Organization of highly acetylated chromatin around sites of heterogeneous nuclear RNA accumulation

Molecular Biology of the Cell

Volumn 9, Issue 9, 1998, Pages 2491-2507

  Hendzel, Michael J ^a   Kruhlak, Michael J ^a   Bazett Jones, David P ^a  

^a UNIVERSITY OF CALGARY   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

HETEROGENEOUS NUCLEAR RNA; HISTONE ACETYLTRANSFERASE; HISTONE DEACETYLASE; HISTONE H3; RIBONUCLEOPROTEIN;

ACETYLATION; ANIMAL CELL; ARTICLE; CELL GRANULE; CELL NUCLEUS; CHROMATIN CONDENSATION; CHROMATIN STRUCTURE; FIBROBLAST; HUMAN; HUMAN CELL; NONHUMAN; PRIORITY JOURNAL;

ANIMALIA; MUNTIACUS MUNTJAK;

EID: 0031713881     PISSN: 10591524     EISSN: None     Source Type: Journal    
DOI: 10.1091/mbc.9.9.2491     Document Type: Article

References (66)

1. Abholhassani-Dadras, S., Vazquez-Nin, G.H., Echeverria, O.M., and Fakan, S. (1996). Image-EELS for in situ estimation of the phosphorus content of RNP granules. J. Micros. 183, 215-222.
2. Alberts, B., Bray, D., Lewis, J., Raff, M., Roberts, K., and Watson, J.D. (1994). Molecular Biology of the Cell, 3rd ed., New York: Garland Publishing, 233.
3. Armstrong, J.A., and Emerson, B.M. (1998). Transcription of chromatin: these are complex times. Curr. Opin. Genet. Dev. 8, 165-172.
4. Bazett-Jones, D.P. (1992). Empirical basis for phosphorus mapping and structure determination of DNA:protein complexes by electron spectroscopic imaging. Microbeam Analysis 2, 69-79.
5. Belmont, A.S., and Bruce, K. (1994). Visualization of G1 chromosomes - a folded, twisted, supercoiled chromonema model of interphase chromatid structure. J. Cell Biol. 127, 287-302.
6. Bernhard, W. (1969). A new staining procedure for electron microscopical cytology. J. Ultrastruct. Res. 27, 250-265.
7. Boffa, L.C., Walker, J., Chen, T.A., Sterner, R., Mariani, M.R., and Allfrey, V.G. (1990). Factors affecting nucleosome structure in transcriptionally active chromatin. Histone acetylation, nascent RNA and inhibitors and RNA synthesis. Eur. J. Biochem. 194, 811-823.
8. 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.
9. Breneman, J.W., Yau, P.M., Swiger, R.R., Teplitz, R., Smith, H.A., Tucker, J.D., and Bradbury, E.M. (1996). Acivity banding of human chromosomes as shown by histone acetylation. Chromosoma 105, 41-49.
10. Bridge, E., Riedel, K.-U., Johansson, B.-M., and Pettersson, U. (1996). Spliced exons of adenovirus late RNAs colocalize with snRNP in a specific nuclear domain. J. Cell Biol. 135, 303-314.
11. Bridge, E., and Pettersson, U. (1996). Nuclear organization of adenovirus RNA biogenesis. Exp. Cell Res. 229, 233-239.
12. Carter, K.C., Bowman, D., Carrington, W., Fogarty, K., McNeil, J.A., Fay, F.S., and Lawrence, J.B. (1993). A three-dimensional view of precursor messenger RNA metabolism within the mammalian nucleus. Science 259, 1330-1334.
13. Carter, K.C., Taneja, K.L., and Lawrence, J.B. (1991). Discrete nuclear domains of poly(A) RNA and their relationship to the functional organization of the nucleus. J. Cell Biol. 115, 1191-1202.
14. Clemson, C.M., and Lawrence, J.B. (1996). Multifunctional compartments in the nucleus: insights from DNA and RNA localization. J. Cell. Biochem. 62, 81-190.
15. Covault, J., and Chalkley, R. (1980). The identification of distinct populations of acetylated histone. J. Biol. Chem. 255, 9110-9116.
16. Davie, J.R. (1996). Histone modifications, chromatin structure, and the nuclear matrix. J. Cell. Biochem. 62, 454-466.
17. Davie, J.R. (1998). Covalent modification of histones: expression from chromatin templates. Curr. Opin. Genet. Dev. 8, 173-178.
18. Davie, J.R., and Hendzel, M.J. (1994). The multiple functions of dynamic histone acetylation. J. Cell. Biochem. 55, 98-105.
19. Fakan, S (1994). Perichromatin fibrils are in situ forms of nascent transcripts. Trends Cell Biol. 4, 86-90.
20. 3H-uridine incorporation as visualized by high resolution autoradiography. Exp. Cell Res. 79, 431-444.
21. Fakan, S., Leser, G., and Martin, T.E. (1984). Ultrastructural distribution of nuclear ribonucleoproteins as visualized by immunocytochemistry on thin sections. J. Cell Biol. 98, 358-363.
22. Fakan, S., and Nobis, P. (1978). Ultrastructural localization of transcription sites and of RNA distribution during the cell cycle of synchronized CHO cells. Exp. Cell Res. 113, 327-337.
23. Fakan, S., and Puvion, E. (1980). The ultrasrructural visualizationof nucleolar and extranucleolar RNA synthesis and distribution. Int. Rev. Cytol. 65, 255-299.
24. Fay, F.S., Taneja, K.L., Shenoy, S., Lifshitz, L., and Singer, R.H. (1997). Quantitative digital analysis of diffuse and concentrated nuclear distributions of nascent transcripts, SC35, and poly(A). Exp. Cell Res. 231, 23-37.
25. Ferreira, J., Paolella, G., Ramos, C., and Lamond, A.I. (1997). Spatial organization of large-scale chromatin domains in the nucleus: a magnified view of single chromosome territories. J. Cell Biol. 139, 1597-1610.
26. Fu, X.D., and Maniatis, T. (1990). Ractor required for mammalian spliceosome assembly is localized to discrete regions in the nucleus. Nature 343, 437-441.
27. Garcia-Ramirez, M., Rocchini, C., and Ausio, J. (1995). Modulation of chromatin folding by histone acetylation. J. Biol. Chem. 270, 17923-17928.
28. Grande, M.A., van der Kraan, I., de Jong, L., and van Driel, R. (1997). Nuclear distribution of transcription factors in relation to sites of transcription and RNA polymerase II. J. Cell Sci. 110, 1781-1791.
29. Hendzel, M.J., and Bazett-Jones, D.P. (1996). Probing nuclear ultrastructure by electron spectroscopic imaging (ESI). J. Microsc. 182, 1-14.
30. Hendzel, M.J., Delcuve, G.P., and Davie, J.R. (1991). Histone deacetylase is a component of the internal nuclear matrix. J. Biol. Chem. 266, 21936-21942.
31. Hendzel, M.J., Kruhlak, M.J., and Bazett-Jones, D.P. (1998). Electron spectroscopic imaging and correlative fluorescent microscopy of the cell nucleus. Scanning (in press).
32. Hendzel, M.J., Sun, J.-M., Chen, H.Y., Rattner, J.B., and Davie, J.R. (1994). Histone acetyltransferase is associated with the nuclear matrix. J. Biol. Chem. 269, 22894-22901.
33. + RNA. J. Cell Biol. 126, 877-899.
34. Huang, S., and Spector, D.L. (1991). Nascent pre-mRNA transcripts are associated with nuclear regions enriched in splicing factors. Genes Dev. 5, 2288-2302.
35. Huang, S., and Spector, D.L. (1996). Dynamic organization of pre-mRNA splicing factors. J. Cell. Biochem. 62, 191-197.
36. Ishov, A.M., Stenberg, R.M., and Maul, G.G. (1997). Human cytomegalovirus immediate early interaction with host nuclear structures: definition of an immediate transcript environment. J. Cell Biol. 138, 5-16.
37. Jackson, D.A., Iborra, F.I., Manders, E.M.M., and Cook, P.R. (1998). Numbers and organization of RNA polymerases, nascent transcript and transcription units in HeLa nuclei. Mol. Biol. Cell 9, 1523-1536.
38. Jeppesen, P. (1997). Histone acetylation: a possible mechanism for the inheritance of cell memory at mitosis. Bioessays 19, 67-74.
39. Kramer, J., Zachar, Z., and Bingham, P.M. (1994). Nuclear pre-mRNA metabolism: channels and tracks. Trends Cell Biol. 4, 35-37.
40. Lamond, A.I., and Earnshaw, W.C. (1998). Structure and function in the nucleus. Science 280, 547-553.
41. Marunis, M.J., Xing, J., and Dreyfuss, G. (1994). The hnRNP F protein: unique primary structure, nucleic acid-binding properties, and subcellular localization. Nucleic Acids Res. 22, 1059-1067.
42. Misteli, T., Caceres, J.F., and Spector, D.L. (1997). The dynamics of a pre-mRNA splicing factor in living cells. Nature 387, 523-527.
43. Misteli, T., and Spector, D.L. (1997). Protein phosphorylation and the nuclear organization of pre-mRNA splicing. Trends Cell Biol. 7, 135-138.
44. Mizzen, C.A., et al. (1996). The TAF(II)250 subunit of TFIID has histone acetyltransferase activity. Cell 87, 1261-1270.
45. Monneron, A., and Bernhard, W. (1969). Fine structural organization of the interphase nucleus in some mammalian cells. J. Ultrastruct. Res. 27, 266-288.
46. Nevins, J.R., and Darnell, J.E., Jr. (1978). Steps in the processing of Ad2 mRNA: poly(A)+ nuclear sequences are conserved and poly(A) addition precedes splicing. Cell 15, 1477-1493.
47. Puvion, E., and Puvion-Dutilleul, F. (1996). Ultrastructure of the ucleus in relation to transcription and splicing: roles of perichromatin fibrils and interchromatin granules. Exp. Cell Res. 229, 217-225.
48. Raska, I. (1995). Nuclear ultrastructures associated with the RNA synthesis and processing. J. Cell. Biochem. 59, 11-26.
49. Rattner, J.B., Hendzel, M.J., Furbee, C.S., Muller, M.T., and Bazett-Jones, D.P. (1996). Topoisomerase II is associated with the mammalian centromere in a cell cycle- and species-specific manner and is required for proper centromere/kinetochore structure. J. Cell Biol. 134, 1097-1107.
50. Reed, R., Griffith, J., and Maniatis, T. (1988). Purification and visualization of native spliceosomes. Cell 53, 949-961.
51. Robinett, C.C., Straight, A., Li, G., Willhelm, C., Sudlow, G., Murray, A., and Belmont, A.S. (1996). In vivo localization of DNA sequences and visualization of large-scale chromatin organization using lac operator/repressor recognition. J. Cell Biol. 135, 1685-1700.
52. II250: a TBP-associated factor implicated in cell-cycle regulation. Nature 362, 175-179.
53. Schwarz, P.M., Felthauser, A., Fletcher, T.M., and Hansen, J.C. (1996). Reversible oligonucleosome self-association: dependence on divalent cations and core histone tail domains. Biochemistry 35 4009-4015.
54. Sharp, P.A. (1988). RNA splicing and genes. JAMA 260, 3035-3041.
55. Spector, D. L. (1990). Higher order nuclear organization: three-dimensional distribution of small nuclear ribonucleoprotein particles. Proc. Natl. Acad. Sci. USA 87, 147-151.
56. Spector, D.L. (1996). Nuclear organization and gene expression. Exp. Cell Res. 229, 189-197.
57. Spector, D.L., Fu, X.-D., and Maniatis, T. (1991). Associations between distinct pre-mRNA splicing components and the cell nucleus. EMBO J. 11, 3467-3481.
58. Strouboulis, J., and Wolffe, A.P. (1996). Functional compartmentalization of the nucleus. J. Cell Sci. 109, 1991-2000.
59. Thiry, M. (1993). Differential location of nucleic acids within interchromatin granule clusters. Eur. J. Cell Biol. 62, 259-269.
60. Thiry, M. (1995). Behaviour of interchromatin granules during the cell cycle. Eur. J. Cell Biol. 68, 14-24.
61. van Steensel, B., Brink, M., van der Meulen, K., van Binnendijk, E.P., Wansink, D.G., de Jong, L., de Kloet, E.R., and van Driel, R. (1995). Localization of the glucocorticoid receptor in discrete clusters in the cell nucleus. J. Cell Sci. 108, 3003-3011.
62. Visa, N., Puvion-Dutilleul, F., Harper, F., Bachellerie, J.-P., and Puvion, E. (1993). Intranuclear distribution of poly(A) RNA determined by electron microscope in situ hybridization. Exp. Cell Res. 208, 19-34.
63. Wassef, M. (1979). A cytochemical study of interchromatin granules. J. Ultrastruct. Res. 69, 121-133.
64. Xing, Y., Johnson, C.V., Dobner, P.R., and Lawrence, J.B. (1993). Higher-level organization of individual gene transcription and RNA splicing. Science 259, 1326-1330.
65. Xing, Y., Johnson, C.V., Moen, P.T., Jr., McNeil, J.A., and Lawrence, J.B. (1995). Nonrandom gene organization: structural arrangements of specific pre-mRNA transcription and splicing with SC-35 domains. J. Cell Biol. 131, 1635-1647.
66. Zirbel, R.M., Mathieu, U.R., Kurz, A., Cremer, T., and Lichter, P. (1993). Evidence for a nuclear compartment of transcription and splicing located at chromosome domain boundaries. Chromosome Res. 1, 93-106.