Higher order chromatin architecture in the cell nucleus: On the way from structure to function

Biology of the Cell

Volumn 96, Issue 8, 2004, Pages 555-567

  Cremer, Thomas ^a   Küpper, Katrin ^a   Dietzel, Steffen ^a   Fakan, Stanislav ^b  

^a UNIVERSITY OF MUNICH   (Germany)

^b UNIVERSITY OF LAUSANNE   (Switzerland)

Author keywords

Chromatin domain; Chromosome territory; Electron microscopy; Fluorescence in situ hybridization; Interchromatin compartment; Interchromatin granule cluster; Live cell microscopy; Perichromatin fibril

Indexed keywords

CELL NUCLEUS; CHROMATIN; CHROMATIN STRUCTURE; CHROMOSOME; CYTOARCHITECTURE; ELECTRON MICROSCOPY; FLUORESCENCE MICROSCOPY; GENETIC TRANSCRIPTION; HUMAN; NONHUMAN; PRIORITY JOURNAL; REVIEW; RNA SPLICING;

EID: 9444281491     PISSN: 02484900     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.biolcel.2004.07.002     Document Type: Short Survey

References (111)

1. B. Alberts A. Johnson J. Lewis M. Raff K. Roberts P. Walter Molecular Biology of the Cell 2002 Garland Publishing Inc New York and London
2. B. Albrecht A.V. Failla A. Schweitzer C. Cremer Spatially modulated illumination microscopy allows axial distance resolution in the nanometer range Appl. Opt. 41 2002 80-87
3. G.S. Baird D.A. Zacharias R.Y. Tsien Biochemistry, mutagenesis, and oligomerization of DsRed, a red fluorescent protein from coral Proc. Natl. Acad. Sci. USA 97 2000 11984-11989
4. A. Belmont Dynamics of chromatin, proteins, and bodies within the cell nucleus Curr. Opin. Cell. Biol. 15 2003 304-310
5. A.S. Belmont Large-scale chromatin structure. In: C. Nicolini (Ed.). Genome structure and function 1997 Kluwer Academic Publishers Dordrecht, The Netherlands 261-278
6. A.S. Belmont K. Bruce Visualization of G1 chromosomes: A folded, twisted, supercoiled chromonema model of interphase chromatid structure J. Cell Biol. 127 1994 287-302
7. A.S. Belmont S. Dietzel A.C. Nye Y.G. Strukov T. Tumbar Large-scale chromatin structure and function Curr. Opin. Cell Biol. 11 1999 307-311
8. A.S. Belmont A.F. Straight In vivo visualization of chromosomes using lac operator-repressor binding Trends Cell Biol. 8 1998 121-124
9. R. Berezney D.D. Dubey J.A. Huberman Heterogeneity of eukaryotic replicons, replicon clusters, and replication foci Chromosoma 108 2000 471-484
10. H. Bornfleth K. Sätzler R. Eils C. Cremer High precision distance measurements and volume-conserving segmentation of objects near and below the resolution limit in three-dimensional confocal fluorescence microscopy J. Microsc. 189 1998 118-136
11. J.M. Bridger P. Lichter. In: W.A. Bickmore (Ed.) Chromosome structural analysis: A practical approach 1999 Oxford University Press 209
12. J.H. Bull P. Harnden Efficient nuclear FISH on paraffin-embedded tissue sections using microwave pretreatment Biotechniques 26 1999 416-418
13. B. Burke C.L. Stewart Life at the edge: The nuclear envelope and human disease Nat. Rev. Mol. Cell Biol. 3 2002 575-585
14. K.C. Carter K.L. Taneja J.B. Lawrence Discrete nuclear domains of poly(A) RNA and their relationship to the functional organization of the nucleus J. Cell Biol. 115 1991 1191-1202
15. D. Chen S. Huang Nucleolar components involved in ribosome biogenesis cycle between the nucleolus and nucleoplasm in interphase cells J. Cell Biol. 153 2001 169-176
16. T. Cheutin A.J. McNairn T. Jenuwein D.M. Gilbert P.B. Singh T. Misteli Maintenance of stable heterochromatin domains by dynamic HP1 binding Science 299 2003 721-725
17. J.R. Chubb W.A. Bickmore Considering nuclear compartmentalization in the light of nuclear dynamics Cell 112 2003 403-406
18. J.R. Chubb S. Boyle P. Perry W.A. Bickmore Chromatin motion is constrained by association with nuclear compartments in human cells Curr. Biol. 12 2002 439-445
19. C.V. Clevenger A.L. Epstein Identification of a nuclear protein component of interchromatin granules using a monoclonal antibody and immunogold electron microscopy Exp. Cell Res. 151 1984 194-207
20. D. Cmarko P.J. Verschure T.E. Martin M.E. Dahmus S. Krause X.D. Fu et al. Ultrastructural analysis of transcription and splicing in the cell nucleus after bromo-UTP microinjection Mol. Biol. Cell 10 1999 211-223
21. D. Cmarko P.J. Verschure A.P. Otte R. Van Driel S. Fakan Polycomb group gene silencing proteins are concentrated in the perichromatin compartment of the mammalian nucleus J. Cell Sci. 116 2003 335-343
22. D.L. Court J.A. Sawitzke L.C. Thomason Genetic engineering using homologous recombination Annu. Rev. Genet. 36 2002 361-388
23. C. Cremer C. Münkel M. Granzow A. Jauch S. Dietzel R. Eils et al. Nuclear architecture and the induction of chromosomal aberrations Mutat. Res. 366 1996 97-116
24. M. Cremer K. Kupper B. Wagler L. Wizelman J. Von Hase Y. Weiland et al. Inheritance of gene density-related higher order chromatin arrangements in normal and tumor cell nuclei J. Cell Biol. 162 2003 809-820
25. T. Cremer C. Cremer Chromosome territories, nuclear architecture and gene regulation in mammalian cells Nat. Rev. Genet. 2 2001 292-301
26. T. Cremer A. Kurz R. Zirbel S. Dietzel B. Rinke E. Schröck Role of chromosome territories in the functional compartmentalization of the cell nucleus Cold Spring Harb. Symp. Quant. Biol. 58 1993 777-792
27. a S. Dietzel R. Eils K. Sützler H. Bornfleth A. Jauch C. Cremer et al. Evidence against a looped structure of the inactive human X-chromosome territory Exp. Cell Res. 240 1998 187-196
28. b S. Dietzel A. Jauch D. Kienle G. Qu H. Holtgreve-Grez R. Eils et al. Separate and variably shaped chromosome arm domains are disclosed by chromosome arm painting in human cell nuclei Chromosome Res. 6 1998 25-33
29. R.W. Dirks K.C. Daniel A.K. Raap RNAs radiate from gene to cytoplasm as revealed by fluorescence in situ hybridization J. Cell Sci. 108 Pt 7 1995 2565-2572
30. B. Dubertret P. Skourides D.J. Norris V. Noireaux A.H. Brivanlou A. Libchaber In vivo imaging of quantum dots encapsulated in phospholipid micelles Science 298 2002 1759-1762
31. S.R. Dundas S. Boyle C.O. Bellamy W. Hawkins O.J. Garden J.A. Ross et al. Dual Y-chromosome painting and immunofluorescence staining of archival human liver transplant biopsies J. Histochem. Cytochem. 49 2001 1321-1322
32. M. Dundr T. Misteli Functional architecture in the cell nucleus Biochem. J. 356 2001 297-310
33. M. Dyba S.W. Hell Focal spots of size lambda/23 open up far-field fluorescence microscopy at 33 nm axial resolution Phys. Rev. Lett. 88 2002 163901
34. M. Eriksson W.T. Brown L.B. Gordon M.W. Glynn J. Singer L. Scott et al. Recurrent de novo point mutations in lamin A cause Hutchinson-Gilford progeria syndrome Nature 423 2003 293-298
35. A. Esa A.E. Coleman P. Edelmann S. Silva C.G. Cremer S. Janz Conformational differences in the 3-D nanostructure of the immunoglobulin heavy-chain locus, a hotspot of chromosomal translocations in B lymphocytes Cancer Genet. Cytogenet. 127 2001 168-173
36. C.H. Eskiw D.P. Bazett-Jones The promyelocytic leukemia nuclear body: sites of activity? Biochem. Cell Biol. 80 2002 301-310
37. A.V. Failla U. Spoeri B. Albrecht A. Kroll C. Cremer Nanosizing of fluorescent objects by spatially modulated illumination microscopy Appl. Opt. 41 2002 7275-7283
38. S. Fakan Perichromatin fibrils are in situ forms of nascent transcripts Trends Cell Biol. 4 1994 86-90
39. S. Fakan W. Bernhard Localisation of rapidly and slowly labelled nuclear RNA as visualized by high resolution autoradiography Exp. Cell Res. 67 1971 129-141
40. S. Fakan G. Leser T.E. Martin Ultrastructural distribution of nuclear ribonucleoproteins as visualized by immunocytochemistry on thin sections J. Cell Biol. 98 1984 358-363
41. S. Fakan E. Puvion The ultrastructural visualization of nucleolar and extranucleolar RNA synthesis and distribution Int. Rev. Cytol. 65 1980 255-299
42. S. Fakan E. Puvion G. Sphor Localization and characterization of newly synthesized nuclear RNA in isolate rat hepatocytes Exp. Cell Res. 99 1976 155-164
43. C. Fauth D. Zink Corrigendum Cytometry 52A 2003 56
44. F.S. Fay K.L. Taneja S. Shenoy L. Lifshitz R.H. Singer Quantitative digital analysis of diffuse and concentrated nuclear distributions of nascent transcripts, SC35 and poly(A) Exp. Cell Res. 231 1997 27-37
45. R. Festenstein S.N. Pagakis K. Hiragami D. Lyon A. Verreault B. Sekkali et al. Modulation of heterochromatin protein 1 dynamics in primary Mammalian cells Science 299 2003 719-721
46. S.M. Görisch K. Richter M.O. Scheuermann H. Herrmann P. Lichter Diffusion-limited compartmentalization of mammalian cell nuclei assessed by microinjected macromolecules Exp. Cell Res. 289 2003 282-294
47. Y. Gruenbaum R.D. Goldman R. Meyuhas E. Mills A. Margalit A. Fridkin et al. The nuclear lamina and its functions in the nucleus Int. Rev. Cytol. 226 2003 1-62
48. M.G. Gustafsson D.A. Agard J.W. Sedat I5M: 3D widefield light microscopy with better than 100 nm axial resolution J. Microsc. 195 Pt 1 1999 10-16
49. P. Heun A. Taddei S.M. Gasser From snapshots to moving pictures: New perspectives on nuclear organization Trends Cell Biol. 11 2001 519-525
50. S. Huang T.J. Deerinck M.H. Ellisman D.L. Spector In vivo analysis of the stability and transport of nuclear poly(A) + RNA J. Cell Biol. 126 1994 877-899
51. D.A. Jackson A. Pombo 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 1998 1285-1295
52. D.A. Jackson A.B. Hassan R.J. Errington P.R. Cook Visualization of focal sites of transcription within human nuclei Embo J. 12 1993 1059-1065
53. S.M. Janicki D.L. Spector Nuclear choreography: Interpretations from living cells Curr. Opin. Cell Biol. 15 2003 149-157
54. E.A. Jares-Erijman T.M. Jovin FRET Imaging Nat. Biotechnol. 21 2003 1387-1395
55. F. Jaunin S. Fakan DNA replication and nuclear architecture J. Cell Biochem. 85 2002 1-9
56. F. Jaunin A.E. Visser D. Cmarko J.A. Aten S. Fakan Fine structural in situ analysis of nascent DNA movement following DNA replication Exp. Cell Res. 260 2000 313-323
57. Z. Kam B. Hanser M.G. Gustafsson D.A. Agard J.W. Sedat Computational adaptive optics for live three-dimensional biological imaging Proc. Natl. Acad. Sci. USA 98 2001 3790-3795
58. T. Kanda K.F. Sullivan G.M. Wahl Histone-Gfp fusion protein enables sensitive analysis of chromosome dynamics in living mammalian cells Curr. Biol. 8 1998 377-385
59. H. Kimura P.R. Cook Kinetics of core histones in living human cells: little exchange of H3 and H4 and some rapid exchange of H2B J. Cell Biol. 153 2001 1341-1353
60. T. Kues A. Dickmanns R. Luhrmann R. Peters U. Kubitscheck High intranuclear mobility and dynamic clustering of the splicing factor U1 snRNP observed by single particle tracking Proc. Natl. Acad. Sci. USA 98 2001 12021-12026
61. A.I. Lamond D.L. Spector Nuclear speckles: A model for nuclear organelles Nat. Rev. Mol. Cell Biol. 4 2003 605-612
62. J. Lemke J. Claussen S. Michel I. Chudoba P. Muhlig M. Westermann et al. The DNA-based structure of human chromosome 5 in interphase Am. J. Hum. Genet. 71 2002 1051-1059
63. N.L. Mahy P.E. Perry W.A. Bickmore Gene density and transcription influence the localization of chromatin outside of chromosome territories detectable by FISH J. Cell Biol. 159 2002 753-763
64. N.L. Mahy P.E. Perry S. Gilchrist R.A. Baldock W.A. Bickmore Spatial organization of active and inactive genes and noncoding DNA within chromosome territories J. Cell Biol. 157 2002 579-589
65. M. Malatesta C. Zancanaro T.E. Martin E.K. Chan F. Amalric R. Luhrmann et al. Cytochemical and immunocytochemical characterization of nuclear bodies during hibernation Eur. J. Cell Biol. 65 1994 82-93
66. E.M.M. Manders J. Stap J. Strackee R. Van Driel J.A. Aten Dynamic behavior of DNA replication domains Exp. Cell Res. 226 1996 328-335
67. E.M.M. Manders H. Kimura P.R. Cook Direct imaging of DNA in living cells reveals the dynamics of chromosome formation J. Cell Biol. 144 1999 813-821
68. L. Manuelidis Active nucleolus organizers are precisely positioned in adult central nervous system cells but not in neuroectodermal tumor cells J. Neuropathol. Exp. Neurol. 43 1984 225-241
69. W.F. Marshall Order and disorder in the nucleus Curr. Biol. 12R 2002 185-192
70. T.E. Martin C.S. Okamura Immunocytochemistry of nuclear hnRNP complexes. In: H. Busch (Ed.). The Cell Nucleus, vol. 9 1981 Academic Press New York 119-144
71. G. Martou U. De Boni Nuclear topology of murine, cerebellar Purkinje neurons: Changes as a function of development Exp. Cell Res. 256 2000 131-139
72. J.G. McNally W.G. Muller D. Walker R. Wolford G.L. Hager The glucocorticoid receptor: Rapid exchange with regulatory sites in living cells Science 287 2000 1262-1265
73. T. Misteli J.F. Caceres D.L. Spector The dynamics of a pre-mRNA splicing factor in living cells Nature 387 1997 523-527
74. C. Molenaar A. Abdulle A. Gena H.J. Tanke R.W. Dirks Poly(A) + RNAs roam the cell nucleus and pass through speckle domains in transcriptionally active and inactive cells J. Cell Biol. 165 2004 191-202
75. A. Monneron W. Bernhard Fine structural organization of the interphase nucleus in some mammalian cells J. Ultrastruct. Res. 27 1969 266-288
76. C. Münkel R. Eils S. Dietzel D. Zink C. Mehring G. Wedemann et al. Compartmentalization of interphase chromosomes observed in simulation and experiment J. Mol. Biol. 285 1999 1053-1065
77. R.E. Nash E. Puvion W. Bernhard Perichromatin fibrils as components of rapidly labeled extranucleolar RNA J. Ultrastruct. Res. 53 1975 395-405
78. S.C. Ogg A.I. Lamond Cajal bodies and coilin-moving towards function J. Cell Biol. 159 2002 17-21
79. T. Pederson Dynamics and genome-centricity of interchromatin domains in the nucleus Nat. Cell Biol. 4 2002 E287-E291
80. R.D. Phair T. Misteli High mobility of proteins in the mammalian cell nucleus Nature 404 2000 604-609
81. J.C. Politz E.S. Browne D.E. Wolf T. Pederson Intranuclear diffusion and hybridization state of oligonucleotides measured by fluorescence correlation spectroscopy in living cells Proc. Natl. Acad. Sci. USA 95 1998 6043-6048
82. J.C. Politz R.A. Tuft T. Pederson R.H. Singer Movement of nuclear poly(A) RNA throughout the interchromatin space in living cells Curr. Biol. 9 1999 285-291
83. E. Puvion F. Puvion-Dutilleul Ultrastructure of the nucleus in relation to transcription and splicing: Roles of perichromatin fibrils and interchromatin granules Exp. Cell Res. 229 1996 217-225
84. E. Puvion A. Viron C. Assens E.H. Leduc P. Jeanteur Immunocytochemical identification of nuclear structures containing snRNPs in isolated rat liver cells J. Ultrastruct. Res. 87 1984 180-189
85. C.C. Robinett A. Straight G. Li C. Willhelm G. Sudlow A. Murray et al. In vivo localization of DNA sequences and visualization of large-scale chromatin organization using lac operator/repressor recognition J. Cell Biol. 135 1996 1685-1700
86. L. Schermelleh J. Walter Long term live cell confocal microscopy GIT Imaging Microsc. 4 2002 47-50
87. L. Schmiedeberg K. Weisshart S. Diekmann G. Meyer Zu Hoerste P. Hemmerich High- and low-mobility populations of HP1 in heterochromatin of mammalian cells Mol. Biol. Cell 15 2004 2819-2833
88. G. Seisenberger M.U. Ried T. Endress H. Buning M. Hallek C. Bräuchle Real-time single-molecule imaging of the infection pathway of an adeno-associated virus Science 294 2001 1929-1932
89. Y. Shav-Tal X. Darzacq S.M. Shenoy D. Fusco S.M. Janicki D.L. Spector et al. Dynamics of single mRNPs in nuclei of living cells Science 304 2004 1797-1800
90. R.D. Shelby K.M. Hahn K.F. Sullivan Dynamic elastic behavior of alpha-satellite DNA domains visualized in situ in living human cells J. Cell Biol. 135 1996 545-557
91. L.S. Shopland C.V. Johnson M. Byron J. McNeil J.B. Lawrence Clustering of multiple specific genes and gene-rich R-bands around SC-35 domains: evidence for local euchromatic neighborhoods J. Cell Biol. 162 2003 981-990
92. R.T. Simpson In vivo methods to analyze chromatin structure Curr. Opin. Genet. Dev. 9 1999 225-229
93. I. Solovei A. Cavallo L. Schermelleh F. Jaunin C. Scasselati D. Cmarko et al. Spatial preservation of nuclear chromatin architecture during three-dimensional fluorescence in situ hybridization (3D-FISH) Exp. Cell Res. 276 2002 10-23
94. I. Solovei J. Walter M. Cremer F. Habermann L. Schermelleh T. Cremer Fish on three dimensionally preserved nuclei. In: B. Beatty S. Mai J. Squire (Eds.). FISH: A practical approach 2002 Oxford University Press 119-157
95. I. Solovei N. Grandi R. Knoth B. Volk T. Cremer Postnatal changes of pericentromeric heterochromatin and nucleoli in postmitotic Purkinje cells during murine cerebellum development Cytogenet. Genome Res. 105 2004 302-310
96. D.L. Spector The dynamics of chromosome organization and gene regulation Annu. Rev. Biochem. 72 2003 573-608
97. D.L. Spector W.H. Schrier H. Busch Immunoelectron microscopic localization of snRNPs Biol. Cell 49 1983 1-10
98. D.L. Spector X.D. Fu T. Maniatis Associations between distinct pre-mRNA splicing components and the cell nucleus Embo J. 10 1991 3467-3481
99. P. Sung L. Krejci S. Van Komen M.G. Sehorn Rad51 recombinase and recombination mediators J. Biol. Chem. 278 2003 42729-42732
100. J. Swoger J. Huisken E.H. Stelzer Multiple imaging axis microscopy improves resolution for thick-sample applications Opt. Lett. 28 2003 1654-1656
101. S. Tashiro J. Walter A. Shinohara N. Kamada T. Cremer Rad51 accumulation at sites of DNA damage and in postreplicative chromatin J. Cell Biol 150 2000 283-291
102. A. Trentani P.S. Testillano M.C. Risueno M. Biggiogera Visualization of transcription sites at the electron microscope Eur. J. Histochem. 47 2003 195-200
103. R. Van Driel P.F. Fransz P.J. Verschure The eukaryotic genome: A system regulated at different hierarchical levels J. Cell Sci. 116 2003 4067-4075
104. P.J. Verschure I. Van Der Kraan E.M. Manders D. Hoogstraten A.B. Houtsmuller R. Van Driel Condensed chromatin domains in the mammalian nucleus are accessible to large macromolecules Embo Rep. 4 2003 861-866
105. N. Visa F. Puvion-Dutilleul F. Harper J.P. Bachellerie E. Puvion Intranuclear distribution of poly(A) RNA determined by electron microscope in situ hybridization Exp Cell Res. 208 1993 19-34
106. A.E. Visser F. Jaunin S. Fakan J.A. Aten High resolution analysis of interphase chromosome domains J. Cell Sci. 113 Pt 14 2000 2585-2593
107. E.V. Volpi E. Chevret T. Jones R. Vatcheva J. Williamson S. Beck et al. Large-scale chromatin organization of the major histocompatibility complex and other regions of human chromosome 6 and its response to interferon in interphase nuclei J. Cell Sci. 113 Pt 9 2000 1565-1576
108. D.G. Wansink W. Schul I. Van Der Kraan B. Van Steensel R. Van Driel L. De Jong Fluorescent labeling of nascent RNA reveals transcription by RNA polymerase II in domains scattered throughout the nucleus J. Cell Biol. 122 1993 283-293
109. R.R. Williams S. Broad D. Sheer J. Ragoussis Subchromosomal positioning of the epidermal differentiation complex (EDC) in keratinocyte and lymphoblast interphase nuclei Exp. Cell Res. 272 2002 163-175
110. D. Zink T. Cremer Cell nucleus: Chromosome dynamics in nuclei of living cells Curr. Biol. 8 1998 R321-R324
111. D. Zink T. Cremer R. Saffrich R. Fischer M.F. Trendelenburg W. Ansorge et al. Structure and dynamics of human interphase chromosome territories in vivo Hum. Genet. 102 1998 241-251