Lineage-specific distribution of high levels of genomic 5-hydroxymethylcytosine in mammalian development

Cell Research

Volumn 21, Issue 9, 2011, Pages 1332-1342

  Ruzov, Alexey ^a,b   Tsenkina, Yanina ^b   Serio, Andrea ^c   Dudnakova, Tatiana ^d   Fletcher, Judy ^b   Bai, Yu ^b   Chebotareva, Tatiana ^b   Pells, Steve ^b   Hannoun, Zara ^b   Sullivan, Gareth ^b   Chandran, Siddharthan ^c   Hay, David C ^b   Bradley, Mark ^c   Wilmut, Ian ^b   De Sousa, Paul ^b,e  

^a UNIVERSITY OF NOTTINGHAM   (United Kingdom)

^b UNIVERSITY OF EDINBURGH   (United Kingdom)

^c UNIVERSITY OF EDINBURGH   (United Kingdom)

^d WESTERN GENERAL HOSPITAL   (United Kingdom)

^e Roslin Cells Limited   (United Kingdom)

Author keywords

5 hydroxymethylcytosine; 5 methylcytosine; CpG methylation; epigenetics; mammalian development; pluripotency; stem cells

Indexed keywords

5 HYDROXYMETHYLCYTOSINE; 5 METHYLCYTOSINE; 5-HYDROXYMETHYLCYTOSINE; ANTIBODY; CYTOSINE; DRUG DERIVATIVE; INTERMEDIATE FILAMENT PROTEIN; NERVE PROTEIN; NESTIN;

ANIMAL; ARTICLE; BONE MARROW; CELL CULTURE; CELL DIFFERENTIATION; CELL LINEAGE; CPG ISLAND; CYTOLOGY; DNA METHYLATION; EMBRYO DEVELOPMENT; EMBRYONIC STEM CELL; GROWTH, DEVELOPMENT AND AGING; HUMAN; HUMAN GENOME; IMMUNOLOGY; METABOLISM; MOUSE; NERVE CELL; PLURIPOTENT STEM CELL; ZYGOTE;

5-METHYLCYTOSINE; ANIMALS; ANTIBODIES; BONE MARROW; CELL DIFFERENTIATION; CELL LINEAGE; CELLS, CULTURED; CPG ISLANDS; CYTOSINE; DNA METHYLATION; EMBRYONIC DEVELOPMENT; EMBRYONIC STEM CELLS; GENOME, HUMAN; HUMANS; INDUCED PLURIPOTENT STEM CELLS; INTERMEDIATE FILAMENT PROTEINS; MICE; NERVE TISSUE PROTEINS; NEURONS; ZYGOTE;

MAMMALIA;

EID: 80052473600     PISSN: 10010602     EISSN: 17487838     Source Type: Journal    
DOI: 10.1038/cr.2011.113     Document Type: Article

References (35)

1. Bird A. DNA methylation patterns and epigenetic memory. Genes Dev 2002; 16:6-21. (Pubitemid 34049633)
2. Reik W, Dean W, Walter J. Epigenetic reprogramming in mammalian development. Science 2001; 293:1089-1093. (Pubitemid 32758081)
3. Surani MA, Hayashi K, Hajkova P. Genetic and epigenetic regulators of pluripotency. Cell 2007; 128:747-762. (Pubitemid 46273582)
4. Tahiliani M, Koh KP, Shen Y, et al. Conversion of 5-methylcytosine to 5-hydroxymethylcytosine in mammalian DNA by MLL partner TET1. Science 2009; 324:930-935.
5. Kriaucionis S, Heintz N. The nuclear DNA base 5-hydroxymethylcytosine is present in Purkinje neurons and the brain. Science 2009; 324:929-930.
6. Ito S, D'Alessio AC, Taranova OV, et al. Role of Tet proteins in 5mC to 5hmC conversion, ES-cell self-renewal and inner cell mass specification. Nature 2010; 466:1129-1133.
7. Jin SG, Kadam S, Pfeifer GP. Examination of the specificity of DNA methylation profiling techniques towards 5-methylcytosine and 5-hydroxymethylcytosine. Nucleic Acids Res 2010; 38:e125.
8. Hayatsu H, Shiragami M. Reaction of bisulfite with the 5-hydroxymethyl group in pyrimidines and in phage DNAs. Biochemistry 1979; 18:632-637.
9. Huang Y, Pastor WA, Shen Y, et al. The behaviour of 5- hydroxymethylcytosine in bisulfite sequencing. PLoS One 2010; 5:e8888.
10. Nestor C, Ruzov A, Meehan R, Dunican D. Enzymatic approaches and bisulphite sequencing cannot distinguish between 5-methylcytosine and 5-hydroxymethylcytosine in DNA. Biotechniques 2010; 48:317-319.
11. Valinluck V, Tsai HH, Rogstad DK, Burdzy A, Bird A, Sowers LC. Oxidative damage to methyl-CpG sequences inhibits the binding of the methyl-CpG binding domain (MBD) of methyl-CpG binding protein 2 (MeCP2). Nucleic Acids Res 2004; 32:4100-4108. (Pubitemid 39232282)
12. Globisch D, Münzel M, Müller M, et al. Tissue distribution of 5-hydroxymethylcytosine and search for active demethylation intermediates. PLoS One 2010; 5:e15367.
13. Ko M, Huang Y, Jankowska AM, et al. Impaired hydroxylation of 5-methylcytosine in myeloid cancers with mutant TET2. Nature 2010; 468:839-843.
14. Szwagierczak A, Bultmann S, Schmidt CS, Spada F, Leonhardt H. Sensitive enzymatic quantification of 5-hydroxymethylcytosine in genomic DNA. Nucleic Acids Res 2010; 38:e181.
15. Hay DC, Fletcher J, Payne C, et al. Highly efficient differentiation of hESC to functional hepatic endoderm requires ActivinA and Wnt3a signalling. Proc Natl Acad Sci USA 2008; 105:12301-12306.
16. Takahashi K, Tanabe K, Ohnuki M, et al. Induction of pluripotent stem cells from adult human fibroblasts by defined factors. Cell 2007; 131:861-872. (Pubitemid 350138099)
17. Feng S, Jacobsen SE, Reik W. Epigenetic reprogramming in mammalian development. Science 2010; 330:622-627.
18. Mayer W, Niveleau A, Walter J, Fundele R, Haaf T. Demethylation of the zygotic paternal genome. Nature 2000; 403:501-502. (Pubitemid 30082186)
19. Iqbal K, Jin SG, Pfeifer GP, Szabó PE. Reprogramming of the paternal genome upon fertilization involves genome-wide oxidation of 5-methylcytosine. Proc Natl Acad Sci USA 2011; 108:3642-3647.
20. Oswald J, Engemann S, Lane N, et al. Active demethylation of the paternal genome in the mouse zygote. Curr Biol 2000; 10:475-478. (Pubitemid 30247337)
21. Wislet-Gendebien S, Wautier PF, Leprince B. Astrocytic and neuronal fate of mesenchymal stem cells expressing nestin. Brain Res Bull 2005; 68:95-102. (Pubitemid 41698881)
22. Wiese C, Rolletschek A, Kania G, et al. Nestin expression-a property of multi-lineage progenitor cells? Cell Mol Life Sci 2004; 61:2510-2522. (Pubitemid 39586514)
23. Murrell W, Féron F, Wetzig A, et al. Multipotent stem cells from adult olfactory mucosa. Dev Dyn 2005; 233:496-515. (Pubitemid 40734050)
24. Merkle FT, Tramontin AD, Garcia-Verdugo JM, Alvarez-Buylla A. Radial glia give rise to adult neural stem cells in the subventricular zone. Proc Natl Acad Sci USA 2004; 101:17528-17532. (Pubitemid 39657437)
25. Merkle FT, Alvarez-Buylla A. Neural stem cells in mammalian development. Curr Opin Cell Biol 2006; 18:704-709. (Pubitemid 44767726)
26. Doetsch F, Caille I, Lim DA, García-Verdugo JM, Alvarez-Buylla A. Subventricular zone astrocytes are neural stem cells in the adult mammalian brain. Cell 1999; 97:703-716. (Pubitemid 29278045)
27. Seri JM, García-Verdugo BS, McEwen A, Alvarez-Buylla A. Astrocytes give rise to new neurons in the adult mammalian hippocampus. J Neurosci 2001; 21:7153-7160. (Pubitemid 32846963)
28. Deng W, Aimone JB, Gage FH. New neurons and new memories: How does adult hippocampal neurogenesis affect learning and memory? Nat Rev Neurosci 2010; 11:339-350.
29. Song CX, Szulwach KE, Fu Y, et al. Selective chemical labeling reveals the genome-wide distribution of 5-hydroxymethylcytosine. Nat Biotechnol 2011; 29:68-72.
30. Meissner A, Mikkelsen TS, Gu H, et al. Genome-scale DNA methylation maps of pluripotent and differentiated cells. Nature 2008; 454:766-770.
31. Mohn F, Weber M, Rebhan M, et al. Lineage-specific polycomb targets and de novo DNA methylation define restriction and potential of neuronal progenitors. Mol Cell 2008; 30:755-766.
32. Fletcher JM, Ferrier PM, Gardner JO, et al. Variations in humanized and defined culture conditions supporting derivation of new human embryonic stem cell lines. Cloning Stem Cells 2006; 8:319-334. (Pubitemid 46146039)
33. De Sousa PA, Gardner J, Sneddon S, et al. Clinically failed eggs as a source of normal human embryo stem cells. Stem Cell Res 2009; 2:188-197.
34. Beaujean N, Taylor J, Gardner J, et al. Effect of limited DNA methylation reprogramming in the normal sheep embryo on somatic cell nuclear transfer. Biol Reprod 2004; 71:185-193. (Pubitemid 38915324)
35. Koch P, Opitz T, Steinbeck JA, Ladewig J, Brüstle O. A rosette-type, self-renewing human ES cell-derived neural stem cell with potential for in vitro instruction and synaptic integration. Proc Natl Acad Sci USA 2009; 106:3225-3230.