The epigenomic interface between genome and environment in common complex diseases

Briefings in Functional Genomics

Volumn 9, Issue 5-6, 2010, Pages 477-485

  Bell, Christopher G ^a   Beck, Stephan ^a  

^a UNIVERSITY COLLEGE LONDON   (United Kingdom)

Author keywords

Common disease; Complex traits; Epigenetics; Epigenomics; Gene environment interaction; Genomics

Indexed keywords

DNA BINDING PROTEIN; HISTONE H3; UNTRANSLATED RNA; ZINC FINGER PROTEIN;

ARTICLE; CHROMATIN; CHRONIC DISEASE; CPG ISLAND; DISEASE MARKER; DNA METHYLATION; EPIGENETICS; GENOTYPE ENVIRONMENT INTERACTION; HAPLOTYPE; HISTONE MODIFICATION; HUMAN; SINGLE NUCLEOTIDE POLYMORPHISM; ANIMAL; COMPUTER PROGRAM; DIET; ENVIRONMENT; EVOLUTION; GENERAL ASPECTS OF DISEASE; GENETICS; GENOME; NEOPLASM; REVIEW;

ANIMALS; BIOLOGICAL EVOLUTION; DIET; DISEASE; DNA METHYLATION; ENVIRONMENT; EPIGENOMICS; GENOME; HUMANS; NEOPLASMS; SOFTWARE;

EID: 78651351984     PISSN: 20412649     EISSN: 20412657     Source Type: Journal    
DOI: 10.1093/bfgp/elq026     Document Type: Article

References (80)

1. Alberts B, Johnson A, Lewis J, et al. Molecular Biology of the Cell. New York: Garland Science. London: Taylor & Francis, 2008.
2. Richards EJ. Inherited epigenetic variation-revisiting soft inheritance. Nat RevGenet 2006;7:395-401.
3. Margueron R, Reinberg D. Chromatin structure and the inheritance of epigenetic information. Nat Rev Genet 2010; 11:285-96.
4. Berger SL, Kouzarides T, Shiekhattar R, et al. An operational definition of epigenetics. Genes Dev 2009;23:781-3.
5. Robertson KD. DNA methylation and human disease. Nat Rev Genet 2005;6:597-610.
6. Duret L. Mutation patterns in the human genome: more variable than expected. PLoS Biol 2009;7:e1000028.
7. Saxonov S, Berg P, Brutlag DL. A genome-wide analysis of CpG dinucleotides in the human genome distinguishes two distinct classes of promoters. Proc Natl Acad Sci USA 2006; 103:1412-7.
8. Suzuki MM, Bird A. DNA methylation landscapes: provocative insights from epigenomics. Nat Rev Genet 2008;9:465-76.
9. Zemach A, McDaniel IE, Silva P, et al. Genome-wide evolutionary analysis of eukaryotic DNA methylation. Science 2010;328:916-9.
10. Reik W. Stability and flexibility of epigenetic gene regulation in mammalian development. Nature 2007;447: 425-32.
11. Jirtle RL, Skinner MK. Environmental epigenomics and disease susceptibility. Nat RevGenet 2007;8:253-62.
12. Ramsahoye BH, Biniszkiewicz D, Lyko F, et al. Non-CpG methylation is prevalent in embryonic stem cells and may be mediated by DNA methyltransferase 3a. Proc Natl Acad Sci USA 2000;97:5237-42.
13. Lister R, Pelizzola M, Dowen RH, et al. Human DNA methylomes at base resolution show widespread epigenomic differences. Nature 2009;462:315-22.
14. Laurent L, Wong E, Li G, et al. Dynamic changes in the human methylome during differentiation. Genome Res 2010;20:320-31.
15. Feinberg AP. Genome-scale approaches to the epigenetics of common human disease. Virchows Arch 2010;456:13-21.
16. Kriaucionis S, Heintz N. The nuclear DNA base 5-hydroxymethylcytosine is present in Purkinje neurons and the brain. Science 2009;324:929-30.
17. Meissner A, Mikkelsen TS, Gu H, et al. Genome-scale DNA methylation maps of pluripotent and differentiated cells. Nature 2008;454:766-70.
18. Thomson JP, Skene PJ, Selfridge J, et al. CpG islands influence chromatin structure via the CpG-binding protein Cfp1. Nature 2010;464:1082-6.
19. Smith AE, Hurd PJ, Bannister AJ, et al. Heritable gene repression through the action of a directed DNA methyltransferase at a chromosomal locus. J Biol Chem 2008;283: 9878-85.
20. Blackledge NP, Zhou JC, Tolstorukov MY, et al. CpG islands recruit a histone H3 lysine 36 demethylase. Mol Cell 2010;38:179-90.
21. Kouzarides T. Chromatin modifications and their function. Cell 2007;128:693-705.
22. Eckhardt F, Lewin J, Cortese R, et al. DNA methylation profiling of human chromosomes 6, 20 and 22. Nat Genet 2006;38:1378-85.
23. Kerkel K, Spadola A, Yuan E, et al. Genomic surveys by methylation-sensitive SNP analysis identify sequence-dependent allele-specific DNA methylation. Nat Genet 2008;40:904-8.
24. Murrell A, Rakyan VK, Beck S. From genome to epigenome. HumMol Genet 2005;14(Spec No 1):R3-10.
25. Zhang D, Cheng L, Badner JA, et al. Genetic control of individual differences in gene-specific methylation in human brain. AmJHum Genet 2010;86:411-9.
26. Schalkwyk LC, Meaburn EL, Smith R, et al. Allelic skewing of DNA methylation is widespread across the genome. AmJHum Genet 2010;86:196-212.
27. Shoemaker R, Deng J, Wang W, et al. Allele-specific methylation is prevalent and is contributed by CpG-SNPs in the human genome. Genome Res 2010;20:883-9.
28. McDaniell R, Lee BK, Song L, et al. Heritable individual-specific and allele-specific chromatin signatures in humans. Science 2010;328:235-9.
29. Feinberg AP. Phenotypic plasticity and the epigenetics of human disease. Nature 2007;447:433-40.
30. Wilson MJ, Shivapurkar N, Poirier LA. Hypomethylation of hepatic nuclear DNA in rats fed with a carcinogenic methyl-deficient diet. BiochemJ 1984;218:987-990.
31. Gluckman PD, Hanson MA, Cooper C, et al. Effect of in utero and early-life conditions on adult health and disease. NEnglJMed 2008;359:61-73.
32. Heijmans BT, Tobi EW, Stein AD, et al. Persistent epigenetic differences associated with prenatal exposure to famine in humans. Proc Natl Acad Sci USA 2008;105: 17046-9.
33. Feinberg AP. Epigenetics at the epicenter of modern medicine. JAMA 2008;299:1345-50.
34. Esteller M. Cancer epigenomics: DNA methylomes and histone-modification maps. Nat Rev Genet 2007;8: 286-98.
35. Xie H, Wang M, Bonaldo Mde F, etal. Epigenomic analysis of Alu repeats in human ependymomas. Proc Natl Acad Sci USA 2010;107:6952-7.
36. Irizarry RA, Ladd-Acosta C, Wen B, et al. The human colon cancer methylome shows similar hypo- and hypermethylation at conserved tissue-specific CpG island shores. Nat Genet 2009;41:178-86.
37. De Smet C, Loriot A. DNA hypomethylation in cancer: epigenetic scars of a neoplastic journey. Epigenetics 2010;5:206-13.
38. Baylin SB, Ohm JE. Epigenetic gene silencing in cancer - a mechanism for early oncogenic pathway addiction? NatRev Cancer 2006;6:107-16.
39. Collado M, Gil J, Efeyan A, et al. Tumour biology: senescence in premalignant tumours. Nature 2005;436:642.
40. Harris AL. Hypoxia-a key regulatory factor in tumour growth. Nat Rev Cancer 2002;2:38-47.
41. Shahrzad S, Bertrand K, Minhas K, et al. Induction of DNA hypomethylation by tumor hypoxia. Epigenetics 2007;2: 119-25.
42. Pal A, Srivastava T, Sharma MK, etal. Aberrant methylation and associated transcriptional mobilization of Alu elements contributes to genomic instability in hypoxia. JCellMolMed 2009; [Epub ahead of print] June 5, 2009 (in press).
43. Feinberg AP, Ohlsson R, Henikoff S. The epigenetic progenitor origin of human cancer. Nat Rev Genet 2006;7: 21-33.
44. Edwards CA, Ferguson-Smith AC. Mechanisms regulating imprinted genes in clusters. Curr Opin Cell Biol 2007;19: 281-9.
45. Cui H, Cruz-Correa M, Giardiello FM, et al. Loss of IGF2 imprinting: a potential marker of colorectal cancer risk. Science 2003;299:1753-55.
46. Hitchins MP, Wong JJ, Suthers G, et al. Inheritance of a cancer-associated MLH1 germ-line epimutation. N Engl J Med 2007;356:697-705.
47. Wareham KA, Lyon MF, Glenister PH, et al. Age related reactivation of an X-linked gene. Nature 1987;327:725-7.
48. Fraga MF, Ballestar E, Paz MF, et al. Epigenetic differences arise during the lifetime of monozygotic twins. Proc Natl Acad SciUSA 2005;102:10604-9.
49. Bjornsson HT, Sigurdsson MI, Fallin MD, et al. Intra-individual change over time in DNA methylation with familial clustering. JAMA 2008;299:2877-83.
50. Christensen BC, Houseman EA, Marsit CJ, et al. Aging and environmental exposures alter tissue-specific DNA methylation dependent upon CpG island context. PLoS Genet 2009;5:e1000602.
51. Teschendorff AE, Menon U, Gentry-Maharaj A, et al. Age-dependent DNA methylation of genes that are suppressed in stem cells is a hallmark of cancer. Genome Res 2010;20:440-6.
52. Rakyan VK, Down TA, Maslau S, et al. Human aging-associated DNA hypermethylation occurs preferentially at bivalent chromatin domains. Genome Res 2010;20: 434-9.
53. Bernstein BE, Mikkelsen TS, Xie X, et al. A bivalent chromatin structure marks key developmental genes in embryonic stem cells. Cell 2006;125:315-26.
54. Bjornsson HT, Fallin MD, Feinberg AP. An integrated epigenetic and genetic approach to common human disease. TrendsGenet 2004;20:350-8.
55. Murgatroyd C, Patchev AV, Wu Y, et al. Dynamic DNA methylation programs persistent adverse effects of early-life stress. NatNeurosci 2009;12:1559-66.
56. Tsankova N, Renthal W, Kumar A, et al. Epigenetic regulation in psychiatric disorders. Nat Rev Neurosci 2007;8: 355-67.
57. Maze I, Covington HE 3rd, Dietz DM, et al. Essential role of the histone methyltransferase G9a in cocaine-induced plasticity. Science 2010;327:213-6.
58. Mill J, Tang T, Kaminsky Z, et al. Epigenomic profiling reveals DNA-methylation changes associated with major psychosis. Am J Hum Genet 2008;82:696-711.
59. Javierre BM, Fernandez AF, Richter J, et al. Changes in the pattern of DNA methylation associate with twin discordance in systemic lupus erythematosus. GenomeRes 2010;20: 170-9.
60. Wallace C, Smyth DJ, Maisuria-Armer M, et al. The imprinted DLK1-MEG3 gene region on chromosome 14q32.2 alters susceptibility to type 1 diabetes. Nat Genet 2010;42:68-71.
61. Kong A, Steinthorsdottir V, Masson G, et al. Parental origin of sequence variants associated with complex diseases. Nature 2009;462:868-74.
62. Gaulton KJ, Nammo T, Pasquali L, et al. A map of open chromatin in human pancreatic islets. Nat Genet 2010;42: 255-9.
63. Bhandare R, Schug J, Le Lay J, et al. Genome-wide analysis of histone modifications in human pancreatic islets. Genome Res 2010;20:428-33.
64. Feinberg AP, Irizarry RA. Evolution in health and medicine Sackler colloquium: stochastic epigenetic variation as a driving force of development, evolutionary adaptation, and disease. Proc Natl Acad Sci USA 2010; 107(Suppl No 1):1757-64.
65. Zemojtel T, Kielbasa SM, Arndt PF, et al. Methylation and deamination of CpGs generate p53-binding sites on a genomic scale. Trends Genet 2009;25:63-6.
66. Hark AT, Schoenherr CJ, Katz DJ, et al. CTCF mediates methylation-sensitive enhancer-blocking activity at the H19/Igf 2 locus. Nature 2000;405:486-9.
67. Akey JM. Constructing genomic maps of positive selection in humans: where do we go from here? Genome Res 2009; 19:711-22.
68. Schmidl C, Klug M, Boeld TJ, et al. Lineage-specific DNA methylation in T cells correlates with histone methylation and enhancer activity. Genome Res 2009;19:1165-74.
69. Teschendorff AE, Menon U, Gentry-Maharaj A, et al. An epigenetic signature in peripheral blood predicts active ovarian cancer. PLoS One 2009;4:e8274.
70. Bell CG, Teschendorff AE, Rakyan VK, et al. Genome-wide DNA methylation analysis for diabetic nephropathy in type 1 diabetes mellitus. BMC Med Genomics 2010;3:33.
71. Laird PW. Principles and challenges of genome-wide DNA methylation analysis. Nat Rev Genet 2010;11:191-203.
72. Bibikova M, Le J, Barnes B, et al. Genome-wide DNA methylation profiling using Infinium assay. Epigenomics 2009;1:177-200.
73. Weber M, Davies JJ, Wittig D, et al. Chromosome-wide and promoter-specific analyses identify sites of differential DNA methylation in normal and transformed human cells. Nat Genet 2005;37:853-62.
74. Huang Y, Pastor WA, Shen Y, et al. The behaviour of 5-hydroxymethylcytosine in bisulfite sequencing. PLoS One 2010;5:e8888.
75. Flusberg BA, Webster DR, Lee JH, etal. Direct detection of DNA methylation during single-molecule, real-time sequencing. NatMethods 2010;7:461-5.
76. Clarke J, Wu HC, Jayasinghe L, et al. Continuous base identification for single-molecule nanopore DNA sequencing. NatNanotechnol 2009;4:265-70.
77. Park PJ. ChIP-seq: advantages and challenges of a maturing technology. Nat RevGenet 2009;10:669-80.
78. Bell CG, Beck S. Advances in the identification and analysis of allele-specific expression. GenomeMed 2009;1:56.
79. Karberg S. Switching on epigenetic therapy. Cell 2009;139: 1029-31.
80. Willyard C. The saving switch. NatMed 2010;16:18-21.