Time-resolved microscopy of chromatin in vitro and in vivo

Photochemistry and Photobiology

Volumn 81, Issue 3, 2005, Pages 548-555

  Davis, Sara K ^a   Bardeen, Christopher J ^b  

^a Cardinal Health   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; HISTONE;

BLEACHING; CELL CULTURE; CELL NUCLEUS; CHEMISTRY; CHROMATIN; CONFERENCE PAPER; CONFOCAL MICROSCOPY; CONFORMATION; GENE EXPRESSION; INSTRUMENTATION; METABOLISM; METHODOLOGY; OSMOLARITY; PHOTOCHEMISTRY; TIME; ULTRASTRUCTURE;

CELL NUCLEUS; CELLS, CULTURED; CHROMATIN; DNA; GENE EXPRESSION; HISTONES; MICROSCOPY, CONFOCAL; NUCLEIC ACID CONFORMATION; OSMOLAR CONCENTRATION; PHOTOBLEACHING; PHOTOCHEMISTRY; TIME;

EUKARYOTA;

EID: 21244491983     PISSN: 00318655     EISSN: None     Source Type: Journal    
DOI: 10.1562/2004-08-14-IR-275.1     Document Type: Conference Paper

References (51)

1. Wolffe, A. (1998) Chromalin: Structure and Function. Academic Press, San Diego.
2. Widom, J. (1998) Structure, dynamics, and function of chromatin in vitro. Annu. Rev. Biophys. Biomol. Struct. 27, 285-327.
3. Cremer, T. and C. Cremer (2001) Chromosome territories, nuclear architecture and gene regulation in mammalian cells. Nat. Rev. Genet. 2, 292-301.
4. Belmont, A. S., S. Dietzel, A. C. Nye, Y. G. Strukov and T. Tumbar (1999) Large-scale chromatin structure and function. Curr. Opin. Cell. Biol. 11, 307-311.
5. Wolffe, A. P. and J. C. Hansen (2001) Nuclear visions: functional flexibility from structural instability. Cell 104, 631-634.
6. Davie, J. R. (1997) Nuclear matrix, dynamic histone acetylation and transcriptionally active chromatin. Mol. Biol. Rep. 24, 197-207.
7. Davis, S. K. and C. J. Bardeen (2003) Cross-linking of histone proteins to DNA by UV illumination of chromatin stained with Hoechst 33342. Photochem. Photobiol. 77, 675-679.
8. Lalwani, R., S. Maiti and S. Mukherji (1995) Involvement of HI and other chromatin proteins in the formation of DNA-protein cross-links induced by visible light in the presence of methylene blue. J. Photochem. Photobiol. B: Biol. 27, 117-122.
9. Hansen, J. C. (2002) Conformational dynamics of the chromatin fiber in solution. Annu. Rev. Biophys. Biomol. Struct. 31, 361-392.
10. Garcia-Perez, A. I., E. A. Lopez-Beltran, P. Kluner, J. Luque, P. Ballesteros and S. Cerdan (1999) Molecular crowding and viscosity as determinants of translational diffusion of metabolites in subcellular organelles. Arch. Biochem. Biophys. 362, 329-338.
11. Magde, D., E. Elson and W. W. Webb (1972) Thermodynamic fluctuations in a reacting system - measurement by fluctuation correlation spectroscopy. Phys. Rev. Lett. 29, 705-708.
12. Qian, H., M. P. Sheetz and E. L. Elson (1991) Single particle tracking: analysis of diffusion and flow in two-dimensional systems. Biophys. J. 60, 910-921.
13. Axelrod, D., D. E. Koppel, J. Schlessinger, E. Elson and W. W. Webb (1976) Mobility measurement by analysis of fluorescence photo-bleaching recovery kinetics. Biophys. J. 16, 1055-1069.
14. Phair, R. D. and T. Misteli (2000) High mobility of proteins in the mammalian cell nucleus. Nature 404, 604-609.
15. Misteli, T., A. Gunjan, R. Hock, M. Bustin and D. T. Brown (2000) Dynamic binding of histone HI to chromatin in living cells. Nature 408, 877-881.
16. Lever, M. A., J. P. H. Th'ng, X. Sun and M. J. Hendzel (2000) Rapid exchange of histone H 1.1 on chromatin of living human cells. Nature 408, 873-876.
17. Abney, J. R., B. Cutler, M. L. Fillbach, D. Axelrod and B. A. Scalettar (1997) Chromatin dynamics in interphase nuclei and its implications for nuclear structure. J. Cell. Biol. 137, 1459-1468.
18. Arndt-Jovin, D. J. and T. M. Jovin (1989) Fluorescence labeling and microscopy of DNA. Methods Cell Biol. 30, 417-448.
19. 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. 8, 377-385.
20. Cicerone, M. T., F. R. Blackburn and M. D. Ediger (1995) Anomalous diffusion of probe molecules in polystyrene: evidence for spatially heterogeneous segmental dynamics. Macromolecules 28, 8224-8232.
21. Smith, B. A. and H. M. McConnell (1978) Determination of molecular motion in membranes using periodic pattern photobleaching. Proc. Natl. Acad. Sci. USA 75, 2759-2763.
22. Davoust, J., P. F. Devaux and L. Leger (1982) Fringe pattern photobleaching, a new method for the measurement of transport coefficients of biological macromolecules. EMBO J. 1, 1233-1238.
23. Lanni, F. and B. R. Ware (1982) Modulation detection of fluorescence photobleaching recovery. Rev. Sci. Inst. 53, 905-908.
24. Hattori, M., H. Shimizu and H. Yokoyama (1996) Fluorescence correlation spectroscopy with traveling interference fringe excitation. Rev. Sci. Inst. 67, 4064-4071.
25. Margineantu, D., R. A. Capaldi and A. H. Marcus (2000) Dynamics of the mitochondrial reticulum in live cells using Fourier imaging correlation spectroscopy and digital video microscopy. Biophys. J. 79, 1833-1849.
26. Davis, S. K. and C. J. Bardeen (2002) Using two-photon standing waves and patterned photobleaching to measure diffusion from nanometers to microns in biological systems. Rev. Sci. Inst. 73, 2128-2135.
27. Bailey, B., D. L. Farkas, D. L. Taylor and F. Lanni (1993) Enhancement of axial resolution in fluorescence microscopy by standing-wave excitation. Nature 366, 44-48.
28. Gustafsson, M. G. L., D. A. Agard and J. W. Sedat (1999) I5M: 3D widefield light microscopy with better than 100 nm axial resolution. J. Microsc. 195, 10-16.
29. Hell, S. W., M. Schrader and H. T. M. van der Voort (1997) Far-field fluorescence microscopy with three dimensional resolution in the 100 nm range. J. Microsc. 187, 1-7.
30. Davis, S. K. and C. J. Bardeen (2004) The connection between chromatin motion on the 100 nm length scale and core histone dynamics in live XTC-2 cells and isolated nuclei. Biophys. J. 86, 555-564.
31. Marshall, W. F., A. Straight, J. F. Marko, J. Swedlow, A. Dernburg, A. Belmont, A. W. Murray, D. A. Agard and J. W. Sedat (1997) Interphase chromosomes undergo constrained diffusional motion in living cells. Curr. Biol. 7, 930-939.
32. Heun, P., T. Laroche, K. Shimada, P. Furrer and S. M. Gasser (2001) Chromosome dynamics in the yeast interphase nucleus. Science 294, 2181-2186.
33. Vazquez, J., A. S. Belmont and J. W. Sedat (2001) Multiple regimes of constrained chromosome motion are regulated in the interphase Drosophila nucleus. Curr. Biol. 11, 1227-1239.
34. Chubb, J. R., S. Boyle, P. Perry and W. A. Bickmore (2002) Chromatin motion is constrained by association with nuclear compartments in human cells. Curr. Biol. 12, 439-445.
35. Bornfleth, H., P. Edelmann, D. Zink, T. Cremer and C. Cremer (1999) Quantitative motion analysis of subchromosomal foci in living cells using four-dimensional microscopy. Biophys. J. 77, 2871-2886.
36. Zimmerman, S. B. (1993) Macromolecular crowding effects on macromolecular interactions: some implications for genome structure and function. Biochim. Biophys. Acta 1216, 175-185.
37. Marshall, W. F. (2002) Order and disorder in the nucleus. Curr. Biol. 12, R185-R192.
38. Gerchman, S. E. and V. Ramakrishnan (1987) Chromatin higher order structure studied by neutron scattering and scanning transmission electron microscopy. Proc. Natl. Acad. Sci. USA 84, 7802-7806.
39. Clark, D. J. and T. Kimura (1990) Electrostatic mechanism of chromatin folding. J. Mol. Biol. 211, 883-896.
40. Meersseman, G., S. Pennings and E. M. Bradbury (1992) Mobile nucleosomes - a general behavior. EMBO J. 11, 2951-2959.
41. Weischet, W. O. (1979) On the de novo formation of compact oligonucleosomes at high ionic strength. Evidence for nucleosomal sliding in high salt. Nucleic Acids Res. 7, 291-304.
42. Thorne, A. W., P. D. Gary and C. Crane-Robinson (1998) Extraction and separation of core histones and non-histone chromosomal proteins. In Chromatin - A Practical Approach (Edited by H. Gould), pp. 35-58. Oxford University Press, New York.
43. Spadafora, C., P. Oudet and P. Chambon (1979) Rearrangement of chromatin structure induced by increasing ionic strength and temperature. Eur. J. Biochem. 100, 225-235.
44. Jackson, V. (1999) Formaldehyde cross-linking for studying nucleosomal dynamics. Methods 17, 125-139.
45. Pederson, T. (2000) Half a century of the "nulear matrix". Mol. Cell Biol. 11, 799-805.
46. Caserta, M., L. Verdone and E. D. Mauro (2002) Aspects of nucleosomal positional flexibility and fluidity. ChemBioChem 3, 1172-1182.
47. Becker, P. B. (2002) Nucleosome sliding: facts and fiction. EMBO J. 21, 4749-41753.
48. Tong, J. K., C. A. Hassig, G. R. Schnitzler, R. E. Kingston and S. L. Schreiber (1998) Chromatin deacetylation by an ATP-dependent nucleosome remodeling complex. Nature 395, 917-921.
49. Hamiche, A., R. Sandaltzopoulos, D. A. Gdula and C. Wu (1999) ATP-dependent histone octamer sliding mediated by the chromatin remodeling complex NURF. Cell 97, 833-842.
50. Guschin, D., P. A. Wade, N. Kikyo and A. P. Wolffe (2000) ATP-dependent histone octamer mobilization and histone deacetylation mediated by the Mi-2 chromatin remodeling complex. Biochem. 39, 5238-5245.
51. Guschin, D., T. M. Geiman, N. Kikyo, D. J. Tremethick, A. P. Wolffe and P. A. Wade (2000) Multiple ISWI ATPase complexes from X-enopus laevis. J. Biol. Chem. 275, 35248-35255.