Intra-monozygotic twin pair discordance and longitudinal variation of whole-genome scale DNA methylation in adults

PLoS ONE

Volumn 10, Issue 8, 2015, Pages

  Zhang, Na ^a,b   Zhao, Shumin ^a   Zhang, Su Hua ^a,b   Chen, Jinzhong ^b   Lu, Daru ^b   Shen, Min ^a   Li, Chengtao ^a  

^a INSTITUTE OF FORENSIC SCIENCE   (China)

^b FUDAN UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; GENETIC MARKER;

ADULT; AGED; ARTICLE; BLOOD SAMPLING; CONTROLLED STUDY; CPG ISLAND; DNA METHYLATION; EPIGENETICS; FEMALE; GENE LOCUS; GENETIC PROCEDURES; GENETIC STABILITY; GENETIC VARIABILITY; GENOME ANALYSIS; HUMAN; LONGITUDINAL STUDY; MALE; MONOZYGOTIC TWINS; PYROSEQUENCING; REPRODUCIBILITY; SANGER SEQUENCING; TWIN DISCORDANCE; FORENSIC GENETICS; GENETIC EPIGENESIS; GENETIC MARKER; GENETICS; HUMAN GENOME; MIDDLE AGED; MULTIGENE FAMILY; PROMOTER REGION;

ADULT; AGED; CPG ISLANDS; DNA METHYLATION; EPIGENESIS, GENETIC; FEMALE; FORENSIC GENETICS; GENETIC MARKERS; GENOME, HUMAN; HUMANS; MALE; MIDDLE AGED; MULTIGENE FAMILY; PROMOTER REGIONS, GENETIC; REPRODUCIBILITY OF RESULTS; TWINS, MONOZYGOTIC;

EID: 84941901978     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0135022     Document Type: Article

References (50)

1. von Wurmb-Schwark N, Schwark T, Christiansen L, Lorenz D, Oehmichen M. The use of different multiplex PCRs for twin zygosity determination and its application in forensic trace analysis. Legal medicine. 2004; 6(2):125-30. doi: 10.1016/j.legalmed.2003.12.002 PMID: 15039056
2. Andrew T, Calloway CD, Stuart S, Lee SH, Gill R, Clement G, et al. A twin study of mitochondrial DNA polymorphisms shows that heteroplasmy at multiple sites is associated with mtDNA variant 16093 but not with zygosity. PLoS One. 6(8):e22332. Epub 2011/08/23. doi: 10.1371/journal.pone.0022332 PONE-D-11-04709 [pii]. PMID: 21857921; PubMed Central PMCID: PMC3153933
3. Edwards TM, Myers JP. Environmental exposures and gene regulation in disease etiology. Environmental health perspectives. 2007; 115(9):1264-70. doi: 10.1289/ehp.9951 PMID: 17805414; PubMed Central PMCID: PMC1964917
4. Fleischmann T, Fulde G. Emergency medicine in modern Europe. Emergency medicine Australasia: EMA. 2007; 19(4):300-2. doi: 10.1111/j.1742-6723.2007.00991.x PMID: 17655630
5. Jaenisch R, Bird A. Epigenetic regulation of gene expression: how the genome integrates intrinsic and environmental signals. Nature genetics. 2003; 33 Suppl:245-54. doi: 10.1038/ng1089 PMID: 12610534
6. Jirtle RL, Skinner MK. Environmental epigenomics and disease susceptibility. Nature reviews Genetics. 2007; 8(4):253-62. doi: 10.1038/nrg2045 PMID: 17363974
7. Ushijima T, Watanabe N, Okochi E, Kaneda A, Sugimura T, Miyamoto K. Fidelity of the methylation pattern and its variation in the genome. Genome research. 2003; 13(5):868-74. doi: 10.1101/gr.969603 PMID: 12727906; PubMed Central PMCID: PMC430912
8. Riggs AD, Xiong Z, Wang L, LeBon JM. Methylation dynamics, epigenetic fidelity and X chromosome structure. Novartis Foundation symposium. 1998; 214:214-25; discussion 25-32. PMID: 9601020
9. Dolinoy DC, Weidman JR, Jirtle RL. Epigenetic gene regulation: linking early developmental environment to adult disease. Reproductive toxicology. 2007; 23(3):297-307. doi: 10.1016/j.reprotox.2006.08. 012 PMID: 17046196
10. Heijmans BT, Kremer D, Tobi EW, Boomsma DI, Slagboom PE. Heritable rather than age-related environmental and stochastic factors dominate variation in DNA methylation of the human IGF2/H19 locus. Human molecular genetics. 2007; 16(5):547-54. doi: 10.1093/hmg/ddm010 PMID: 17339271
11. Kuratomi G, Iwamoto K, Bundo M, Kusumi I, Kato N, Iwata N, et al. Aberrant DNA methylation associated with bipolar disorder identified from discordant monozygotic twins. Molecular psychiatry. 2008; 13 (4):429-41. doi: 10.1038/sj.mp.4002001 PMID: 17471289
12. Petronis A, Gottesman II, Kan P, Kennedy JL, Basile VS, Paterson AD, et al. Monozygotic twins exhibit numerous epigenetic differences: clues to twin discordance? Schizophrenia bulletin. 2003; 29(1):169-78. PMID: 12908672
13. Oates NA, van Vliet J, Duffy DL, Kroes HY, Martin NG, Boomsma DI, et al. Increased DNA methylation at the AXIN1 gene in a monozygotic twin from a pair discordant for a caudal duplication anomaly. American journal of human genetics. 2006; 79(1):155-62. doi: 10.1086/505031 PMID: 16773576; PubMed Central PMCID: PMC1474116
14. Kaminsky ZA, Tang T, Wang SC, Ptak C, Oh GH, Wong AH, et al. DNA methylation profiles in monozygotic and dizygotic twins. Nature genetics. 2009; 41(2):240-5. doi: 10.1038/ng.286 PMID: 19151718
15. Javierre BM, Fernandez AF, Richter J, Al-Shahrour F, Martin-Subero JI, Rodriguez-Ubreva J, et al. Changes in the pattern of DNA methylation associate with twin discordance in systemic lupus erythematosus. Genome research. 2010; 20(2):170-9. doi: 10.1101/gr.100289.109 PMID: 20028698; PubMed Central PMCID: PMC2813473
16. Rakyan VK, Beyan H, Down TA, Hawa MI, Maslau S, Aden D, et al. Identification of type 1 diabetesassociated DNA methylation variable positions that precede disease diagnosis. PLoS genetics. 2011; 7 (9):e1002300. doi: 10.1371/journal.pgen.1002300 PMID: 21980303; PubMed Central PMCID: PMC3183089
17. Martin N, Boomsma D, Machin G. A twin-pronged attack on complex traits. Nature genetics. 1997; 17 (4):387-92. doi: 10.1038/ng1297-387 PMID: 9398838
18. Gervin K, Vigeland MD, Mattingsdal M, Hammero M, Nygard H, Olsen AO, et al. DNA methylation and gene expression changes in monozygotic twins discordant for psoriasis: identification of epigenetically dysregulated genes. PLoS genetics. 2012; 8(1):e1002454. doi: 10.1371/journal.pgen.1002454 PMID: 22291603; PubMed Central PMCID: PMC3262011
19. Martino D, Loke YJ, Gordon L, Ollikainen M, Cruickshank MN, Saffery R, et al. Longitudinal, genomescale analysis of DNA methylation in twins from birth to 18 months of age reveals rapid epigenetic change in early life and pair-specific effects of discordance. Genome biology. 2013; 14(5):R42. doi:10.1186/gb-2013-14-5-r42 PMID: 23697701
20. Gordon L, Joo JE, Powell JE, Ollikainen M, Novakovic B, Li X, et al. Neonatal DNA methylation profile in human twins is specified by a complex interplay between intrauterine environmental and genetic factors, subject to tissue-specific influence. Genome research. 2012; 22(8):1395-406. doi: 10.1101/gr. 136598.111 PMID: 22800725; PubMed Central PMCID: PMC3409253
21. Wang D, Liu X, Zhou Y, Xie H, Hong X, Tsai HJ, et al. Individual variation and longitudinal pattern of genome-wide DNA methylation from birth to the first two years of life. Epigenetics. 2012; 7(6):594-605. doi: 10.4161/epi.20117 PMID: 22522910; PubMed Central PMCID: PMC3398988
22. Boks MP, Derks EM, Weisenberger DJ, Strengman E, Janson E, Sommer IE, et al. The relationship of DNA methylation with age, gender and genotype in twins and healthy controls. PloS one. 2009; 4(8): e6767. doi: 10.1371/journal.pone.0006767 PMID: 19774229; PubMed Central PMCID: PMC2747671
23. Gervin K, Hammero M, Akselsen HE, Moe R, Nygard H, Brandt I, et al. Extensive variation and low heritability of DNA methylation identified in a twin study. Genome research. 2011; 21(11):1813-21. doi:10.1101/gr.119685.110 PMID: 21948560; PubMed Central PMCID: PMC3205566
24. Fraga MF, Ballestar E, Paz MF, Ropero S, Setien F, Ballestar ML, et al. Epigenetic differences arise during the lifetime of monozygotic twins. Proceedings of the National Academy of Sciences of the United States of America. 2005; 102(30):10604-9. doi: 10.1073/pnas.0500398102 PMID: 16009939; PubMed Central PMCID: PMC1174919
25. Rakyan VK, Down TA, Maslau S, Andrew T, Yang TP, Beyan H, et al. Human aging-associated DNA hypermethylation occurs preferentially at bivalent chromatin domains. Genome research. 2010; 20 (4):434-9. doi: 10.1101/gr.103101.109 PMID: 20219945; PubMed Central PMCID: PMC2847746
26. Teschendorff AE, Menon U, Gentry-Maharaj A, Ramus SJ, Weisenberger DJ, Shen H, et al. Agedependent DNA methylation of genes that are suppressed in stem cells is a hallmark of cancer. Genome research. 2010; 20(4):440-6. doi: 10.1101/gr.103606.109 PMID: 20219944; PubMed Central PMCID: PMC2847747
27. Bollati V, Schwartz J, Wright R, Litonjua A, Tarantini L, Suh H, et al. Decline in genomic DNA methylation through aging in a cohort of elderly subjects. Mechanisms of ageing and development. 2009; 130 (4):234-9. doi: 10.1016/j.mad.2008.12.003 PMID: 19150625; PubMed Central PMCID: PMC2956267
28. Murphy SK, Huang Z, Hoyo C. Differentially methylated regions of imprinted genes in prenatal, perinatal and postnatal human tissues. PloS one. 2012; 7(7):e40924. doi: 10.1371/journal.pone.0040924 PMID: 22808284; PubMed Central PMCID: PMC3396645
29. Bjornsson HT, Sigurdsson MI, Fallin MD, Irizarry RA, Aspelund T, Cui H, et al. Intra-individual change over time in DNA methylation with familial clustering. JAMA: the journal of the American Medical Association. 2008; 299(24):2877-83. doi: 10.1001/jama.299.24.2877 PMID: 18577732; PubMed Central PMCID: PMC2581898
30. Feinberg AP, Irizarry RA, Fradin D, Aryee MJ, Murakami P, Aspelund T, et al. Personalized epigenomic signatures that are stable over time and covary with body mass index. Science translational medicine. 2010; 2(49):49ra67. doi: 10.1126/scitranslmed.3001262 PMID: 20844285; PubMed Central PMCID: PMC3137242
31. Teschendorff AE, Marabita F, Lechner M, Bartlett T, Tegner J, Gomez-Cabrero D, et al. A beta-mixture quantile normalization method for correcting probe design bias in Illumina Infinium 450 k DNA methylation data. Bioinformatics. 2013; 29(2):189-96. doi: 10.1093/bioinformatics/bts680 PMID: 23175756; PubMed Central PMCID: PMC3546795
32. Marabita F, Almgren M, Lindholm ME, Ruhrmann S, Fagerstrom-Billai F, Jagodic M, et al. An evaluation of analysis pipelines for DNA methylation profiling using the Illumina HumanMethylation450 BeadChip platform. Epigenetics: official journal of the DNA Methylation Society. 2013; 8(3):333-46. doi: 10.4161/ epi.24008 PMID: 23422812; PubMed Central PMCID: PMC3669124
33. Du P, Zhang X, Huang CC, Jafari N, Kibbe WA, Hou L, et al. Comparison of Beta-value and M-value methods for quantifying methylation levels by microarray analysis. BMC bioinformatics. 2010; 11:587. doi: 10.1186/1471-2105-11-587 PMID: 21118553; PubMed Central PMCID: PMC3012676
34. Sandoval J, Heyn H, Moran S, Serra-Musach J, Pujana MA, Bibikova M, et al. Validation of a DNA methylation microarray for 450,000 CpG sites in the human genome. Epigenetics: official journal of the DNA Methylation Society. 2011; 6(6):692-702. PMID: 21593595
35. Wieczorek G, Asemissen A, Model F, Turbachova I, Floess S, Liebenberg V, et al. Quantitative DNA methylation analysis of FOXP3 as a new method for counting regulatory T cells in peripheral blood and solid tissue. Cancer Res. 2009; 69(2):599-608. Epub 2009/01/17. 69/2/599 [pii] doi: 10.1158/0008- 5472.CAN-08-2361 PMID: 19147574
36. Varley KE, Gertz J, Bowling KM, Parker SL, Reddy TE, Pauli-Behn F, et al. Dynamic DNA methylation across diverse human cell lines and tissues. Genome Res. 23(3):555-67. Epub 2013/01/18. gr.147942.112 [pii] doi: 10.1101/gr.147942.112 PMID: 23325432; PubMed Central PMCID: PMC3589544
37. Davies MN, Volta M, Pidsley R, Lunnon K, Dixit A, Lovestone S, et al. Functional annotation of the human brain methylome identifies tissue-specific epigenetic variation across brain and blood. Genome Biol. 13(6):R43. Epub 2012/06/19. gb-2012-13-6-r43 [pii] doi: 10.1186/gb-2012-13-6-r43 PMID: 22703893; PubMed Central PMCID: PMC3446315
38. Baron U, Turbachova I, Hellwag A, Eckhardt F, Berlin K, Hoffmuller U, et al. DNA methylation analysis as a tool for cell typing. Epigenetics. 2006; 1(1):55-60. Epub 2007/11/14. 2643 [pii]. PMID: 17998806
39. Meissner A. Epigenetic modifications in pluripotent and differentiated cells. Nat Biotechnol. 28 (10):1079-88. Epub 2010/10/15. nbt.1684 [pii] doi: 10.1038/nbt.1684 PMID: 20944600
40. Accomando WP, Wiencke JK, Houseman EA, Nelson HH, Kelsey KT. Quantitative reconstruction of leukocyte subsets using DNA methylation. Genome Biol. 15(3):R50. Epub 2014/03/07. gb-2014-15-3- r50 [pii] doi: 10.1186/gb-2014-15-3-r50 PMID: 24598480; PubMed Central PMCID: PMC4053693
41. Lu TP, Chen KT, Tsai MH, Kuo KT, Hsiao CK, Lai LC, et al. Identification of genes with consistent methylation levels across different human tissues. Sci Rep. 4:4351. Epub 2014/03/13. srep04351 [pii] doi: 10.1038/srep04351 PMID: 24619003; PubMed Central PMCID: PMC3950633
42. Gordon L, Joo JH, Andronikos R, Ollikainen M, Wallace EM, Umstad MP, et al. Expression discordance of monozygotic twins at birth: effect of intrauterine environment and a possible mechanism for fetal programming. Epigenetics: official journal of the DNA Methylation Society. 2011; 6(5):579-92. PMID: 21358273
43. Shoemaker R, Deng J, Wang W, Zhang K. Allele-specific methylation is prevalent and is contributed by CpG-SNPs in the human genome. Genome research. 2010; 20(7):883-9. doi: 10.1101/gr.104695.109 PMID: 20418490; PubMed Central PMCID: PMC2892089
44. Dedeurwaerder S, Defrance M, Calonne E, Denis H, Sotiriou C, Fuks F. Evaluation of the Infinium Methylation 450K technology. Epigenomics. 2011; 3(6):771-84. doi: 10.2217/epi.11.105 PMID: 22126295
45. Bibikova M, Fan JB. GoldenGate assay for DNA methylation profiling. Methods in molecular biology. 2009; 507:149-63. doi: 10.1007/978-1-59745-522-0-12 PMID: 18987813
46. Bibikova M, Lin Z, Zhou L, Chudin E, Garcia EW, Wu B, et al. High-throughput DNA methylation profiling using universal bead arrays. Genome research. 2006; 16(3):383-93. doi: 10.1101/gr.4410706 PMID: 16449502; PubMed Central PMCID: PMC1415217
47. Irizarry RA, Ladd-Acosta C, Carvalho B, Wu H, Brandenburg SA, Jeddeloh JA, et al. Comprehensive high-throughput arrays for relative methylation (CHARM). Genome research. 2008; 18(5):780-90. doi: 10.1101/gr.7301508 PMID: 18316654; PubMed Central PMCID: PMC2336799
48. Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, et al. Bioconductor: open software development for computational biology and bioinformatics. Genome Biol. 2004; 5(10):R80. Epub 2004/10/06. gb-2004-5-10-r80 [pii] doi: 10.1186/gb-2004-5-10-r80 PMID: 15461798; PubMed Central PMCID: PMC545600
49. Dereeper A, Guignon V, Blanc G, Audic S, Buffet S, Chevenet F, et al. Phylogeny.fr: robust phylogenetic analysis for the non-specialist. Nucleic acids research. 2008; 36(Web Server issue):W465-9. doi: 10.1093/nar/gkn180 PMID: 18424797; PubMed Central PMCID: PMC2447785
50. Dereeper A, Audic S, Claverie JM, Blanc G. BLAST-EXPLORER helps you building datasets for phylogenetic analysis. BMC evolutionary biology. 2010; 10:8. doi: 10.1186/1471-2148-10-8 PMID: 20067610; PubMed Central PMCID: PMC2821324