Evaluating genome-wide DNA methylation changes in mice by Methylation Specific Digital Karyotyping

BMC Genomics

Volumn 9, Issue , 2008, Pages

  Boon, Kathy ^a   Tomfohr, John K ^a   Bailey, Nathaniel W ^a   Garantziotis, Stavros ^a   Li, Zhuowei ^a   Brass, David M ^a,b   Maruoka, Shuichiro ^a   Hollingsworth, John W ^b   Schwartz, David A ^a,c,d  

^a NATIONAL HEART LUNG AND BLOOD INSTITUTE   (United States)

^b DUKE UNIVERSITY MEDICAL CENTER   (United States)

^c DEPARTMENT OF MEDICINE   (United States)

^d UNIVERSITY OF COLORADO   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; DNA METHYLTRANSFERASE 1; DNA METHYLTRANSFERASE 3A; DNA METHYLTRANSFERASE 3B; GENOMIC DNA; HEAT SHOCK PROTEIN 90; JANUS KINASE 2; PHOSPHODIESTERASE; RIBONUCLEASE; SUPPRESSOR OF CYTOKINE SIGNALING; TRANSCRIPTION FACTOR NFAT; ZINC FINGER PROTEIN;

ARTICLE; CELL POPULATION; CONTROLLED STUDY; DIET THERAPY; DISEASE MODEL; DNA ISOLATION; DNA METHYLATION; DNA MODIFICATION; ENVIRONMENTAL EXPOSURE; EPIGENETICS; EXPERIMENTAL MODEL; GENE EXPRESSION PROFILING; GENE FREQUENCY; GENE LOCATION; GENE LOCUS; GENETIC TRANSCRIPTION; INTERMETHOD COMPARISON; KARYOTYPING; MOUSE; NONHUMAN; POLYMERASE CHAIN REACTION; RESPIRATORY TRACT ALLERGY; SEQUENCE ANALYSIS; SERIAL ANALYSIS OF GENE EXPRESSION; ANIMAL; C57BL MOUSE; FEMALE; GENE EXPRESSION REGULATION; GENE LIBRARY; GENETIC EPIGENESIS; GENOMICS; MATERNAL NUTRITION; METHODOLOGY; PREGNANCY;

MUS;

ANIMALS; DNA METHYLATION; EPIGENESIS, GENETIC; FEMALE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, DEVELOPMENTAL; GENE LIBRARY; GENOMICS; KARYOTYPING; MICE; MICE, INBRED C57BL; PREGNANCY; PRENATAL NUTRITIONAL PHYSIOLOGICAL PHENOMENA;

EID: 58249106881     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-9-598     Document Type: Article

References (25)

1. Esteller M Cancer epigenomics: DNA methylomes and histone-modification maps Nat Rev Genet 2007, 8(4):286-298. 10.1038/nrg2005 17339880
2. Robertson KD DNA methylation and human disease Nat Rev Genet 2005, 6(8):597-610. 10.1038/nrg1655 16136652
3. Waterland RA Michels KB Epigenetic Epidemiology of the Developmental Origins Hypothesis Annual Review of Nutrition 2007, 27(1):363-388. 10.1146/annurev.nutr.27.061406.093705 17465856
4. Jirtle RL Skinner MK Environmental epigenomics and disease susceptibility Nat Rev Genet 2007, 8(4):253-262. 10.1038/nrg2045 17363974
5. Waterland RA Jirtle RL Early nutrition, epigenetic changes at transposons and imprinted genes, and enhanced susceptibility to adult chronic diseases Nutrition 2004, 20(1):63-68. 10.1016/j.nut.2003.09.011 14698016
6. Zilberman D Henikoff S Genome-wide analysis of DNA methylation patterns Development 2007, 134(22):3959-3965. 10.1242/dev.001131 17928417
7. Hu M Yao J Cai L Bachman KE Brule van den F Velculescu V Polyak K Distinct epigenetic changes in the stromal cells of breast cancers Nat Genet 2005, 37(8):899-905. 10.1038/ng1596 16007089
8. Hu M Yao J Polyak K Methylation-specific digital karyotyping Nat Protocols 2006, 1(3):1621-1636. 10.1038/nprot.2006.278
9. Hollingsworth J Maruoka S Boon K Garantziotis S Li Z Tomfohr J Bailey N Potts E Whitehead G Brass D Schwartz DA In utero supplementation with methyl-donors enhances allergic airway disease in mice Journal of Clinical Investigation 2008, 118(10):3462-3469. 2542847 18802477
10. Wang T Maierhofer C Speicher MR Lengauer C Vogelstein B Kinzler KW Velculescu VE Digital karyotyping PNAS 2002, 99(25):16156-16161. 138581 12461184 10.1073/pnas.202610899
11. Saha S Sparks AB Rago C Akmaev V Wang CJ Vogelstein B Kinzler KW Velculescu VE Using the transcriptome to annotate the genome Nat Biotech 2002, 20(5):508-512. 10.1038/nbt0502-508
12. Robertson N Mehrdad Oveisi-Fordorei M Zuyderduyn SD Richard J Varhol RJ Fjell C Marra M Jones S Siddiqui A DiscoverySpace: An interactive data analysis application Genome Biology 2007, 8(I):R6-R13. 1839122 17210078 10.1186/gb-2007-8-1-r6
13. Boon K Edwards J Siu I Olschner D Eberhart C Marra M Strausberg R Riggins G Comparison of medulloblastoma and normal neural transcriptomes identifies a restricted set of activated genes Oncogene 2003, 22(48):7687-7694. 10.1038/sj.onc.1207043 14576832
14. Mueller W Nutt CL Ehrich M Riemenschneider MJ von Deimling A Boom van den D Louis DN Downregulation of RUNX3 and TES by hypermethylation in glioblastoma Oncogene 2006, 26(4):583-593. 10.1038/sj.onc.1209805 16909125
15. Subramaniam M Chan J Soong R Ito K Ito Y Yeoh K Salto-Tellez M Putti T RUNX3 inactivation by frequent promoter hypermethylation and protein mislocalization constitute an early event in breast cancer progression Breast Cancer Res Treat 2009, 113(1):113-121. 10.1007/s10549-008-9917-4 18256927
16. Fujii S Ito K Ito Y Ochiai A Enhancer of Zeste Homologue 2 (EZH2) Down-regulates RUNX3 by Increasing Histone H3 Methylation J Biol Chem 2008, 283(25):17324-17332. 10.1074/jbc.M800224200 18430739 2427338
17. Akimzhanov A Krenacs L Schlegel T Klein-Hessling S Bagdi E Stelkovics E Kondo E Chuvpilo S Wilke P Avots A Gattenlohner S Muller-Hermelink H Palmetshofer A Serfling E Epigenetic Changes and Suppression of the Nuclear Factor of Activated T Cell 1 (NFATC1) Promoter in Human Lymphomas with Defects in Immunoreceptor Signaling Am J Pathol 2008, 172(1):215-224. 2189623 18156209 10.2353/ajpath.2008.070294
18. Lee MG Wynder C Cooch N Shiekhattar R An essential role for CoREST in nucleosomal histone 3 lysine 4 demethylation Nature 2005, 437(7057):432-435. 16079794
19. Lakowski B Roelens I Jacob S CoREST-like complexes regulate chromatin modification and neuronal gene expression Journal of Molecular Neuroscience 2006, 29(3):227-239. 10.1385/JMN:29:3:227 17085781
20. Tews B Roerig P Hartmann C Hahn M Felsberg J Blaschke B Sabel M Kunitz A Toedt G Neben K Benner A Deimling A von Reifenberger G Lichter P Hypermethylation and transcriptional downregulation of the CITED4 gene at 1p34.2 in oligodendroglial tumours with allelic losses on 1p and 19q Oncogene 2007, 26(34):5010-5016. 10.1038/sj.onc.1210297 17311001
21. Waterland RA Assessing the Effects of High Methionine Intake on DNA Methylation J Nutr 2006, 136(6):1706S-1710. 16702343
22. Ng PWC Ruan Y Paired-end diTagging for transcriptome and genome analysis John Wiley & Sons, Inc 2007 2007.
23. Nielsen K Hogh AL Emmersen J DeepSAGE - digital transcriptomics with high sensitivity, simple experimental protocol and multiplexing of samples Nucl Acids Res 2006, 34(19):e133. 1636492 17028099 10.1093/nar/ gkl714
24. Herman JG Graff JR Myohanen S Nelkin BD Baylin SB Methylation-specific PCR: A novel PCR assay for methylation status of CpG islands PNAS 1996, 93(18):9821-9826. 38513 8790415 10.1073/pnas.93.18.9821
25. Li L-C Dahiya R MethPrimer: Designing primers for methylation PCRs Bioinformatics 2002, 18(11):1427-1431. 10.1093/bioinformatics/18.11.1427 12424112