Human aging-associated DNA hypermethylation occurs preferentially at bivalent chromatin domains

Genome Research

Volumn 20, Issue 4, 2010, Pages 434-439

  Rakyan, Vardhman K ^a   Down, Thomas A ^b   Maslau, Siarhei ^b   Andrew, Toby ^c   Yang, Tsun Po ^d   Beyan, Huriya ^a   Whittaker, Pamela ^d   McCann, Owen T ^d   Finer, Sarah ^a   Valdes, Ana M ^c   Leslie, R David ^a   Deloukas, Panogiotis ^d   Spector, Timothy D ^c  

^a QUEEN MARY UNIVERSITY OF LONDON   (United Kingdom)

^b UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^c ST THOMAS HOSPITAL   (United Kingdom)

^d WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

DNA;

AGING; ARTICLE; BLOOD SAMPLING; CD4 LYMPHOCYTE COUNT; CHEEK; CHROMATIN; CONTROLLED STUDY; DNA METHYLATION; GENE REPLICATION; HUMAN; HUMAN CELL; NORMAL HUMAN; PRIORITY JOURNAL; PROMOTER REGION;

ADULT; AGED; AGING; BLOOD CELLS; CELL LINE, TUMOR; CELL TRANSFORMATION, NEOPLASTIC; CHROMATIN; COHORT STUDIES; DNA METHYLATION; EPIGENESIS, GENETIC; FEMALE; GENE EXPRESSION REGULATION, DEVELOPMENTAL; GENES, DEVELOPMENTAL; HUMANS; MALE; MIDDLE AGED; NEOPLASMS; PROMOTER REGIONS, GENETIC; SUBSTRATE SPECIFICITY; TWINS; YOUNG ADULT;

EID: 77950657253     PISSN: 10889051     EISSN: 15495469     Source Type: Journal    
DOI: 10.1101/gr.103101.109     Document Type: Article

References (20)

1. Azuara V, Perry P, Sauer S, Spivakov M, Jørgensen HF, John RM, Gouti M, Casanova M, Warnes G, Merkenschlager M, et al. 2006. Chromatin signatures of pluripotent cell lines. Nat Cell Biol 8: 532-538.
2. Barski A, Cuddapah S, Cui K, Roh TY, Schones DE,Wang Z,Wei G, Chepelev I, Zhao K. 2007. High-resolution profiling of histone methylations in the human genome. Cell 129: 823-837.
3. Bernstein BE, Mikkelsen TS, Xie X, Kamal M, Huebert DJ, Cuff J, Fry B, Meissner A, Wernig M, Plath K, et al. 2006. A bivalent chromatin structure marks key developmental genes in embryonic stem cells. Cell 125: 315-326.
4. Bibikova M, Le J, Barnes R, Saedinia-Melnyk S, Zhou L, Shen R, Gunderson KL. 2009. Genome-wide DNA methylation profiling using Infinium® assay. Epigenomics 1: 177-200.
5. Bjornsson HT, Sigurdsson MI, Fallin MD, Irizarry RA, Aspelund T, Cui H, Yu W, Rongione MA, Ekström TJ, Harris TB, et al. 2008. Intra-individual change over time in DNA methylation with familial clustering. JAMA 299: 2877-2883.
6. Boks MP, Derks EM, Weisenberger DJ, Strengman E, Janson E, Sommer IE, Kahn RS, Ophoff RA. 2009. The relationship of DNA methylation with age, gender and genotype in twins and healthy controls. PLoS One 4: e6767. doi: 10.1371/journal.pone.0006767.
7. Christensen BC, Houseman EA, Marsit CJ, Zheng S, Wrensch MR, Wiemels JL, Nelson HH, Karagas MR, Padbury JF, Bueno R, et al. 2009. Aging and environmental exposures alter tissue-specific DNA methylation dependent upon CpG island context. PLoS Genet 5: e1000602. doi:10.1371/journal.pgen.1000602.
8. Cui K, Zang C, Roh TY, Schones DE, Childs RW, Peng W, Zhao K. 2009. Chromatin signatures in multipotent human hematopoietic stem cells indicate the fate of bivalent genes during differentiation. Cell Stem Cell 4: 80-93.
9. Dorus S, Vallender EJ, Evans PD, Anderson JR, Gilbert SL, Mahowald M, Wyckoff GJ, Malcom CM, Lahn BT. 2004. Accelerated evolution of nervous system genes in the origin of Homo sapiens. Cell 119: 1027-1040.
10. Eisenberg E, Levanon EY. 2003. Human housekeeping genes are compact. Trends Genet 19: 362-365.
11. Figueroa ME, Skrabanek L, Li Y, Jiemjit A, Fandy TE, Paietta E, Fernandez H, Tallman MS, Greally JM, Carraway H, et al. 2009. MDS and secondary AML display unique patterns and abundance of aberrant DNA methylation. Blood 114: 3448-3458.
12. Fraga MF, Ballestar E, Paz MF, Ropero S, Setien F, Ballestar ML, Heine-Suñer D, Cigudosa JC, Urioste M, Benitez J, et al. 2005. Epigenetic differences arise during the lifetime of monozygotic twins. Proc Natl Acad Sci 102: 10604-10609.
13. Meissner A, Mikkelsen TS, Gu H, Wernig M, Hanna J, Sivachenko A, Zhang X, Bernstein BE, Nusbaum C, Jaffe DB, et al. 2008. Genome-scale DNA methylation maps of pluripotent and differentiated cells. Nature 454: 766-770.
14. Ohm JE, Baylin SB. 2007. Stem cell chromatin patterns: An instructive mechanism for DNA hypermethylation? Cell Cycle 6: 1040-1043.
15. Ohm JE, McGarvey KM, Yu X, Cheng L, Schuebel KE, Cope L, Mohammad HP, Chen W, Daniel VC, Yu W, et al. 2007. A stem cell-like chromatin pattern may predispose tumor suppressor genes to DNA hypermethylation and heritable silencing. Nat Genet 39: 237-242.
16. Rossi DJ, Bryder D, Zahn JM, Ahlenius H, Sonu R, Wagers AJ, Weissman IL. 2005. Cell intrinsic alterations underlie hematopoietic stem cell aging. Proc Natl Acad Sci 102: 9194-9199.
17. Schlesinger Y, Straussman R, Keshet I, Farkash S, Hecht M, Zimmerman J, Eden E, Yakhini Z, Ben-Shushan E, Reubinoff BE, et al. 2007. Polycomb-mediated methylation on Lys27 of histone H3 pre-marks genes for de novo methylation in cancer. Nat Genet 39: 232-236.
18. Vijg J, Campisi J. 2008. Puzzles, promises and a cure for ageing. Nature 454: 1065-1071.
19. Widschwendter M, Fiegl H, Egle D, Mueller-Holzner E, Spizzo G, Marth C, Weisenberger DJ, Campan M, Young J, Jacobs I, et al. 2007. Epigenetic stem cell signature in cancer. Nat Genet 39: 157-158.
20. Zhao XD, Han X, Chew JL, Liu J, Chiu KP, Choo A, Orlov YL, Sung WK, Shahab A, Kuznetsov VA, et al. 2007.Whole-genome mapping of histone H3 Lys4 and 27 trimethylations reveals distinct genomic compartments in human embryonic stem cells. Cell Stem Cell 1: 286-298.