Organization of chromatin in the interphase mammalian cell

Micron

Volumn 36, Issue 2, 2005, Pages 95-108

  Dehghani, Hesam ^a   Dellaire, Graham ^a   Bazett Jones, David P ^a,b  

^a HOSPITAL FOR SICK CHILDREN RESEARCH INSTITUTE   (Canada)

^b UNIVERSITY OF TORONTO   (Canada)

Author keywords

Chromatin; Chromosome; Electron spectroscopic imaging; Imaging techniques; Interphase; Models; Nucleus

Indexed keywords

CELL BIOLOGY; CHROMATIN; ELECTRON SPECTROSCOPIC IMAGING (ESI); FLUORESCENCE MICROSCOPY;

CELLS; CHROMOSOMES; ELECTRON SPECTROSCOPY; IMAGING TECHNIQUES; STRUCTURE (COMPOSITION); TRANSMISSION ELECTRON MICROSCOPY;

CYTOLOGY;

DNA;

ANIMAL; CHROMATIN; ELECTRON MICROSCOPY; ERYTHROCYTE; HUMAN; INTERPHASE; METHODOLOGY; PHYSIOLOGY; REVIEW; ULTRASTRUCTURE;

ANIMALS; CHROMATIN; DNA; ERYTHROCYTES; HUMANS; INTERPHASE; MICROSCOPY, ELECTRON;

EUKARYOTA; MAMMALIA;

EID: 11144321432     PISSN: 09684328     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.micron.2004.10.003     Document Type: Review

References (88)

1. R. Abranches, A.F. Beven, L. Aragon-Alcaide, and P.J. Shaw Transcription sites are not correlated with chromosome territories in wheat nuclei Journal of Cell Biology 143 1 1998 5 12
2. K. Ahmad, and S. Henikoff Epigenetic consequences of nucleosome dynamics Cell 111 3 2002 281 284
3. K. Ahmad, and S. Henikoff The histone variant H3.3 marks active chromatin by replication-independent nucleosome assembly Molecular Cell 9 6 2002 1191 1200
4. D.P. Bazett-Jones, and M.J. Hendzel Electron spectroscopic imaging of chromatin Methods 17 2 1999 188 200
5. A.S. Belmont, and K. Bruce Visualization of G1 chromosomes: a folded, twisted, supercoiled chromonema model of interphase chromatid structure Journal of Cell Biology 127 2 1994 287 302
6. A.S. Belmont, S. Dietzel, A.C. Nye, Y.G. Strukov, and T. Tumbar Large-scale chromatin structure and function Current Opinion in Cell Biology 11 3 1999 307 311
7. W. Bernhard A new staining procedure for electron microscopical cytology Journal of Ultrastructure Research 27 3 1969 250 265
8. F.M. Boisvert, M.J. Hendzel, and D.P. Bazett-Jones Promyelocytic leukemia (PML) nuclear bodies are protein structures that do not accumulate RNA Journal of Cell Biology 148 2 2000 283 292
9. S. Boyle, S. Gilchrist, J.M. Bridger, N.L. Mahy, J.A. Ellis, and W.A. Bickmore The spatial organization of human chromosomes within the nuclei of normal and emerin-mutant cells Human Molecular Genetetics 10 3 2001 211 219
10. J.M. Bridger, S. Boyle, I.R. Kill, and W.A. Bickmore Re-modelling of nuclear architecture in quiescent and senescent human fibroblasts Current Biology 10 3 2000 149 152
11. C.J. Brown, A. Ballabio, J.L. Rupert, R.G. Lafreniere, M. Grompe, R. Tonlorenzi, and H.F. Willard A gene from the region of the human X inactivation centre is expressed exclusively from the inactive X chromosome Nature 349 1991 38 44
12. K.E. Brown, S.S. Guest, S.T. Smale, K. Hahm, M. Merkenschlager, and A.G. Fisher Association of transcriptionally silent genes with Ikaros complexes at centromeric heterochromatin Cell 91 1997 845 854
13. D.E. Comings The rationale for an ordered arrangement of chromatin in the interphase nucleus American Journal of Human Genetics 20 5 1968 440 460
14. T. Cremer, and C. Cremer Chromosome territories, nuclear architecture and gene regulation in mammalian cells. Nature reviews Genetics 2 4 2001 292 301
15. T. Cremer, C. Cremer, T. Schneider, H. Baumann, L. Hens, and M. Kirsch-Volders Analysis of chromosome positions in the interphase nucleus of Chinese hamster cells by laser-UV-microirradiation experiments Human Genetetics 62 3 1982 201 209
16. T. Cremer, A. Kurz, R. Zirbel, S. Dietzel, B. Rinke, E. Schrock, M.R. Speicher, U. Mathieu, A. Jauch, and P. Emmerich Role of chromosome territories in the functional compartmentalization of the cell nucleus Cold Spring Harbor Symposia on Quantitative Biology 58 1993 777 792
17. T. Cremer, G. Kreth, H. Koester, R.H. Fink, R. Heintzmann, M. Cremer, I. Solovei, D. Zink, and C. Cremer Chromosome territories, interchromatin domain compartment, and nuclear matrix: an integrated view of the functional nuclear architecture Critical Reviews in Eukaryotic Gene Expression 10 2 2000 179 212
18. J.A. Croft, J.M. Bridger, S. Boyle, P. Perry, P. Teague, and W.A. Bickmore Differences in the localization and morphology of chromosomes in the human nucleus Journal of Cell Biology 145 6 1999 1119 1131
19. H.G. Davies, and J.V. Small Structural units in chromatin and their orientation on membranes Nature 217 134 1968 1122 1125
20. H.G. Davies, and M. Spencer The variation in the structure of erythrocyte nuclei with fixation Journal of Cell Biology 14 1962 445 458
21. G. Dellaire, R. Nisman, and D.P. Bazett-Jones Correlative light and electron spectroscopic imaging of chromatin in situ Methods in Enzymology 375 2004 456 478
22. A.F. Dernburg, K.W. Broman, J.C. Fung, W.F. Marshall, J. Philips, D.A. Agard, and J.W. Sedat Perturbation of nuclear architecture by long-distance chromosome interactions Cell 85 1996 745 759
23. E. De Robertis Electron microscopic observations on the submicroscopic morphology of the meiotic nucleus and chromosomes The Journal of Biophysical and Biochemical Cytology 2 6 1956 785 796
24. S. Dietzel, K. Schiebel, G. Little, P. Edelmann, G.A. Rappold, R. Eils, C. Cremer, and T. Cremer The 3D positioning of ANT2 and ANT3 genes within female X chromosome territories correlates with gene activity Experimental Cell Research 252 2 1999 363 375
25. S. Fakan Perichromatin fibrils are in situ forms of nascent transcripts Trends in Cell Biology 4 3 1994 86 90
26. S. Fakan, G. Leser, and T.E. Martin Ultrastructural distribution of nuclear ribonucleoproteins as visualized by immunocytochemistry on thin sections Journal of Cell Biology 98 1 1984 358 363
27. A.L. Fisher, and M. Caudy Groucho proteins: transcriptional corepressors for specific subsets of DNA-binding transcription factors in vertebrates and invertebrates Genes and Development 12 13 1998 1931 1940
28. C. Francastel, M.C. Walters, M. Groudine, and D.I.K. Martin A functional enhancer suppresses silencing of a transgene and prevents its localization close to centromeric heterochromatin Cell 99 1999 259 269
29. J. Gall Chromosome fibers from an interphase nucleus Science 139 1963 120 121
30. I.K. Greaves, W. Rens, M.A. Ferguson-Smith, D. Griffin, and J.A. Marshall Graves Conservation of chromosome arrangement and position of the X in mammalian sperm suggests functional significance Chromosome Research 11 5 2003 503 512
31. S.I. Grewal, and D. Moazed Heterochromatin and epigenetic control of gene expression Science 301 5634 2003 798 802
32. J.D. Griffith, and G. Christiansen Electron microscope visualization of chromatin and other DNA-protein complexes Annual Review of Biophysics and Bioengineering 7 1978 19 35
33. A.D. Hollenbach, J.E. Sublett, C.J. McPherson, and G. Grosveld The Pax3-FKHR oncoprotein is unresponsive to the Pax3-associated repressor hDaxx EMBO Journal 18 13 1999 3702 3711
34. A. Kurz, S. Lampel, J.E. Nickolenko, J. Bradl, A. Benner, R.M. Zirbel, T. Cremer, and P. Lichter Active and inactive genes localize preferentially in the periphery of chromosome territories Journal of Cell Biology 135 5 1996 1195 1205
35. J.T. Lee, L.S. Davidow, and D. Warshawsky Tsix, a gene antisense to Xist at the X-inactivation centre Nature Genetics 21 1999 400 404
36. Y. Li, J.R. Danzer, P. Alvarez, A.S. Belmont, and L.L. Wallrath Effects of tethering HP1 to euchromatic regions of the Drosophila genome Development 130 9 2003 1817 1824
37. P. Lichter, and T. Cremer Chromosome analysis by non-isotopic in situ hybridization D.E. Rooney B.H. Czepulkowski Human Cytogenetics - A Practical Approach 1992 IRL Oxford 157 192
38. P. Lichter, T. Cremer, J. Borden, L. Manuelidis, and D.C. Ward Delineation of individual human chromosomes in metaphase and interphase cells by in situ suppression hybridization using recombinant DNA libraries Human Genetics 80 3 1988 224 234
39. N.L. Mahy, P.E. Perry, and W.A. Bickmore Gene density and transcription influence the localization of chromatin outside of chromosome territories detectable by FISH Journal of Cell Biology 159 5 2002 753 763
40. N.L. Mahy, P.E. Perry, S. Gilchrist, R.A. Baldock, and W.A. Bickmore Spatial organization of active and inactive genes and noncoding DNA within chromosome territories Journal of Cell Biology 157 4 2002 579 589
41. C. Maison, D. Bailly, A.H. Peters, J.P. Quivy, D. Roche, A. Taddei, M. Lachner, T. Jenuwein, and G. Almouzni Higher-order structure in pericentric heterochromatin involves a distinct pattern of histone modification and an RNA component Nature Genetics 30 3 2002 329 334
42. M. Malecki, A. Hsu, L. Truong, and S. Sanchez Molecular immunolabeling with recombinant single-chain variable fragment (scFv) antibodies designed with metal-binding domains Proceedings of the National Academy of Sciences of the United States of America 99 1 2002 213 218
43. R. Marmorstein Protein modules that manipulate histone tails for chromatin regulation. Nature reviews Molecular Cell Biology 2 6 2001 422 432
44. W.F. Marshall, A.F. Dernburg, B. Harmon, D.A. Agard, and J.W. Sedat Specific interactions of chromatin with the nuclear envelope: positional determination within the nucleus in Drosophila melanogaster Molecular Biology of the Cell 7 5 1996 825 842
45. G. Mascetti, S. Carrara, and L. Vergani Relationship between chromatin compactness and dye uptake for in situ chromatin stained with DAPI Cytometry 44 2001 113 119
46. M.D. Meneghini, M. Wu, and H.D. Madhani Conserved histone variant H2A.Z protects euchromatin from the ectopic spread of silent heterochromatin Cell 112 5 2003 725 736
47. A.E. Mirsky, and H. Ris The composition and structure of isolated chromosomes The Journal of General Physiology 34 5 1951 475 492
48. G. Mizuguchi, X. Shen, J. Landry, W.H. Wu, S. Sen, and C. Wu ATP-driven exchange of histone H2AZ variant catalyzed by SWR1 chromatin remodeling complex Science 303 5656 2004 343 348
49. A. Monneron, and W. Bernhard Fine structural organization of the interphase nucleus in some mammalian cells Journal of Ultrastructure Research 27 3 1969 266 288
50. A. Myc, F. Traganos, J. Lara, M.R. Melamed, and Z. Darzynkiewicz Unstainable DNA in cell nuclei Cytometry 13 1992 389 394
51. R. Nagele, T. Freeman, L. McMorrow, and H.Y. Lee Precise spatial positioning of chromosomes during prometaphase: evidence for chromosomal order Science 270 5243 1995 1831 1835
52. R.E. Nash, E. Puvion, and W. Bernhard Perichromatin fibrils as components of rapidly labeled extranucleolar RNA Journal of Ultrastructure Research 53 3 1975 395 405
53. R. Nisman, G. Dellaire, Y. Ren, R. Li, and D.P. Bazett-Jones Application of quantum dots as probes for correlative fluorescence, conventional, and energy-filtered transmission electron microscopy The Journal of Histochemistry and Cytochemistry: Official Journal of the Histochemistry Society 52 1 2004 13 18
54. M. Nogami, A. Kohda, H. Taguchi, M. Nakao, T. Ikemura, and K. Okumura Relative locations of the centromere and imprinted SNRPN gene within chromosome 15 territories during the cell cycle in HL60 cells Journal of Cell Science 113 12 2000 2157 2165
55. D.E. Olins, and A.L. Olins Physical studies of isolated eucaryotic nuclei Journal of Cell Biology 53 3 1972 715 736
56. A.L. Olins, and D.E. Olins Spheroid chromatin units (ν bodies) Science 183 122 1974 330 332
57. D.E. Olins, and A.L. Olins Chromatin history: our view from the bridge. Nature reviews Molecular Cell Biology 4 10 2003 809 814
58. P. Oudet, M. Gross-Bellard, and P. Chambon Electron microscopic and biochemical evidence that chromatin structure is a repeating unit Cell 4 4 1975 281 300
59. M. Pal-Bhadra, B.A. Leibovitch, S.G. Gandhi, M. Rao, U. Bhadra, J.A. Birchler, and S.C. Elgin Heterochromatic silencing and HP1 localization in Drosophila are dependent on the RNAi machinery Science 303 5658 2004 669 672
60. R.J. Palstra, B. Tolhuis, E. Splinter, R. Nijmeijer, F. Grosveld, and W. de Laat The beta-globin nuclear compartment in development and erythroid differentiation Nature Genetics 35 2 2003 190 194
61. P. Petrov, and W. Bernhard Experimentally induced changes of extranucleolar ribonucleoprotein components of the interphase nucleus Journal of Ultrastructure Research 35 3 1971 386 402
62. R.D. Phair, and T. Misteli High mobility of proteins in the mammalian cell nucleus Nature 404 6778 2000 604 609
63. E. Puvion, A. Viron, and F.X. Xu High resolution autoradiographical detection of RNA in the interchromatin granules of DRB-treated cells Experimental Cell Research 152 2 1984 357 367
64. C. Rabl Über Zelltheilung Morphol. Jahrbuch 10 1885 214 330
65. T. Ragoczy, A. Telling, T. Sawado, M. Groudine, and S.T. Kosak A genetic analysis of chromosome territory looping: diverse roles for distal regulatory elements Chromosome Research 11 5 2003 513 525
66. Y. Ren, M.J. Kruhlak, and D.P. Bazett-Jones Same serial section correlative light and energy-filtered transmission electron microscopy The Journal of Histochemistry and Cytochemistry: Official Journal of the Histochemistry Society 51 5 2003 605 612
67. H. Ris, and D.F. Kubai Chromosome structure Annual Review of Genetics 4 1970 263 294
68. M.S. Santisteban, M.P. Montmasson, F. Giroud, X. Ronot, and G. Brugal Fluorescence image cytometry of nuclear DNA content versus chromatin pattern: a comparative study of ten fluorochromes The Journal of Histochemistry and Cytochemistry: Official Journal of the Histochemistry Society 40 11 1992 1789 1797
69. A. Saveliev, C. Everett, T. Sharpe, Z. Webster, and R. Festenstein DNA triplet repeats mediate heterochromatin-protein-1-sensitive variegated gene silencing Nature 422 6934 2003 909 913
70. D.L. Spector, X.D. Fu, and T. Maniatis Associations between distinct pre-mRNA splicing components and the cell nucleus EMBO Journal 10 11 1991 3467 3481
71. S.M. Stack, D.B. Brown, and W.C. Dewey Visualization of interphase chromosomes Journal of Cell Science 26 1977 281 299
72. G.S. Stein, J.B. Lian, A.J. van Wijnen, J.L. Stein, A. Javed, M. Montecino, S.K. Zaidi, D. Young, J.Y. Choi, S. Gutierrez, and S. Pockwinse Nuclear microenvironments support assembly and organization of the transcriptional regulatory machinery for cell proliferation and differentiation Journal of Cellular Biochemistry 91 2 2004 287 302
73. A. Taddei, C. Maison, D. Roche, and G. Almouzni Reversible disruption of pericentric heterochromatin and centromere function by inhibiting deacetylases Nature Cell Biology 3 2 2001 114 120
74. J. Tajbakhsh, H. Luz, H. Bornfleth, S. Lampel, C. Cremer, and P. Lichter Spatial distribution of GC- and AT-rich DNA sequences within human chromosome territories Experimental Cell Research 255 2 2000 229 237
75. G. Thiel, M. Lietz, and M. Hohl How mammalian transcriptional repressors work European Journal of Biochemistry 271 2004 2855 2862
76. A. Verdel, S. Jia, S. Gerber, T. Sugiyama, S. Gygi, S.I. Grewal, and D. Moazed RNAi-mediated targeting of heterochromatin by the RITS complex Science 303 5658 2004 672 676
77. P.J. Verschure, I. van der Kraan, E.M. Manders, and R. van Driel Spatial relationship between transcription sites and chromosome territories Journal of Cell Biology 147 1 1999 13 24
78. P.J. Verschure, I. van der Kraan, E.M. Manders, D. Hoogstraten, A.B. Houtsmuller, and R. van Driel Condensed chromatin domains in the mammalian nucleus are accessible to large macromolecules EMBO Reports 4 9 2003 861 866
79. A.E. Visser, R. Eils, A. Jauch, G. Little, P.J. Bakker, T. Cremer, and J.A. Aten Spatial distributions of early and late replicating chromatin in interphase chromosome territories Experimental Cell Research 243 2 1998 398 407
80. E.V. Volpi, E. Chevret, T. Jones, R. Vatcheva, J. Williamson, S. Beck, R.D. Campbell, M. Goldsworthy, S.H. Powis, J. Ragoussis, J. Trowsdale, and D. Sheer Large-scale chromatin organization of the major histocompatibility complex and other regions of human chromosome 6 and its response to interferon in interphase nuclei Journal of Cell Science 113 9 2000 1565 1576
81. C. Weierich, A. Brero, S. Stein, J. von Hase, C. Cremer, T. Cremer, and I. Solovei Three-dimensional arrangements of centromeres and telomeres in nuclei of human and murine lymphocytes Chromosome Research 11 5 2003 485 502
82. R.R.E. Williams, S. Board, D. Sheer, and J. Ragoussis Subchromosomal positioning of the epidermal differentiation complex (EDC) in keratinocyte and lymphoblast interphase nuclei Experimental Cell Research 272 2002 163 175
83. S. Wischnitzer The submicroscopic morphology of the interphase nucleus International Review of Cytology 34 1973 1 48
84. S.L. Wolfe The fine structure of isolated chromosomes Journal of Ultrastructure Research 12 1965 104 112
85. S.L. Wolfe, and P.G. Martin The ultrastructure and strandedness of chromosomes from two species of Vicia Experimental Cell Research 50 1 1968 140 150
86. C.L. Woodcock Ultrastructure of inactive chromatin Journal of Cell Biology 59 1973 368a
87. C.L. Woodcock, J.P. Safer, and J.E. Stanchfield Structural repeating units in chromatin. I. Evidence for their general occurrence Experimental Cell Research 97 1976 101 110
88. C.L. Woodcock, H.E. Sweetman, and L.L. Frado Structural repeating units in chromatin. II. Their isolation and partial characterization Experimental Cell Research 97 1976 111 119