Dynamic instability of genomic methylation patterns in pluripotent stem cells

Epigenetics and Chromatin

Volumn 3, Issue 1, 2010, Pages

  Ooi, Steen K T ^a,f   Wolf, Daniel ^b   Hartung, Odelya ^c   Agarwal, Suneet ^c   Daley, George Q ^c,d,e   Goff, Stephen P ^b   Bestor, Timothy H ^a  

^a Och Spine at New York Presbyterian Hospitals   (United States)

^b Children's Hospital Boston ^*  (United States)

^c BOSTON CHILDREN S HOSPITAL   (United States)

^d BRIGHAM AND WOMEN S HOSPITAL   (United States)

^e HARVARD MEDICAL SCHOOL   (United States)

^f UNIVERSITY COLLEGE LONDON   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

DNA METHYLTRANSFERASE; DNA METHYLTRANSFERASE DNMT3L; UNCLASSIFIED DRUG; VIRUS DNA;

ANIMAL CELL; ARTICLE; CONTROLLED STUDY; DNA METHYLATION; FEMALE; FLOW CYTOMETRY; GENE EXPRESSION; GENOMIC INSTABILITY; MALE; MOUSE; NONHUMAN; PLURIPOTENT STEM CELL; PRIORITY JOURNAL; SEX CHROMOSOME; SEX DIFFERENCE;

EID: 77957901287     PISSN: None     EISSN: 17568935     Source Type: Journal    
DOI: 10.1186/1756-8935-3-17     Document Type: Article

References (39)

1. Epigenetic decisions in mammalian germ cells. CB Schaefer SK Ooi TH Bestor D Bourc'his, Science 2007 316 398 399 10.1126/science.1137544 17446388
2. Dnmt3L and the establishment of maternal genomic imprints. D Bourc'his GL Xu CS Lin B Bollman TH Bestor, Science 2001 294 2536 2539 10.1126/science. 1065848 11719692
3. Meiotic catastrophe and retrotransposon reactivation in male germ cells lacking Dnmt3L. D Bourc'his TH Bestor, Nature 2004 431 96 99 10.1038/nature02886 15318244
4. DNMT3L connects unmethylated lysine 4 of histone H3 to de novo methylation of DNA. SK Ooi C Qiu E Bernstein K Li D Jia Z Yang H Erdjument-Bromage P Tempst SP Lin CD Allis, et al. Nature 2007 448 714 717 10.1038/nature05987 17687327 (Pubitemid 47236857)
5. The DNA methyltransferase-like protein DNMT3L stimulates de novo methylation by Dnmt3a. F Chedin MR Lieber CL Hsieh, Proc Natl Acad Sci USA 2002 99 16916 16921 10.1073/pnas.262443999 12481029
6. DNMT3L stimulates the DNA methylation activity of Dnmt3a and Dnmt3b through a direct interaction. I Suetake F Shinozaki J Miyagawa H Takeshima S Tajima, J Biol Chem 2004 279 27816 27823 10.1074/jbc.M400181200 15105426
7. De novo methylation, expression, and infectivity of retroviral genomes introduced into embryonal carcinoma cells. CL Stewart H Stuhlmann D Jahner R Jaenisch, Proc Natl Acad Sci USA 1982 79 4098 4102 10.1073/pnas.79.13.4098 6955793
8. De novo DNA cytosine methyltransferase activities in mouse embryonic stem cells. H Lei SP Oh M Okano R Juttermann KA Goss R Jaenisch E Li, Development 1996 122 3195 3205 8898232
9. Chromatin and sequence features that define the fine and gross structure of genomic methylation patterns. JR Edwards AH O'Donnell RA Rollins HE Peckham C Lee MH Milekic B Chanrion Y Fu T Su H Hibshoosh, et al. Genome Res 2010 20 972 980 10.1101/gr.101535.109 20488932
10. Dynamic analysis of proviral induction and De Novo methylation: implications for a histone deacetylase-independent, methylation density-dependent mechanism of transcriptional repression. MC Lorincz D Schubeler SC Goeke M Walters M Groudine DI Martin, Mol Cell Biol 2000 20 842 850 10.1128/MCB.20.3.842-850.2000 10629041
11. Cytosine methylation: remaining faithful. SK Ooi TH Bestor, Curr Biol 2008 18 174 176 10.1016/j.cub.2007.12.045 18302924
12. Targeted mutation of the DNA methyltransferase gene results in embryonic lethality. E Li TH Bestor R Jaenisch, Cell 1992 69 915 926 10.1016/0092-8674(92) 90611-F 1606615
13. UHRF1 plays a role in maintaining DNA methylation in mammalian cells. M Bostick JK Kim PO Esteve A Clark S Pradhan SE Jacobsen, Science 2007 317 1760 1764 10.1126/science.1147939 17673620
14. The SRA protein Np95 mediates epigenetic inheritance by recruiting Dnmt1 to methylated DNA. J Sharif M Muto SI Takebayashi I Suetake A Iwamatsu TA Endo J Shinga Y Mizutani-Koseki T Toyoda K Okamura, et al. Nature 2007 450 7171 908 12 10.1038/nature06397 17994007
15. The multi-domain protein Np95 connects DNA methylation and histone modification. A Rottach C Frauer G Pichler IM Bonapace F Spada H Leonhardt, Nucleic Acids Res 38 1796 1804 10.1093/nar/gkp1152 20026581
16. Altered imprinted gene methylation and expression in completely ES cell-derived mouse fetuses: association with aberrant phenotypes. W Dean L Bowden A Aitchison J Klose T Moore JJ Meneses W Reik R Feil, Development 1998 125 2273 2282 9584126
17. Epigenetic instability in ES cells and cloned mice. D Humpherys K Eggan H Akutsu K Hochedlinger WM Rideout D Biniszkiewicz R Yanagimachi R Jaenisch, Science 2001 293 95 97 10.1126/science.1061402 11441181
18. Global hypomethylation of the genome in XX embryonic stem cells. I Zvetkova A Apedaile B Ramsahoye JE Mermoud LA Crompton R John R Feil N Brockdorff, Nat Genet 2005 37 1274 1279 10.1038/ng1663 16244654
19. DNA methyltransferases Dnmt3a and Dnmt3b are essential for de novo methylation and mammalian development. M Okano DW Bell DA Haber E Li, Cell 1999 99 247 257 10.1016/S0092-8674(00)81656-6 10555141
20. Epigenetic control of mouse Oct-4 gene expression in embryonic stem cells and trophoblast stem cells. N Hattori K Nishino YG Ko J Ohgane S Tanaka K Shiota, J Biol Chem 2004 279 17063 17069 10.1074/jbc.M309002200 14761969
21. TRIM28 mediates primer binding site-targeted silencing of murine leukemia virus in embryonic cells. D Wolf SP Goff, Cell 2007 131 46 57 10.1016/j.cell.2007.07.026 17923087
22. Embryonic stem cells use ZFP809 to silence retroviral DNAs. D Wolf SP Goff, Nature 2009 458 1201 1204 10.1038/nature07844 19270682
23. Instability of retroviral DNA methylation in embryonic stem cells. S Minoguchi H Iba, Stem Cells 2008 26 1166 1173 10.1634/stemcells.2007-1106 18323407
24. Retrovirus silencing, variegation, extinction, and memory are controlled by a dynamic interplay of multiple epigenetic modifications. S Yao T Sukonnik T Kean RR Bharadwaj P Pasceri J Ellis, Mol Ther 2004 10 27 36 10.1016/j.ymthe. 2004.04.007 15233939
25. Lineage-specific polycomb targets and de novo DNA methylation define restriction and potential of neuronal progenitors. F Mohn M Weber M Rebhan TC Roloff J Richter MB Stadler M Bibel D Schubeler, Mol Cell 2008 30 755 766 10.1016/j.molcel.2008.05.007 18514006
26. Directly reprogrammed fibroblasts show global epigenetic remodeling and widespread tissue contribution. N Maherali R Sridharan W Xie J Utikal S Eminli K Arnold M Stadtfeld R Yachechko J Tchieu R Jaenisch, et al. Cell Stem Cell 2007 1 55 70 10.1016/j.stem.2007.05.014 18371336
27. Dnmt3L cooperates with the Dnmt3 family of de novo DNA methyltransferases to establish maternal imprints in mice. K Hata M Okano H Lei E Li, Development 2002 129 1983 1993 11934864
28. Cooperativity between DNA methyltransferases in the maintenance methylation of repetitive elements. G Liang MF Chan Y Tomigahara YC Tsai FA Gonzales E Li PW Laird PA Jones, Mol Cell Biol 2002 22 480 491 10.1128/MCB.22.2.480-491.2002 11756544
29. Establishment and maintenance of genomic methylation patterns in mouse embryonic stem cells by Dnmt3a and Dnmt3b. T Chen Y Ueda JE Dodge Z Wang E Li, Mol Cell Biol 2003 23 5594 5605 10.1128/MCB.23.16.5594-5605.2003 12897133
30. A bivalent chromatin structure marks key developmental genes in embryonic stem cells. BE Bernstein TS Mikkelsen X Xie M Kamal DJ Huebert J Cuff B Fry A Meissner M Wernig K Plath, et al. Cell 2006 125 315 326 10.1016/j.cell.2006.02. 041 16630819
31. Conversion of 5-methylcytosine to 5-hydroxymethylcytosine in mammalian DNA by MLL partner TET1. M Tahiliani KP Koh Y Shen WA Pastor H Bandukwala Y Brudno S Agarwal LM Iyer DR Liu L Aravind A Rao, Science 2009 324 930 935 10.1126/science.1170116 19372391
32. The SRA domain of UHRF1 flips 5-methylcytosine out of the DNA helix. H Hashimoto JR Horton X Zhang M Bostick SE Jacobsen X Cheng, Nature 2008 455 826 829 10.1038/nature07280 18772888
33. Decatenation checkpoint deficiency destabilizes the stem cell genome. M Damelin TH Bestor, Cell Cycle 2006 5 345 346 16479155
34. From Protocol 5: De Novo Isolation of ES Cell Lines from Blastocysts. A Nagy M Gertsenstein K Vintersten R Behringer, Manipulating the Mouse Embryo: A Laboratory Manual Cold Spring Harbor Press 2003
35. DNA-methylation analysis by the bisulfite-assisted genomic sequencing method. P Hajkova O el-Maarri S Engemann J Oswald A Olek J Walter, Methods Mol Biol 2002 200 143 154 11951649
36. QUMA: quantification tool for methylation analysis. Y Kumaki M Oda M Okano, Nucleic Acids Res 2008 36 170 175 10.1093/nar/gkn294 18487274
37. Biological functions of DNA methyltransferase 1 require its methyltransferase activity. M Damelin TH Bestor, Mol Cell Biol 2007 27 3891 3899 10.1128/MCB.00036-07 17371843
38. Suv39h-mediated histone H3 lysine 9 methylation directs DNA methylation to major satellite repeats at pericentric heterochromatin. B Lehnertz Y Ueda AA Derijck U Braunschweig L Perez-Burgos S Kubicek T Chen E Li T Jenuwein AH Peters, Curr Biol 2003 13 1192 1200 10.1016/S0960-9822(03)00432-9 12867029
39. MethPrimer: designing primers for methylation PCRs. LC Li R Dahiya, Bioinformatics 2002 18 1427 1431 10.1093/bioinformatics/18.11.1427 12424112