Epigenetic aspects of differentiation

Journal of Cell Science

Volumn 117, Issue 19, 2004, Pages 4355-4363

  Arney, Katharine L ^a   Fisher, Amanda G ^a  

^a IMPERIAL COLLEGE SCHOOL OF MEDICINE   (United Kingdom)

Author keywords

Chromatin; Differentiation; Epigenetic

Indexed keywords

CIS ACTING ELEMENT; TRANSCRIPTION FACTOR;

ARTICLE; CELL DIFFERENTIATION; CELL DIVISION; CELL MANIPULATION; CELL NUCLEUS; CELL TYPE; CHROMATIN STRUCTURE; CONSTITUTIVE HETEROCHROMATIN; EPIGENETICS; EUCHROMATIN; GENE ACTIVITY; GENE EXPRESSION; GENE EXPRESSION PROFILING; GENE LOCUS; GENE REPRESSION; GENE SILENCING; GENETIC CODE; GENETIC TRANSCRIPTION; HERITABILITY; HETEROCHROMATIN; HUMAN; MOLECULAR MODEL; NONHUMAN; PRIORITY JOURNAL; SIGNAL TRANSDUCTION;

ANIMALS; CELL DIFFERENTIATION; CELL NUCLEUS; CHROMATIN; EUCHROMATIN; GROWTH AND DEVELOPMENT; HETEROCHROMATIN; HUMANS;

EID: 5444263735     PISSN: 00219533     EISSN: None     Source Type: Journal    
DOI: 10.1242/jcs.01390     Document Type: Article

References (60)

1. Aagaard, L., Laible, G., Selenko, P., Schmid, M., Dorn, R., Schotta, G., Kuhfittig, S., Wolf, A., Lebersorger, A., Singh, P. B. et al. (1999). Functional mammalian homologues of the Drosophila PEV-modifier Su(var)3-9 encode centromere-associated proteins which complex with the heterochromatin component M31. EMBO J. 18, 1923-1938.
2. Ahmad, K. and Henikoff, S. (2002a). Histone H3 variants specify modes of chromatin assembly. Proc. Natl. Acad. Sci. USA 99, 16477-16484.
3. Ahmad, K. and Henikoff, S. (2002b). The histone variant H3.3 marks active chromatin by replication-independent nucleosome assembly. Mol. Cell 9, 1191-1200.
4. Alcobia, I., Dilao, R. and Parreira, L. (2000). Spatial associations of centromeres in the nuclei of hematopoietic cells: evidence for cell-type-specific organizational patterns. Blood 95, 1608-1615.
5. Alcobia, I., Quina, A. S., Neves, H., Clode, N. and Parreira, L. (2003). The spatial organization of centromeric heterochromatin during normal human lymphopoiesis: evidence for ontogenically determined spatial patterns. Exp. Cell Res. 290 358-369.
6. Arney, K. L., Bao, S., Bannister, A. J., Kouzarides, T. and Surani, M. A. (2002). Histone methylation defines epigenetic asymmetry in the mouse zygote. Int. J. Dev. Biol. 46, 317-320.
7. Attwood, J. T., Yung, R. L. and Richardson, B. C. (2002). DNA methylation and the regulation of gene transcription. Cell. Mol. Life Sci. 59, 241-257.
8. Ayyanathan, K., Lechner, M. S., Bell, P., Maul, G. G., Schultz, D. C., Yamada, Y., Tanaka, K., Torigoe, K. and Rauscher, F. J. (2003). Regulated recruitment of HP1 to a euchromatic gene induces mitotically heritable, epigenetic gene silencing: a mammalian cell culture model of gene variegation. Genes Dev. 17, 1855-1869.
9. Azuara, V., Brown, K. E., Williams, R. R., Webb, N., Dillon, N., Festenstein, R., Buckle, V., Merkenschlager, M. and Fisher, A. G. (2003). Heritable gene silencing in lymphocytes delays chromatid resolution without affecting the timing of DNA replication. Nat. Cell Biol. 5, 668-674.
10. Bae, E., Calhoun, V. C., Levine, M., Lewis, E. B. and Drewell, R. A. (2002). Characterization of the intergenic RNA profile at abdominal-A and Abdominal-B in the Drosophila bithorax complex. Proc. Natl. Acad. Sci. USA 99, 16847-16852.
11. Bailis, J. M. and Forsburg, S. L. (2003). It's all in the timing: linking S phase to chromatin structure and chromosome dynamics. Cell Cycle 2, 303-306.
12. Bannister, A. J., Zegerman, P., Partridge, J. F., Miska, E. A., Thomas, J.O., Allshire, R. C. and Kouzarides, T. (2001). Selective recognition of methylated lysine 9 on histone H3 by the HP1 chromo domain. Nature 410, 120-124.
13. Barr, M. L. and Bertram, E. G. (1949). A morphological distinction between neurones of the male and female, and the behaviour of the nucleolar satellite during accelerated nucleoprotein synthesis. Nature 163, 676-677.
14. Bauer, U. M., Daujat, S., Nielsen, S. J., Nightingale, K. and Kouzarides, T. (2002). Methylation at arginine 17 of histone H3 is linked to gene activation. EMBO Rep. 3, 39-44.
15. Beil, M., Durschmied, D., Paschke, S., Schreiner, B., Nolte, U., Bruel, A. and Irinopoulou, T. (2002). Spatial distribution patterns of interphase centromeres during retinoic acid-induced differentiation of promyelocytic leukemia cells. Cytometry 47 217-225.
16. Boggs, B. A., Connors, B., Sobel, R. E., Chinault, A. C. and Allis, C. D. (1996). Reduced levels of histone H3 acetylation on the inactive X chromosome in human females. Chromosoma 105, 303-309.
17. Bosch, A. and Suau, P. (1995). Changes in core histone variant composition in differentiating nefurons: the roles of differential turnover and synthesis rates. Eur. J. Cell Biol. 68 220-225.
18. Bottardi, S., Aumont, A., Grosveld, F. and Milot, E. (2003). Developmental stage-specific epigenetic control of human beta globin gene expression is potentiated in hematopoietic progenitor cells prior to their transcriptional activation. Blood 102, 3989-3997.
19. Cammas, F., Oulad-Abdelghani, M., Vonesch, J. L., Huss-Garcia, Y., Chambon, P. and Losson, R. (2002). Cell differentiation induces TIF1beta association with centromeric heterochromatin via an HP1 interaction. J. Cell Sci. 115, 3439-3448.
20. Cao, R., Wang, L., Wang, H., Xia, L., Erdjument-Bromage, H., Tempst, P., Jones, R. S. and Zhang, Y. (2002). Role of histone H3 lysine 27 methylation in Polycomb-group silencing. Science 298 1039-1043.
21. Carrel, L., Cottle, A. A., Goglin, K. C. and Willard, H. F. (1999). A first-generation X-inactivation profile of the human X chromosome. Proc. Natl. Acad. Sci. USA 96, 14440-14444.
22. Chadwick, B. P. and Willard, H. F. (2003). Chromatin of the Barr body: histone and non-histone proteins associated with or excluded from the inactive X chromosome. Hum. Mol. Genet. 12, 2167-2178.
23. Claus, R. and Lubbert, M. (2003). Epigenetic targets in hematopoietic malignancies. Oncogene 22, 6489-6496.
24. Cook, P. R. (2003). Nongenic transcription, gene regulation and action at a distance. J. Cell Sci. 116, 4483-4491.
25. Cosma, M. P. (2002). Ordered recruitment: gene-specific mechanism of transcription activation. Mol. Cell 10, 227-236.
26. Costanzi, C. and Pehrson, J. R. (1998). Histone macroH2A1 is concentrated in the inactive X chromosome of female mammals. Nature 393, 599-601.
27. Czermin, B., Melfi, R., McCabe, D., Seitz, V., Imhof, A. and Pirrotta, V. (2002). Drosophila enhancer of Zeste/ESC complexes have a histone H3 methyltransferase activity that marks chromosomal Polycomb sites. Cell 111, 185-196.
28. Daujat, S., Bauer, U. M., Shah, V., Turner, B., Berger, S. and Kouzarides, T. (2002). Crosstalk between CARM1 methylation and CBP acetylation on histone H3. Curr Biol. 12, 2090-2097.
29. Drewell, R. A., Bae, E., Burr, J. and Lewis, E. B. (2002). Transcription defines the embryonic domains of cis-regulatory activity at the Drosophila bithorax complex. Proc. Natl Acad. Sci. USA 99, 16853-16858.
30. Fischle, W., Wang, Y. and Allis, C. D. (2003). Binary switches and modification cassettes in histone biology and beyond. Nature 425, 475-479.
31. Fitzpatrick, D. R. and Wilson, C. B. (2003). Methylation and demethylation in the regulation of genes, cells, and responses in the immune system. Clin. Immunol. 109, 37-45.
32. Francastel, C., Magis, W. and Groudine, M. (2001). Nuclear relocation of a transactivator subunit precedes target gene activation. Proc. Natl. Acad. Sci. USA 98, 12120-12125.
33. Fuks, F., Hurd, P. J., Deplus, R. and Kouzarides, T. (2003). The DNA methyltransferases associate with HP1 and the SUV39H1 histone methyltransferase. Nucleic Acids Res. 31, 2305-2312.
34. Gilbert, D. M. (2002). Replication timing and transcriptional control: beyond cause and effect. Curr. Opin. Cell Biol. 14, 377-383.
35. Gilbert, N., Boyle, S., Sutherland, H., de Las Heras, J., Allan, J., Jenuwein, T. and Bickmore, W. A. (2003). Formation of facultative heterochromatin in the absence of HP1. EMBO J. 22 5540-5550.
36. Gribnau, J., Diderich, K., Pruzina, S., Calzolari, R. and Fraser, P. (2000). Intergenic transcription and developmental remodeling of chromatin subdomains in the human beta-globin locus. Mol. Cell 5, 377-386.
37. Haaf, T., Steinlein, C. and Schmid, M. (1990). Nucleolar transcriptional activity in mouse Sertoli cells is dependent on centromere arrangement. Exp. Cell Res. 191, 157-160.
38. Hall, I. M., Shankaranarayana, G. D., Noma, K., Ayoub, N., Cohen, A. and Grewal, S. I. (2002). Establishment and maintenance of a heterochromatin domain. Science 297, 2232-2237.
39. Havas, K., Whitehouse, I. and Owen-Hughes, T. (2001). ATP-dependent chromatin remodeling activities. Cell. Mol. Life Sci. 58, 673-682.
40. Heard, E. (2004). Recent advances in X-chromosome inactivation. Curr. Opin. Cell Biol. 16, 247-255.
41. Henikoff, S., Ahmad, K., Platero, J. S. and van Steensel, B. (2000). Heterochromatic deposition of centromeric histone H3-like proteins. Proc. Natl. Acad. Sci. USA 97, 716-721.
42. Huang, Y. (2002). Transcriptional silencing in Saccharomyces cerevisiae and Schizosaccharomyces pombe. Nucleic Acids Res. 30, 1465-1482.
43. Huelsken, J. and Behrens, J. (2002). The Wnt signalling pathway. J. Cell Sci. 115, 3977-3978.
44. Im, H., Park, C., Feng, Q., Johnson, K. D., Kiekhaefer, C. M., Choi, K., Zhang, Y. and Bresnick, E. H. (2003). Dynamic regulation of histone H3 methylated at lysine 79 within a tissue-specific chromatin domain. J. Biol. Chem. 278, 18346-18352.
45. Jenuwein, T. and Allis, C. D. (2001). Translating the histone code. Science 293, 1074-1080.
46. Jeppesen, P. and Turner, B. M. (1993).The inactive X chromosome in female mammals is distinguished by a lack of histone H4 acetylation, a cytogenetic marker for gene expression. Cell 74 281-289.
47. Kontaraki, J., Chen, H. H., Riggs, A. and Bonifer, C. (2000). Chromatin fine structure profiles for a developmentally regulated gene: reorganization
48. Su, R. C., Brown, K. E., Saaber, S., Fisher, A. G., Merkenschlager, M. and Smale, S. T. (2004). Dynamic assembly of silent chromatin during thymocyte maturation. Nat. Genet. 36, 502-506.
49. Sullivan, E. J., Kasinathan, S., Kasinathan, P., Robl, J. M. and Collas, P. (2003). Cloned calves from chromatin remodeled in vitro. Biol. Reprod. 70, 146-153.
50. Tagoh, H., Melnik, S., Lefevre, P., Chong, S., Riggs, A. D. and Bonifer, C. (2004). Dynamic reorganization of chromatin structure and selective DNA demethylation prior to stable enhancer complex formation during differentiation of primary hematopoietic cells in vitro. Blood 103, 2950-2955.
51. Tamara, H., Zhang, X., McMillen, D., Singh, P. B., Nakayama, J., Grewal, S. I., Allis, C. D., Cheng, X. and Selker, E. U. (2003). Trimethylated lysine 9 of histone H3 is a mark for DNA methylation in Neurospora crassa. Nat. Genet. 34, 75-79.
52. Trinh, L. A., Ferrini, R., Cobb, B. S., Weinmann, A. S., Hahm, K., Ernst, P., Garraway, I. P., Merkenschlager, M. and Smale, S. T. (2001). Down-regulation of TDT transcription in CD4(+)CD8(+) thymocytes by Ikaros proteins in direct competition with an Ets activator. Genes Dev. 15, 1817-1832.
53. van der Vlag, J. and Otte, A. P. (1999). Transcriptional repression mediated by the human polycomb-group protein EED involves histone deacetylation. Nat. Genet. 23, 474-478.
54. van Driel, R., Fransz, P. F. and Verschure, P. J. (2003). The eukaryotic genome: a system regulated at different hierarchical levels. J. Cell Sci. 116, 4067-4075.
55. van Leeuwen, F., Gafken, P. R. and Gottschling, D. E. (2002). Dot1p modulates silencing in yeast by methylation of the nucleosome core. Cell 109, 745-756.
56. Veeman, M. T., Axelrod, J. D. and Moon, R. T. (2003). A second canon. Functions and mechanisms of beta-catenin-independent Wnt signaling. Dev. Cell 5, 367-377.
57. Volpe, T. A., Kidner, C., Hall, I. M., Teng, G., Grewal, S. I. and Martienssen, R. A. (2002). Regulation of heterochromatic silencing and histone H3 lysine-9 methylation by RNAi. Science 297, 1833-1837.
58. Weintraub, H. and Groudine, M. (1976). Chromosomal subunits in active genes have an altered conformation. Science 193, 848-856.
59. Wu, R. S., Tsai, S. and Bonner, W. M. (1983). Changes in histone H3 composition and synthesis pattern during lymphocyte activation. Biochemistry 22, 3868-3873.
60. Wunsch, A. M., Haas, A. L. and Lough, J. (1987). Synthesis and ubiquitination of histones during myogenesis. Dev. Biol. 119, 85-93.