Epigenetic memory of environmental organisms: A reflection of lifetime stressor exposures

Esteller, 2002, Cancer as an epigenetic disease: DNA methylation and chromatin alterations in human tumours, J. Pathol., 196, 1, 10.1002/path.1024 Kriukiene, 2012, 5-Hydroxymethylcytosine-the elusive epigenetic mark in mammalian DNA, Chem. Soc. Rev., 41, 6916, 10.1039/c2cs35104h Xing, 2012, Recent advance in DNA epigenetic modifications-the sixth base in the genome, Sheng Li Ke Xue Jin Zhan, 43, 164 Gueant, 2013, Floate and fetal programming: a play in epigenomics?, Trends Endocrinol. Metab., 10.1016/j.tem.2013.01.010 Dominguez-Salas, 2012, Maternal nutritional status, C1 metabolism and offspring DNA methylation: a review of current evidence in human subjects, Proc. Natl. Acad. Sci., 71, 154 Alegria-Torres, 2011, Epigenetics and lifestyle, Epigenomics, 3, 267, 10.2217/epi.11.22 Baccarelli, 2009, Epigenetics and environmental chemicals, Curr. Opin. Pediatr., 21, 243, 10.1097/MOP.0b013e32832925cc Morgan, 2007, Microevolution and ecotoxicology of metals in invertebrates, Environ. Sci. Technol., 41, 1085, 10.1021/es061992x Flores, 2013, The role of methylation of DNA in environmental adaptation, Integr. Comp. Biol., 10.1093/icb/ict019 Turner, 2009, Epigenetic responses to environmental change and their evolutionary implications, Philos. Trans. R. Soc. Lond. B: Biol. Sci., 364, 3403, 10.1098/rstb.2009.0125 Dolinoy, 2007, Metastable epialleles, imprinting, and the foetal origins of adult diseases, Pediatr. Res., 61, 30, 10.1203/pdr.0b013e31804575f7 Christensen, 2009, Aging and environmental exposures alter tissue-specific DNA methylation dependent upon CpG island context, PLOS Genet., 5, 1, 10.1371/journal.pgen.1000602 Gomez-Diaz, 2012, Epigenetics of host–pathogen interactions: the road ahead and the road behind, PLoS Pathog., 8, e1003007, 10.1371/journal.ppat.1003007 Egger, 2004, Epigenetics in human disease and prospects for epigenetic therapy, Nature, 429, 457, 10.1038/nature02625 Jirtle, 2003, Epigenetic regulation of gene expression: how the genome integrates intrinsic and environmental signals, Nat. Genet., 33, 245, 10.1038/ng1089 Turner, 2007, Defining an epigenetic code, Nat. Cell Biol., 9, 2, 10.1038/ncb0107-2 Chan, 2008, Convergence of mutation and epigenetic alterations identifies common genes in cancer that predict for poor prognosis, PLOS Med., 5, 823, 10.1371/journal.pmed.0050114 Cui, 2010, A novel mechanism of epigenetic regulation: nucleosome-space occupancy, Biochem. Biophys. Res. Commun., 391, 884, 10.1016/j.bbrc.2009.11.157 Probst, 2009, Epigenetic inheritance during the cell cycle, Nat. Rev. Mol. Cell Biol., 10, 192, 10.1038/nrm2640 Pogribny, 2010, Epigenetic events in tumourigenesis: putting the pieces together, Exp. Oncol., 32, 132 Gronbaek, 2007, Epigenetic changes in cancer, Agric. Prod. Market Inform. Syst., 115, 1039 Thomson, 2010, CpG islands influence chromatin structure via the CpG-binding protein Cfp1, Nature, 464, 1082, 10.1038/nature08924 Butler, 2008, CFP1 interacts with DNMT1 independently of association with the Setd1 histone H3K4 methyltransferase complexes, DNA Cell Biol., 27, 533, 10.1089/dna.2007.0714 Tate, 2010, CXXC finger protein 1 restricts the Setd1A histone H3K4 methyltransferase complex to euchromatin, FASEB J., 277, 210 Herceg, 2011, Epigenetic mechanisms and cancer. An interface between the environment and the genome, Epigenetics, 6, 804, 10.4161/epi.6.7.16262 Tahiliani, 2009, Conversion of 5-methylcytosine to 5-hydroxymethylcytosine in mammalian DNA by MLL partner TET1, Science, 324, 930, 10.1126/science.1170116 Williams, 2011, TET1 and hydroxymethylcytosine in transcription and DNA methylation fidelity, Nature, 473, 343, 10.1038/nature10066 Bird, 2002, DNA methylation patterns and epigenetic memory, Genes Dev., 16, 6, 10.1101/gad.947102 Holliday, 2005, DNA methylation and epigenotypes, Biochemistry (Mosc)., 70, 500, 10.1007/s10541-005-0144-x Godmann, 2009, The dynamic epigenetic program in male germ cells: its role in spermatogenesis, testis cancer, and its response to the environment, Microsc. Res. Tech., 72, 603, 10.1002/jemt.20715 He, 2003, Regulation of flowering time by histone acetylation in Arabidopsis, Science, 302, 1751, 10.1126/science.1091109 Bastow, 2004, Vernalization requires epigenetic silencing of FLC by histone methylation, Nature, 427, 164, 10.1038/nature02269 Burn, 1993, DNA methylation, vernalization, and the initiation of flowering, Proc. Natl. Acad. Sci., 90, 287, 10.1073/pnas.90.1.287 Wilson, 2013, Developmental regulation of neuronal genes by DNA methylation: environmental influences, Int. J. Dev. Neurosci., 10.1016/j.ijdevneu.2013.03.004 Crews, 2010, Epigenetics, brain, behaviour, and the environment, Hormones (Athens), 9, 41, 10.14310/horm.2002.1251 McCarthy, 2008, Epigenetics-new frontiers in neuroendocrinology, Front. Neuroendocrinol., 29, 341, 10.1016/j.yfrne.2008.01.002 Navarro-Martin, 2011, DNA methylation of the gonadal aromatase (cyp19a) promoter is involved in temperature-dependent sex ratio shifts in the European sea bass, PLOS Genet., 7, 1, 10.1371/journal.pgen.1002447 Contractor, 2004, Evidence of gender- and tissue-specific promoter methylation and the potential for ethinylestradiol induced changes in Japanese medaka (Oryzias latipes) estrogen receptor and aromatase genes, Environ. Health, 67, 1 Massicotte, 2011, DNA methylation. A source of random variation in natural populations, Epigenetics, 6, 421, 10.4161/epi.6.4.14532 Lyko, 2010, The honey bee epigenomes: differential methylation of Bbrain DNA in queens and workers, PLoS Biol., 8, 1, 10.1371/journal.pbio.1000506 Moran, 2011, Methylation changes associated with early maturation stages in the Atlantic salmon, BMC Genet., 12, 1, 10.1186/1471-2156-12-86 Fraga, 2005, Epigenetic differences arise during the lifetime of monozygotic twins, Proc. Natl. Acad. Sci., 102, 10604, 10.1073/pnas.0500398102 Pogribny, 2013, DNA methylome alterations in chemical carcinogenesis, Cancer Lett., 334, 39, 10.1016/j.canlet.2012.09.010 Cortessis, 2012, Environmental epigenetics: prospects for studying epigenetic mediation of exposure–response relationships, Hum. Genet., 131, 1565, 10.1007/s00439-012-1189-8 Martinez-Zamudio, 2011, Environmental epigenetics in metal exposure, Epigenetics, 6, 820, 10.4161/epi.6.7.16250 Gore, 2008, Developmental programming and endocrine disruptor effects on reproductive neuroendocrine systems, Front. Neuroendocrinol., 29, 358, 10.1016/j.yfrne.2008.02.002 Crews, 2008, Epigenetics and its implications for behavioral neuroendocrinology, Front. Neuroendocrinol., 29, 344, 10.1016/j.yfrne.2008.01.003 Ho, 2006, Developmental exposure to estradiol and bisphenol A increases susceptibility to prostate carcinogenesis and epigenetically regulates phosphodiesterase type 4 variant 4, Cancer Res., 66, 5624, 10.1158/0008-5472.CAN-06-0516 Michel, 2006, Choline transport for phospholipid synthesis, Exp. Biol. Med., 231, 490, 10.1177/153537020623100503 Locker, 1986, DNA methylation and hepatocarcinogenesis in rats fed a choline-devoid diet, Carcinogenesis, 7, 1309, 10.1093/carcin/7.8.1309 Wilson, 1984, Hypomethylation of hepatic nuclear DNA in rats fed with a carcinogenic methyl-deficient diet, Biochem. J., 218, 987, 10.1042/bj2180987 Ghoshal, 1984, The induction of liver cancer by dietary deficiency of choline and methionine without added carcinogens, Carcinogenesis, 5, 1367, 10.1093/carcin/5.10.1367 Sibani, 2002, Studies of methionine cycle intermediates (SAM, SAH), DNA methylation and the impact of folate deficiency on tumour numbers in Min mice, Carcinogenesis, 23, 61, 10.1093/carcin/23.1.61 Mirbahai, 2013, Disruption of DNA methylation via S-adenosylhomocysteine is a key process in high incidence liver carcinogenesis in fish, J. Proteome Res., 10.1021/pr400195u Barros, 2009, Epigenetics: connecting environment and genotype to phenotype and disease, J. Dent. Res., 88, 400, 10.1177/0022034509335868 Jirtle, 2007, Environmental epigenomics and disease susceptibility, Nat. Rev. Genet., 8, 253, 10.1038/nrg2045 Li, 2003, Environmental exposure, DNA methylation, and gene regulation: lessons from diethylstilbesterol-induced cancers, Ann. N. Y. Acad. Sci., 983, 161, 10.1111/j.1749-6632.2003.tb05971.x Skinner, 2010, Epigenetic transgenerational actions of environmental factors in disease etiology, Trends Endocrinol. Metab., 21, 214, 10.1016/j.tem.2009.12.007 Prins, 2008, Estrogen imprinting: when your epigenetic memories come back to haunt you, Endocrinology, 149, 5919, 10.1210/en.2008-1266 Anway, 2006, Transgenerational effect of the endocrine disruptor vinclozolin on male spermatogenesis, J. Androl., 27, 868, 10.2164/jandrol.106.000349 Newbold, 2000, Proliferative lesions and reproductive tract tumours in male descendants of mice exposed developmentally to diethylstilbestrol, Carcinogenesis, 21, 1355, 10.1093/carcin/21.7.1355 Prins, 2007, Developmental estrogen exposures predispose to prostate carcinogenesis with aging, Reprod. Toxicol., 23, 374, 10.1016/j.reprotox.2006.10.001 Andres, 1984, Persistence, methylation and expression of vitellogenin gene derivatives after injection into fertilized eggs of Xenopus laevis, Nucleic Acids Res., 12, 2283, 10.1093/nar/12.5.2283 Li, 1997, Developmental exposure to diethylstilbestrol elicits demethylation of estrogen-responsive lactoferrin gene in mouse uterus, Cancer Res., 57, 4356 Dolinoy, 2008, The agouti mouse model: an epigenetic biosensor for nutritional and environmental alterations on the foetal epigenome, Nutr. Rev., 66, 1, 10.1111/j.1753-4887.2008.00056.x Dolinoy, 2006, Maternal genistein alters coat colour and protects Avy mouse offspring from obesity by modifying the foetal epigenome, Environ. Health Perspect., 114, 567, 10.1289/ehp.8700 Mirbahai, 2011, DNA methylation in liver tumourigenesis in fish from the environment, Epigenetics, 6, 1319, 10.4161/epi.6.11.17890 Feinberg, 2006, The epigenetic progenitor origin of human cancer, Nat. Rev. Genet., 7, 21, 10.1038/nrg1748 Youngson, 2008, Transgenerational epigenetic effects, Annu. Rev. Genomics Hum. Genet., 9, 233, 10.1146/annurev.genom.9.081307.164445 Reik, 2001, Evolution of imprinting mechanisms: the battle of the sexes begins in the zygote, Nat. Genet., 27, 255, 10.1038/85804 Whitelaw, 2008, Transgenerational epigenetic inheritance in health and disease, Curr. Opin. Genet. Dev., 18, 273, 10.1016/j.gde.2008.07.001 Francis, 1999, Nongenomic transmission across generations of maternal behaviour and stress responses in the rat, Science, 286, 1155, 10.1126/science.286.5442.1155 Weaver, 2004, Epigenetic programming by maternal behaviour, Nat. Neurosci., 7, 847, 10.1038/nn1276 Weaver, 2007, The transcription factor nerve growth factori protein A mediates epigenetic rogramming: altering epigenetic marks by immediate-early genes, J. Neurosci., 27, 1756, 10.1523/JNEUROSCI.4164-06.2007 Anway, 2005, Epigenetic transgenerational actions of endocrine disruptors and male fertility, Science, 308, 1466, 10.1126/science.1108190 Anway, 2006, Epigenetic transgenerational actions of endocrine disruptors, Endocrinology, 147, S43, 10.1210/en.2005-1058 Anway, 2008, Transgenerational effects of the endocrine disruptor vinclozolin on the prostate transcriptome and adult onset disease, Prostate, 68, 517, 10.1002/pros.20724 Anway, 2008, Transgenerational epigenetic programming of the embryonic testis transcriptome, Genomics, 91, 30, 10.1016/j.ygeno.2007.10.002 Anway, 2008, Comparative anti-androgenic actions of vinclozolin and flutamide on transgenerational adult onset disease and spermatogenesis, Reprod. Toxicol., 26, 100, 10.1016/j.reprotox.2008.07.008 Stouder, 2010, Transgenerational effects of the endocrine disruptor vinclozolin on the methylation pattern of imprinted genes in the mouse sperm, Reproduction, 139, 373, 10.1530/REP-09-0340 Nilson, 2012, Environmentally induced epigenetic transgenerational inheritance of ovarian disease, PLoS ONE, 7, e36129, 10.1371/journal.pone.0036129 Inawaka, 2009, Maternal exposure to anti-androgenic compounds, vinclozolin, flutamide and procymidone, has no effects on spermatogenesis and DNA methylation in male rats of subsequent generations, Toxicol. Appl. Pharmacol., 237, 178, 10.1016/j.taap.2009.03.004 Schneider, 2008, Vinclozolin—the lack of a transgenerational effect after oral maternal exposure during organogenesis, Reprod. Toxicol., 25, 352, 10.1016/j.reprotox.2008.04.001 Schneider, 2013, Vinclozolin—No transgenerational inheritance of anti-androgenic effects after maternal exposure during organogenesis via the intraperitoneal route, Reprod. Toxicol., 37, 6, 10.1016/j.reprotox.2012.12.003 Vandegehuchte, 2010, Gene transcription profiles, global DNA methylation and potential transgenerational epigenetic effects related to Zn exposure history in Daphnia magna, Environ. Pollut., 158, 3323, 10.1016/j.envpol.2010.07.023 Vandegehuchte, 2009, Occurance of DNA methylation in Daphnia magna and influence of multigeneration Cd exposure, Environ. Int., 35, 700, 10.1016/j.envint.2009.01.002 Vandegehuchte, 2009, Quantitative DNA methylation in Daphnia magna and effects of multigeneration Zn exposure, Comp. Biochem. Physiol., 150, 343 Vandegehuchte, 2010, Direct and transgenerational impact on Daphnia magna of chemicals with a known effect on DNA methylation, Comp. Biochem. Physiol., 151, 278 Vandegehuchte, 2011, Epigenetics and its implications for ecotoxicology, Ecotoxicology, 20, 607, 10.1007/s10646-011-0634-0 Harris, 2012, Daphnia as an emerging epigenetic model organism, Genet. Res. Int., 2012, 1, 10.1155/2012/147892 Goodman, 2010, What do we need to know prior to thinking about incorporating an epigenetic evaluation into safety assessments?, Toxicol. Sci., 116, 375, 10.1093/toxsci/kfq133 Moggs, 2004, Epigenetics and cancer. Implications for drug discovery and safety assessment, Toxicol. Appl. Pharmacol., 196, 422, 10.1016/j.taap.2004.01.009 Legler, 2010, Epigenetics: an emerging field in environmental toxicology, Integr. Environ. Assess Manag., 6, 314, 10.1002/ieam.40 Sved, 1990, The expected equilibrium of the CpG dinucleotide in vertebrate genomes under a mutation model, Proc. Natl. Acad. Sci., 87, 4692, 10.1073/pnas.87.12.4692 Guerrero-Bosagna, 2005, Environmental signaling and evolutionary change: can exposure of pregnant mammals to environmental estrogens lead to epigenetically induced evolutionary changes in embryos?, Evol. Dev., 7, 341, 10.1111/j.1525-142X.2005.05033.x Ahmad, 2006, Anguilla anguilla L., oxidative stress biomarkers: an in situ study of freshwater wetland ecosystem (Pateira de Fermentelos, Portugal), Chemosphere, 65, 952, 10.1016/j.chemosphere.2006.03.042 Zhou, 2001, Influence of Cu, Zn, Pb, Cd and their heavy metal ion mixture on the DNA methylation level of the fish (Carassius auratus), J. Environ. Sci. (China), 21, 549 Stromqvist, 2010, DNA methylation levels in the 5′ flanking region of the vitellogenin I gene in liver and brain of adult zebrafish (Danio rerio)-sex and tissue differences and effects of 17α-ethinylestradiol exposure, Aquat. Toxicol., 98, 275, 10.1016/j.aquatox.2010.02.023 Scott, 2007, Evidence for estrogenic endocrine disruption in an offshore flatfish, the dab (Limanda limanda), Mar. Environ. Res., 64, 128, 10.1016/j.marenvres.2006.12.013 Lempiainen, 2011, Phenobarbital mediates an epigenetic switch at the constitutive androstane receptor (CAR) target gene Cyp2b10 in the liver of B6C3F1 mice, PLoS ONE, 6, 1, 10.1371/journal.pone.0018216 Phillips, 2009, Phenobarbital elicits unique, early changes in the expression of hepatic genes that affect critical pathways in tumour-prone B6C3F1 mice, Toxicol. Sci., 109, 193, 10.1093/toxsci/kfp050 Phillips, 2009, Multiple genes exhibit phenobarbital-induced constitutive active/androstane receptor-mediated DNA methylation changes during liver tumourigenesis and in liver tumours, Toxicol. Sci., 108, 273, 10.1093/toxsci/kfp031 Bachman, 2006, Phenobarbital induces progressive patterns of GC-rich and gene-specific altered DNA methylation in the liver of tumour-prone B6C3F1 mice, Toxicol. Sci., 91, 393, 10.1093/toxsci/kfj155 Pei, 2009, An overview of hepatocellular carcinoma study by omics-based methods, Acta Biochim. Biophys. Sin. (Shanghai), 41, 1, 10.1093/abbs/gmn001 Brede, 2009, The impact of human-made ecological changes on the genetic architecture of Daphnia species, Proc. Natl. Acad. Sci., 106, 4758, 10.1073/pnas.0807187106 Kerfoot, 2004, Experimental paleoecology (resurrection ecology): chasing Van Valen's Red Queen hypothesis, Limnol. Oceanogr., 49, 1300, 10.4319/lo.2004.49.4_part_2.1300 Eads, 2008, Ecological genomics in Daphnia: stress responses and environmental sex determination, Heredity, 100, 184, 10.1038/sj.hdy.6800999 Furusawa, 2013, Epigenetic feedback regulation accelerates adaptation and evolution, PLoS ONE, 8, e61251, 10.1371/journal.pone.0061251 Paun, 2010, Stable epigenetic effects impact adaptation in allopolyploid orchids (Dactylorhiza: Orchidaceae), Mol. Biol. Evol., 27, 2465, 10.1093/molbev/msq150 Brautigam, 2013, Epigenetic regulation of adaptive responses of forest tree species to the environment, Ecol. Evol., 3, 399, 10.1002/ece3.461 Hirsch, 2013, Epigenetic variation, inheritance, and selection in plant populations, Cold Spring Harb. Symp. Quant. Biol.