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Review Paper

The epigenetic side of human adaptation: hypotheses, evidences and theories

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Pages 1-9 | Received 10 Jul 2014, Accepted 02 Sep 2014, Published online: 21 Nov 2014

References

  • Alkorta-Aranburu G, Beall CM, Witonsky DB, Gebremedhin A, Pritchard JK, Di Rienzo A. 2012. The genetic architecture of adaptations to high altitude in Ethiopia. PLoS Genet 8:e1003110
  • Antequera F. 2003. Structure, function and evolution of CpG island promoters. CMLS 60:1647–1658
  • Bacalini MG, Friso S, Olivieri F, Pirazzini C, Giuliani C, Capri M, Santoro A, et al. 2014. Present and future of anti-ageing epigenetic diets. Mech Ageing Dev 136--137:101--115
  • Barnes SK, Ozanne SE. 2011. Pathways linking the early environment to long-term health and lifespan. Prog Biophys Mol Biol 106:323–336
  • Becker C, Weigel D. 2012. Epigenetic variation: origin and transgenerational inheritance. Curr Opin Plant Biol 15:562–567
  • Bell JT, Pai AA, Pickrell JK, Gaffney DJ, Pique-Regi R, Degner JF, Gilad Y, Pritchard JK. 2011. DNA methylation patterns associate with genetic and gene expression variation in HapMap cell lines. Genome Biol 12:R10
  • Bock C, Paulsen M, Tierling S, Mikeska T, Lengauer T, Walter J. 2006. CpG island methylation in human lymphocytes is highly correlated with DNA sequence, repeats, and predicted DNA structure. PLoS Genet 2:243--252, e26
  • Chen T, Ueda Y, Dodge JE, Wang Z, Li E. 2003. Establishment and maintenance of genomic methylation patterns in mouse embryonic stem cells by Dnmt3a and Dnmt3b. Mol Cell Biol 23:5594–5605
  • Das PM, Ramachandran K, Vanwert J, Ferdinand L, Gopisetty G, Reis IM, Singal R. 2006. Methylation mediated silencing of TMS1/ASC gene in prostate cancer. Mol Cancer 5:28
  • Daxinger L, Whitelaw E. 2012. Understanding transgenerational epigenetic inheritance via the gametes in mammals. Nat Rev Genet 13:153–162
  • Dolinoy DC, Huang D, Jirtle RL. 2007. Maternal nutrient supplementation counteracts bisphenol A-induced DNA hypomethylation in early development. Proc Natl Acad Sci 104:13056–13061
  • Eastman NJ. 1954. Mount Everest in utero. Am J Obstet Gynecol 67:701–711
  • Elango N, Yi SV. 2008. DNA methylation and structural and functional bimodality of vertebrate promoters. Mol Biol Evol 25:1602–1608
  • Feinberg AP, Irizarry RA. 2010. Stochastic epigenetic variation as a driving force of development, evolutionary adaptation, and disease. Proc Natl Acad Sci USA 107(Suppl 1):1757--1764
  • Feng S, Jacobsen SE, Reik W. 2010. Epigenetic reprogramming in plant and animal development. Science (N.Y.) 330:622–627
  • Fraga MF, Ballestar E, Paz MF, Ropero S, Setien F, Ballestar ML, Heine-Suñer D, et al. 2005. Epigenetic differences arise during the lifetime of monozygotic twins. Proc Natl Acad Sci USA 102:10604–10609
  • Franklin TB, Mansuy IM. 2010. Epigenetic inheritance in mammals: evidence for the impact of adverse environmental effects. Neurobiol Dis 39:61–65
  • Fraser HB, Lam LL, Neumann SM, Kobor MS. 2012. Population-specificity of human DNA methylation. Genome Biol 13:R8
  • Fumagalli M, Sironi M, Pozzoli U, Ferrer-Admetlla A, Ferrer-Admettla A, Pattini L, Nielsen R. 2011. Signatures of environmental genetic adaptation pinpoint pathogens as the main selective pressure through human evolution. PLoS Genet 7:e1002355
  • Garagnani P, Bacalini MG, Pirazzini C, Gori D, Giuliani C, Mari D, Di Blasio AM, et al. 2012. Methylation of ELOVL2 gene as a new epigenetic marker of age. Aging Cell 11:1132–1134
  • Gluckman PD, Hanson MA, Spencer HG. 2005. Predictive adaptive responses and human evolution. Trends Ecol Evol 20:527–533
  • Grönniger E, Weber B, Heil O, Peters N, Stäb F, Wenck H, Korn B, et al. 2010. Aging and chronic sun exposure cause distinct epigenetic changes in human skin. PLoS Genet 6:e1000971
  • Hancock AM, Witonsky DB, Alkorta-Aranburu G, Beall CM, Gebremedhin A, Sukernik R, Utermann G, et al. 2011. Adaptations to climate-mediated selective pressures in humans. PLoS Genet 7:e1001375
  • Hannum G, Guinney J, Zhao L, Zhang L, Hughes G, Sadda S, Klotzle B, et al. 2013. Genome-wide methylation profiles reveal quantitative views of human aging rates. Mol Cell 49:359–367
  • Heard E, Martienssen RA. 2014. Transgenerational epigenetic inheritance: myths and mechanisms. Cell 157:95–109
  • Heijmans BT, Tobi EW, Stein AD, Putter H, Blauw GJ, Susser ES, Slagboom PE, Lumey LH. 2008. Persistent epigenetic differences associated with prenatal exposure to famine in humans. Proc Natl Acad Sci 105:17046–17049
  • Henn BM, Cavalli-Sforza LL, Feldman MW. 2012. The great human expansion. Proc Natl Acad Sci USA 109:17758–17764
  • Heyn H, Moran S, Hernando-Herraez I, Sayols S, Gomez A, Sandoval J, Monk D, et al. 2013. DNA methylation contributes to natural human variation. Genome Res 23:1363–1372
  • Irizarry RA, Ladd-Acosta C, Wen B, Wu Z, Montano C, Onyango P, Cui H, et al. 2009. The human colon cancer methylome shows similar hypo- and hypermethylation at conserved tissue-specific CpG island shores. Nat Genet 41:178–186
  • Jablonka E, Lamb MJ. 2005. Evolution in four dimensions: genetic, epigenetic, behavioral, and symbolic variation in the history of life. Cambridge, Massachusetts, USA: The MIT Press
  • Jablonski NG, Chaplin G. 2000. The evolution of human skin coloration. J Hum Evol 39:57–106
  • Jacobsen SC, Brøns C, Bork-Jensen J, Ribel-Madsen R, Yang B, Lara E, Hall E, et al. 2012. Effects of short-term high-fat overfeeding on genome-wide DNA methylation in the skeletal muscle of healthy young men. Diabetologia 55:3341–3349
  • Jähner D, Jaenisch R. 1985. Retrovirus-induced de novo methylation of flanking host sequences correlates with gene inactivity. Nature 315:594–597
  • Jones PA. 2012. Functions of DNA methylation: islands, start sites, gene bodies and beyond. Nat Rev Genet 13:484–492
  • Klironomos FD, Berg J, Collins S. 2013. How epigenetic mutations can affect genetic evolution: model and mechanism. BioEssays: News Rev Mol Cell Dev Biol 35:571–578
  • Laker RC, Wlodek ME, Connelly JJ, Yan Z. 2013. Epigenetic origins of metabolic disease: the impact of the maternal condition to the offspring epigenome and later health consequences. Food Sci Hum Wellness 2:1–11
  • Lambrot R, Xu C, Saint-Phar S, Chountalos G, Cohen T, Paquet M, Suderman M. 2013. Low paternal dietary folate alters the mouse sperm epigenome and is associated with negative pregnancy outcomes. Nat Commun 4:2889. doi: 10.1038/ncomms3889
  • Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, Devon K, et al, International Human Genome Sequencing Consortium. 2001. Initial sequencing and analysis of the human genome. Nature 409:860–921
  • Langley-Evans SC. 2014. Nutrition in early life and the programming of adult disease: a review. J Hum Nutr Diet. doi: 10.1111/jhn.12212
  • Lee D-H, Pfeifer GP. 2003. Deamination of 5-methylcytosines within cyclobutane pyrimidine dimers is an important component of UVB mutagenesis. J Biol Chem 278:10314–10321
  • Liu J, Hutchison K, Perrone-Bizzozero N, Morgan M, Sui J, Calhoun V. 2010. Identification of genetic and epigenetic marks involved in population structure. PLoS One 5:e13209
  • Martin DS, Khosravi M, Grocott MP, Mythen MG. 2010. Concepts in hypoxia reborn. Crit Care 14:315
  • Morgan HD, Sutherland HG, Martin DI, Whitelaw E. 1999. Epigenetic inheritance at the agouti locus in the mouse. Nat Genet 23:314–318
  • Nanduri J, Makarenko V, Reddy VD, Yuan G, Pawar A, Wang N, Khan SA, et al. 2012. Epigenetic regulation of hypoxic sensing disrupts cardiorespiratory homeostasis. Proc Natl Acad Sci USA 109:2515–2520
  • Nielsen D, Hamon S, Yuferov V, Jackson C, Ho A, Ott J, Kreek M. 2010. Ethnic diversity of DNA methylation in the OPRM1 promoter region in lymphocytes of heroin addicts. Hum Genet 127:639–649
  • Okamoto Y, Shinjo K, Shimizu Y, Sano T, Yamao K, Gao W, Fujii M, et al. 2014. Hepatitis virus infection affects DNA methylation in mice with humanized livers. Gastroenterology 146:562–572
  • Okano M, Bell DW, Haber DA, Li E. 1999. DNA methyltransferases Dnmt3a and Dnmt3b are essential for de novo methylation and mammalian development. Cell 99:247–257
  • Park E-S, Park YK, Shin CY, Park SH, Ahn SH, Kim DH, Lim K-H, et al. 2013. Hepatitis B virus inhibits liver regeneration via epigenetic regulation of urokinase-type plasminogen activator. Hepatology (Baltimore, MD) 58:762–776
  • Pirazzini C, Giuliani C, Bacalini MG, Boattini A, Capri M, Fontanesi E, Marasco E, et al. 2012. Space/population and time/age in DNA methylation variability in humans: a study on IGF2/H19 locus in different Italian populations and in mono- and di-zygotic twins of different age. Aging 4:509–520
  • Popp C, Dean W, Feng S, Cokus SJ, Andrews S, Pellegrini M, Jacobsen SE, Reik W. 2010. Genome-wide erasure of DNA methylation in mouse primordial germ cells is affected by AID deficiency. Nature 463:1101–1105
  • Quirin J. 1992. Review of The Oromo of Ethiopia: a history, 1570-- 1860 by Mohammed Hassen. Afr Stud Rev 35:123–125
  • Rakyan VK, Blewitt ME, Druker R, Preis JI, Whitelaw E. 2002. Metastable epialleles in mammals. Trend Genet 18:348–351
  • Rakyan VK, Chong S, Champ ME, Cuthbert PC, Morgan HD, Luu KVK, Whitelaw E. 2003. Transgenerational inheritance of epigenetic states at the murine Axin(Fu) allele occurs after maternal and paternal transmission. Proc Natl Acad Sci USA 100:2538–2543
  • Rando OJ, Verstrepen KJ. 2007. Timescales of genetic and epigenetic inheritance. Cell 128:655–668
  • Razin A, Riggs AD. 1980. DNA methylation and gene function. Science 210:604–610
  • Richards EJ. 2008. Population epigenetics. Curr Opin Genet Dev 18:221–226
  • Rönn T, Volkov P, Davegårdh C, Dayeh T, Hall E, Olsson AH, Nilsson E, et al. 2013. A six months exercise intervention influences the genome-wide DNA methylation pattern in human adipose tissue. PLoS Genet 9:e1003572
  • Sazzini M, Schiavo G, De Fanti S, Martelli PL, Casadio R, Luiselli D. 2014. Searching for signatures of cold adaptations in modern and archaic humans: hints from the brown adipose tissue genes. Heredity (Edinb) 113:259--267
  • Schmitz RJ, Schultz MD, Lewsey MG, O’Malley RC, Urich MA, Libiger O, Schork NJ, Ecker JR. 2011. Transgenerational epigenetic instability is a source of novel methylation variants. Science (New York, N.Y.) 334:369–373
  • Scoccianti C, Ricceri F, Ferrari P, Cuenin C, Sacerdote C, Polidoro S, Jenab M, et al. 2011. Methylation patterns in sentinel genes in peripheral blood cells of heavy smokers: influence of cruciferous vegetables in an intervention study. Epigenetics Off J DNA Methylation Soc 6:1114–1119
  • Shea N, Pen I, Uller T. 2011. Three epigenetic information channels and their different roles in evolution. J Evol Biol 24:1178–1187
  • Skinner MK, Manikkam M, Guerrero-Bosagna C. 2010. Epigenetic transgenerational actions of environmental factors in disease etiology. Trends Endocrinol Metab 21:214–222
  • Smith AK, Kilaru V, Kocak M, Almli LM, Mercer KB, Ressler KJ, Tylavsky FA, Conneely KN. 2014. Methylation quantitative trait loci (meQTLs) are consistently detected across ancestry, developmental stage, and tissue type. BMC Genomics 15:145
  • Song F, Smith JF, Kimura MT, Morrow AD, Matsuyama T, Nagase H, Held WA. 2005. Association of tissue-specific differentially methylated regions (TDMs) with differential gene expression. Proc Natl Acad Sci USA 102:3336–3341
  • Surani MA, Hayashi K, Hajkova P. 2007. Genetic and Epigenetic Regulators of Pluripotency. Cell 128:747–762
  • Terry MB, Ferris JS, Pilsner R, Flom JD, Tehranifar P, Santella RM, Gamble MV, Susser E. 2008. Genomic DNA methylation among women in a multiethnic New York City Birth Cohort. Cancer Epidemiol Biomarkers Prevent 17:2306–2310
  • Tobi EW, Lumey LH, Talens RP, Kremer D, Putter H, Stein AD, Slagboom PE, Heijmans BT. 2009. DNA methylation differences after exposure to prenatal famine are common and timing- and sex-specific. Hum Mol Genet 18:4046–4053
  • Turner BM. 2011. Environmental sensing by chromatin: an epigenetic contribution to evolutionary change. FEBS Letts 585:2032–2040
  • Vivekanandan P, Daniel HD-J, Kannangai R, Martinez-Murillo F, Torbenson M. 2010. Hepatitis B Virus replication induces methylation of both host and viral DNA. J Virol 84:4321–4329
  • Waterland RA, Jirtle RL. 2003. transposable elements: targets for early nutritional effects on epigenetic gene regulation. Mol Cell Biol 23:5293–5300
  • Watson JA, Watson CJ, McCann A, Baugh J. 2010. Epigenetics, the epicenter of the hypoxic response. Epigenetics Off J DNA Methylation Soc 5:293–296
  • Watson JA, Watson CJ, McCrohan A-M, Woodfine K, Tosetto M, McDaid J, Gallagher E, et al. 2009. Generation of an epigenetic signature by chronic hypoxia in prostate cells. Hum Mol Genet 18:3594–3604
  • Xing G, Qualls C, Huicho L, Rivera-Ch M, River-Ch M, Stobdan T, Slessarev M, et al. 2008. Adaptation and mal-adaptation to ambient hypoxia; Andean, Ethiopian and Himalayan patterns. PloS One 3:e2342
  • Yang AS, Estecio MRH, Doshi K, Kondo Y, Tajara EH, Issa J-PJ. 2004. A simple method for estimating global DNA methylation using bisulfite PCR of repetitive DNA elements. Nucl Acids Res 32:e38
  • Yuen RKC, Chen B, Blair JD, Robinson WP, Nelson DM. 2013. Hypoxia alters the epigenetic profile in cultured human placental trophoblasts. Epigenetics Off J DNA Methylation Soc 8:192–202
  • Zhang FF, Cardarelli R, Carroll J, Fulda KG, Kaur M, Gonzalez K, Vishwanatha JK, et al. 2011. Significant differences in global genomic DNA methylation by gender and race/ethnicity in peripheral blood. Epigenetics Off J DNA Methylation Soc 6:623–629

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