Using dna methylation to understand biological consequences of genetic variability

Neurodegenerative Diseases

Volumn 9, Issue 2, 2012, Pages 53-59

  Hernandez, Dena G ^a   Singleton, Andrew B ^a  

^a NATIONAL INSTITUTE ON AGING   (United States)

Author keywords

Genetic variability; Genome wide association; Methylation; Quantitative trait loci

Indexed keywords

BISULFITE; GENOMIC DNA; MEMBRANE METALLOENDOPEPTIDASE;

AGING; ALZHEIMER DISEASE; ATAXIA; CARDIOVASCULAR DISEASE; CHROMATIN STRUCTURE; CPG ISLAND; DIET; DNA METHYLATION; DNA SEQUENCE; EPIGENETICS; FRAGILE X SYNDROME; GENE EXPRESSION; GENE MUTATION; GENETIC ANALYSIS; GENETIC ASSOCIATION; GENETIC VARIABILITY; HISTONE MODIFICATION; HUMAN; LIFESTYLE; METABOLIC DISORDER; MOLECULAR CLONING; MYOPATHY; NUCLEOSOME; PARKINSON DISEASE; PATHOLOGY; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; QUANTITATIVE TRAIT LOCUS MAPPING; REVIEW; SINGLE NUCLEOTIDE POLYMORPHISM; SPINAL MUSCULAR ATROPHY;

ANIMALS; DNA METHYLATION; EPIGENESIS, GENETIC; GENETIC VARIATION; HUMANS; QUANTITATIVE TRAIT LOCI;

EID: 84856707495     PISSN: 16602854     EISSN: 16602862     Source Type: Journal    
DOI: 10.1159/000333097     Document Type: Review

References (60)

1. Hindorff LA, Sethupathy P, Junkins HA, Ramos EM, Mehta JP, Collins FS, Manolio TA: Potential etiologic and functional implications of genome-wide association loci for human diseases and traits. Proc Natl Acad Sci USA 2009; 106: 9362-9367.
2. Hardy J, Trabzuni D, Ryten M: Whole genome expression as a quantitative trait. Biochem Soc Trans 2009; 37: 1276-1277.
3. Mill J: Toward an integrated genetic and epigenetic approach to Alzheimer's disease. Neurobiol Aging 2011; 32: 1188-1191.
4. Doi A, Park IH, Wen B, Murakami P, Aryee MJ, Irizarry R, Herb B, Ladd-Acosta C, Rho J, Loewer S, Miller J, Schlaeger T, Daley GQ, Feinberg AP: Differential methylation of tissue-and cancer-specific CpG island shores distinguishes human induced pluripotent stem cells, embryonic stem cells and fibroblasts. Nat Genet 2009; 41: 1350-1353.
5. Irizarry RA, Ladd-Acosta C, Wen B, Wu Z, Montano C, Onyango P, Cui H, Gabo K, Rongione M, Webster M, Ji H, Potash JB, Sabunciyan S, Feinberg AP: The human colon cancer methylome shows similar hypoand hypermethylation at conserved tissuespecific CpG island shores. Nat Genet 2009; 41: 178-186.
6. Lister R, Pelizzola M, Dowen RH, Hawkins RD, Hon G, Tonti-Filippini J, Nery JR, Lee L, Ye Z, Ngo QM, Edsall L, Antosiewicz-Bourget J, Stewart R, Ruotti V, Millar AH, Thomson JA, Ren B, Ecker JR: Human DNA methylomes at base resolution show widespread epigenomic differences. Nature 2009; 462: 315-322.
7. Dawson MA, Bannister AJ, Gottgens B, Foster SD, Bartke T, Green AR, Kouzarides T: JAK2 phosphorylates histone H3Y41 and excludes HP1alpha from chromatin. Nature 2009; 461: 819-822.
8. Hurd PJ, Bannister AJ, Halls K, Dawson MA, Vermeulen M, Olsen JV, Ismail H, Somers J, Mann M, Owen-Hughes T, Gout I, Kouzarides T: Phosphorylation of histone H3 Thr-45. is linked to apoptosis. J Biol Chem 2009; 284: 16575-16583.
9. Zhao Q, Rank G, Tan YT, Li H, Moritz RL, Simpson RJ, Cerruti L, Curtis DJ, Patel DJ, Allis CD, Cunningham JM, Jane SM: PRMT5-mediated methylation of histone H4R3 recruits DNMT3A, coupling histone and DNA methylation in gene silencing. Nat Struct Mol Biol 2009; 16: 304-311.
10. Fazzari MJ, Greally JM: Introduction to epigenomics and epigenome-wide analysis. Methods Mol Biol 2010; 620: 243-265.
11. Fazzari MJ, Greally JM: Epigenomics: beyond CpG islands. Nat Rev Genet 2004; 5: 446-455. (Pubitemid 38915411)
12. Symonds ME, Sebert SP, Hyatt MA, Budge H: Nutritional programming of the metabolic syndrome. Nat Rev Endocrinol 2009; 5: 604-610.
13. Turunen MP, Aavik E, Yla-Herttuala S: Epigenetics and atherosclerosis. Biochim Biophys Acta 2009; 1790: 886-891.
14. Hang CT, Yang J, Han P, Cheng HL, Shang C, Ashley E, Zhou B, Chang CP: Chromatin regulation by Brg1 underlies heart muscle development and disease. Nature 2010; 466: 62-67.
15. Movassagh M, Choy MK, Goddard M, Bennett MR, Down TA, Foo RS: Differential DNA methylation correlates with differential expression of angiogenic factors in human heart failure. PLoS One 2010; 5:e8564.
16. Zeng W, de Greef JC, Chen YY, Chien R, Kong X, Gregson HC, Winokur ST, Pyle A, Robertson KD, Schmiesing JA, Kimonis VE, Balog J, Frants RR, Ball AR Jr, Lock LF, Donovan PJ, van der Maarel SM, Yokomori K: Specific loss of histone H3 lysine 9 trimethylation and HP1gamma/cohesin binding at D4Z4 repeats is associated with facioscapulohumeral dystrophy (FSHD). PLoS Genet 2009; 5:e1000559.
17. Gheldof N, Tabuchi TM, Dekker J: The active FMR1 promoter is associated with a large domain of altered chromatin conformation with embedded local histone modifications. Proc Natl Acad Sci USA 2006; 103: 12463-12468. (Pubitemid 44267282)
18. Urdinguio RG, Sanchez-Mut JV, Esteller M: Epigenetic mechanisms in neurological diseases: genes, syndromes, and therapies. Lancet Neurol 2009; 8: 1056-1072.
19. Pieper HC, Evert BO, Kaut O, Riederer PF, Waha A, Wullner U: Different methylation of the TNF-alpha promoter in cortex and substantia nigra: implications for selective neuronal vulnerability. Neurobiol Dis 2008; 32: 521-527.
20. Gao HM, Hong JS: Gene-environment interactions: key to unraveling the mystery of Parkinson's disease. Prog Neurobiol 2011; 94: 1-19.
21. Chouliaras L, Rutten BP, Kenis G, Peerbooms O, Visser PJ, Verhey F, van Os J, Steinbusch HW, van den Hove DL: Epigenetic regulation in the pathophysiology of Alzheimer's disease. Prog Neurobiol 2010; 90: 498-510.
22. Portela A, Esteller M: Epigenetic modifications and human disease. Nat Biotechnol 2010; 28: 1057-1068.
23. Razin A, Riggs AD: DNA methylation and gene function. Science 1980; 210: 604-610.
24. Herman JG, Baylin SB: Gene silencing in cancer in association with promoter hypermethylation. N Engl J Med 2003; 349: 2042-2054. (Pubitemid 37448928)
25. Bird AP: CpG-rich islands and the function of DNA methylation. Nature 1986; 321: 209-213. (Pubitemid 16016411)
26. Gardiner-Garden M, Frommer M: CpG islands in vertebrate genomes. J Mol Biol 1987; 196: 261-282. (Pubitemid 17122132)
27. Shen L, Kondo Y, Guo Y, Zhang J, Zhang L, Ahmed S, Shu J, Chen X, Waterland RA, Issa JP: Genome-wide profiling of DNA methylation reveals a class of normally methylated CpG island promoters. PLoS Genet 2007; 3: 2023-2036.
28. Takai D, Jones PA: Comprehensive analysis of CpG islands in human chromosomes 21 and 22. Proc Natl Acad Sci USA 2002; 99: 3740-3745. (Pubitemid 34252176)
29. Zhou H, Hu H, Lai M: Non-coding RNAs and their epigenetic regulatory mechanisms. Biol Cell 2010; 102: 645-655.
30. Maunakea AK, Nagarajan RP, Bilenky M, Ballinger TJ, D'Souza C, Fouse SD, Johnson BE, Hong C, Nielsen C, Zhao Y, Turecki G, Delaney A, Varhol R, Thiessen N, Shchors K, Heine VM, Rowitch DH, Xing X, Fiore C, Schillebeeckx M, Jones SJ, Haussler D, Marra MA, Hirst M, Wang T, Costello JF: Conserved role of intragenic DNA methylation in regulating alternative promoters. Nature 2010; 466: 253-257.
31. Tost J: Epigenetics. Norfolk, Caister Academic Press, 2008.
32. De Pinho RA: The age of cancer. Nature 2000; 408: 248-254.
33. Issa JP: CpG-island methylation in aging and cancer. Curr Top Microbiol Immunol 2000; 249: 101-118.
34. International Parkinson Disease Genomics Consortium, Nalls MA, Plagnol V, Hernandez DG, Sharma M, Sheerin UM, Saad M, Simon-Sanchez J, Schulte C, Lesage S, Sveinbjornsdottir S, Stefansson K, Martinez M, Hardy J, Heutink P, Brice A, Gasser T, Singleton AB, Wood NW: Imputation of sequence variants for identification of genetic risks for Parkinson's disease: a meta-analysis of genome-wide association studies. Lancet 2011; 377: 641-649.
35. Simon-Sanchez J, Schulte C, Bras JM, Sharma M, Gibbs JR, Berg D, Paisan-Ruiz C, Lichtner P, Scholz SW, Hernandez DG, Kruger R, Federoff M, Klein C, Goate A, Perlmutter J, Bonin M, Nalls MA, Illig T, Gieger C, Houlden H, Steffens M, Okun MS, Racette BA, Cookson MR, Foote KD, Fernandez HH, Traynor BJ, Schreiber S, Arepalli S, Zonozi R, Gwinn K, van der Brug M, Lopez G, Chanock SJ, Schatzkin A, Park Y, Hollenbeck A, Gao J, Huang X, Wood NW, Lorenz D, Deuschl G, Chen H, Riess O, Hardy JA, Singleton AB, Gasser T: Genome-wide association study reveals genetic risk underlying Parkinson's disease. Nat Genet 2009; 41: 1308-1312.
36. Matarin M, Brown WM, Scholz S, Simon-Sanchez J, Fung HC, Hernandez D, Gibbs JR, De Vrieze FW, Crews C, Britton A, Langefeld CD, Brott TG, Brown RD Jr, Worrall BB, Frankel M, Silliman S, Case LD, Singleton A, Hardy JA, Rich SS, Meschia JF: A genomewide genotyping study in patients with ischaemic stroke: initial analysis and data release. Lancet Neurol 2007; 6: 414-420. (Pubitemid 46551853)
37. Schymick JC, Scholz SW, Fung HC, Britton A, Arepalli S, Gibbs JR, Lombardo F, Matarin M, Kasperaviciute D, Hernandez DG, Crews C, Bruijn L, Rothstein J, Mora G, Restagno G, Chio A, Singleton A, Hardy J, Traynor BJ: Genome-wide genotyping in amyotrophic lateral sclerosis and neurologically normal controls: first stage analysis and public release of data. Lancet Neurol 2007; 6: 322-328. (Pubitemid 46367937)
38. Gopisetty G, Ramachandran K, Singal R: DNA methylation and apoptosis. Mol Immunol 2006; 43: 1729-1740.
39. Ottaviano YL, Issa JP, Parl FF, Smith HS, Baylin SB, Davidson NE: Methylation of the estrogen receptor gene CpG island marks loss of estrogen receptor expression in human breast cancer cells. Cancer Res 1994; 54: 2552-2555. (Pubitemid 24173735)
40. Richardson B: Impact of aging on DNA methylation. Ageing Res Rev 2003; 2: 245-261. (Pubitemid 38340315)
41. Ehrich M, Turner J, Gibbs P, Lipton L, Giovanneti M, Cantor C, van den Boom D: Cytosine methylation profiling of cancer cell lines. Proc Natl Acad Sci USA 2008; 105: 4844-4849. (Pubitemid 351753834)
42. Bibikova M, Lin Z, Zhou L, Chudin E, Garcia EW, Wu B, Doucet D, Thomas NJ, Wang Y, Vollmer E, Goldmann T, Seifart C, Jiang W, Barker DL, Chee MS, Floros J, Fan JB: Highthroughput DNA methylation profiling using universal bead arrays. Genome Res 2006; 16: 383-393. (Pubitemid 43327509)
43. Clark SJ, Harrison J, Paul CL, Frommer M: High sensitivity mapping of methylated cytosines. Nucleic Acids Res 1994; 22: 2990-2997. (Pubitemid 24260626)
44. Clark SJ, Statham A, Stirzaker C, Molloy PL, Frommer M: DNA methylation: bisulphite modification and analysis. Nat Protoc 2006; 1: 2353-2364.
45. Fraga MF, Esteller M: DNA methylation: a profile of methods and applications. Biotechniques 2002; 33: 632, 634, 636-649.
46. Pomraning KR, Smith KM, Freitag M: Genome-wide high throughput analysis of DNA methylation in eukaryotes. Methods 2009; 47: 142-150.
47. Hatada I, Kato A, Morita S, Obata Y, Nagaoka K, Sakurada A, Sato M, Horii A, Tsujimoto A, Matsubara K: A microarray-based method for detecting methylated loci. J Hum Genet 2002; 47: 448-451. (Pubitemid 34857547)
48. Van Steensel B, Delrow J, Henikoff S: Chromatin profiling using targeted DNA adenine methyltransferase. Nat Genet 2001; 27: 304-308. (Pubitemid 32201852)
49. Huang TH, Perry MR, Laux DE: Methylation profiling of CpG islands in human breast cancer cells. Hum Mol Genet 1999; 8: 459-470. (Pubitemid 29097334)
50. Beck S, Olek A, Walter J: From genomics to epigenomics: a loftier view of life. Nat Biotechnol 1999; 17: 1144.
51. Gu H, Smith ZD, Bock C, Boyle P, Gnirke A, Meissner A: Preparation of reduced representation bisulfite sequencing libraries for genome-scale DNA methylation profiling. Nat Protoc 2011; 6: 468-481.
52. Rauch TA, Pfeifer GP: The MIRA method for DNA methylation analysis. Methods Mol Biol 2009; 507: 65-75.
53. Suzuki M, Greally JM: DNA methylation profiling using Hpa II tiny fragment enrichment by ligation-mediated PCR (HELP). Methods 2010; 52: 218-222.
54. Bock C, Tomazou EM, Brinkman AB, Muller F, Simmer F, Gu H, Jager N, Gnirke A, Stunnenberg HG, Meissner A: Quantitative comparison of genome-wide DNA methylation mapping technologies. Nat Biotechnol 2010; 28: 1106-1114.
55. Hernandez DG, Nalls MA, Gibbs JR, Arepalli S, van der Brug M, Chong S, Moore M, Longo DL, Cookson MR, Traynor BJ, Singleton AB: Distinct DNA methylation changes highly correlated with chronological age in the human brain. Hum Mol Genet 2011; 20: 1164-1172.
56. Gibbs JR, van der Brug MP, Hernandez DG, Traynor BJ, Nalls MA, Lai SL, Arepalli S, Dillman A, Rafferty IP, Troncoso J, Johnson R, Zielke HR, Ferrucci L, Longo DL, Cookson MR, Singleton AB: Abundant quantitative trait loci exist for DNA methylation and gene expression in human brain. PLoS Genet 2010; 6:e1000952.
57. International Parkinson's Disease Genomics Consortium and Wellcome Trust Case Control Consortium: A two-stage meta-analysis identifies several new loci for Parkinson's disease. PLoS Genet 2011; 7:e1002142.
58. Guerreiro RJ, Beck J, Gibbs JR, Santana I, Rossor MN, Schott JM, Nalls MA, Ribeiro H, Santiago B, Fox NC, Oliveira C, Collinge J, Mead S, Singleton A, Hardy J: Genetic variability in CLU and its association with Alzheimer's disease. PLoS One 2010; 5:e9510.
59. Hoglinger GU, Melhem NM, Dickson DW, Sleiman PM, Wang LS, Klei L, Rademakers R, de Silva R, Litvan I, Riley DE, van Swieten JC, Heutink P, Wszolek ZK, Uitti RJ, Vandrovcova J, Hurtig HI, Gross RG, Maetzler W, Goldwurm S, Tolosa E, Borroni B, Pastor P, Group PSPGS, Albin RL, Alonso E, Antonini A, Apfelbacher M, Arnold SE, Avila J, Beach TG, Beecher S, Berg D, Bird TD, Bogdanovic N, Boon AJ, Bordelon Y, Brice A, Budka H, Canesi M, Chiu WZ, Cilia R, Colosimo C, De Deyn PP, de Yebenes JG, Kaat LD, Duara R, Durr A, Engelborghs S, Fabbrini G, Finch NA, Flook R, Frosch MP, Gaig C, Galasko DR, Gasser T, Gearing M, Geller ET, Ghetti B, Graff-Radford NR, Grossman M, Hall DA, Hazrati LN, Hollerhage M, Jankovic J, Juncos JL, Karydas A, Kretzschmar HA, Leber I, Lee VM, Lieberman AP, Lyons KE, Mariani C, Masliah E, Massey LA, McLean CA, Meucci N, Miller BL, Mollenhauer B, Moller JC, Morris HR, Morris C, O'Sullivan SS, Oertel WH, Ottaviani D, Padovani A, Pahwa R, Pezzoli G, Pickering-Brown S, Poewe W, Rabano A, Rajput , Reich SG, Respondek G, Roeber S, Rohrer JD, Ross OA, Rossor MN, Sacilotto G, Seeley WW, Seppi K, Silveira-Moriyama L, Spina S, Srulijes K, St George-Hyslop P, Stamelou M, Standaert DG, Tesei S, Tourtellotte WW, Trenkwalder C, Troakes C, Trojanowski JQ, Troncoso JC, Van Deerlin VM, Vonsattel JP, Wenning GK, White CL, Winter P, Zarow C, Zecchinelli AL, Cantwell LB, Han MR, Dillman A, van der Brug MP, Gibbs JR, Cookson MR, Hernandez DG, Singleton AB, Farrer MJ, Yu CE, Golbe LI, Revesz T, Hardy J, Lees AJ, Devlin B, Hakonarson H, Muller U, Schellenberg GD: Identification of common variants influencing risk of the tauopathy progressive supranuclear palsy. Nat Genet 2011; 43: 699-705.
60. Matevossian A, Akbarian S: Neuronal nuclei isolation from human postmortem brain tissue. J Vis Exp 2008; 20: 914.