Characterization of genome-methylome interactions in 22 nuclear pedigrees

PLoS ONE

Volumn 9, Issue 7, 2014, Pages

  Plongthongkum, Nongluk ^a   Van Eijk, Kristel R ^c   De Jong, Simone ^b   Wang, Tina ^b   Sul, Jae Hoon ^d   Boks, Marco P M ^c   Kahn, René S ^c   Fung, Ho Lim ^a   Ophoff, Roel A ^b,c   Zhang, Kun ^a  

^a UNIVERSITY OF CALIFORNIA SAN DIEGO   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c UNIVERSITY MEDICAL CENTER UTRECHT   (Netherlands)

^d Department of Civil and Environmental Engineering   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BLOOD SAMPLING; CELL POPULATION; DNA METHYLATION; GENE EXPRESSION; GENE FREQUENCY; GENE LINKAGE DISEQUILIBRIUM; GENE MUTATION; GENETIC POLYMORPHISM; GENETIC VARIABILITY; GENOTYPE; HERITABILITY; HUMAN; PEDIGREE ANALYSIS; PHENOTYPE; QUANTITATIVE TRAIT LOCUS; SINGLE NUCLEOTIDE POLYMORPHISM; CPG ISLAND; FEMALE; GENETICS; GENOMICS; HUMAN GENOME; MALE; NUCLEAR FAMILY; PEDIGREE;

CPG ISLANDS; DNA METHYLATION; FEMALE; GENOME, HUMAN; GENOMICS; HUMANS; MALE; NUCLEAR FAMILY; PEDIGREE; POLYMORPHISM, SINGLE NUCLEOTIDE; QUANTITATIVE TRAIT LOCI;

EID: 84904253150     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0099313     Document Type: Article

References (54)

1. McDaniell R, Lee BK, Song L, Liu Z, Boyle AP, et al. (2010) Heritable individual-specific and allele-specific chromatin signatures in humans. Science 328: 235-239.
2. Zhang Y, Rohde C, Reinhardt R, Voelcker-Rehage C, Jeltsch A (2009) Non-imprinted allele-specific DNA methylation on human autosomes. Genome biology 10: R138.
3. Schalkwyk LC, Meaburn EL, Smith R, Dempster EL, Jeffries AR, et al. (2010) Allelic skewing of DNA methylation is widespread across the genome. American journal of human genetics 86: 196-212.
4. Rakyan VK, Down TA, Balding DJ, Beck S (2011) Epigenome-wide association studies for common human diseases. Nature reviews Genetics 12: 529-541.
5. Hannum G, Guinney J, Zhao L, Zhang L, Hughes G, et al. (2013) Genome-wide methylation profiles reveal quantitative views of human aging rates. Molecular cell 49: 359-367.
6. Tycko B (2010) Allele-specific DNA methylation: beyond imprinting. Human molecular genetics 19: R210-220.
7. Feinberg AP (2007) Phenotypic plasticity and the epigenetics of human disease. Nature 447: 433-440.
8. Bell JT, Pai AA, Pickrell JK, Gaffney DJ, Pique-Regi R, et al. (2011) DNA methylation patterns associate with genetic and gene expression variation in HapMap cell lines. Genome biology 12: R10.
9. Fraser HB, Lam LL, Neumann SM, Kobor MS (2012) Population-specificity of human DNA methylation. Genome biology 13: R8.
10. Gertz J, Varley KE, Reddy TE, Bowling KM, Pauli F, et al. (2011) Analysis of DNA methylation in a three-generation family reveals widespread genetic influence on epigenetic regulation. PLoS genetics 7: e1002228.
11. van Eijk KR, de Jong S, Boks MP, Langeveld T, Colas F, et al. (2012) Genetic analysis of DNA methylation and gene expression levels in whole blood of healthy human subjects. BMC genomics 13: 636.
12. Hellman A, Chess A (2010) Extensive sequence-influenced DNA methylation polymorphism in the human genome. Epigenetics & chromatin 3: 11.
13. Shoemaker R, Deng J, Wang W, Zhang K (2010) Allele-specific methylation is prevalent and is contributed by CpG-SNPs in the human genome. Genome research 20: 883-889.
14. Fang F, Hodges E, Molaro A, Dean M, Hannon GJ, et al. (2012) Genomic landscape of human allele-specific DNA methylation. Proceedings of the National Academy of Sciences of the United States of America 109: 7332-7337.
15. Schilling E, El Chartouni C, Rehli M (2009) Allele-specific DNA methylation in mouse strains is mainly determined by cis-acting sequences. Genome research 19: 2028-2035.
16. Diep D, Plongthongkum N, Gore A, Fung HL, Shoemaker R, et al. (2012) Library-free methylation sequencing with bisulfite padlock probes. Nature methods 9: 270-272.
17. Houseman EA, Accomando WP, Koestler DC, Christensen BC, Marsit CJ, et al. (2012) DNA methylation arrays as surrogate measures of cell mixture distribution. BMC Bioinformatics 13: 86.
18. Liu Y, Aryee MJ, Padyukov L, Fallin MD, Hesselberg E, et al. (2013) Epigenome-wide association data implicate DNA methylation as an intermediary of genetic risk in rheumatoid arthritis. Nature biotechnology 31: 142-147.
19. Jaffe AE, Irizarry RA (2014) Accounting for cellular heterogeneity is critical in epigenome-wide association studies. Genome biology 15: R31.
20. Stranger BE, Nica AC, Forrest MS, Dimas A, Bird CP, et al. (2007) Population genomics of human gene expression. Nat Genet 39: 1217-1224. (Pubitemid 47482691)
21. Abecasis GR, Altshuler D, Auton A, Brooks LD, Durbin RM, et al. (2010) A map of human genome variation from population-scale sequencing. Nature 467: 1061-1073.
22. Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MA, et al. (2007) PLINK: a tool set for whole-genome association and population-based linkage analyses. American journal of human genetics 81: 559-575. (Pubitemid 47330214)
23. Xie W, Barr CL, Kim A, Yue F, Lee AY, et al. (2012) Base-resolution analyses of sequence and parent-of-origin dependent DNA methylation in the mouse genome. Cell 148: 816-831.
24. Greaves I, Groszmann M, Dennis ES, Peacock WJ (2012) Trans-chromosomal methylation. Epigenetics: official journal of the DNA Methylation Society 7: 800-805.
25. Gimelbrant A, Hutchinson JN, Thompson BR, Chess A (2007) Widespread monoallelic expression on human autosomes. Science 318: 1136-1140. (Pubitemid 350134896)
26. Hansen KD, Timp W, Bravo HC, Sabunciyan S, Langmead B, et al. (2011) Increased methylation variation in epigenetic domains across cancer types. Nature genetics 43: 768-775.
27. Feinberg AP, Irizarry RA (2010) Evolution in health and medicine Sackler colloquium: Stochastic epigenetic variation as a driving force of development, evolutionary adaptation, and disease. Proceedings of the National Academy of Sciences of the United States of America 107 Suppl 1: 1757-1764.
28. Bastepe M (2007) The GNAS Locus: Quintessential Complex Gene Encoding Gsalpha, XLalphas, and other Imprinted Transcripts. Current genomics 8: 398-414.
29. Plagge A, Kelsey G (2006) Imprinting the Gnas locus. Cytogenetic and genome research 113: 178-187.
30. Luykx JJ, Bakker SC, Lentjes E, Neeleman M, Strengman E, et al. (2013) Genome-wide association study of monoamine metabolite levels in human cerebrospinal fluid. Molecular psychiatry.
31. Degner JF, Pai AA, Pique-Regi R, Veyrieras JB, Gaffney DJ, et al. (2012) DNase I sensitivity QTLs are a major determinant of human expression variation. Nature 482: 390-394.
32. Pickrell JK, Marioni JC, Pai AA, Degner JF, Engelhardt BE, et al. (2010) Understanding mechanisms underlying human gene expression variation with RNA sequencing. Nature 464: 768-772.
33. Zhang D, Cheng L, Badner JA, Chen C, Chen Q, et al. (2010) Genetic control of individual differences in gene-specific methylation in human brain. American journal of human genetics 86: 411-419.
34. Emilsson V, Thorleifsson G, Zhang B, Leonardson AS, Zink F, et al. (2008) Genetics of gene expression and its effect on disease. Nature 452: 423-428. (Pubitemid 351450845)
35. Bibikova M, Barnes B, Tsan C, Ho V, Klotzle B, et al. (2011) High density DNA methylation array with single CpG site resolution. Genomics 98: 288-295.
36. Boyle P, Clement K, Gu H, Smith ZD, Ziller M, et al. (2012) Gel-free multiplexed reduced representation bisulfite sequencing for large-scale DNA methylation profiling. Genome biology 13: R92.
37. Teperino R, Lempradl A, Pospisilik JA (2013) Bridging epigenomics and complex disease: the basics. Cellular and molecular life sciences: CMLS.
38. Drong AW, Nicholson G, Hedman AK, Meduri E, Grundberg E, et al. (2013) The presence of methylation quantitative trait Loci indicates a direct genetic influence on the level of DNA methylation in adipose tissue. PLoS One 8: e55923.
39. Shenker NS, Polidoro S, van Veldhoven K, Sacerdote C, Ricceri F, et al. (2013) Epigenome-wide association study in the European Prospective Investigation into Cancer and Nutrition (EPIC-Turin) identifies novel genetic loci associated with smoking. Human molecular genetics 22: 843-851.
40. Joubert BR, Haberg SE, Nilsen RM, Wang X, Vollset SE, et al. (2012) 450K epigenome-wide scan identifies differential DNA methylation in newborns related to maternal smoking during pregnancy. Environmental health perspectives 120: 1425-1431.
41. Ball MP, Li JB, Gao Y, Lee JH, LeProust EM, et al. (2009) Targeted and genome-scale strategies reveal gene-body methylation signatures in human cells. Nature biotechnology 27: 361-368.
42. Jones PA (2012) Functions of DNA methylation: islands, start sites, gene bodies and beyond. Nature reviews Genetics 13: 484-492.
43. Deng J, Shoemaker R, Xie B, Gore A, LeProust EM, et al. (2009) Targeted bisulfite sequencing reveals changes in DNA methylation associated with nuclear reprogramming. Nat Biotechnol 27: 353-360.
44. Lister R, Pelizzola M, Dowen RH, Hawkins RD, Hon G, et al. (2009) Human DNA methylomes at base resolution show widespread epigenomic differences. Nature 462: 315-322.
45. Stadler MB, Murr R, Burger L, Ivanek R, Lienert F, et al. (2011) DNA-binding factors shape the mouse methylome at distal regulatory regions. Nature 480: 490-495.
46. Dunham I, Kundaje A, Aldred SF, Collins PJ, Davis CA, et al. (2012) An integrated encyclopedia of DNA elements in the human genome. Nature 489: 57-74.
47. Liu Y, Siegmund KD, Laird PW, Berman BP (2012) Bis-SNP: Combined DNA methylation and SNP calling for Bisulfite-seq data. Genome biology 13: R61.
48. Hartwell LH, Hopfield JJ, Leibler S, Murray AW (1999) From molecular to modular cell biology. Nature 402: C47-52.
49. Milo R, Shen-Orr S, Itzkovitz S, Kashtan N, Chklovskii D, et al. (2002) Network motifs: simple building blocks of complex networks. Science 298: 824-827. (Pubitemid 35231534)
50. Becskei A, Serrano L (2000) Engineering stability in gene networks by autoregulation. Nature 405: 590-593.
51. Raj A, Rifkin SA, Andersen E, van Oudenaarden A (2010) Variability in gene expression underlies incomplete penetrance. Nature 463: 913-918.
52. Browning BL, Browning SR (2009) A unified approach to genotype imputation and haplotype-phase inference for large data sets of trios and unrelated individuals. American journal of human genetics 84: 210-223.
53. Howie B, Fuchsberger C, Stephens M, Marchini J, Abecasis GR (2012) Fast and accurate genotype imputation in genome-wide association studies through prephasing. Nat Genet 44: 955-959.
54. Quinlan AR, Hall IM (2010) BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26: 841-842.