Differential subnuclear localization and replication timing of histone H3 lysine 9 methylation states

Molecular Biology of the Cell

Volumn 16, Issue 6, 2005, Pages 2872-2881

  Wu, Rong ^a   Terry, Anna V ^a   Singh, Prim B ^b   Gilbert, David M ^a  

^a SUNY UPSTATE MEDICAL UNIVERSITY   (United States)

^b RESEARCH CENTER BORSTEL   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

4',6 DIAMIDINO 2 PHENYLINDOLE; HISTONE H3; LYSINE; METHYLTRANSFERASE; METHYLTRANSFERASE G9A; UNCLASSIFIED DRUG;

ANIMAL CELL; ARTICLE; CELL CYCLE S PHASE; CELL DIVISION; CELL NUCLEUS; CHROMATIN; CHROMOSOME; CONTROLLED STUDY; DNA SYNTHESIS; EPITOPE MAPPING; HETEROCHROMATIN; HUMAN; HUMAN CELL; MOUSE; NONHUMAN; NUCLEOLUS; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN FUNCTION; PROTEIN LOCALIZATION; PROTEIN METHYLATION;

ANIMALS; ANTIBODIES, MONOCLONAL; CELL LINE, TUMOR; CELL NUCLEUS; CHO CELLS; CRICETINAE; CRICETULUS; DNA; EPIGENESIS, GENETIC; EPITOPES; FLUORESCENT DYES; HETEROCHROMATIN; HISTONE-LYSINE N-METHYLTRANSFERASE; HISTONES; HUMANS; INDOLES; LYSINE; METHYLATION; MICE; MICROSCOPY, CONFOCAL; S PHASE;

CRICETINAE; MAMMALIA; MURINAE;

EID: 19644381697     PISSN: 10591524     EISSN: None     Source Type: Journal    
DOI: 10.1091/mbc.E04-11-0997     Document Type: Article

References (47)

1. Aparicio, J. G., Viggianl, C. J., Gibson, D. G., and Aparlcio, O. M. (2004). The Rpd3-Sin3 histone deacetyiase regulates replication timing and enables intra-S origin control in Saccharomyces cerevisiae, Mol. Cell. Biol. 24, 4769-4780.
2. Bernard, P., Maure, J. F., Partridge, J. F., Genier, S., Javerzat, J. P., and Allshire, R. C. (2001). Requirement of heterochromatin for cohesion at centromeres. Science 2539-2541.
3. Bozhenok, L., Wade, P. A., and Varga-Weisz, P. (2002). WSTF-ISWI chromatin remodeling complex targets heterochromatic replication foci, EMBO J. 23, 2231-2241.
4. Cowell, I. G. et al. (2002). Heterochromatin, HP1 and methylation at lysine 9 of histone H3 in animals. Chromosoma 332, 22-36.
5. Delaval, K., and Feil, R. (2004). Epigenetic regulation of mammalian genomic imprinting. Curr, Opin. Genet. Dev. 14, 188-195.
6. Dimitrova, D. S., and Berezney, R. (2002). The spatio-temporal organization of DNA replication sites is identical in primary, immortalized and transformed mammalian cells. J. Cell Sci. 135, 4037-4051.
7. Dimitrova, D. S., and Gilbert, D. M. (1999). The spatial position and replication riming of chromosomal domains are both established in early G1-phase. Mol. Cell 4, 983-993.
8. Gilbert, D. M. (2002). Replication timing and transcriptional control: beyond cause and effect. Curr. Opin. Cell Biol. 34, 377-383.
9. Heard, E. (2004). Recent advances in X-chromosome inactivation, Curr. Opin. Cell Biol. 36, 247-255.
10. Jackson, D. A., and Pombo, A. (1998). Replicon clusters are stable units of chromosome structure: evidence that nuclear organization contributes to the efficient activation and propagation of S phase in human cells, J. Cell Biol. 140, 1285-1295.
11. Kourmouli, N., Dialynas, G., Petraki, C., Pyrpasopoulou, A., Singh, P. B., Georgatos, S. D., and Theodoropoulos, P. A. (2001). Binding of heterochromatin protein 1 to the nuclear envelope is regulated by a soluble form of tubulin. J. Biol. Chem. 276, 13007-13014.
12. Kourmouli, N. et al. (2004). Heterochromatin and tri-methylated lysine 20 of histone H4 in animals. J. Cell Sci. 117, 2491-2501.
13. Kourmouli, N., Theodoropoulos, P. A., Dialynas, G., Bakou, A., Politou, A. S., Cowell, I. G., Singh, P. B., and Georgatos, S. D. (2000). Dynamic associations of heterochromarin protein 1 with the nuclear envelope, EMBO J. 19, 6558-6568.
14. Leonhardt, H., Rahn, H. P., Weinzierl, P., Sporbert, A., Cremer, T., Zink, D., and Cardoso, M. C. (2000). Dynamics of DNA replication factories in living cells. J. Cell Biol. 149, 271-280.
15. Litt, M. D., Simpson, M., Gaszner, M., Allis, C. D., and Felsenfeld, G. (2001a). Correlation between histone lysine methylation and developmental changes at the chicken beta-globin locus. Science 293, 2453-2455.
16. Litt, M. D., Simpson, M., Recillas-Targa, F., Prioleau, M. N., and Felsenfeld, G. (2001b). Transitions in histone acetylation reveal boundaries of three separately regulated neighboring loci. EMBO J. 20, 2224-2235.
17. Ma, H., Samarabandu, J., Devdhar, R. S., Acharya, R., Cheng, P., Meng, C., and Berezney, R. (1998). Spatial and temporal dynamics of DNA replication sites in mammalian cells. J. Cell Biol. 243, 1415-1425.
18. Makatsori, D., Kourmouli, N., Polioudaki, H., Shultz, L. D., McLean, K., Theodoropoulos, P. A., Singh, P. B., and Georgatos, S. D. (2004). The inner nuclear membrane protein lamin B receptor forms distinct microdomains and links epigenerically marked chromatin to the nuclear envelope. J. Biol. Chem. 279, 25567-25573.
19. McNairn, A. J., and Gilbert, D. M. (2003). Epigenomic replication: linking epigenetics to DNA replication. Bioessays 25, 647-656.
20. Misteli, T. (2004). Spatial positioning; a new dimension in genome function. Cell 119, 153-156.
21. Noma, K., Allis, C. D., and Grewal, S. I. (2001). Transitions in distinct histone H3 methylation patterns at the heterochromatin domain boundaries. Science 293, 1150-1155.
22. O'Keefe, R. T., Henderson, S. C., and Spector, D. L. (1992). Dynamic organization of DNA replication in mammalian cell nuclei-spatially and temporally defined replication of chromosome-specific alpha-satellite DNA sequences. J. Cell Biol. 116, 1095-1110.
23. Ogawa, H., Ishiguro, K., Gaubatz, S., Livingston, D. M., and Nakatani, V. (2002). A complex with chromatin modifiers that occupies E2F- and Mycresponsive genes in GO cells. Science 296, 1132-1136.
24. Perez-Burgos, L., Peters, A. H., Opravil, S., Kauer, M., Mechtler, K., and Jenuwein, T. (2004). Generation and characterization of methyl-lysine histone antibodies. Methods Enzymol. 376, 234-254.
25. Peters, A. H. et al (2003). Partitioning and plasticity of repressive histone methylation states in mammalian chromatin. Mol. Cell 12, 1577-1589.
26. Peters, A. H. et al. (2001). Loss of the Suv39h histone methyltransferases impairs mammalian heterochromatin and genome stability. Cell 107, 323-337.
27. Polioudaki, H., Kourmouli, N., Drosou, V., Bakou, A., Theodoropoulos, P. A., Singh, P. B., Giannakouros, T., and Georgatos, S. D. (2001). Histones H3/H4 form a tight complex with the inner nuclear membrane protein LBR and heterochromatin protein 1. EMBO Rep. 2, 920-925.
28. Rea, S. et al. (2000). Regulation of chromatin structure by site-specific histone H3 methyltransferases. Nature 406, 593-599.
29. Rice, J. C., Briggs, S. D., Ueberheide, B., Barber, C. M., Shabanowitz, J., Hunt, D. F., Shinkai, Y., and Allis, C. D. (2003). Histone methyltransferases direct different degrees of methylation to define distinct chromatin domains. Mol. Cell 12, 1591-1598.
30. Sadoni, N., Cardoso, M. C., Stelzer, E. H., Leonhardt, H., and Zink, D. (2004). Stable chromosomal units determine the spatial and temporal organization of DNA replication. J. Cell Sci. 117, 5353-5365.
31. Santos-Rosa, H., Schneider, R., Bannister, A. J., Sherriff, J., Bernstein, B. E., Emre, N. C., Schreiber, S. L., Mellor, J., and Kouzarides, T. (2002). Active genes are tri-methylated at K4 of histone H3. Nature 419, 407-411.
32. Schotta, G., Lachner, M., Sarma, K., Ebert, A., Sengupta, R., Reuter, G., Reinberg, D., and Jenuwein, T. (2004). A silencing pathway to induce H3-K9 and H4-K20 trimethylation at constitutive heterochromatin. Genes Dev. 18, 1251-1262.
33. Schultz, D. C., Ayyanathan, K., Negorev, D., Maul, G. G., and Rauscher, F. J., 3rd. (2002). SETDB1, a novel KAP-1-associated histone H3, lysine 9-specific methyltransferase that contributes to HP1-mediated silencing of euchromatic genes by KRAB zinc-finger proteins. Genes Dev. 16, 919-932.
34. Singh, P. B., and Georgatos, S. D. (2002). HP 1, facts, open questions, and speculation. J. Struct. Biol. 140, 10-16.
35. Tachibana, M., Sugimoto, K., Fukushima, T., and Shinkai, Y. (2001). Set domain-containing protein, G9a, is a novel lysine-preferring mammalian histone methyltransferase with hyperactivify and specific selectivity to lysines 9 and 27 of histone H3. J. Biol. Chem. 276, 25309-25317.
36. Tachibana, M. et al. (2002). G9a histone methyltransferase plays a dominant role in euchromatic histone H3 lysine 9 methylation and is essential for early embryogenesis. Genes Dev. 16, 1779-1791.
37. Taddei, A., Hediger, F., Neumann, F. R., and Gasser, S. M. (2004). The function of nuclear architecture: a genetic approach. Annu. Rev. Genet. 38, 305-345.
38. Tamaru, 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 DMA methylation in Neurospora crassa. Nat. Genet. 34, 75-79.
39. Vogelauer, M., Rubbi, L., Lucas, I., Brewer, B. J., and Grunstein, M. (2002). Histone acerylation regulates the time of replication origin firing. Mol. Cell 10, 1223-1233.
40. Wang, H., An, W., Cao, R., Xia, L., Erdjument-Bromage, H., Chatton, B., Tempsr, P., Roeder, R. G., and Zhang, V. (2003). mAM facilitates conversion by ESET of dimethyl to trimethyl lysine 9 of histone H3 to cause transcriptional repression. Mol. Cell 12, 475-487.
41. Waterborg, J. H. (1993). Dynamic methylation of alfalfa histone H3. J. Biol. Chem. 268, 4918-4921.
42. Williams, R. R., and Fisher, A. G. (2003). Chromosomes, positions pleasel! Nat. Cell Biol. 5, 388-3890.
43. Wu, R., Terry, A. V., and Gilbert, D. M. (2004). Observing nuclear structure/chromatin changes with fluorescently-labelled antibodies. In: Methods in Molecular Biology: Nuclear Reprogramming, vol., ed. S. Pells, Totowa, NJ: Humana Press (in press).
44. Zappulla, D. C., Sternglanz, R., and Leatherwood, J. (2002). Control of replication timing by a transcriptional silencer. Curr. Biol. 12, 869-875.
45. Zhang, J., Xu, F., Hashimshony, T., Keshet, I., and Cedar, H. (2002), Establishment of transcriptional competence in early and late S phase. Nature 420, 198-202.
46. Zhang, X., Yang, Z., Khan, S. I., Horton, I. R., Tamaru, H., Selker, E. U., and Cheng, X. (2003). Structural basis for the product specificity of histone lysine methyltransferases. Mol. Cell 12, 177-185.
47. Zink, D., Bornfleth, H., Visser, A., Cremer, C., and Cremer, T. (1999). Organization of early and late replicating DNA in human chromosome territories. Exp. Cell Res. 247, 176-188.