Genome-wide conserved consensus transcription factor binding motifs are hyper-methylated

BMC Genomics

Volumn 11, Issue 1, 2010, Pages

  Choy, Mun Kit ^a   Movassagh, Mehregan ^a   Goh, Hock Guan ^b   Bennett, Martin R ^a   Down, Thomas A ^c   Foo, Roger S Y ^a  

^a UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^b UNIVERSITI TUNKU ABDUL RAHMAN   (Malaysia)

^c UNIVERSITY OF CAMBRIDGE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

TRANSCRIPTION FACTOR;

ARTICLE; BINDING SITE; CHROMATIN IMMUNOPRECIPITATION; CONTROLLED STUDY; CPG ISLAND; DNA BINDING MOTIF; DNA METHYLATION; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETIC CONSERVATION; GENOME ANALYSIS; HEART; HUMAN; HUMAN TISSUE; MALE; NORMAL HUMAN; PROTEIN BINDING; PROTEIN DNA INTERACTION; PROTEIN MOTIF; SPERM; CONSENSUS SEQUENCE; GENETIC DATABASE; GENETICS; HEART MUSCLE; HUMAN GENOME; METABOLISM; NUCLEOTIDE SEQUENCE; SPERMATOZOON;

BASE SEQUENCE; BINDING SITES; CONSENSUS SEQUENCE; CPG ISLANDS; DATABASES, GENETIC; DNA METHYLATION; GENOME, HUMAN; HUMANS; MALE; MYOCARDIUM; PROTEIN BINDING; SPERMATOZOA; TRANSCRIPTION FACTORS;

EID: 77957174102     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-11-519     Document Type: Article

References (30)

1. 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. 10.1038/nature08514, 2857523, 19829295.
2. Laurent L, Wong E, Li G, Huynh T, Tsirigos A, Ong CT, Low HM, Kin Sung KW, Rigoutsos I, Loring J, Wei CL. Dynamic changes in the human methylome during differentiation. Genome Res 20:320-331. 10.1101/gr.101907.109, 2840979, 20133333.
3. Ball MP, Li JB, Gao Y, Lee JH, LeProust EM, Park IH, Xie B, Daley GQ, Church GM. Targeted and genome-scale strategies reveal gene-body methylation signatures in human cells. Nat Biotechnol 2009, 27:361-368. 10.1038/nbt.1533, 19329998.
4. Jaenisch R, Bird A. Epigenetic regulation of gene expression: how the genome integrates intrinsic and environmental signals. Nat Genet 2003, (33 Suppl):245-254. 10.1038/ng1089, 12610534.
5. Fraga MF, Ballestar E, Paz MF, Ropero S, Setien F, Ballestar ML, Heine-Suner D, Cigudosa JC, Urioste M, Benitez J, Boix-Chornet M, Sanchez-Aguilera A, Ling C, Carlsson E, Poulsen P, Vaag A, Stephan Z, Spector TD, Wu YZ, Plass C, Esteller M. Epigenetic differences arise during the lifetime of monozygotic twins. Proc Natl Acad Sci USA 2005, 102:10604-10609. 10.1073/pnas.0500398102, 1174919, 16009939.
6. Christensen BC, Houseman EA, Marsit CJ, Zheng S, Wrensch MR, Wiemels JL, Nelson HH, Karagas MR, Padbury JF, Bueno R, Sugarbaker DJ, Yeh RF, Wiencke JK, Kelsey KT. Aging and environmental exposures alter tissue-specific DNA methylation dependent upon CpG island context. PLoS Genet 2009, 5:e1000602. 10.1371/journal.pgen.1000602, 2718614, 19680444.
7. Rakyan VK, Down TA, Maslau S, Andrew T, Yang TP, Beyan H, Whittaker P, McCann OT, Finer S, Valdes AM, Leslie RD, Deloukas P, Spector TD. Human aging-associated DNA hypermethylation occurs preferentially at bivalent chromatin domains. Genome Res 20:434-9. 10.1101/gr.103101.109, 20219945.
8. Esteller M. Epigenetics in cancer. N Engl J Med 2008, 358:1148-1159. 10.1056/NEJMra072067, 18337604.
9. Jirtle RL, Skinner MK. Environmental epigenomics and disease susceptibility. Nat Rev Genet 2007, 8:253-262. 10.1038/nrg2045, 17363974.
10. Weaver IC, Cervoni N, Champagne FA, D'Alessio AC, Sharma S, Seckl JR, Dymov S, Szyf M, Meaney MJ. Epigenetic programming by maternal behavior. Nat Neurosci 2004, 7:847-854. 10.1038/nn1276, 15220929.
11. Kucharski R, Maleszka J, Foret S, Maleszka R. Nutritional control of reproductive status in honeybees via DNA methylation. Science 2008, 319:1827-1830. 10.1126/science.1153069, 18339900.
12. Miller CA, Sweatt JD. Covalent modification of DNA regulates memory formation. Neuron 2007, 53:857-869. 10.1016/j.neuron.2007.02.022, 17359920.
13. Metivier R, Gallais R, Tiffoche C, Le Peron C, Jurkowska RZ, Carmouche RP, Ibberson D, Barath P, Demay F, Reid G, Benes V, Jeltsch A, Gannon F, Salbert G. Cyclical DNA methylation of a transcriptionally active promoter. Nature 452:45-50. 10.1038/nature06544, 18322525.
14. Tachibana M, Matsumura Y, Fukuda M, Kimura H, Shinkai Y. G9a/GLP complexes independently mediate H3K9 and DNA methylation to silence transcription. Embo J 2008, 27:2681-2690. 10.1038/emboj.2008.192, 2572175, 18818694.
15. Turker MS. Gene silencing in mammalian cells and the spread of DNA methylation. Oncogene 2002, 21:5388-5393. 10.1038/sj.onc.1205599, 12154401.
16. Han L, Lin IG, Hsieh CL. Protein binding protects sites on stable episomes and in the chromosome from de novo methylation. Mol Cell Biol 2001, 21:3416-3424. 10.1128/MCB.21.10.3416-3424.2001, 100263, 11313467.
17. Gebhard C, Benner C, Ehrich M, Schwarzfischer L, Schilling E, Klug M, Dietmaier W, Thiede C, Holler E, Andreesen R, Rehli M. General transcription factor binding at CpG islands in normal cells correlates with resistance to de novo DNA methylation in cancer cells. Cancer Res 70:1398-1407. 10.1158/0008-5472.CAN-09-3406, 20145141.
18. Jones PA, Takai D. The role of DNA methylation in mammalian epigenetics. Science 2001, 293:1068-1070. 10.1126/science.1063852, 11498573.
19. Adams RL. DNA methylation. The effect of minor bases on DNA-protein interactions. Biochem J 1990, 265:309-320. 1136889, 2405840.
20. Bell AC, Felsenfeld G. Methylation of a CTCF-dependent boundary controls imprinted expression of the Igf2 gene. Nature 2000, 405:482-485. 10.1038/35013100, 10839546.
21. 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 5:e8564. 10.1371/journal.pone.0008564, 2797324, 20084101.
22. Down TA, Rakyan VK, Turner DJ, Flicek P, Li H, Kulesha E, Graf S, Johnson N, Herrero J, Tomazou EM, Thorne NP, Backdahl L, Herberth M, Howe KL, Jackson DK, Miretti MM, Marioni JC, Birney E, Hubbard TJ, Durbin R, Tavare S, Beck S. A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis. Nat Biotechnol 2008, 26:779-785. 10.1038/nbt1414, 2644410, 18612301.
23. Farnham PJ. Insights from genomic profiling of transcription factors. Nat Rev Genet 2009, 10:605-616. 10.1038/nrg2636, 2846386, 19668247.
24. McGowan PO, Sasaki A, D'Alessio AC, Dymov S, Labonté B, Szyf M, Turecki G, Meaney MJ. Epigenetic regulation of the glucocorticoid receptor in human brain associates with childhood abuse. Nat Neurosci 2009, 12:342-8. 10.1038/nn.2270, 2944040, 19234457.
25. Straussman R, Nejman D, Roberts D, Steinfeld I, Blum B, Benvenisty N, Simon I, Yakhini Z, Cedar H. Developmental programming of CpG island methylation profiles in the human genome. Nat Struct Mol Biol 2009, 16:564-571. 10.1038/nsmb.1594, 19377480.
26. Macleod D, Charlton J, Mullins J, Bird AP. Sp1 sites in the mouse aprt gene promoter are required to prevent methylation of the CpG island. Genes Dev 1994, 8:2282-2292. 10.1101/gad.8.19.2282, 7958895.
27. Adamson DL, Money-Kyrle AR, Harding SE. Functional evidence for a cyclic-AMP related mechanism of action of the beta(2)-adrenoceptor in human ventricular myocytes. J Mol Cell Cardiol 2000, 32:1353-1360. 10.1006/jmcc.2000.1171, 10860775.
28. Kolasinska-Zwierz P, Down T, Latorre I, Liu T, Liu XS, Ahringer J. Differential chromatin marking of introns and expressed exons by H3K36me3. Nat Genet 2009, 41:376-381. 10.1038/ng.322, 2648722, 19182803.
29. Quinlan AR, Hall IM. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 2010, 26:841-842. 10.1093/bioinformatics/btq033, 2832824, 20110278.
30. Gardiner-Garden M, Frommer M. CpG islands in vertebrate genomes. J Mol Biol 1987, 196:261-82. 10.1016/0022-2836(87)90689-9, 3656447.