Global nature of dynamic protein-chromatin interactions in vivo: Three-dimensional genome scanning and dynamic interaction networks of chromatin proteins

Molecular and Cellular Biology

Volumn 24, Issue 14, 2004, Pages 6393-6402

  Phair, Robert D ^c   Scaffidi, Paola ^a   Elbi, Cem ^a   Vecerová, Jaromíra ^d   Dey, Anup ^b   Ozato, Keiko ^b   Brown, David T ^e   Hager, Gordon ^a   Bustin, Michael ^a   Misteli, Tom ^a  

^a NATIONAL CANCER INSTITUTE   (United States)

^b EUNICE KENNEDY SHRIVER NATIONAL INSTITUTE OF CHILD HEALTH AND HUMAN DEVELOPMENT   (United States)

^c BioInformatics Services   (United States)

^d INSTITUTE OF EXPERIMENTAL MEDICINE   (Czech Republic)

^e UNIVERSITY OF MISSISSIPPI MEDICAL CENTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BINDING PROTEIN; CHROMATIN BINDING PROTEIN; UNCLASSIFIED DRUG;

ANIMAL CELL; ARTICLE; BINDING SITE; BLEACHING; CHROMATIN; GENE EXPRESSION; GENE STRUCTURE; GENOME; HUMAN; HUMAN CELL; MOUSE; NONHUMAN; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN PROTEIN INTERACTION; STEADY STATE;

ANIMALS; CELL LINE; CHROMATIN; DNA-BINDING PROTEINS; FLUORESCENCE RECOVERY AFTER PHOTOBLEACHING; GENOME; HUMANS; MODELS, BIOLOGICAL; PROTEIN BINDING; RECOMBINANT FUSION PROTEINS;

ANIMALIA;

EID: 3042760021     PISSN: 02707306     EISSN: None     Source Type: Journal    
DOI: 10.1128/MCB.24.14.6393-6402.2004     Document Type: Article

References (65)

1. Ahmad, K., and S. Henikoff. 2001. Modulation of a transcription factor counteracts heterochromatic gene silencing in Drosophila. Cell 104:839-847.
2. Akaike, H. 1974. A new look at statistical model identification. IEEE Trans. Auto. Control 19:716-723.
3. Becker, M., C. Baumann, S. John, D. A. Walker, M. Vigneron, J. G. McNally, and G. L. Hager. 2002. Dynamic behavior of transcription factors on a natural promoter in living cells. EMBO Rep. 3:1188-1194.
4. Bell, B. M. 2001. Approximating the marginal likelihood estimate for models with random parameters. Appl. Math. Comput. 119:57-75.
5. Bonaldi, T., G. Langst, R. Strohner, P. B. Becker, and M. E. Bianchi. 2002. The DNA chaperone HMGB1 facilitates ACF/CHRAC-dependent nucleosome sliding. EMBO J. 21:6865-6873.
6. Bustin, M. 1999. Regulation of DNA-dependent activities by the functional motifs of the high-mobility-group chromosomal proteins. Mol. Cell. Biol. 19:5237-5246.
7. Catez, F., D. T. Brown, T. Misteli, and M. Bustin. 2002. Competition between histone H1 and HMGN proteins for chromatin binding sites. EMBO Rep. 3:760-766.
8. Catez, F., Y. Huan, K. J. Tracey, R. Reeves, T. Misteli, and M. Bustin. 2004. A network of dynamic interations between histone H1 and HMG proteins in chromatin. Mol. Cell. Biol. 24:4321-4328.
9. Chalfie, M., Y. Tu, G. Euskirchen, W. Ward, and D. Prasher. 1994. Green fluorescent protein as a marker for gene expression. Science 263:802-805.
10. Chen, D., C. S. Hinkley, R. W. Henry, and S. Huang. 2002. TBP dynamics in living human cells: constitutive association of TBP with mitotic chromosomes. Mol. Biol. Cell 13:276-284.
11. Cheng, T. H., and M. R. Gartenberg. 2000. Yeast heterochromatin is a dynamic structure that requires silencers continuously. Genes Dev. 14:452-463.
12. Cheutin, T., S. A. Gorski, K. M. May, P. B. Singh, and T. Misteli. 2004. In vivo dynamics of Swi6 in yeast: evidence for a stochastic model of heterochromatin. Mol. Cell. Biol. 24:3157-3167.
13. Cheutin, T., A. J. McNairn, T. Jenuwein, D. M. Gilbert, P. B. Singh, and T. Misteli. 2003. Maintenance of stable heterochromatin domains by dynamic HP1 binding. Science 299:721-725.
14. Cobelli, C., and D. M. Foster. 1998. Compartmental models: theory and practice using the SAAM II software system. Adv. Exp. Med. Biol. 445:79-101.
15. Dey, A., F. Chitsaz, A. Abbasi, T. Misteli, and K. Ozato. 2003. The double bromodomain protein Brd4 binds to acetylated chromatin during interphase and mitosis. Proc. Natl. Acad. Sci. USA 100:8758-8763.
16. Dou, Y., J. Bowen, Y. Liu, and M. A. Gorovsky. 2002. Phosphorylation and an ATP-dependent process increase the dynamic exchange of H1 in chromatin. J. Cell Biol. 158:1161-1170.
17. Dundr, M., U. Hoffmann-Rohrer, Q. Hu, I. Grummt, L. I. Rothblum, R. D. Phair, and T. Misteli. 2002. A kinetic framework for a mammalian RNA polymerase in vivo. Science 298:1623-1626.
18. Dundr, M., J. G. McNally, J. Cohen, and T. Misteli. 2002. Quantitation of GFP-fusion proteins in single living cells. J. Struct. Biol. 140:92-99.
19. Eissenberg, J. C., and S. C. R. Elgin. 2000. The HP1 protein family: getting a grip on chromatin. Curr. Opin. Gen. Dev. 10:204-210.
20. Elbi, C., T. Misteli, and G. L. Hager. 2002. Recruitment of dioxin receptor to active transcription sites. Mol. Biol. Cell 13:2001-2015.
21. Elbi, C. C., D. A. Walker, G. Romero, W. P. Sullivan, D. O. Toft, G. L. Hager, and D. B. DeFranco. 2004. Molecular chaperones function as steroid receptor nuclear mobility factors. Proc. Natl. Acad. Sci. USA 101:2876-2881.
22. Felsenfeld, G., and M. Groudine. 2003. Controlling the double helix. Nature 421:448-453.
23. Festenstein, R., S. N. Pagakis, K. Hiragami, D. Lyon, A. Verreault, B. Sekkali, and D. Kioussis. 2003. Modulation of heterochromatin protein 1 dynamics in primary mammalian cells. Science 299:719-721.
24. Fletcher, T. M., N. Xiao, G. Mautino, C. T. Baumann, R. Wolford, B. S. Warren, and G. L. Hager. 2002. ATP-dependent mobilization of the glucocorticoid receptor during chromatin remodeling. Mol. Cell. Biol. 22:3255-3263.
25. Freeman, B. C., and K. R. Yamamoto. 2002. Disassembly of transcriptional regulatory complexes by molecular chaperones. Science 296:2232-2235.
26. Goytisolo, F. A., S. E. Gerchman, X. Yu, C. Rees, V. Graziano, V. Ramakrishnan, and J. O. Thomas. 1996. Identification of two DNA-binding sites on the globular domain of histone H5. EMBO J. 15:3421-3429.
27. Grewal, S. I., and S. C. Elgin. 2002. Heterochromatin: new possibilities for the inheritance of structure. Curr. Opin. Genet. Dev. 12:178-187.
28. Gunjan, A., B. T. Alexander, D. B. Sittman, and D. T. Brown. 1999. Effects of H1 histone variant overexpression on chromatin structure. J. Biol. Chem. 274:37950-37956.
29. Hager, G. L., C. Elbi, and M. Becker. 2002. Protein dynamics in the nuclear compartment. Curr. Opin. Genet. Dev. 12:137-141.
30. He, L., A. Weber, and D. Levens. 2000. Nuclear targeting determinants of the far upstream element binding protein, a c-myc transcription factor. Nucleic Acids Res. 28:4558-4565.
31. Hoogstraten, D., A. L. Nigg, H. Heath, L. H. Mullenders, R. van Driel, J. H. Hoeijmakers, W. Vermeulen, and A. B. Houtsmuller. 2002. Rapid switching of TFIIH between RNA polymerase I and II transcription and DNA repair in vivo. Mol. Cell 10:1163-1174.
32. Houtsmuller, A. B., S. Rademakers, A. L. Nigg, D. Hoogstraten, J. H. Hoeijmakers, and W. Vermeulen. 1999. Action of DNA repair endonuclease ERCC1/XPF in living cells. Science 284:958-961.
33. Houtsmuller, A. B., and W. Vermeulen. 2001. Macromolecular dynamics in living cell nuclei revealed by fluorescence redistribution after photobleaching. Histochem. Cell Biol. 115:13-21.
34. Kanda, T., K. F. Sullivan, and G. M. Wahl. 1998. Histone-GFP fusion protein enables sensitive analysis of chromosome dynamics in living mammalian cells. Curr. Biol. 26:377-385.
35. Kimura, H., and P. R. Cook. 2001. Kinetics of core histones in living human cells: little exchange of H3 and H4 and some rapid exchange of H2B. J. Cell Biol. 153:1341-1353.
36. Kimura, H., K. Sugaya, and P. R. Cook. 2002. The transcription cycle of RNA polymerase II in living cells. J. Cell Biol. 159:777-782.
37. Labrador, M., and V. G. Corces. 2002. Setting the boundaries of chromatin domains and nuclear organization. Cell 111:151-154.
38. Lemon, B., and R. Tjian. 2000. Orchestrated response: a symphony of transcription factors for gene control. Genes Dev. 14:2551-2569.
39. Lever, M. A., J. P. H. Th'ng, X. Sun, and M. J. Hendzel. 2000. Rapid exchange of histone H1.1 on chromatin in living cells. Nature 408:873-876.
40. Lippincott-Schwartz, J., E. Snapp, and A. Kenworthy. 2001. Studying protein dynamics in living cells. Nat. Rev. Mol. Cell Biol. 2:444-456.
41. McNally, J. G., W. G. Muller, D. Walker, R. Wolford, and G. L. Hager. 2000. The glucocorticoid receptor: rapid exchange with regulatory sites in living cells. Science 287:1262-1265.
42. Meyvis, T. K., S. C. De Smedt, P. Van Oostveldt, and J. Demeester. 1999. Fluorescence recovery after photobleaching: a versatile tool for mobility and interaction measurements in pharmaceutical research. Pharm. Res. 16:1153-1162.
43. Misteli, T. 2001. Protein dynamics: implications for nuclear architecture and gene expression. Science 291:843-847.
44. Misteli, T., A. Gunjan, R. Hock, M. Bustin, and D. T. Brown. 2000. Dynamic binding of histone H1 to chromatin in living cells. Nature 408:877-881.
45. Naar, A. M., B. D. Lemon, and R. Tjian. 2001. Transcriptional coactivator complexes. Annu. Rev. Biochem. 70:475-501.
46. Nagaich, A. K., D. A. Walker, R. Wolford, and G. L. Hager. 2004. Rapid periodic binding and displacement of the glucocorticoid receptor during chromatin remodeling. Mol. Cell 14:163-174.
47. Orphanides, G., and D. Reinberg. 2002. A unified theory of gene expression. Cell 108:439-451.
48. Pederson, T. 2001. Protein mobility within the nucleus-what are the right moves? Cell 104:635-638.
49. Phair, R. D., S. Gorski, and T. Misteli. 2004. Measurement of dynamic protein binding to chromatin in vivo using photobleaching microscopy. Methods Enzymol. 375:393-414.
50. Phair, R. D., and T. Misteli. 2000. High mobility of proteins in the mammalian cell nucleus. Nature 404:604-609.
51. Phair, R. D., and T. Misteli. 2001. Kinetic modelling approaches to in vivo imaging. Nat. Rev. Mol. Cell Biol. 2:898-907.
52. Prymakowsa-Bosak, M., T. Misteli, J. E. Herrera, H. Shirakawa, Y. Birger, S. Garfield, and M. Bustin. 2001. Mitotic phosphorylation prevents the binding of HMGN proteins to chromatin. Mol. Cell. Biol. 21:5169-5178.
53. Purich, D. L., and R. D. Allison. 2000. Handbook of biochemical kinetics. Academic Press, San Diego, Calif.
54. Roix, J., and T. Misteli. 2002. Genomes, proteomes, and dynamic networks in the cell nucleus. Histochem. Cell Biol. 118:105-116.
55. Scaffidi, P., T. Misteli, and M. E. Bianchi. 2002. Release of chromatin protein HMGB1 by necrotic cells triggers inflammation. Nature 418:191-195.
56. Schaaf, M. J., and J. A. Cidlowski. 2003. Molecular determinants of glucocorticoid receptor mobility in living cells: the importance of ligand affinity. Mol. Cell. Biol. 23:1922-1934.
57. Schaufele, F., J. F. Enwright III, X. Wang, C. Teoh, R. Srihari, R. Erickson, O. A. MacDougald, and R. N. Day. 2001. CCAAT/enhancer binding protein alpha assembles essential cooperating factors in common subnuclear domains. Mol. Endocrinol. 15:1665-1676.
58. Sporbert, A., A. Gahl, R. Ankerhold, H. Leonhardt, and M. C. Cardoso. 2002. DNA polymerase clamp shows little turnover at established replication sites but sequential de novo assembly at adjacent origin clusters. Mol. Cell 10:1355-1365.
59. Stavreva, D. A., W. G. Muller, G. L. Hager, C. L. Smith, and J. G. McNally. 2004. Rapid glucocorticoid receptor exchange at a promoter is coupled to transcription and regulated by chaperones and proteasomes. Mol. Cell. Biol. 24:2682-2697.
60. Stenoien, D. L., K. Patel, M. G. Mancini, M. Dutertre, C. L. Smith, B. W. O'Malley, and M. A. Mancini. 2001. FRAP reveals that mobility of oestrogen receptor-α is ligand and proteasome-dependent. Nat. Cell Biol. 3:15-23.
61. Strahl, B. D., and C. D. Allis. 2000. The language of covalent histone modifications. Nature 403:41-45.
62. Thomas, J. O., and A. A. Travers. 2001. HMG1 and 2, and related 'architectural' DNA-binding proteins. Trends Biochem. Sci. 26:167-174.
63. Verkman, A. S. 2002. Solute and macromolecule diffusion in cellular aqueous compartments. Trends Biochem. Sci. 27:27-33.
64. Woodcock, C. L., and S. Dimitrov. 2001. Higher-order structure of chromatin and chromosomes. Curr. Opin. Genet. Dev. 11:130-135.
65. Yin, X., M. F. Landay, W. Han, E. S. Levitan, S. C. Watkins, R. M. Levenson, D. L. Farkas, and E. V. Prochownik. 2001. Dynamic in vivo interactions among Myc network members. Oncogene 20:4650-4664.