Epigenetic characterization of the early embryo with a chromatin immunoprecipitation protocol applicable to small cell populations

Nature Genetics

Volumn 38, Issue 7, 2006, Pages 835-841

  O'Neill, Laura P ^a   VerMilyea, Matthew D ^a   Turner, Bryan M ^a  

^a UNIVERSITY DEPARTMENT OF MEDICINE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

HISTONE; HISTONE H3K9; HISTONE H4; OCTAMER TRANSCRIPTION FACTOR 4; TRANSCRIPTION FACTOR CDX2; UNCLASSIFIED DRUG;

ACETYLATION; ANIMAL CELL; ANIMAL TISSUE; ARTICLE; BLASTOCYST; CDX2 GENE; CFC1 GENE; CHROMATIN IMMUNOPRECIPITATION; CONTROLLED STUDY; EMBRYO; EMBRYONIC STEM CELL; GENE; GENE SILENCING; GENETIC EPIGENESIS; HHEX GENE; INNER CELL MASS; MOUSE; NKX GENE; NONHUMAN; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN METHYLATION; PROTEIN MODIFICATION; REGULATOR GENE;

ANIMALS; BLASTOCYST; CELL COUNT; CELL LINE; CHROMATIN IMMUNOPRECIPITATION; EPIGENESIS, GENETIC; GENE SILENCING; GENES, REGULATOR; HISTONES; MICE; POLYMERASE CHAIN REACTION; PROMOTER REGIONS (GENETICS); STEM CELLS;

EID: 33745549658     PISSN: 10614036     EISSN: 15461718     Source Type: Journal    
DOI: 10.1038/ng1820     Document Type: Article

References (50)

1. Smith, A.G. Embryo-derived stem cells: of mice and men. Annu. Rev. Cell Dev. Biol. 17, 435-462 (2001).
2. Ralston, A. & Rossant, J. Genetic regulation of stem cell origins in the mouse embryo. Clin. Genet. 68, 106-112 (2005).
3. Chambers, I. et al. Functional expression cloning of Nanog, a pluripotency sustaining factor in embryonic stem cells. Cell 113, 643-655 (2003).
4. Mitsui, K. et al. The homeoprotein Nanog is required for maintenance of pluripotency in mouse epiblast and ES cells. Cell 113, 631-642 (2003).
5. Boyer, L.A. et al. Core transcriptional regulatory circuitry in human embryonic stem cells. Cell 122, 947-956 (2005).
6. Arney, K.L. & Fisher, A.G. Epigenetic aspects of differentiation. J. Cell Sci. 117, 4355-4363 (2004).
7. Santos, F. & Dean, W. Epigenetic reprogramming during early development in mammals. Reproduction 127, 643-651 (2004).
8. Szutorisz, H. & Dillon, N. The epigenetic basis for embryonic stem cell pluripotency. Bioessays 27, 1286-1293 (2005).
9. Gilbert, N., Gilchrist, S. & Bickmore, W.A. Chromatin organization in the mammalian nucleus. Int. Rev. Cytol. 242, 283-336 (2005).
10. Merkenschlager, M. et al. Centromeric repositioning of coreceptor loci predicts their stable silencing and the CD4/CD8 lineage choice. J. Exp. Med. 200, 1437-1444 (2004).
11. Perry, P. et al. A dynamic switch in the replication timing of key regulator genes in embryonic stem cells upon neural induction. Cell Cycle 3, 1645-1650 (2004).
12. Sproul, D., Gilbert, N. & Bickmore, W.A. The role of chromatin structure in regulating the expression of clustered genes. Nat. Rev. Genet. 6, 775-781 (2005).
13. Wiblin, A.E., Cui, W., Clark, A.J. & Bickmore, W.A. Distinctive nuclear organisation of centromeres and regions involved in pluripotency in human embryonic stem cells. J. Cell Sci. 118, 3861-3868 (2005).
14. Margueron, R., Trojer, P. & Reinberg, D. The key to development: interpreting the histone code? Curr. Opin. Genet. Dev. 15, 163-176 (2005).
15. Nightingale, K.P., O'Neill, L.P. & Turner, B.M. Histone modifications: signalling receptors and potential elements of a heritable epigenetic code. Curr. Opin. Genet. Dev. 16, 125-136 (2006).
16. Baxter, J. et al. Histone hypomethylation is an indicator of epigenetic plasticity in quiescent lymphocytes. EMBO J. 23, 4462-4472 (2004).
17. Martens, J.H. et al. The profile of repeat-associated histone lysine methylation states in the mouse epigenome. EMBO J. 24, 800-812 (2005).
18. Rice, J.C. et al. Histone methyltransferases direct different degrees of methylation to define distinct chromatin domains. Mol. Cell 12, 1591-1598 (2003).
19. Schneider, R. et al. Histone H3 lysine 4 methylation patterns in higher eukaryotic genes. Nat. Cell Biol. 6, 73-77 (2004).
20. Fischle, W. et al. Regulation of HP1-chromatin binding by histone H3 methylation and phosphorylation. Nature 438, 1116-1122 (2005).
21. Sims, R.J. III et al. Human but not yeast CHD1 binds directly and selectively to histone H3 methylated at lysine 4 via its tandem chromodomains. J. Biol. Chem. 280, 41789-41792 (2005).
22. Gregory, R.I. et al. Inhibition of histone deacetylases alters allelic chromatin conformation at the imprinted U2af1-rs1 locus in mouse embryonic stem cells. J. Biol. Chem. 277, 11728-11734 (2002).
23. Hattori, N. et al. Epigenetic control of mouse Oct-4 gene expression in embryonic stem cells and trophoblast stem cells. J. Biol. Chem. 279, 17063-17069 (2004).
24. O'Neill, L.P. et al. X-linked genes in female embryonic stem cells carry an epigenetic mark prior to the onset of X inactivation. Hum. Mol. Genet. 12, 1783-1790 (2003).
25. Szutorisz, H. et al. Formation of an active tissue-specific chromatin domain initiated by epigenetic marking at the embryonic stem cell stage. Mol. Cell. Biol. 25, 1804-1820 (2005).
26. Handyside, A.H. & Hunter, S. A rapid procedure for visualising the inner cell mass and trophectoderm nuclei of mouse blastocysts in situ using polynucleotide-specific fluorochromes. J. Exp. Zool. 231, 429-434 (1984).
27. Harvey, M.B. & Kaye, P.L. Insulin increases the cell number of the inner cell mass and stimulates morphological development of mouse blastocysts in vitro. Development 110, 963-967 (1990).
28. Adjaye, J. et al. Primary differentiation in the human blastocyst: comparative molecular portraits of inner cell mass and trophectoderm cells. Stem Cells 23, 1514-1525 (2005).
29. Rugg-Gunn, P.J., Ferguson-Smith, A.C. & Pedersen, R.A. Epigenetic status of human embryonic stem cells. Nat. Genet. 37, 585-587 (2005).
30. Pokholok, D.K. et al. Genome-wide map of nucleosome acetylation and methylation in yeast. Cell 122, 517-527 (2005).
31. Lachner, M., O'Sullivan, R.J. & Jenuwein, T. An epigenetic road map for histone lysine methylation. J. Cell Sci. 116, 2117-2124 (2003).
32. Schubeler, D. et al. The histone modification pattern of active genes revealed through genome-wide chromatin analysis of a higher eukaryote. Genes Dev. 18, 1263-1271 (2004).
33. Strumpf, D. et al. Cdx2 is required for correct cell fate specification and differentiation of trophectoderm in the mouse blastocyst. Development 132, 2093-2102 (2005).
34. Vakoc, C.R., Mandat, S.A., Olenchock, B.A. & Blobel, G.A. Histone H3 lysine 9 methylation and HP1gamma are associated with transcription elongation through mammalian chromatin. Mol. Cell 19, 381-391 (2005).
35. Solter, D. & Knowles, B.B. Immunosurgery of mouse blastocyst. Proc. Natl. Acad. Sci. USA 72, 5099-5102 (1975).
36. Jones, P.A. & Martienssen, R. A blueprint for a Human Epigenome Project: the AACR Human Epigenome Workshop. Cancer Res. 65, 11241-11246 (2005).
37. Hebbes, T.R., Thorne, A.W. & Crane-Robinson, C. A direct link between core histone acetylation and transcriptionally active chromatin. EMBO J. 7, 1395-1402 (1988).
38. O'Neill, L.P. & Turner, B.M. Histone H4 acetylation distinguishes coding regions of the human genome from heterochromatin in a differentiation-dependent but transcription-independent manner. EMBO J. 14, 3946-3957 (1995).
39. Orlando, V. Mapping chromosomal proteins in vivo by formaldehyde- crosslinked-chromatin immunoprecipitation. Trends Biochem. Sci. 25, 99-104 (2000).
40. Geisberg, J.V. & Struhl, K. Quantitative sequential chromatin immunoprecipitation, a method for analyzing co-occupancy of proteins at genomic regions in vivo. Nucleic Acids Res. 32, e151 (2004).
41. Kuo, M.H. & Allis, C.D. In vivo cross-linking and immunoprecipitation for studying dynamic Protein:DNA associations in a chromatin environment. Methods 19, 425-433 (1999).
42. Robyr, D. & Grunstein, M. Genomewide histone acetylation microarrays. Methods 31, 83-89 (2003).
43. Suka, N., Suka, Y., Carmen, A.A., Wu, J. & Grunstein, M. Highly specific antibodies determine histone acetylation site usage in yeast heterochromatin and euchromatin. Mol. Cell 8, 473-479 (2001).
44. Gregory, R.I. & Feil, R. Analysis of chromatin in limited numbers of cells: a PCR-SSCP based assay of allele-specific nuclease sensitivity. Nucleic Acids Res. 27, e32 (1999).
45. Santos, F. et al. Epigenetic marking correlates with developmental potential in cloned bovine preimplantation embryos. Curr. Biol. 13, 1116-1121 (2003).
46. Schneider, I. Cell lines derived from late embryonic stages of Drosophila melanogaster. J. Embryol. Exp. Morphol. 27, 353-365 (1972).
47. Norris, D.P. et al. Evidence that random and imprinted Xist expression is controlled by preemptive methylation. Cell 77, 41-51 (1994).
48. O'Neill, L.P. et al. A developmental switch in H4 acetylation upstream of Xist plays a role in X chromosome inactivation. EMBO J. 18, 2897-2907 (1999).
49. Turner, B.M. & Fellows, G. Specific antibodies reveal ordered and cell-cycle-related use of histone-H4 acetylation sites in mammalian cells. Eur. J. Biochem. 179, 131-139 (1989).
50. White, D.A., Belyaev, N.D. & Turner, B.M. Preparation of site-specific antibodies to acetylated histones. Methods 19, 417-424 (1999).