Gene dynamics and nuclear architecture during differentiation

Differentiation

Volumn 76, Issue 1, 2008, Pages 41-56

  Schöfer, Christian ^a   Weipoltshammer, Klara ^a  

^a Medical University of Vienna   (Austria)

Author keywords

Chromatin organization; Chromosome territory; Gene expression; Nuclear structure; Transcription

Indexed keywords

DNA METHYLTRANSFERASE;

CELL COMPARTMENTALIZATION; CELL DIFFERENTIATION; CELL NUCLEUS; CELL NUCLEUS MEMBRANE; CHROMATIN; CONFERENCE PAPER; CYTOARCHITECTURE; GENE ACTIVATION; GENE CONTROL; GENE EXPRESSION; GENE INTERACTION; GENE SILENCING; GENE TRANSLOCATION; GENETIC ANALYSIS; HETEROCHROMATIN; NONHUMAN; PRIORITY JOURNAL; TRANSCRIPTION INITIATION;

EID: 38149053614     PISSN: 03014681     EISSN: 14320436     Source Type: Journal    
DOI: 10.1111/j.1432-0436.2007.00218.x     Document Type: Conference Paper

References (150)

1. Albiez, H., Cremer, M., Tiberi, C., Vecchio, L., Schermelleh, L., Dittrich, S., Kupper, K., Joffe, B., Thormeyer, T., von Hase, J., Yang, S., Rohr, K., Leonhardt, H., Solovei, I., Cremer, C., Fakan, S. Cremer, T. (2006) Chromatin domains and the interchromatin compartment form structurally defined and functionally interacting nuclear networks. Chromosome Res 14 : 707 733.
2. Andrulis, E.D., Neiman, A.M., Zappulla, D.C. Sternglanz, R. (1998) Perinuclear localization of chromatin facilitates transcriptional silencing. Nature 394 : 592 595.
3. Arsuaga, J., Greulich-Bode, K.M., Vazquez, M., Bruckner, M., Hahnfeldt, P., Brenner, D.J., Sachs, R. Hlatky, L. (2004) Chromosome spatial clustering inferred from radiogenic aberrations. Int J Radiat Biol 80 : 507 515.
4. Bacher, C.P., Guggiari, M., Brors, B., Augui, S., Clerc, P., Avner, P., Eils, R. Heard, E. (2006) Transient colocalization of X-inactivation centres accompanies the initiation of X inactivation. Nat Cell Biol 8 : 293 299.
5. Bartova, E., Kozubek, S., Jirsova, P., Kozubek, M., Gajova, H., Lukasova, E., Skalnikova, M., Ganova, A., Koutna, I. Hausmann, M. (2002) Nuclear structure and gene activity in human differentiated cells. J Struct Biol 139 : 76 89.
6. Bartova, E., Krejci, J., Harnicarova, A. Kozubek, S. (2007) Differentiation of human embryonic stem cells induces condensation of chromosome territories and formation of heterochromatin protein 1 foci. Differentiation DOI :.
7. Berezney, R. Coffey, D.S. (1977) Nuclear matrix: isolation and characterization of a framework structure from rat liver nuclei. J Mol Biol 73 : 616 637.
8. Biggiogera, M., Cisterna, B., Spedito, A., Vecchio, L. Malatesta, M. (2007) Perichromatin fibrils as early markers of transcriptional alterations. Differentiation DOI :.
9. Blobel, G. (1985) Gene gating: a hypothesis. Proc Natl Acad Sci USA 82 : 8527 8529.
10. Bolzer, A., Kreth, G., Solovei, I., Koehler, D., Saracoglu, K., Fauth, C., Muller, S., Eils, R., Cremer, C., Speicher, M.R. Cremer, T. (2005) Three-dimensional maps of all chromosomes in human male fibroblast nuclei and prometaphase rosettes. PLoS Biol 3 : 826 842.
11. Boveri, T. (1909) Die Blastomerenkerne von Ascaris megalocephala und die Theorie der Chromosomenindividualität. Archiv Zellforschung 3 : 181 286.
12. Boyle, S., Gilchrist, S., Bridger, J.M., Mahy, N.L., Ellis, J.A. Bickmore, W.A. (2001) The spatial organization of human chromosomes within the nuclei of normal and emerin-mutant cells. Hum Mol Genet 10 : 211 219.
13. Branco, M.R. Pombo, A. (2006) Intermingling of chromosome territories in interphase suggests role in translocations and transcription-dependent associations. PLoS Biol 4 : e138.
14. Branco, M.R. Pombo, A. (2007) Chromosome organization: new facts, new models. Trends Cell Biol 17 : 127 134.
15. Brero, A., Easwaran, H.P., Nowak, D., Grunewald, I., Cremer, T., Leonhardt, H. Cardoso, M.C. (2005) Methyl CpG-binding proteins induce large-scale chromatin reorganization during terminal differentiation. J Cell Biol 169 : 733 743.
16. Brickner, D.G., Cajigas, I., Fondufe-Mittendorf, Y., Ahmed, S., Lee, P.C., Widom, J. Brickner, J.H. (2007) H2A.Z-mediated localization of genes at the nuclear periphery confers epigenetic memory of previous transcriptional state. PLoS Biol 5 : e81.
17. Brickner, J.H. Walter, P. (2004) Gene recruitment of the activated INO1 locus to the nuclear membrane. PLoS Biol 2 : e342.
18. Brown, J.M., Leach, J., Reittie, J.E., Atzberger, A., Lee-Prudhoe, J., Wood, W.G., Higgs, D.R., Iborra, F.J. Buckle, V.J. (2006) Coregulated human globin genes are frequently in spatial proximity when active. J Cell Biol 172 : 177 187.
19. Brown, K.E., Amoils, S., Horn, J.M., Buckle, V.J., Higgs, D.R., Merkenschlager, M. Fisher, A.G. (2001) Expression of alpha- and beta-globin genes occurs within different nuclear domains in haemopoietic cells. Nat Cell Biol 3 : 602 606.
20. Brown, K.E., Guest, S.S., Smale, S.T., Hahm, K., Merkenschlager, M. Fisher, A.G. (1997) Association of transcriptionally silent genes with Ikaros complexes at centromeric heterochromatin. Cell 91 : 845 854.
21. Cabal, G.G., Genovesio, A., Rodriguez-Navarro, S., Zimmer, C., Gadal, O., Lesne, A., Buc, H., Feuerbach-Fournier, F., Olivo-Marin, J.C., Hurt, E.C. Nehrbass, U. (2006) SAGA interacting factors confine sub-diffusion of transcribed genes to the nuclear envelope. Nature 441 : 770 773.
22. Caron, H., van Schaik, B., van der Mee, M., Baas, F., Riggins, G., van Sluis, P., Hermus, M.C., van Asperen, R., Boon, K., Voute, P.A., Heisterkamp, S., van Kampen, A. Versteeg, R. (2001) The human transcriptome map: clustering of highly expressed genes in chromosomal domains. Science 291 : 1289 1292.
23. Carpenter, A.E., Memedula, S., Plutz, M.J. Belmont, A.S. (2005) Common effects of acidic activators on large-scale chromatin structure and transcription. Mol Cell Biol 25 : 958 968.
24. Casolari, J.M., Brown, C.R., Drubin, D.A., Rando, O.J. Silver, P.A. (2005) Developmentally induced changes in transcriptional program alter spatial organization across chromosomes. Genes Dev 19 : 1188 1198.
25. Casolari, J.M., Brown, C.R., Komili, S., West, J., Hieronymus, H. Silver, P.A. (2004) Genome-wide localization of the nuclear transport machinery couples transcriptional status and nuclear organization. Cell 117 : 427 439.
26. Chambeyron, S. Bickmore, W.A. (2004a) Chromatin decondensation and nuclear reorganization of the HoxB locus upon induction of transcription. Genes Dev 18 : 1119 1130.
27. Chambeyron, S. Bickmore, W.A. (2004b) Does looping and clustering in the nucleus regulate gene expression? Curr Opin Cell Biol 16 : 256 262.
28. Chambeyron, S., Da Silva, N.R., Lawson, K.A. Bickmore, W.A. (2005) Nuclear re-organisation of the Hoxb complex during mouse embryonic development. Development 132 : 2215 2223.
29. Chuang, C.H., Carpenter, A.E., Fuchsova, B., Johnson, T., de Lanerolle, P. Belmont, A.S. (2006) Long-range directional movement of an interphase chromosome site. Curr Biol 16 : 825 831.
30. Chubb, J.R., Boyle, S., Perry, P. Bickmore, W.A. (2002) Chromatin motion is constrained by association with nuclear compartments in human cells. Curr Biol 12 : 439 445.
31. Cisterna, B., Necchi, D., Prosperi, E. Biggiogera, M. (2006) Small ribosomal subunits associate with nuclear myosin and actin in transit to the nuclear pores. Faseb J 20 : 1901 1903.
32. Clemson, C.M., Hall, L.L., Byron, M., McNeil, J. Lawrence, J.B. (2006) The X chromosome is organized into a gene-rich outer rim and an internal core containing silenced nongenic sequences. Proc Natl Acad Sci USA 103 : 7688 7693.
33. Cmarko, D., Verschure, P.J., Martin, T.E., Dahmus, M.E., Krause, S., Fu, X.D., van Driel, R. Fakan, S. (1999) Ultrastructural analysis of transcription and splicing in the cell nucleus after bromo-UTP microinjection. Mol Biol Cell 10 : 211 223.
34. Cohen, B.A., Mitra, R.D., Hughes, J.D. Church, G.M. (2000) A computational analysis of whole-genome expression data reveals chromosomal domains of gene expression. Nat Genet 26 : 183 186.
35. Cook, P.R. (2002) Predicting three-dimensional genome structure from transcriptional activity. Nat Genet 32 : 347 352.
36. Cremer, M., von Hase, J., Volm, T., Brero, A., Kreth, G., Walter, J., Fischer, C., Solovei, I., Cremer, C. Cremer, T. (2001) Non-random radial higher-order chromatin arrangements in nuclei of diploid human cells. Chromosome Res 9 : 541 567.
37. Cremer, T., Cremer, M., Dietzel, S., Muller, S., Solovei, I. Fakan, S. (2006) Chromosome territories - a functional nuclear landscape. Curr Opin Cell Biol 18 : 307 316.
38. Cremer, T., Kurz, A., Zirbel, R.M., Dietzel, S., Rinke, B., Schröck, E., Speicher, M.R., Mathieu, U., Jauch, A., Emmerich, P., Scherthan, H., Ried, T., Cremer, C. Lichter, P. (1993) Role of chromosome territories in the functional compartmentalization of the cell nucleus. Cold Spring Harbour Sympos Quant Biol 58 : 777 792.
39. Croft, J.A., Bridger, J.M., Boyle, S., Perry, P., Teague, P. Bickmore, W.A. (1999) Differences in the localization and morphology of chromosomes in the human nucleus. J Cell Biol 145 : 1119 1131.
40. Dehghani, H., Dellaire, G. Bazett-Jones, D.P. (2005) Organization of chromatin in the interphase mammalian cell. Micron 36 : 95 108.
41. Dekker, J., Rippe, K., Dekker, M. Kleckner, N. (2002) Capturing chromosome conformation. Science 295 : 1306 1311.
42. de Laat, W. Grosveld, F. (2003) Spatial organization of gene expression: the active chromatin hub. Chromosome Res 11 : 447 459.
43. Dellaire, G., Nisman, R. Bazett-Jones, D.P. (2004) Correlative light and electron spectroscopic imaging of chromatin in situ. Methods Enzymol 375 : 456 478.
44. Dernburg, A.F., Broman, K.W., Fung, J.C., Marshall, W.F., Philips, J., Agard, D.A. Sedat, J.W. (1996) Perturbation of nuclear architecture by long-distance chromosome interactions. Cell 85 : 745 759.
45. Dickinson, P., Cook, P.R. Jackson, D.A. (1990) Active RNA polymerase I is fixed within the nucleus of HeLa cells. EMBO 9 : 2207 2214.
46. Dietzel, S., Schiebel, K., Little, G., Edelmann, P., Rappold, G.A., Eils, R., Cremer, C. Cremer, T. (1999) The 3D positioning of ANT2 and ANT3 genes within female X chromosome territories correlates with gene activity. Exp Cell Res 252 : 363 375.
47. Dostie, J., Richmond, T.A., Arnaout, R.A., Selzer, R.R., Lee, W.L., Honan, T.A., Rubio, E.D., Krumm, A., Lamb, J., Nusbaum, C., Green, R.D. Dekker, J. (2006) Chromosome conformation capture carbon copy (5C): a massively parallel solution for mapping interactions between genomic elements. Genome Res 16 : 1299 1309.
48. Espada, J., Ballestar, E., Fraga, M.F., Villar-Garea, A., Juarranz, A., Stockert, J.C., Robertson, K.D., Fuks, F. Esteller, M. (2004) Human DNA methyltransferase 1 is required for maintenance of the histone H3 modification pattern. J Biol Chem 279 : 37175 37184.
49. Espada, J., Ballestar, E., Santoro, R., Fraga, M.F., Villar-Garea, A., Nemeth, A., Lopez-Serra, L., Ropero, S., Aranda, A., Orozco, H., Moreno, V., Juarranz, A., Stockert, J.C., Langst, G., Grummt, I., Bickmore, W. Esteller, M. (2007) Epigenetic disruption of ribosomal RNA genes and nucleolar architecture in DNA methyltransferase 1 (Dnmt1) deficient cells. Nucleic Acids Res 35 : 2191 2198.
50. Fakan, S. Bernhard, W. (1973) Nuclear labelling after prolonged 3H-uridine incorporation as visualized by high resolution autoradiography. Exp Cell Res 79 : 431 444.
51. Francastel, C., Magis, W. Groudine, M. (2001) Nuclear relocation of a transactivator subunit precedes target gene activation. Proc Natl Acad Sci USA 98 : 12120 12125.
52. Fraser, P. (2006) Transcriptional control thrown for a loop. Curr Opin Genet Dev 16 : 490 495.
53. Gerlich, D., Beaudouin, J., Kalbfuss, B., Daigle, N., Eils, R. Ellenberg, J. (2003) Global chromosome positions are transmitted through mitosis in mammalian cells. Cell 112 : 751 764.
54. Gilbert, N., Boyle, S., Fiegler, H., Woodfine, K., Carter, N.P. Bickmore, W.A. (2004) Chromatin architecture of the human genome: gene-rich domains are enriched in open chromatin fibers. Cell 118 : 555 566.
55. Gilbert, N., Boyle, S., Sutherland, H., de Las Heras, J., Allan, J., Jenuwein, T. Bickmore, W.A. (2003) Formation of facultative heterochromatin in the absence of HP1. Embo J 22 : 5540 5550.
56. Gilbert, N., Thomson, I., Boyle, S., Allan, J., Ramsahoye, B. Bickmore, W.A. (2007) DNA methylation affects nuclear organization, histone modifications, and linker histone binding but not chromatin compaction. J Cell Biol 177 : 401 411.
57. Goldman, R.D., Gruenbaum, Y., Moir, R.D., Shumaker, D.K. Spann, T.P. (2002) Nuclear lamins: building blocks of nuclear architecture. Genes Dev 16 : 533 547.
58. Gotzmann, J. Foisner, R. (1999) Lamins and lamin-binding proteins in functional chromatin organization. Crit Rev Eukaryot Gene Expr 9 : 257 265.
59. Grimaud, C., Bantignies, F., Pal-Bhadra, M., Ghana, P., Bhadra, U. Cavalli, G. (2006) RNAi components are required for nuclear clustering of Polycomb group response elements. Cell 124 : 957 971.
60. Hancock, R. (2004) Internal organisation of the nucleus: assembly of compartments by macromolecular crowding and the nuclear matrix model. Biol Cell 96 : 595 601.
61. Harmon, B. Sedat, J. (2005) Cell-by-cell dissection of gene expression and chromosomal interactions reveals consequences of nuclear reorganization. PLoS Biol 3 : e67.
62. Harnicarova, A., Kozubek, S., Pachernik, J., Krejci, J. Bartova, E. (2006) Distinct nuclear arrangement of active and inactive c-myc genes in control and differentiated colon carcinoma cells. Exp Cell Res 312 : 4019 4035.
63. Hlatky, L., Sachs, R.K., Vazquez, M. Cornforth, M.N. (2002) Radiation-induced chromosome aberrations: insights gained from biophysical modeling. Bioessays 24 : 714 723.
64. Hofmann, W.A., Johnson, T., Klapczynski, M., Fan, J.L. de Lanerolle, P. (2006) From transcription to transport: emerging roles for nuclear myosin I. Biochem Cell Biol 84 : 418 426.
65. Hutchison, N. Weintraub, H. (1985) Localization of DNAase I-sensitive sequences to specific regions of interphase nuclei. Cell 43 : 471 482.
66. Iborra, F.J. (2007) Can visco-elastic phase separation, macromolecular crowding and colloidal physics explain nuclear organisation? Theor Biol Med Model 4 : 15.
67. Iborra, F.J., Pombo, A., McManus, J., Jackson, D.A. Cook, P.R. (1996) The topology of transcription by immobilized polymerases. Exp Cell Res 229 : 167 173.
68. Jackson, D.A. Cook, P.R. (1985) Transcription occurs at a nucleoskeleton. EMBO 4 : 919 925.
69. Jackson, D.A., Hassan, A.B., Errington, R.J. Cook, P.R. (1993) Visualization of focal sites of transcription within human nuclei. EMBO J 12 : 1059 1065.
70. Kioussis, D. (2005) Gene regulation: kissing chromosomes. Nature 435 : 579 580.
71. Klose, R.J., Kallin, E.M. Zhang, Y. (2006) JmjC-domain-containing proteins and histone demethylation. Nat Rev Genet 7 : 715 727.
72. Kosak, S.T. Groudine, M. (2004) Form follows function: the genomic organization of cellular differentiation. Genes Dev 18 : 1371 1384.
73. Kosak, S.T., Skok, J.A., Medina, K.L., Riblet, R., Le Beau, M.M., Fisher, A.G. Singh, H. (2002) Subnuclear compartmentalization of immunoglobulin loci during lymphocyte development. Science 296 : 158 162.
74. Koutna, I., Krontorad, P., Svoboda, Z., Bartova, E., Kozubek, M. Kozubek, S. (2007) New insights into gene positional clustering and its properties supported by large-scale analysis of various differentiation pathways. Genomics 89 : 81 88.
75. Kupper, K., Kolbl, A., Biener, D., Dittrich, S., von Hase, J., Thormeyer, T., Fiegler, H., Carter, N.P., Speicher, M.R., Cremer, T. Cremer, M. (2007) Radial chromatin positioning is shaped by local gene density, not by gene expression. Chromosoma 116 : 285 306.
76. Kuroda, M., Tanabe, H., Yoshida, K., Oikawa, K., Saito, A., Kiyuna, T., Mizusawa, H. Mukai, K. (2004) Alteration of chromosome positioning during adipocyte differentiation. J Cell Sci 117 : 5897 5903.
77. Kurukuti, S., Tiwari, V.K., Tavoosidana, G., Pugacheva, E., Murrell, A., Zhao, Z., Lobanenkov, V., Reik, W. Ohlsson, R. (2006) CTCF binding at the H19 imprinting control region mediates maternally inherited higher-order chromatin conformation to restrict enhancer access to Igf2. Proc Natl Acad Sci USA 103 : 10684 10689.
78. Kurz, A., Lampel, S., Nickolenko, J.E., Bradl, J., Benner, A., Zirbel, R.M., Cremer, T. Lichter, P. (1996) Active and inactive genes localize preferentially in the periphery of chromosome territories. J Cell Biol 135 : 1195 1205.
79. Lachner, M., O'Carroll, D., Rea, S., Mechtler, K. Jenuwein, T. (2001) Methylation of histone H3 lysine 9 creates a binding site for HP1 proteins. Nature 410 : 116 120.
80. Lanctot, C., Cheutin, T., Cremer, M., Cavalli, G. Cremer, T. (2007) Dynamic genome architecture in the nuclear space: regulation of gene expression in three dimensions. Nat Rev Genet 8 : 104 115.
81. Mahy, N.L., Perry, P.E. Bickmore, W.A. (2002a) Gene density and transcription influence the localization of chromatin outside of chromosome territories detectable by FISH. J Cell Biol 159 : 753 763.
82. Mahy, N.L., Perry, P.E., Gilchrist, S., Baldock, R.A. Bickmore, W.A. (2002b) Spatial organization of active and inactive genes and noncoding DNA within chromosome territories. J Cell Biol 157 : 579 589.
83. Maison, C. Almouzni, G. (2004) HP1 and the dynamics of heterochromatin maintenance. Nat Rev Mol Cell Biol 5 : 296 304.
84. Malhas, A., Lee, C.F., Sanders, R., Saunders, N.J. Vaux, D.J. (2007) Defects in lamin B1 expression or processing affect interphase chromosome position and gene expression. J Cell Biol 176 : 593 603.
85. Manuelidis, L. (1984) Different central nervous system cell types display distinct and nonrandom arrangements of satellite DNA sequences. Proc Natl Acad Sci USA 81 : 3123 3127.
86. Manuelidis, L. Borden, J. (1988) Reproducible compartmentalization of individual chromosome domains in human CNS cells revealed by in situ hybridization and 3-D reconstruction. Chromosoma 96 : 397 410.
87. Marenduzzo, D., Faro-Trindade, I. Cook, P.R. (2007) What are the molecular ties that maintain genomic loops? Trends Genet 23 : 126 133.
88. Margalit, A., Brachner, A., Gotzmann, J., Foisner, R. Gruenbaum, Y. (2007) Barrier-to-autointegration factor - a BAFfling little protein. Trends Cell Biol 17 : 202 208.
89. Marshall, W.F., Straight, A., Marko, J.F., Swedlow, J., Dernburg, A., Belmont, A., Murray, A.W., Agard, D.A. Sedat, J.W. (1997) Interphase chromosomes undergo constrained diffusional motion in living cells. Curr Biol 7 : 930 939.
90. Masny, P.S., Bengtsson, U., Chung, S.A., Martin, J.H., van Engelen, B., van der Maarel, S.M. Winokur, S.T. (2004) Localization of 4q35.2 to the nuclear periphery: is FSHD a nuclear envelope disease? Hum Mol Genet 13 : 1857 1871.
91. McManus, K.J., Stephens, D.A., Adams, N.M., Islam, S.A., Freemont, P.S. Hendzel, M.J. (2006) The transcriptional regulator CBP has defined spatial associations within interphase nuclei. PLoS Comput Biol 2 : 1271 1283.
92. Meaburn, K.J., Cabuy, E., Bonne, G., Levy, N., Morris, G.E., Novelli, G., Kill, I.R. Bridger, J.M. (2007) Primary laminopathy fibroblasts display altered genome organization and apoptosis. Aging Cell 6 : 139 153.
93. Meaburn, K.J., Levy, N., Toniolo, D. Bridger, J.M. (2005) Chromosome positioning is largely unaffected in lymphoblastoid cell lines containing emerin or A-type lamin mutations. Biochem Soc Trans 33 : 1438 1440.
94. Menon, B.B., Sarma, N.J., Pasula, S., Deminoff, S.J., Willis, K.A., Barbara, K.E., Andrews, B. Santangelo, G.M. (2005) Reverse recruitment: the Nup84 nuclear pore subcomplex mediates Rap1/Gcr1/Gcr2 transcriptional activation. Proc Natl Acad Sci USA 102 : 5749 5754.
95. Morey, C., Da Silva, N.R., Perry, P. Bickmore, W.A. (2007) Nuclear reorganisation and chromatin decondensation are conserved, but distinct, mechanisms linked to Hox gene activation. Development 134 : 909 919.
96. Murrell, A., Heeson, S. Reik, W. (2004) Interaction between differentially methylated regions partitions the imprinted genes Igf2 and H19 into parent-specific chromatin loops. Nat Genet 36 : 889 893.
97. Neusser, M., Schubel, V., Koch, A., Cremer, T. Muller, S. (2007) Evolutionarily conserved, cell type and species-specific higher order chromatin arrangements in interphase nuclei of primates. Chromosoma 116 : 307 320.
98. Osborne, C.S., Chakalova, L., Brown, K.E., Carter, D., Horton, A., Debrand, E., Goyenechea, B., Mitchell, J.A., Lopes, S., Reik, W. Fraser, P. (2004) Active genes dynamically colocalize to shared sites of ongoing transcription. Nat Genet 36 : 1065 1071.
99. Parada, L.A., Roix, J.J. Misteli, T. (2003) An uncertainty principle in chromosome positioning. Trends Cell Biol 13 : 393 396.
100. Park, P.C. De Boni, U. (1996) Transposition of DNase hypersensitive chromatin to the nuclear periphery coincides temporally with nerve growth factor-induced up-regulation of gene expression in PC12 cells. Proc Natl Acad Sci USA 93 : 11646 11651.
101. Pederson, T. (2000) Half a century of "the nuclear matrix." Mol Biol Cell 11 : 799 805.
102. Pestic-Dragovich, L., Stojiljkovic, L., Philimonenko, A.A., Nowak, G., Ke, Y., Settlage, R.E., Shabanowitz, J., Hunt, D.F., Hozak, P. de Lanerolle, P. (2000) A myosin I isoform in the nucleus. Science 290 : 337 341.
103. Peters, A.H.F.M., ÓCarroll, D., Scherthan, H., Mechtler, K., Sauer, S., Schöfer, C., Weipoltshammer, K., Pagani, M., Lachner, M., Kohlmaier, A., Opravil, S., Doyle, M. Jenuwein, T. (2001) Loss of the Suv39h histone methyltransferases impairs mammalian heterochromatin and genome stability. Cell 107 : 323 337.
104. Philimonenko, V.V., Zhao, J., Iben, S., Dingova, H., Kysela, K., Kahle, M., Zentgraf, H., Hofmann, W.A., de Lanerolle, P., Hozak, P. Grummt, I. (2004) Nuclear actin and myosin I are required for RNA polymerase I transcription. Nat Cell Biol 6 : 1165 1172.
105. Pickersgill, H., Kalverda, B., de Wit, E., Talhout, W., Fornerod, M. van Steensel, B. (2006) Characterization of the Drosophila melanogaster genome at the nuclear lamina. Nat Genet 38 : 1005 1014.
106. Pombo, A., Ferreira, J., Bridge, E. Carmo-Fonseca, M. (1994) Adenovirus replication and transcription sites are spatially separated in the nucleus of infected cells. Embo J 13 : 5075 5085.
107. Ragoczy, T., Bender, M.A., Telling, A., Byron, R. Groudine, M. (2006) The locus control region is required for association of the murine beta-globin locus with engaged transcription factories during erythroid maturation. Genes Dev 20 : 1447 1457.
108. Saccone, S., Federico, C. Bernardi, G. (2002) Localization of the gene-richest and the gene-poorest isochores in the interphase nuclei of mammals and birds. Gene 300 : 169 178.
109. Sarma, N.J., Haley, T.M., Barbara, K.E., Buford, T.D., Willis, K.A. Santangelo, G.M. (2007) Glucose-responsive regulators of gene expression in Saccharomyces cerevisiae function at the nuclear periphery via a reverse recruitment mechanism. Genetics 175 : 1127 1135.
110. Scheuermann, M.O., Tajbakhsh, J., Kurz, A., Saracoglu, K., Eils, R. Lichter, P. (2004) Topology of genes and nontranscribed sequences in human interphase nuclei. Exp Cell Res 301 : 266 279.
111. Schmid, M., Arib, G., Laemmli, C., Nishikawa, J., Durussel, T. Laemmli, U.K. (2006) Nup-PI: the nucleopore-promoter interaction of genes in yeast. Mol Cell 21 : 379 391.
112. Schöfer, C., Janácek, J., Weipoltshammer, K., Pourani, J. Hozak, P. (2004) Mapping of cellular compartments based on ultrastructural immunogold labeling. J Struct Biol 147 : 128 135.
113. Schübeler, D., Francastel, C., Cimbora, D.M., Reik, A., Martin, D.I.K. Groudine, M. (2000) Nuclear localization and histone acetylation: a pathway for chromatin opening and transcriptional activation of the human β-globin locus. Genes Dev 14 : 940 950.
114. Shi, Y., Lan, F., Matson, C., Mulligan, P., Whetstine, J.R., Cole, P.A. Casero, R.A. (2004) Histone demethylation mediated by the nuclear amine oxidase homolog LSD1. Cell 119 : 941 953.
115. Shopland, L.S., Lynch, C.R., Peterson, K.A., Thornton, K., Kepper, N., Hase, J., Stein, S., Vincent, S., Molloy, K.R., Kreth, G., Cremer, C., Bult, C.J. O'Brien, T.P. (2006) Folding and organization of a contiguous chromosome region according to the gene distribution pattern in primary genomic sequence. J Cell Biol 174 : 27 38.
116. Simeone, A., Acampora, D., Arcioni, L., Andrews, P.W., Boncinelli, E. Mavilio, F. (1990) Sequential activation of HOX2 homeobox genes by retinoic acid in human embryonal carcinoma cells. Nature 346 : 763 766.
117. Simonis, M., Klous, P., Splinter, E., Moshkin, Y., Willemsen, R., de Wit, E., van Steensel, B. de Laat, W. (2006) Nuclear organization of active and inactive chromatin domains uncovered by chromosome conformation capture-on-chip (4C). Nat Genet 38 : 1348 1354.
118. Smallwood, A., Esteve, P.O., Pradhan, S. Carey, M. (2007) Functional cooperation between HP1 and DNMT1 mediates gene silencing. Genes Dev 21 : 1169 1178.
119. Smetana, K., Schöfer, C., Mosgöller, W., Wachtler, F., Schwarzacher, H.G., Jiraskova, I. Ochs, R. (1993) Cytochemistry of satellite nucleoli in human lymphocytes. Acta Histochem 95 : 228 231.
120. Spilianakis, C.G., Lalioti, M.D., Town, T., Lee, G.R. Flavell, R.A. (2005) Interchromosomal associations between alternatively expressed loci. Nature 435 : 637 645.
121. Splinter, E., Heath, H., Kooren, J., Palstra, R.J., Klous, P., Grosveld, F., Galjart, N. de Laat, W. (2006) CTCF mediates long-range chromatin looping and local histone modification in the beta-globin locus. Genes Dev 20 : 2349 2354.
122. Sullivan, G.J., Bridger, J.M., Cuthbert, A.P., Newbold, R.F., Bickmore, W.A. McStay, B. (2001) Human acrocentric chromosomes with transcriptionally silent nucleolar organizer regions associate with nucleoli. EMBO J 20 : 2867 2874.
123. Sun, H.B., Shen, J. Yokota, H. (2000) Size-dependent positioning of human chromosomes in interphase nuclei. Biophys J 79 : 184 190.
124. Tachibana, M., Sugimoto, K., Fukushima, T. Shinkai, Y. (2001) Set domain-containing protein, G9a, is a novel lysine-preferring mammalian histone methyltransferase with hyperactivity and specific selectivity to lysines 9 and 27 of histone H3. J Biol Chem 276 : 25309 25317.
125. Taddei, A., Hediger, F., Neumann, F.R., Bauer, C. Gasser, S.M. (2004) Separation of silencing from perinuclear anchoring functions in yeast Ku80, Sir4 and Esc1 proteins. Embo J 23 : 1301 1312.
126. Taddei, A., Van Houwe, G., Hediger, F., Kalck, V., Cubizolles, F., Schober, H. Gasser, S.M. (2006) Nuclear pore association confers optimal expression levels for an inducible yeast gene. Nature 441 : 774 778.
127. Thomson, I., Gilchrist, S., Bickmore, W.A. Chubb, J.R. (2004) The radial positioning of chromatin is not inherited through mitosis but is established de novo in early G1. Curr Biol 14 : 166 172.
128. Tumbar, T. Belmont, A.S. (2001) Interphase movements of a DNA chromosome region modulated by VP16 transcriptional activator. Nat Cell Biol 3 : 134 139.
129. Verschure, P.J., van der Kraan, I., Manders, E.M.M. van Driel, R. (1999) Spatial relationship between transcription sites and chromosome territories. J Cell Biol 147 : 13 24.
130. Visser, A.E., Jaunin, F., Fakan, S. Aten, J.A. (2000) High resolution analysis of interphase chromosome domains. J Cell Sci 113 : 2585 2593.
131. Vlcek, S. Foisner, R. (2007) Lamins and lamin-associated proteins in aging and disease. Curr Opin Cell Biol 19 : 298 304.
132. Volpi, E.V., Chevret, E., Jones, T., Vatcheva, R., Williamson, J., Beck, S., Campbell, R.D., Goldsworthy, M., Powis, S.H., Ragoussis, J., Trowsdale, J. Sheer, D. (2000) 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 : 1565 1576.
133. Vreugde, S., Ferrai, C., Miluzio, A., Hauben, E., Marchisio, P.C., Crippa, M.P., Bussi, M. Biffo, S. (2006) Nuclear myosin VI enhances RNA polymerase II-dependent transcription. Mol Cell 23 : 749 755.
134. Wachtler, F., Schöfer, C., Mosgöller, W., Weipoltshammer, K., Schwarzacher, H.G., Guichaoua, M., Hartung, M., Stahl, A., Berge-Lefranc, J.L., Gonzalez, I. Sylvester, J. (1992) Human Ribosomal RNA gene repeats are localized in the dense fibrillar component of nucleoli: light and electron microscopic in situ hybridization in human sertoli cells. Exp Cell Res 198 : 135 143.
135. Walter, H. Brooks, D.E. (1995) Phase separation in cytoplasm, due to macromolecular crowding, is the basis for microcompartmentation. FEBS Lett 361 : 135 139.
136. Walter, J., Schermelleh, L., Cremer, M., Tashiro, S. Cremer, T. (2003) Chromosome order in HeLa cells changes during mitosis and early G1, but is stably maintained during subsequent interphase stages. J Cell Biol 160 : 685 697.
137. Wansink, D.G., Schul, W., van der Kraan, I., van Steensel, B., van Driel, R. de Jong, L. (1993) Fluorescent labeling of nascent RNA reveals transcription by RNA polymerase Ii in domains scattered throughout the nucleus. J Cell Biol 122 : 283 293.
138. Wanzenböck, E.M., Schöfer, C., Schweizer, D. Bachmair, A. (1997) Ribosomal transcription units integrated via t-DNA transformation associate with the nucleolus and do not require upstream repeat sequences for activity in Arabidopsis thaliana. Plant J 11 : 1007 1016.
139. Waye, J.S. Willard, H.F. (1989) Concerted evolution of alpha satellite DNA: evidence for species specificity and a general lack of sequence conservation among alphoid sequences of higher primates. Chromosoma 98 : 273 279.
140. Weipoltshammer, K., Schöfer, C., Almeder, M., Philimonenko, V.V., Frei, K., Wachtler, F. Hozak, P. (1999) Intranuclear anchoring of repetitive DNA sequences: centromeres, telomeres, and ribosomal DNA. J Cell Biol 147 : 1409 1418.
141. Weipoltshammer, K., Schöfer, C., Almeder, M., Sylvester, J. Wachtler, F. (1996) Spatial distribution of sex chromosomes and ribosomal genes: a study on human lymphocytes and testicular cells. Cytogenet Cell Genet 73 : 108 113.
142. Wiesmeijer, K., Krouwels, I.M., Tanke, H.J. Dirks, R.W. (2007) Chromatin movement visualized with photoactivable GFP-labeled H4. Differentiation DOI :.
143. Williams, R.R., Azuara, V., Perry, P., Sauer, S., Dvorkina, M., Jorgensen, H., Roix, J., McQueen, P., Misteli, T., Merkenschlager, M. Fisher, A.G. (2006) Neural induction promotes large-scale chromatin reorganisation of the Mash1 locus. J Cell Sci 119 : 132 140.
144. Williams, R.R., Broad, S., Sheer, D. Ragoussis, J. (2002) Subchromosomal positioning of the epidermal differentiation complex (EDC) in keratinocyte and lymphoblast interphase nuclei. Exp Cell Res 272 : 163 175.
145. Wissmann, M., Yin, N., Muller, J.M., Greschik, H., Fodor, B.D., Jenuwein, T., Vogler, C., Schneider, R., Gunther, T., Buettner, R., Metzger, E. Schule, R. (2007) Cooperative demethylation by JMJD2C and LSD1 promotes androgen receptor-dependent gene expression. Nat Cell Biol 9 : 347 353.
146. Xie, X., Mikkelsen, T.S., Gnirke, A., Lindblad-Toh, K., Kellis, M. Lander, E.S. (2007) Systematic discovery of regulatory motifs in conserved regions of the human genome, including thousands of CTCF insulator sites. Proc Natl Acad Sci USA 104 : 7145 7150.
147. Xu, N., Tsai, C.L. Lee, J.T. (2006) Transient homologous chromosome pairing marks the onset of X inactivation. Science 311 : 1149 1152.
148. Zhao, Z., Tavoosidana, G., Sjolinder, M., Gondor, A., Mariano, P., Wang, S., Kanduri, C., Lezcano, M., Sandhu, K.S., Singh, U., Pant, V., Tiwari, V., Kurukuti, S. Ohlsson, R. (2006) Circular chromosome conformation capture (4C) uncovers extensive networks of epigenetically regulated intra- and interchromosomal interactions. Nat Genet 38 : 1341 1347.
149. Zink, D., Amaral, M.D., Englmann, A., Lang, S., Clarke, L.A., Rudolph, C., Alt, F., Luther, K., Braz, C., Sadoni, N., Rosenecker, J. Schindelhauer, D. (2004) Transcription-dependent spatial arrangements of CFTR and adjacent genes in human cell nuclei. J Cell Biol 166 : 815 825.
150. Zirbel, R.M., Mathieu, U.R., Kurz, A., Cremer, T. Lichter, P. (1993) Evidence for a nuclear compartment of transcription and splicing located at chromosome domain boundaries. Chromosome Res 1 : 93 106.