Patterns of DNA methylation in animals: An ecotoxicological perspective

Integrative and Comparative Biology

Volumn 54, Issue 1, 2014, Pages 77-86

  Head, Jessica A ^a  

^a UNIVERSITY OF MICHIGAN   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

POLLUTANT;

ANIMAL; COMPARATIVE STUDY; DNA METHYLATION; DRUG EFFECTS; ECOTOXICOLOGY; GENE EXPRESSION REGULATION; GENETICS; INVERTEBRATE; PHYSIOLOGY; POLLUTANT; PROCEDURES; SPECIES DIFFERENCE; TOXICITY; VERTEBRATE;

ANIMALS; DNA METHYLATION; ECOTOXICOLOGY; ENVIRONMENTAL POLLUTANTS; GENE EXPRESSION REGULATION; INVERTEBRATES; SPECIES SPECIFICITY; VERTEBRATES;

EID: 84903648157     PISSN: 15407063     EISSN: 15577023     Source Type: Journal    
DOI: 10.1093/icb/icu025     Document Type: Conference Paper

References (81)

1. Aina R, Sgorbati S, Santagostino A, Labra M, Ghiani A, Citterio S. 2004. Specific hypomethylation of DNA is induced by heavy metals in white clover and industrial hemp. Physiol Plant 121:472-80. (Pubitemid 38927697)
2. Anway MD, Cupp AS, Uzumcu M, Skinner MK. 2005. Epigenetic transgenerational actions of endocrine disruptors and male fertility. Science 308:1466-9. (Pubitemid 40791300)
3. Baccarelli A, Bollati V. 2009. Epigenetics and environmental chemicals. Curr Opin Pediatr 21:243.
4. Basu N, Goodrich JM, Head JA. 2014. Ecogenetics of mercury: from genetic polymorphisms and epigenetics to risk assessment and decision-making. Environ Toxicol Chem 33:1248-58.
5. Basu N, Head JA, Nam DH, Pilsner JR, Carva n MJ, Chan HM, Goetz FW, Murphy CA, Rouvinen-Watt K, Scheuhammer AM. 2013. Effects of methylmercury on epigenetic markers in three model species: mink, chicken and yellow perch. Comp Biochem Physiol C Toxicol Pharmacol 1 57:322-7.
6. Bird AP. 1985. CpG-rich islands and the function of DNA methylation. Nature 321:209-13.
7. Bird A. 2002. DNA methylation patterns and epigenetic memory Genes Dev 16 6-21. (Pubitemid 34049633)
8. BogdanovićO, Long SW, van Heeringen SJ, Brinkman AB, Gómez-Skarmeta JL, Stunnenberg HG, Jones PL, Veenstra GJC. 2011. Temporal uncoupling of the DNA methylome and transcriptional repression during embryogenesis. Genome Res 21:1313-27.
9. Bonasio R, Li Q, Lian J, Mutti NS, Jin L, Zhao H, Zhang P, Wen P, Xiang H, Ding Y, et al. 2012. Genome-wide and caste-specific DNA methylomes of the ants Camponotus floridanus and Harpegnathos saltator. Curr Biol 22:1755-64.
10. Bossdorf O, Richards CL, Pigliucci M. 2008. Epigenetics for ecologists. Ecol Lett 11:106-15.
11. Bull JJ. 1980. Sex determination in reptiles. Q Rev Biol 55:3-21.
12. Contr actor RG, Foran CM, Li S, Willett KL. 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. J Toxicol Environ Health A 67:1-22. (Pubitemid 38117528)
13. Crews D, McLachlan JA. 2006. Epigenetics, evolution, endocrine disruption, health, and disease. Endocrinology 147:s4-10.
14. Devlin RH, Nagahama Y. 2 002. Sex determination and sex differentiation in fish: an overview of genetic, physiological, and environmental influences. Aquaculture 208:191-364. (Pubitemid 34641603)
15. Dobbs KB, Rodriguez M, Sudano MJ, Ortega MS, Hansen PJ. 2013. Dynamics of DNA methylation during early development of the Preimplantation Bovine Embryo. PLoS One 8:e66230.
16. Dunwell TL, McGuffin LJ, Dunwell JM, Pfeifer GP. 2013. The mysterious presence of a 5-methylcytosine oxidase in the Drosophila genome. Cell Cycle 12:3357-65.
17. Fang X, Corrales J, Thornton C, Scheffler BE, Willett KL. 2013. Global and gene specific DNA methylation changes during zebrafish development. Comp Biochem Physiol B Biochem Mol Biol 166:99-108.
18. Faulk C, Dolinoy DC. 2011. Timing is everything: the when and how of environmentally induced changes in the epigenome of animals. Epigenetics 6:791-7.
19. Feng S, Cokus SJ, Zhang X, Chen PY, Bostick M, Goll MG, Hetze J, Jain J, Strauss AH, Halpern ME. 2010. Conservation and divergence of methylation patterning in plants and animals. Proc Natl Acad Sci USA 107:8689-94.
20. Flohr L, Fuzinatto CF, Melegari SP, Matias WG. 2012. Effects of exposure to soluble fraction of industrial solid waste on lipid peroxidation and DNA methylation in erythrocytes of Oreochromis niloticus, as assessed by quantification of MDA and m5dC rates. Ecotoxicol Environ Saf 76:63-70.
21. Flores K, Wolschin F, Corneveaux JJ, Allen AN, Huentelman MJ, Amdam GV. 20 12. Genome-wide association between DNA methylation and alternative splicing in an invertebrate. BMC Genomics 13:480.
22. Frésard L, Morisson M, Brun JM, Collin A, Pain B, Minvielle F, Pitel F. 2013. Epigenetics and phenotypic variability: some interesting insights from birds. Genet Select Evol 45:16.
23. Frésard L, Leroux S, Servin B, Gourichon D, Dehais P, San Cristobal M, Marsaud N, Vignoles F, Beh'hom B, Coville JL, et al. 2014. Transcriptome-wide investigation of genomic imprinting in chicken. Nucleic acids Res 42:3768-82.
24. Gao F, Liu X, Wu X, Wang X, Gong D, Lu H, Xia Y, Song Y, Wang J, Du J, et al. 2012. Differential DNA methylation in discrete developmental stages of the parasit ic nematode Trichinella spiralis. Genome Biol 13:R100.
25. Gavery MR, Roberts SB. 2013. Predominant intragenic methylation is associated with gene expression characteristics in a bivalve mollusc. Peer J 1:e215.
26. Glastad KM, Hunt BG, Yi SV, Goodisman MAD. 2011. DNA methylation in insects: on the brink of the epigenomic era. Insect Mol Biol 20:553-65.
27. Hala D, Huggett DB, Burggren WW. 2014. Environmental stressors and the epigenome. Drug Discov Today: Technol 12:e3-8.
28. Head JA, Dolinoy DC, Basu N. 2012. Epigenetics for ecotoxicologists. Environ Toxicol Chem 31:221-7.
29. Head JA,Mittal K,Basu N Forthcoming 2014. Application of the LUminometric Methylation Assay (LUMA) to ecological species; tissue quality requirements and a survey of DNA methylation levels in animals. Mol Ecol Resour. Doi:10.1111/1755-0998.12 244.
30. Jabbari K, Cacció S, Päs de Barros JP, Desgrés J, Bernardi G. 1997. Evolutionary changes in CpG and methylation levels in the genome of vertebrates. Gene 205:109-18. (Pubitemid 28029604)
31. Jiang L, Zhang J, Wang JJ, Wang L, Zhang L, Li G, Yang X, Ma X, Sun X, Cai J, et al. 2013. Sperm, but not oocyte, DNA methylome is inherited by zebrafish early embryos. Cell 153:773-84.
32. Jirtle RL, S kinner MK. 2007. Environmental epigenomics and disease susceptibility. Nat Rev Genet 8:253-62. (Pubitemid 46439287)
33. Kille P, Andre J, Anderson C, Ang HN, Bruford MW, Bundy JG, Donnelly R, Hodson ME, Juma G, Lahive E, et al. 2013. DNA sequence variation and methylation in an arsenic tolerant earthworm population. Soil Biol Biochem 57:524-32.
34. Kronforst MR, Gilley DC, Strassmann JE, Queller DC. 2008. DNA methylation is widespread across social Hymenoptera. Curr Biol 18:R287-8. (Pubitemid 351458687)
35. Kucharski R, Maleszka J, Foret S, Maleszka R. 2008. Nutritional control of reproductive status in honeybees via DNA methylation. Science 319:1827-30. (Pubitemid 351451590)
36. Law JA, Jacobsen SE. 2010. Establishing, maintaining and modifying DNA methylation patterns in plants and animals. Nat Rev Genet 11:204-20.
37. Lee DH, Jacobs DR, Porta M. 2009. Hypothesis: a unifying mechanism for nutrition and chemicals as lifelong modulators of DNA hypomethylation. Environ Health Perspect 117:1799.
38. Li Q, Li N, Hu X, Li J, Du Z, Chen L, Yin G, Duan J, Zhang H, Zhao Y, et al. 2011. Genome-wide mapping of DNA methylation in chicken. PLoS One 6:e19428.
39. Lister R, Mukamel EA, Nery JR, Urich M, Puddifoot CA, Johnson ND, Lucero J, Huang Y, Dwork AJ, Schultz MD, et al. 2013. Global epigenomic reconfiguration during mammalian brain development. Science 341:1237905.
40. Lloyd VK , Brisson JA, Fitzpatrick KA, McEachern LA, Verhulst EC. 2012. The epigenetics of emerging and nonmodel organisms. Genet Res Int 2012:491204.
41. Long HK, Sims D, Heger A, Blackledge NP, Kutter C, Wright ML, Grützner F, Odom DT, Patient R, Ponting CP, et al. 2013. Epigenetic conservation at gene regulatory elements revealed by non-methylated DNA profiling in seven vertebrates. eLife 2:e00348.
42. Luo J, Yu Y, Zhang H, Tian F, Chang S, Cheng H, Song J. 2011. Down-regulation of promoter methylation level of CD4 gene after MDV infection in MD-susceptible chicken line. BMC Proc 5(Suppl l4):S7.
43. Lyko F, Ramsahoye BH, Jaenisch R. 2000. Development: DNA methylation in Drosophila melanogaster. Nature 408:538-40.
44. Lyko F, Foret S, Kucharski R, Wolf S, Falckenhayn C, Maleszka R. 2010. The honey bee epigenomes: differential methylation of brain DNA in queens and workers. PLoS Biol 8:e1000506.
45. MacKay AB, Mhanni AA, McGowan RA, Krone PH. 2007. Immunological detection of changes in genomic DNA methylation during early zebrafish development. Genome 50:778-5.
46. Mandrioli M, Volpi N. 2003. The genome of the lepidopteran Mamestra brassicae has a vertebrate-like content of methylcytosine. Genetica 119:187-91. (Pubitemid 37365118)
47. Manikkam M, Guerrero-Bosagna C, Tracey R, Haque MM, Skinner MK. 2012. Transgenerational actions of environmental compounds on reproductive disease and identification of epigen etic biomarkers of ancestral exposures. PLoS One 7:e31901.
48. Matsumoto Y, Buemio A, Chu R, Vafaee M, Crews D. 2013. Epigenetic control of gonadal aromatase (cyp19a1) in temperature-dependent sex determina tion of red-eared slider turtles. PLoS One 8:e63599.
49. Mhanni AA, McGowan RA. 2004. Global changes in genomic methylation levels during early development of the zebrafish embryo. Dev Genes Evol 214:412-7.
50. Michalak P. 2014 Evidence for maternal imprinting of 45S ribosomal RNA genes in Xenopus hybrids. Gen Genes Evol 224 125-8.
51. Mirbahai L, Yin G, Bignell JP, Li N, Williams TD, Chipman JK. 2011. DNA methylation in liver tumorigenesis in fish from the environment. Epigenetics 6:1319-33.
52. Mirbahai L, Southam AD, Sommer U, Williams TD, Bignell JP, Lyons BP, Viant MR, Chipman JK. 2013. Disruption of DNA methylation via S-Adenosylhomocysteine is a key process in high incidence liver carcinogenesis in fish. J Proteome Res 12:2895-904.
53. Morgan HD, Santos F, Green K, Dean W, Reik W. 2005. Epigenetic reprogramming in mammals. Hum Mol Genet 14(Suppl. 1):R47-58. (Pubitemid 40542620)
54. Navarro-Martín L, Viñas J, Ribas L, Daz N, Gutiérrez A, Di Croce L, Piferrer F. 2011. DNA methylation of the gonadal aromatase (cyp19a) promoter is involved in temperaturedependent sex ratio shifts in the European sea bass. PLoS Genet 7:e1002447.
55. Onishchen ko N, Karpova N, Sabri F, Castren E, Ceccatelli S. 2008. Long-lasting depression-like behavior and epigenetic changes of BDNF gene expression induced by perinatal exposure to methylmercury. J Neurochem 106:1378-87 .
56. Patalano S, Hore TA, Reik W, Sumner S. 2012. Shifting behaviour: epigenetic reprogramming in eusocial insects. Curr Opin Cell Biol 24:367-73.
57. Park J, Peng Z, Zeng J, Elango N, Park T, Wheeler D, Werren JH, Soojin VY. 2011. Comparative analyses of DNA methylation and sequence evolution using Nasonia genomes. Mol Biol Evol 28:3345-54.
58. Pierron F, Baillon L, Sow M, Got reau S, Gonzalez P. 2014. Effect of low-dose cadmium exposure on DNA methylation in the endangered European eel. Environ Sci Technol 48:797-803.
59. Pilsner JR, Lazarus AL, Nam DH, Letcher RJ, Sonne C, Dietz R, Basu N. 2010. Mercury-Associated DNA hypomethylation in polar bear brains via the LUminometric Methylation Assay: a sensitive method to study epigenetics in wildlife. Mol Ecol 19:307-14.
60. Ponger L, Li WH. 2005. Evolutionary diversification of DNA methyltransferases in eukaryotic genomes. Mol Biol Evol 22:1119-28. (Pubitemid 40471424)
61. Potok ME, Nix DA, Parnell TJ, Cairns BR. 2013. Reprogramming the maternal zebrafish genome after fertilization to match the paternal methylation pattern. Cell 153:759-72.
62. Rai K, Huggins IJ, James SR, Karpf AR, Jones DA, Cairns BR. 2008. DNA demethylation in zebrafish involv es the coupling of a deaminase, a glycosylase, and gadd45. Cell 135:1201-12.
63. Reik W, Dean W, Walter J. 2001. Epigenetic reprogramming in mammalian development. Science 293:1089-93. (Pubitemid 32758081)
64. Renfree MB, Hore TA, Shaw G, Marshall Graves JA, Pask AJ. 2009. Evolution of genomic imprinting: insights from marsupials and monotremes. Annu Rev Genomics Hum Genet 10:241-62.
65. Robertson KD , Jones PA. 2000. DNA methylation: past, present and future directions. Carcinogenesis 21:461-7. (Pubitemid 30137931)
66. Santos F, Hendrich B, Reik W, Dean W. 2002. Dynamic reprogramming of DNA methylation in the early mouse embryo. Dev Biol 241:172-82. (Pubitemid 34066770)
67. Shorter KR, Crossland JP, Webb D, Szalai G, Felder MR, Vrana PB. 2012. Peromyscus as a mammalian epigenetic model. Genet Res Int 2012:179159.
68. Skinner MK. 2008. What is an epigenetic transgenerational phenotype? F3 or F2. Reprod Toxicol 25:2-6.
69. Suzuki MM, Bird A. 2008. DNA methylation landscapes: provocative insights from epigenomics. Nat Rev Genet 9:465-76. (Pubitemid 351693975)
70. Vandegehuchte MB Lemiére F Janssen CR. 2009. Quantitative DNA-methylation in Daphnia magna and effects of multigeneration Zn exposure. Comp Biochem Physiol C Toxicol Pharmacol 150 343-8.
71. Vandegehuchte MB, Janssen CR. 2011. Epigenetics and its implications for ecotoxicology. Ecotoxicology 20:607-24.
72. Vandegehuchte MB, Janssen CR. 2014. Epigenetics in an ecotoxicological context. Mutat Res/Genet Toxicol Environ Mutagen 764-765:36-45.
73. Varriale A, Bernardi G. 2006 a. DNA methylation and body temperature in fishes. Gene 385:111-21. (Pubitemid 44828323)
74. Varriale A, Bernardi G. 2006 b . DNA methylation in reptiles. Gene 385:122-7. (Pubitemid 44828320)
75. Veenstra GJC, Wolffe AP. 2001. Constitutive genomic methylation during embryonic development of Xenopus. Biochim Biophys Acta 1521:39-44. (Pubitemid 33020764)
76. Warner DA, Uller T, Shine R. 2013. Transgenerational sex determination: the embryonic environment experienced by a male affects offspring sex ratio. Sci Rep 3:2709.
77. Watt F, Molloy PL. 1988. Cytosine methylation prevents binding to DNA of a HeLa cell transcription factor required for optimal expression of the adenovi rus major late promoter. Genes Dev 2:1136-43.
78. Wu H, Zhang Y. 2014. Reversing DNA methylation: mechanisms, genomics, and biological functions. Cell 156:45-68.
79. Yauk C, Polyzos A, Rowan-Carroll A, Somers CM, Godschalk RW, Van Schooten FJ, Berndt ML, Pogribny IP, Koturbash I, Williams A, et al. 2008. Germ-line mutations, DNA damage, and global hypermethylation in mice exposed to particulate air pollution in an urban/industrial location. Proc Natl Acad Sci USA 105:605-10. (Pubitemid 351171755)
80. Yokomine T, Hata K, Tsudzuki M, Sasaki H. 2006. Evolution of the vertebrate DNMT3 gene family: a possible link between existence of DNMT3L and genomic imprinting. Cytogenet Genome Res 113:75-80.
81. Zemach A, McDaniel IE, Silva P, Zilberman D. 2010. Genome-wide evolutionary analysis of eukaryotic DNA methylation. Science 328:916-9.