Allele-specific chromatin immunoprecipitation studies show genetic influence on chromatin state in human genome

PLoS Genetics

Volumn 3, Issue 5, 2007, Pages 768-778

  Kadota, Mitsutaka ^a   Yang, Howard H ^a   Hu, Nan ^a   Wang, Chaoyu ^a   Hu, Ying ^a   Taylor, Philip R ^a   Buetow, Kenneth H ^a   Lee, Maxwell P ^a  

^a NATIONAL CANCER INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ENZYME ANTIBODY; HISTONE H3; RNA POLYMERASE II; HISTONE;

ARTICLE; CELL LINE; CHROMATIN; CHROMATIN IMMUNOPRECIPITATION; EPIGENETICS; GENETIC POLYMORPHISM; HUMAN; HUMAN GENOME; HYPOTHESIS; INHERITANCE; LYMPHOBLASTOID CELL; PEDIGREE; PROTEIN MODIFICATION; SINGLE NUCLEOTIDE POLYMORPHISM; ACETYLATION; ADOLESCENT; ADULT; ALLELE; ANTIBODY SPECIFICITY; BASE PAIRING; CHILD; CLUSTER ANALYSIS; FEMALE; GENETICS; GENOME; MALE; METABOLISM; METHODOLOGY; MIDDLE AGED; PRINCIPAL COMPONENT ANALYSIS; PROMOTER REGION;

ACETYLATION; ADOLESCENT; ADULT; ALLELES; ANTIBODY SPECIFICITY; BASE PAIRING; CHILD; CHROMATIN; CHROMATIN IMMUNOPRECIPITATION; CLUSTER ANALYSIS; FEMALE; GENOME, HUMAN; HISTONES; HUMANS; INHERITANCE PATTERNS; MALE; MIDDLE AGED; PRINCIPAL COMPONENT ANALYSIS; PROMOTER REGIONS (GENETICS);

EID: 34249725088     PISSN: 15537390     EISSN: 15537404     Source Type: Journal    
DOI: 10.1371/journal.pgen.0030081     Document Type: Article

References (30)

1. Cheung VG, Conlin LK, Weber TM, Arcaro M, Jen KY, et al. (2003) Natural variation in human gene expression assessed in lymphoblastoid cells. Nat Genet 33: 422-425.
2. Enard W, Khaitovich P, Klose J, Zollner S, Heissig F, et al. (2002) Intra- and interspecific variation in primate gene expression patterns. Science 296: 340-343.
3. Johnson NA, Porter AH (2000) Rapid speciation via parallel, directional selection on regulatory genetic pathways. J Theor Biol 205: 527-542.
4. Levine M, Tjian R (2003) Transcription regulation and animal diversity. Nature 424: 147-151.
5. Yan H, Yuan W, Velculescu VE, Vogelstein B, Kinzler KW (2002) Allelic variation in human gene expression. Science 297: 1143.
6. Brem RB, Yvert G, Clinton R, Kruglyak L (2002) Genetic dissection of transcriptional regulation in budding yeast. Science 296: 752-755.
7. Morley M, Molony CM, Weber TM, Devlin JL, Ewens KG, et al. (2004) Genetic analysis of genome-wide variation in human gene expression. Nature 430: 743-747.
8. Schadt EE, Monks SA, Drake TA, Lusis AJ, Che N, et al. (2003) Genetics of gene expression surveyed in maize, mouse and man. Nature 422: 297-302.
9. Lo HS, Wang Z, Hu Y, Yang HH, Gere S, et al. (2003) Allelic variation in gene expression is common in the human genome. Genome Res 13: 1855-1862.
10. Ge B, Gurd S, Gaudin T, Dore C, Lepage P, et al. (2005) Survey of allelic expression using EST mining. Genome Res 15: 1584-1591.
11. Lin W, Yang HH, Lee MP (2005) Allelic variation in gene expression identified through computational analysis of the dbEST database. Genomics 86: 518-527.
12. Pant PV, Tao H, Beilharz EJ, Ballinger DG, Cox DR, et al. (2006) Analysis of allelic differential expression in human white blood cells. Genome Res 16: 331-339.
13. Knight JC, Keating BJ, Rockett KA, Kwiatkowski DP (2003) In vivo characterization of regulatory polymorphisms by allele-specific quantification of RNA polymerase loading. Nat Genet 33: 469-475.
14. Tao H, Cox DR, Frazer KA (2006) Allele-specific KRT1 expression is a complex trait. PLoS Genet 2: e93. doi:10.1371/journal.pgen.0020093
15. Jenuwein T, Allis CD (2001) Translating the histone code. Science 293: 1074-1080.
16. Morgan HD, Sutherland HG, Martin DI, Whitelaw E (1999) Epigenetic inheritance at the agouti locus in the mouse. Nat Genet 23: 314-318.
17. Rassoulzadegan M, Grandjean V, Gounon P, Vincent S, Gillot I, et al. (2006) RNA-mediated non-mendelian inheritance of an epigenetic change in the mouse. Nature 441: 469-474.
18. Lee MP, DeBaun MR, Mitsuya K, Galonek HL, Brandenburg S, et al. (1999) Loss of imprinting of a paternally expressed transcript, with antisense orientation to KVLQT1, occurs frequently in Beckwith-Wiedemann syndrome and is independent of insulin-like growth factor II imprinting. Proc Natl Acad Sci U S A 96: 5203-5208.
19. Sandovici I, Leppert M, Hawk PR, Suarez A, Linares Y, et al. (2003) Familial aggregation of abnormal methylation of parental alleles at the IGF2/H19 and IGF2R differentially methylated regions. Hum Mol Genet 12: 1569-1578.
20. Silva AJ, White R (1988) Inheritance of allelic blueprints for methylation patterns. Cell 54: 145-152.
21. Chan TL, Yuen ST, Kong CK, Chan YW, Chan AS, et al. (2006) Heritable germline epimutation of MSH2 in a family with hereditary nonpolyposis colorectal cancer. Nat Genet 38: 1178-1183.
22. Hitchins MP, Wong JJ, Suthers G, Suter CM, Martin DI, et al. (2007) Inheritance of a cancer-associated MLH1 germ-line epimutation. N Engl J Med 356: 697-705.
23. Suter CM, Martin DI, Ward RL (2004) Germline epimutation of MLH1 in individuals with multiple cancers. Nat Genet 36: 497-501.
24. Fraga MF, Ballestar E, Paz MF, Ropero S, Setien F, et al. (2005) Epigenetic differences arise during the lifetime of monozygotic twins. Proc Natl Acad Sci U S A 102: 10604-10609.
25. Reuter G, Spierer P (1992) Position effect variegation and chromatin proteins. Bioessays 14: 605-612.
26. Rakyan VK, Chong S, Champ ME, Cuthbert PC, Morgan HD, et al. (2003) Transgenerational inheritance of epigenetic states at the murine Axin(Fu) allele occurs after maternal and paternal transmission. Proc Natl Acad Sci U S A 100: 2538-2543.
27. Banks JA, Masson P, Fedoroff N (1988) Molecular mechanisms in the developmental regulation of the maize Suppressor-mutator transposable element. Genes Dev 2: 1364-1380.
28. Bender J, Fink GR (1995) Epigenetic control of an endogenous gene family is revealed by a novel blue fluorescent mutant of Arabidopsis. Cell 83: 725-734.
29. Stam M, Belele C, Dorweiler JE, Chandler VL (2002) Differential chromatin structure within a tandem array 100 kb upstream of the maize b1 locus is associated with paramutation. Genes Dev 16: 1906-1918.
30. Irizarry RA, Hobbs B, Collin F, Beazer-Barclay YD, Antonellis KJ, et al. (2003) Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics 4: 249-264.