Chromatin signatures of pluripotent cell lines

Nature Cell Biology

Volumn 8, Issue 5, 2006, Pages 532-538

  Azuara, Véronique ^a   Perry, Pascale ^a   Sauer, Stephan ^a   Spivakov, Mikhail ^a   Jørgensen, Helle F ^a   John, Rosalind M ^a,b   Gouti, Mina ^a,c   Casanova, Miguel ^a   Warnes, Gary ^d   Merkenschlager, Matthias ^a   Fisher, Amanda G ^a  

^a HAMMERSMITH HOSPITAL   (United Kingdom)

^b CARDIFF UNIVERSITY   (United Kingdom)

^c Academy of Athens Biomedical Research Foundation   (Greece)

^d IMPERIAL CANCER RESEARCH FUND   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

EED PROTEIN, MOUSE; REPRESSOR PROTEIN;

ANIMAL; ARTICLE; CARCINOMA; CELL CULTURE; CELL LINE; CHROMATIN; DNA REPLICATION TIMING; DOWN REGULATION; GENE EXPRESSION PROFILING; GENETIC EPIGENESIS; GENETIC MARKER; GENETICS; HEMATOPOIETIC STEM CELL; METABOLISM; MOUSE; MULTIPOTENT STEM CELL; PLURIPOTENT STEM CELL; T LYMPHOCYTE;

ANIMALS; CARCINOMA; CELL LINE; CELLS, CULTURED; CHROMATIN; DNA REPLICATION TIMING; DOWN-REGULATION; EPIGENESIS, GENETIC; GENE EXPRESSION PROFILING; GENETIC MARKERS; HEMATOPOIETIC STEM CELLS; MICE; MULTIPOTENT STEM CELLS; PLURIPOTENT STEM CELLS; REPRESSOR PROTEINS; T-LYMPHOCYTES;

EID: 33646872978     PISSN: 14657392     EISSN: 14764679     Source Type: Journal    
DOI: 10.1038/ncb1403     Document Type: Article

References (37)

1. Terskikh, A. V. et al. From hematopoiesis to neuropoiesis: evidence of overlapping genetic programs. Proc. Natl Acad. Sci. USA 98, 7934–7939 (2001).
2. Ivanova, N. B. et al. A stem cell molecular signature. Science 298, 601–604 (2002).
3. Ramalho-Santos, M., Yoon, S., Matsuzaki, Y., Mulligan, R. C. & Melton, D. A. “Stemness”: transcriptional profiling of embryonic and adult stem cells. Science 298, 597–600 (2002).
4. Fortunel, N. O. et al. Comment on “‘Stemness’: transcriptional profiling of embryonic and adult stem cells” and “a stem cell molecular signature”. Science 302, 393 (2003).
5. Evsikov, A. V. & Solter, D. Comment on “‘Stemness’: transcriptional profiling of embryonic and adult stem cells” and “a stem cell molecular signature”. Science 302, 393 (2003).
6. Vogel, G. Stem cells. ‘Stemness’ genes still elusive. Science 302, 371 (2003).
7. Bernstein, B. E. et al. Genomic maps and comparative analysis of histone modifications in human and mouse. Cell 120, 169–181 (2005).
8. 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).
9. Woodfine, K. et al. Replication timing of the human genome. Hum. Mol. Genet. 13, 191–202 (2004).
10. 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).
11. Hiratani, I., Leskovar, A. & Gilbert, D. M. Differentiation-induced replication-timing changes are restricted to AT-rich/long interspersed nuclear element (LINE)-rich isochores. Proc. Natl Acad. Sci. USA 101, 16861–16866 (2004).
12. Gilbert, N. et al. Chromatin architecture of the human genome: gene-rich domains are enriched in open chromatin fibers. Cell 118, 555–566 (2004).
13. Rugg-Gunn, P. J., Ferguson-Smith, A. C. & Pedersen, R. A. Epigenetic status of human embryonic stem cells. Nature Genet. 37, 585–587 (2005).
14. Evans, M. & Hunter, S. Source and nature of embryonic stem cells. C. R. Biol. 325, 1003–1007 (2002).
15. Schubeler, D. et al. Genome-wide DNA replication profile for Drosophila melanogaster: a link between transcription and replication timing. Nature Genet. 32, 438–442 (2002).
16. Azuara, V. et al. Heritable gene silencing in lymphocytes delays chromatid resolution without affecting the timing of DNA replication. Nature Cell Biol. 5, 668–674 (2003).
17. Gilbert, D. M. In search of the holy replicator. Nature Rev. Mol. Cell Biol. 5, 848–855 (2004).
18. Spooncer, E., Heyworth, C. M., Dunn, A. & Dexter, T. M. Self-renewal and differentiation of interleukin-3-dependent multipotent stem cells are modulated by stromal cells and serum factors. Differentiation 31, 111–118 (1986).
19. Nutt, S. L., Heavey, B., Rolink, A. G. & Busslinger, M. Commitment to the B-lymphoid lineage depends on the transcription factor Pax5. Nature 401, 556–562 (1999).
20. Chambers, I. & Smith, A. Self-renewal of teratocarcinoma and embryonic stem cells. Oncogene 23, 7150–7160 (2004).
21. Hogan, B. L., Taylor, A. & Adamson, E. Cell interactions modulate embryonal carcinoma cell differentiation into parietal or visceral endoderm. Nature 291, 235–237 (1981).
22. Jones-Villeneuve, E. M., Rudnicki, M. A., Harris, J. F. & McBurney, M. W. Retinoic acid-induced neural differentiation of embryonal carcinoma cells. Mol. Cell Biol. 3, 2271–2279 (1983).
23. Williams, R. R. et al. Neural induction promotes large-scale chromatin reorganisation of the Mash1 locus. J. Cell Sci. 119, 132–140 (2006).
24. Montgomery, N. D. et al. The murine polycomb group protein Eed is required for global histone H3 lysine-27 methylation. Curr. Biol. 15, 942–947 (2005).
25. Peters, A. H. & Schubeler, D. Methylation of histones: playing memory with DNA. Curr. Opin. Cell Biol. 17, 230–238 (2005).
26. Morin-Kensicki, E. M., Faust, C., LaMantia, C. & Magnuson, T. Cell and tissue requirements for the gene eed during mouse gastrulation and organogenesis. Genesis 31, 142–146 (2001).
27. Faust, C., Lawson, K. A., Schork, N. J., Thiel, B. & Magnuson, T. The Polycomb-group gene eed is required for normal morphogenetic movements during gastrulation in the mouse embryo. Development 125, 4495–4506 (1998).
28. Silva, J. et al. Establishment of histone H3 methylation on the inactive X chromosome requires transient recruitment of Eed––Enx1 polycomb group complexes. Dev. Cell 4, 481–495 (2003).
29. Plath, K. et al. Role of histone H3 lysine 27 methylation in X inactivation. Science 300, 131–135 (2003).
30. Vogelauer, M., Rubbi, L., Lucas, I., Brewer, B. J. & Grunstein, M. Histone acetylation regulates the time of replication origin firing. Mol. Cell 10, 1223–1233 (2002).
31. Lin, C. M., Fu, H., Martinovsky, M., Bouhassira, E. & Aladjem, M. I. Dynamic alterations of replication timing in mammalian cells. Curr. Biol. 13, 1019–1028 (2003).
32. Zhang, J., Xu, F., Hashimshony, T., Keshet, I. & Cedar, H. Establishment of transcriptional competence in early and late S phase. Nature 420, 198–202 (2002).
33. Ballas, N. & Mandel, G. The many faces of REST oversee epigenetic programming of neuronal genes. Curr. Opin. Neurobiol. 15, 500–506 (2005).
34. Hansen, R. S., Canfield, T. K., Lamb, M. M., Gartler, S. M. & Laird, C. D. Association of fragile X syndrome with delayed replication of the FMR1 gene. Cell 73, 1403–1409 (1993).
35. Gomez, M. & Brockdorff, N. Heterochromatin on the inactive X chromosome delays replication timing without affecting origin usage. Proc. Natl Acad. Sci. USA 101, 6923–6928 (2004).
36. Wang, J. et al. Imprinted X inactivation maintained by a mouse Polycomb group gene. Nature Genet. 28, 371–375 (2001).
37. Vandesompele, J. et al. Accurate normalization of real-time quantitative RT––PCR data by geometric averaging of multiple internal control genes. Genome Biol. 3, DOI: 10.1186/gb-2002-3-7-research0034 (2002).