Challenges in nutrition-related DNA methylation studies

Biomolecular Concepts

Volumn 3, Issue 2, 2012, Pages 151-160

  Niculescu, Mihai D ^a  

^a University of North Carolina   (United States)

Author keywords

DNA methylation; epigenetics; genomic variability; nutrition

Indexed keywords

EID: 84874081773     PISSN: 18685021     EISSN: 1868503X     Source Type: Journal    
DOI: 10.1515/bmc-2011-0052     Document Type: Review

References (67)

1. Gluckman PD, Hanson MA, Low FM. The role of developmental plasticity and epigenetics in human health. Birth Defects Res C Embryo Today 2011; 93: 12-8.
2. Gravina S, Vijg J. Epigenetic factors in aging and longevity. Pflugers Arch 2010; 459: 247-58.
3. Skinner MK. Role of epigenetics in developmental biology and transgenerational inheritance. Birth Defects Res C Embryo Today 2011; 93: 51-5.
4. Niculescu MD, Lupu DS. Nutritional influence on epigenetics and effects on longevity. Curr Opin Clin Nutr Metab Care 2011; 14: 35-40.
5. Mohr F, Dohner K, Buske C, Rawat VP. TET genes: new players in DNA demethylation and important determinants for stemness. Exp Hematol 2011; 39: 272-81.
6. Simmons R. Epigenetics and maternal nutrition: nature v. nurture. Proc Nutr Soc 2011; 70: 73-81.
7. Hanley B, Dijane J, Fewtrell M, Grynberg A, Hummel S, Junien C, Koletzko B, Lewis S, Renz H, Symonds M, Gros M, Harthoorn L, Mace K, Samuels F, Van Der Beek EM. Metabolic imprinting, programming and epigenetics-a review of present priorities and future opportunities. Br J Nutr 2010; 104 Suppl 1: S1-25.
8. de Jager CA, Kovatcheva A. Summary and discussion: methodologies to assess long-term effects of nutrition on brain function. Nutr Rev 2010; 68 Suppl 1: S53-8.
9. Laird PW. Principles and challenges of genome-wide DNA meth-ylation analysis. Nat Rev Genet 2010; 11: 191-203.
10. Hawkins RD, Hon GC, Ren B. Next-generation genomics: an integrative approach. Nat Rev Genet 2010; 11: 476-86.
11. Ordovas JM, Robertson R, Cleirigh EN. Gene-gene and gene-environment interactions defining lipid-related traits. Curr Opin Lipidol 2011; 22: 129-36.
12. Cucu NV. DNA methylation. In Niculescu MD, Haggarty P, editors. Nutrition in epigenetics. Ames, IA: John Wiley & Sons, 2011: 15-46.
13. Bonifer C, Cockerill PN. Chromatin mechanisms regulating gene expression in health and disease. Adv Exp Med Biol 2011; 711: 12-25.
14. Niculescu MD, Zeisel SH. Diet, methyl donors and DNA methy-lation: interactions between dietary folate, methionine and cho-line. J Nutr 2002; 132: 2333S-5S.
15. Mehedint MG, Niculescu MD, Craciunescu CN, Zeisel SH. Choline deficiency alters global histone methylation and epige-netic marking at the Re1 site of the calbindin 1 gene. FASEB J 2010; 24: 184-95.
16. Ferguson-Smith AC. Genomic imprinting: the emergence of an epigenetic paradigm. Nat Rev Genet 2011; 12: 565-75.
17. Abramowitz LK, Bartolomei MS. Genomic imprinting: recognition and marking of imprinted loci. Curr Opin Genet Dev 2011; 22: 1-7.
18. Masahiro K. Genomic imprinting in mammals-epigenetic parental memories. Differentiation 2011; 82: 51-6.
19. Kaminen-Ahola NJ, Ahola AI, Whitelaw E. Epigenetic inheritance: both mitotic and meiotic. In Niculescu MD, Haggarty P, editors. Nutrition in epigenetics. Ames: John Wiley & Sons, 2011: 87-103.
20. Tahiliani M, Koh KP, Shen Y, Pastor WA, Bandukwala H, Brudno Y, Agarwal S, Iyer LM, Liu DR, Aravind L, Rao A. Conversion of 5-methylcytosine to 5-hydroxymethylcytosine in mammalian DNA by MLL partner TET1. Science 2009; 324: 930-5.
21. Williams K, Christensen J, Pedersen MT, Johansen J V, Cloos PA, Rappsilber J, Helin K. TET1 and hydroxymethylcytosine in transcription and DNA methylation fidelity. Nature 2011; 473: 343-8.
22. Hake SB. Chromatin modifications. In Niculescu MD, Haggarty P, editors. Nutrition in epigenetics. Ames: John Wiley & Sons, 2011: 47-71.
23. Zhu B, Reinberg D. Epigenetic inheritance: uncontested? Cell Res 2011; 21: 435-41.
24. Sato F, Tsuchiya S, Meltzer SJ, Shimizu K. MicroRNAs and epi-genetics. FEBS J 2011; 278: 1598-609.
25. Fabbri M. Roles of RNAi and other micro-RNAs in the regulation of epigenetic processes. In Niculescu MD, Haggarty P, editors. Nutrition in epigenetics. Ames, IA: John Wiley & Sons, 2011: 73-86.
26. Haley SL, Moyer-Mileur LJ, Lane RH, Joss-Moore LA. Maternal nutrition and developmental outcomes. In Niculescu MD, Haggarty P, editors. Nutrition in epigenetics. Ames, IA: John Wiley & Sons, 2011; 193-208.
27. Steegers-Theunissen RP, Obermann-Borst SA, Kremer D, Lindemans J, Siebel C, Steegers EA, Slagboom PE, Heijmans BT. Periconceptional maternal folic acid use of 400 microg per day is related to increased methylation of the IGF2 gene in the very young child. PLoS One 2009; 4: e7845.
28. Burdge GC, Lillycrop KA, Phillips ES, Slater-Jefferies JL, Jackson AA, Hanson MA. Folic acid supplementation during the juvenile-pubertal period in rats modifies the phenotype and epigenotype induced by prenatal nutrition. J Nutr 2009; 139: 1054-60.
29. James SJ, Melnyk S, Jernigan S, Pavliv O, Trusty T, Lehman S, Seidel L, Gaylor DW, Cleves MA. A functional polymorphism in the reduced folate carrier gene and DNA hypomethy-lation in mothers of children with autism. Am J Med Genet B Neuropsychiatr Genet 2010; 153B: 1209-20.
30. Niculescu MD, Craciunescu CN, Zeisel SH. Dietary choline defi-ciency alters global and gene-specific DNA methylation in the developing hippocampus of mouse fetal brains. FASEB J 2006; 20: 43-9.
31. Davison JM, Mellott TJ, Kovacheva VP, Blusztajn JK. Gestational choline supply regulates methylation of histone H3, expression of histone methyltransferases G9a (Kmt1c) and Suv39h1 (Kmt1a), and DNA methylation of their genes in rat fetal liver and brain. J Biol Chem 2009; 284: 1982-9.
32. Kovacheva VP, Mellott TJ, Davison JM, Wagner N, Lopez-Coviella I, Schnitzler AC, Blusztajn JK. Gestational choline deficiency causes global and Igf2 gene DNA hypermethylation by up-regulation of Dnmt1 expression. J Biol Chem 2007; 282: 31777-88.
33. Oliva J, Bardag-Gorce F, Li J, French BA, Nguyen SK, Lu SC, French SW. Betaine prevents Mallory-Denk body formation in drug-primed mice by epigenetic mechanisms. Exp Mol Pathol 2009; 86: 77-86.
34. Milagro FI, Campion J, Garcia-Diaz DF, Goyenechea E, Paternain L, Martinez JA. High fat diet-induced obesity modi-fies the methylation pattern of leptin promoter in rats. J Physiol Biochem 2009; 65: 1-9.
35. Dudley KJ, Sloboda DM, Connor KL, Beltrand J, Vickers MH. Offspring of mothers fed a high fat diet display hepatic cell cycle inhibition and associated changes in gene expression and DNA methylation. PLoS ONE 2011; 6: e21662.
36. Unterberger A, Szyf M, Nathanielsz P, Cox L. Organ and ges-tational age effects of maternal nutrient restriction on global methylation in fetal baboons. J Med Primatol 2009; 38: 219-27.
37. Tobi EW, Lumey LH, Talens RP, Kremer D, Putter H, Stein AD, Slagboom PE, Heijmans BT. DNA methylation differences after exposure to prenatal famine are common and timing-and sex-specific. Hum Mol Genet 2009; 18: 4046-53.
38. van Straten EME, Bloks VW, Huijkman NCA, Baller JFW, Meer H V, Lutjohann D, Kuipers F, Plosch T. The liver X-receptor gene promoter is hypermethylated in a mouse model of prenatal protein restriction. Am J Physiol Regul Integr Comp Physiol 2010; 298: R275-82.
39. Jousse C, Parry L, Langlais SL, Maurin A, Averous J, Bruhat A, Carraro V, Tost J, Letteron P, Chen P, Jockers R, Launay J, Mallet J, Fafournoux P. Perinatal undernutrition affects the methyla-tion and expression of the leptin gene in adults: implication for the understanding of metabolic syndrome. FASEB J 2011; 25: 3271-8.
40. Gong L, Pan YX, Chen H. Gestational low protein diet in the rat mediates Igf2 gene expression in male offspring via altered hepatic DNA methylation. Epigenetics 2010; 5: 619-26.
41. Godfrey KM, Sheppard A, Gluckman PD, Lillycrop KA, Burdge GC, McLean C, Rodford J, Slater-Jefferies JL, Garratt E, Crozier SR, Emerald BS, Gale CR, Inskip HM, Cooper C, Hanson MA. Epigenetic gene promoter methylation at birth is associated with child's later adiposity. Diabetes 2011; 60: 1528-34.
42. Sauer J, Jang H, Zimmerly EM, Kim K-C, Liu Z, Chanson A, Smith DE, Mason JB, Friso S-W, Choi S. Ageing, chronic alcohol consumption and folate are determinants of genomic DNA methylation, p16 promoter methylation and the expression of p16 in the mouse colon. Br J Nutr 2010; 104: 24-30.
43. Uthus E, Begaye A, Ross S, Zeng H. The von Hippel-Lindau (VHL) tumor-suppressor gene is down-regulated by selenium deficiency in Caco-2 cells and rat colon mucosa. Biol Trace Elem Res 2011; 142: 223-31.
44. Dolinoy DC, Weidman JR, Waterland RA, Jirtle RL. Maternal genistein alters coat color and protects Avy mouse offspring from obesity by modifying the fetal epigenome. Environ Health Perspect 2006; 114: 567-72.
45. Zeisel SH. Nutritional genomics: defining the dietary requirement and effects of choline. J Nutr 2011; 141: 531-4.
46. Zeisel SH. Choline: clinical nutrigenetic/nutrigenomic approaches for identification of functions and dietary requirements. World Rev Nutr Diet 2010; 101: 73-83.
47. Pogribny IP, Shpyleva SI, Muskhelishvili L, Bagnyukova T V, Jill James S, Beland FA. Role of DNA damage and alterations in cytosine DNA methylation in rat liver carcinogenesis induced by a methyl-deficient diet. Mutat Res 2009; 669: 56-62.
48. Engeham SF, Haase A, Langley-Evans SC. Supplementation of a maternal low-protein diet in rat pregnancy with folic acid ameliorates programming effects upon feeding behaviour in the absence of disturbances to the methionine-homocysteine cycle. Br J Nutr 2010; 103: 996-1007.
49. Min H. Effects of dietary supplementation of high-dose folic acid on biomarkers of methylating reaction in vitamin B(12)-deficient rats. Nutr Res Pract 2009; 3: 122-7.
50. Heijmans BT, Tobi EW, Stein AD, Putter H, Blauw GJ, Susser ES, Slagboom PE, Lumey LH. Persistent epigenetic differences associated with prenatal exposure to famine in humans. PNAS 2008; 105: 17046-9.
51. Lillycrop KA. Effect of maternal diet on the epigenome: implications for human metabolic disease. Proc Nutr Soc 2011; 70: 64-72.
52. Faulk C, Dolinoy DC. Timing is everything: the when and how of environmentally induced changes in the epigenome of animals. Epigenetics 2011; 6: 791-7.
53. Dolinoy DC, Huang D, Jirtle RL. Maternal nutrient supplementation counteracts bisphenol A-induced DNA hypomethylation in early development. PNAS 2007; 104: 13056-61.
54. Morgan DK, Whitelaw E. The case for transgenerational epi-genetic inheritance in humans. Mamm Genome 2008; 19: 394-7.
55. Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, Devon K, Dewar K, Doyle M, FitzHugh W, Funke R, Gage D, Harris K, Heaford A, Howland J, Kann L, Lehoczky J, LeVine R, McEwan P, McKernan K, Meldrim J, Mesirov JP, Miranda C, Morris W, Naylor J, Raymond C, Rosetti M, Santos R, Sheridan A, Sougnez C, Stange-Thomann N, Stojanovic N, Subramanian A, Wyman D, Rogers J, Sulston J, Ainscough R, Beck S, Bentley D, Burton J, Clee C, Carter N, Coulson A, Deadman R, Deloukas P, Dunham A, Dunham I, Durbin R, French L, Grafham D, Gregory S, Hubbard T, Humphray S, Hunt A, Jones M, Lloyd C, McMurray A, Matthews L, Mercer S, Milne S, Mullikin JC, Mungall A, Plumb R, Ross M, Shownkeen R, Sims S, Waterston RH, Wilson RK, Hillier LW, McPherson JD, Marra MA, Mardis ER, Fulton LA, Chinwalla AT, Pepin KH, Gish WR, Chissoe SL, Wendl MC, Delehaunty KD, Miner TL, Delehaunty A, Kramer JB, Cook LL, Fulton RS, Johnson DL, Minx PJ, Clifton SW, Hawkins T, Branscomb E, Predki P, Richardson P, Wenning S, Slezak T, Doggett N, Cheng J, Olsen A, Lucas S, Elkin C, Uberbacher E, Frazier M, Gibbs RA, Muzny DM, Scherer SE, Bouck JB, Sodergren EJ, Worley KC, Rives CM, Gorrell JH, Metzker ML, Naylor SL, Kucherlapati RS, Nelson DL, Weinstock GM, Sakaki Y, Fujiyama A, Hattori M, Yada T, Toyoda A, Itoh T, Kawagoe C, Watanabe H, Totoki Y, Taylor T, Weissenbach J, Heilig R, Saurin W, Artiguenave F, Brottier P, Bruls T, Pelletier E, Robert C, Wincker P, Rosenthal A, Platzer M, Nyakatura G, Taudien S, Smith DR, Doucette-Stamm L, Rubenfield M, Weinstock K, Lee HM, Dubois J, Yang H, Yu J, Wang J, Huang G, Gu J, Hood L, Rowen L, Madan A, Qin S, Davis RW, Federspiel NA, Abola AP, Proctor MJ, Roe BA, Chen F, Pan H, Ramser J, Lehrach H, Reinhardt R, McCombie WR, Bastide M, Dedhia N, Blöcker H, Hornischer K, Nordsiek G, Agarwala R, Aravind L, Bailey JA, Bateman A, Batzoglou S, Birney E, Bork P, Brown DG, Burge CB, Cerutti L, Chen H, Church D, Clamp M, Copley RR, Doerks T, Eddy SR, Eichler EE, Furey TS, Galagan J, Gilbert JGR, Harmon C, Hayashizaki Y, Haussler D, Hermjakob H, Hokamp K, Jang W, Johnson LS, Jones TA, Kasif S, Kaspryzk A, Kennedy S, Kent WJ, Kitts P, Koonin E V, Korf I, Kulp D, Lancet D, Lowe TM, McLysaght A, Mikkelsen T, Moran JV, Mulder N, Pollara VJ, Ponting CP, Schuler G, Schultz J, Slater G, Smit AFA, Stupka E, Szustakowki J, Thierry-Mieg D, Thierry-Mieg J, Wagner L, Wallis J, Wheeler R, Williams A, Wolf YI, Wolfe KH, Yang S, Yeh R, Collins F, Guyer MS, Peterson J, Felsenfeld A, Wetterstrand KA, Myers RM, Schmutz J, Dickson M, Grimwood J, Cox DR, Olson MV, Kaul R, Raymond C, Shimizu N, Kawasaki K, Minoshima S, Evans GA, Athanasiou M, Schultz R. Initial sequencing and analysis of the human genome. Nature 2001; 409: 860-921.
56. Dolinoy DC, Weinhouse C, Jones TR, Rozek LS, Jirtle RL. Variable histone modifications at the A(vy) metastable epiallele. Epigenetics 2010; 5: 637-44.
57. Alkan C, Coe BP, Eichler EE. Genome structural variation discovery and genotyping. Nat Rev Genet 2011; 12: 363-76.
58. Robinson MD, Stirzaker C, Statham AL, Coolen MW, Song JZ, Nair SS, Strbenac D, Speed TP, Clark SJ. Evaluation of affinity-based genome-wide DNA methylation data: effects of CpG density, amplification bias, and copy number variation. Genome Res 2010; 20: 1719-29.
59. Bell JT, Spector TD. A twin approach to unraveling epigenetics. Trends Genet 2011; 27: 116-25.
60. Bruder CEG, Piotrowski A, Gijsbers AACJ, Andersson R, Erickson S, Ståhl TD, Menzel U, Sandgren J, Tell DV, Poplawski A, Crowley M, Crasto C, Partridge EC, Tiwari H, Allison DB, Komorowski J, Ommen GB, Boomsma DI, Pedersen NL, Dunnen JT, Wirdefeldt K, Dumanski JP. Phenotypically concordant and discordant monozygotic twins display different DNA copy-number-variation profiles. Am J Hum Genet 2008; 82: 763-71.
61. + T cells with epigenetic immune lineage analysis. J Immunol 2011; 186: 92-102.
62. Gupta R, Nagarajan A, Wajapeyee N. Advances in genome-wide DNA methylation analysis. Biotechniques 2010; 49: iii-xi.
63. Szulwach KE, Li X, Li Y, Song C, Han JW, Kim S, Namburi S, Hermetz K, Kim JJ, Rudd MK, Yoon Y, Ren B, He C, Jin P. Integrating 5-hydroxymethylcytosine into the epigenomic landscape of human embryonic stem cells. PLoS Genet 2011; 7: e1002154.
64. Down TA, Rakyan VK, Turner DJ, Flicek P, Li H, Kulesha E, Gräf S, Johnson N, Herrero J, Tomazou EM, Thorne NP, Bäckdahl L, Herberth M, Howe KL, Jackson DK, Miretti MM, Marioni JC, Birney E, Hubbard TJ, Durbin R, Tavar é S, Beck S. A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis. Nat Biotechnol 2008; 26: 779-85.
65. Houseman EA, Christensen BC, Yeh R-F, Marsit CJ, Karagas MR, Wrensch M, Nelson HH, Wiemels J, Zheng S, Wiencke JK, Kelsey KT. Model-based clustering of DNA methylation array data: a recursive-partitioning algorithm for high-dimensional data arising as a mixture of beta distributions. BMC Bioinformatics 2008; 9: 365.
66. Hirst M, Marra MA. Next generation sequencing based approaches to epigenomics. Brief Funct Genomics 2010; 9: 455-65.
67. Dolinoy DC. The agouti mouse model: an epigenetic biosensor for nutritional and environmental alterations on the fetal epi-genome. Nutr Rev 2008; 66: S7-11.