645.
M. Pascual, et al. Impact of TLR4 on behavioral and cognitive dysfunctions associated with alcohol-induced neuroinflammatory damage. Brain Behav Immun 2011; 25 Suppl 1: S80-91.

Prescribed Drugs
A. Duenas-Gonzalez, et al. Valproic acid as epigenetic cancer drug: preclinical, clinical and transcriptional effects on solid tumors. Cancer treatment reviews 2008; 34: 206-222.
M.M. Brouwers, et al. Hypospadias: a transgenerational effect of diethylstilbestrol? Hum Reprod 2006; 21: 666-669.
R.R. Newbold, et al. Adverse effects of the model environmental estrogen diethylstilbestrol are transmitted to subsequent generations. Endocrinology 2006; 147: S11-17.
M. Fukuchi, et al. Valproic acid induces up- or down-regulation of gene expression responsible for the neuronal excitation and inhibition in rat cortical neurons through its epigenetic actions. Neurosci Res 2009; 65: 35-43.
T.C. Karagiannis, et al. The epigenetic modifier, valproic acid, enhances radiation sensitivity. Epigenetics 2006; 1: 131-137.
B. Monti, et al. Biochemical, molecular and epigenetic mechanisms of valproic acid neuroprotection. Current molecular pharmacology 2009; 2: 95-109.
L. Travaglini, et al. Epigenetic reprogramming of breast cancer cells by valproic acid occurs regardless of estrogen receptor status. Int J Biochem Cell Biol 2009; 41: 225-234.
E.W. Tung & L.M. Winn. Epigenetic modifications in valproic acid-induced teratogenesis. Toxicol Appl Pharmacol 2010; 248: 201-209.

Cancer
P. Blancafort, et al. Writing and rewriting the epigenetic code of cancer cells: from engineered proteins to small molecules. Mol Pharmacol 2013; 83: 563-576.
J.A. Colacino, et al. Pretreatment dietary intake is associated with tumor suppressor DNA methylation in head and neck squamous cell carcinomas. Epigenetics 2012; 7: 883-891.
A. Papi, et al. Epigenetic modifiers as anticancer drugs: effectiveness of valproic acid in neural crest-derived tumor cells. Anticancer Res 2010; 30: 535-540.
R. Verma, et al. In vitro profiling of epigenetic modifications underlying heavy metal toxicity of tungsten-alloy and its components. Toxicol Appl Pharmacol 2011; 253: 178-187.

Disease and Miscellaneous
T. Schlinzig, et al. Epigenetic modulation at birth - altered DNA-methylation in white blood cells after Caesarean section. Acta Paediatr 2009; 98: 1096-1099.
A. Esteki-Zadeh, et al. Human cytomegalovirus infection is sensitive to the host cell DNA methylation state and alters global DNA methylation capacity. Epigenetics 2012; 7: 585-593.
K.M. Bakulski, et al. Genome-wide DNA methylation differences between late-onset Alzheimer's disease and cognitively normal controls in human frontal cortex. J Alzheimers Dis 2012; 29: 571-588.
L. Gong, et al. Gestational low protein diet in the rat mediates Igf2 gene expression in male offspring via altered hepatic DNA methylation. Epigenetics 2010; 5: 619-626.

IVF
D. Lucifero, et al. Potential significance of genomic imprinting defects for reproduction and assisted reproductive technology. Hum Reprod Update 2004; 10: 3-18.
M.K. Skinner & M.D. Anway. Seminiferous cord formation and germ-cell programming: epigenetic transgenerational actions of endocrine disruptors. Ann N Y Acad Sci 2005; 1061: 18-32.
M.K. Skinner, et al. Epigenetic transgenerational inheritance of somatic transcriptomes and epigenetic control regions. Genome Biol 2012; 13: R91.
C. Feng, et al. General imprinting status is stable in assisted reproduction-conceived offspring. Fertil Steril 2011; 96: 1417-1423 e1419.
L. Li, et al. Genome-wide DNA methylation patterns in IVF-conceived mice and their progeny: a putative model for ART-conceived humans. Reprod Toxicol 2011; 32: 98-105.
H.Y. Zheng, et al. Study of DNA methylation patterns of imprinted genes in children born after assisted reproductive technologies reveals no imprinting errors: A pilot study. Exp Ther Med 2011; 2: 751-755.

Psychology/Psychiatry
H.M. Abdolmaleky, et al. Methylomics in psychiatry: Modulation of gene-environment interactions may be through DNA methylation. Am J Med Genet B Neuropsychiatr Genet 2004; 127B: 51-59.
J. Auta, et al. DNA-methylation gene network dysregulation in peripheral blood lymphocytes of schizophrenia patients. Schizophr Res 2013; 150: 312-318.
A.S. Brown & E.S. Susser. Prenatal nutritional deficiency and risk of adult schizophrenia. Schizophr Bull 2008; 34: 1054-1063.
J.J. Byrnes, et al. Multigenerational effects of adolescent morphine exposure on dopamine D2 receptor function. Psychopharmacology (Berl) 2013; 227: 263-272.
L. Chouliaras, et al. Histone deacetylase 2 in the mouse hippocampus: attenuation of age-related increase by caloric restriction. Curr Alzheimer Res 2013; 10: 868-876.
L. Chouliaras, et al. Age-related increase in levels of 5-hydroxymethylcytosine in mouse hippocampus is prevented by caloric restriction. Curr Alzheimer Res 2012; 9: 536-544.
T.J. Crow. 'The missing genes: what happened to the heritability of psychiatric disorders?'. Mol Psychiatry 2011; 16: 362-364.
T.J. Crow. Schizophrenia as variation in the sapiens-specific epigenetic instruction to the embryo. Clin Genet 2012; 81: 319-324.
T. Delport & I. Pollard. Changing perspective on obesity: genetic and environmental health consequences in the offspring. Eubios Journal of Asian and International Bioethics 2010; 20: 170-173.
B.G. Dias & K.J. Ressler. Parental olfactory experience influences behavior and neural structure in subsequent generations. Nat Neurosci 2014; 17: 86-96.
E. Dong, et al. Upregulation of TET1 and downregulation of APOBEC3A and APOBEC3C in the parietal cortex of psychotic patients. Transl Psychiatry 2012; 2: e159.
J. Elia, et al. Attention-deficit/hyperactivity disorder genomics: update for clinicians. Curr Psychiatry Rep 2012; 14: 579-589.
C. Ernst, et al. Alternative splicing, methylation state, and expression profile of tropomyosin-related kinase B in the frontal cortex of suicide completers. Arch Gen Psychiatry 2009; 66: 22-32.
K. Fekete, et al. Perinatal folate supply: relevance in health outcome parameters. Maternal & child nutrition 2010; 6 Suppl 2: 23-38.
E.M. Frans, et al. Autism risk across generations: a population-based study of advancing grandpaternal and paternal age. JAMA psychiatry 2013; 70: 516-521.
D.P. Gavin & S. Akbarian. Epigenetic and post-transcriptional dysregulation of gene expression in schizophrenia and related disease. Neurobiol Dis 2012; 46: 255-262.

Chapter 8: Environmental Epigenetics and Risk Assessment/Remediation

D.C. Dolinoy, et al. Maternal nutrient supplementation counteracts bisphenol A-induced DNA hypomethylation in early development. Proc Natl Acad Sci U S A 2007; 104: 13056-13061.
M.D. Anway, et al. Epigenetic transgenerational actions of endocrine disruptors and male fertility. Science 2005; 308: 1466-1469.
C. Guerrero-Bosagna, et al. Environmentally induced epigenetic transgenerational inheritance of altered Sertoli cell transcriptome and epigenome: molecular etiology of male infertility. PLoS One 2013; 8: e59922.
H.D. Morgan, et al. Epigenetic inheritance at the agouti locus in the mouse. Nat Genet 1999; 23: 314-318.
A.T. Moynihan, et al. Histone deacetylase inhibitors and a functional potent inhibitory effect on human uterine contractility. Am J Obstet Gynecol 2008; 199: 167 e161-167.
O. Pelkonen. Environmental influences on human foetal and placental xenobiotic metabolism. Eur J Clin Pharmacol 1980; 18: 17-24.
M.K. Skinner & M.D. Anway. Seminiferous cord formation and germ-cell programming: epigenetic transgenerational actions of endocrine disruptors. Ann N Y Acad Sci 2005; 1061: 18-32.
J.M. Swanson, et al. Developmental origins of health and disease: environmental exposures. Semin Reprod Med 2009; 27: 391-402.
M. Szyf. The dynamic epigenome and its implications in toxicology. Toxicol Sci 2007; 100: 7-23.
A. Toren, et al. Pediatric cancer: environmental and genetic aspects. Pediatr Hematol Oncol 1996; 13: 319-331.
T.Y. Zhang & M.J. Meaney. Epigenetics and the environmental regulation of the genome and its function. Annu Rev Psychol 2010; 61: 439-466, C431-433.
J. Guthman & B. Mansfield. The implications of environmental epigenetics: a new direction for geographic inquiry on health, space, and nature-society relations. Progress in Human Geography 2012; 37: 486-504.
R.P. Arasaradnam, et al. A review of dietary factors and its influence on DNA methylation in colorectal carcinogenesis. Epigenetics 2008; 3: 193-198.
R. Verma, et al. In vitro profiling of epigenetic modifications underlying heavy metal toxicity of tungsten-alloy and its components. Toxicol Appl Pharmacol 2011; 253: 178-187.

Chapter 9: Epigenetics: The Ethical, Legal, and Regulatory Challenges
T. Delport & I. Pollard. Changing perspective on obesity: genetic and environmental health consequences in the offspring. Eubios Journal of Asian and International Bioethics 2010; 20: 170-173.
C. Dupras, et al. Epigenetics and the Environment in Bioethics. Bioethics 2012.
J. Elia, et al. Attention-deficit/hyperactivity disorder genomics: update for clinicians. Curr Psychiatry Rep 2012; 14: 579-589.
M.H. Johnson. The problematic in-vitro embryo in the age of epigenetics. Reprod Biomed Online 2005; 10 Suppl 1: 88-96.
M. Loi, et al. Social Epigenetics and Equality of Opportunity. Public health ethics 2013; 6: 142-153.
M.A. Rothstein, et al. The ghost in our genes: legal and ethical implications of epigenetics. Health Matrix Clevel 2009; 19: 1-62.
M.A. Rothstein, et al. Ethical implications of epigenetics research. Nat Rev Genet 2009; 10: 224.
D. Ziech, et al. The role of epigenetics in environmental and occupational carcinogenesis. Chem Biol Interact 2010; 188: 340-349.
L. Daxinger & E. Whitelaw. Understanding transgenerational epigenetic inheritance via the gametes in mammals. Nat Rev Genet 2012; 13: 153-162.
F. Khan. Preserving human potential as freedom: a framework for regulating epigenetic harms. Health Matrix Clevel 2010; 20: 259-323.
R. Chadwick & A. O'Connor. Epigenetics and personalized medicine: prospects and ethical issues. Personalized Medicine 2013; 10: 463-471.
G. Gestri, et al. Six3 functions in anterior neural plate specification by promoting cell proliferation and inhibiting Bmp4 expression. Development 2005; 132: 2401-2413.
M. Hedlund. Epigenetic Responsibility. Medicine Studies 2012; 3: 171-183.
C.J. Weiner. Transgenerational Tort Liability for Epigenetic Disease. DePaul J Health Care L 2010; 13: 319-338.
J. Guthman & B. Mansfield. The implications of environmental epigenetics: a new direction for geographic inquiry on health, space, and nature-society relations. Progress in Human Geography 2012; 37: 486-504.
M. Loi, et al. Social Epigenetics and Equality of Opportunity. Public health ethics 2013; 6: 142-153.

Chapter 10: Epigenetics and Privacy Considerations
F.F. Costa. Big data in biomedicine. Drug Discov Today 2013.
J. Elia, et al. Attention-deficit/hyperactivity disorder genomics: update for clinicians. Curr Psychiatry Rep 2012; 14: 579-589.
S.D. Kahn. On the future of genomic data. Science 2011; 331: 728-729.

Chapter 11: Summary of Challenges and an Agenda for Development and Remediation