The eukaryotic genome: A system regulated at different hierarchical levels

Journal of Cell Science

Volumn 116, Issue 20, 2003, Pages 4067-4075

  van Driel, Roel ^a   Fransz, Paul F ^a   Verschure, Pernette J ^a  

^a UNIVERSITY OF AMSTERDAM   (Netherlands)

Author keywords

Chromatin; Gene expression; Histone code; Nuclear organization

Indexed keywords

DNA; HISTONE;

CELL COMPARTMENTALIZATION; CELL NUCLEUS; CELL STRUCTURE; CHROMATIN STRUCTURE; DNA METHYLATION; EUKARYOTE; GENE ACTIVITY; GENE CLUSTER; GENE CONTROL; GENE EXPRESSION REGULATION; GENE FUNCTION; GENE LOCUS; GENE SEQUENCE; GENETIC ORGANIZATION; GENETIC TRANSCRIPTION; GENOME ANALYSIS; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN MODIFICATION; REGULATORY MECHANISM; REVIEW; TRANSCRIPTION TERMINATION;

ANIMALS; BASE SEQUENCE; CHROMATIN; DNA METHYLATION; EUKARYOTIC CELLS; GENE EXPRESSION REGULATION; GENOME; HISTONES; HUMANS; NUCLEAR MATRIX; PROMOTER REGIONS (GENETICS); TRANSCRIPTION, GENETIC;

EUKARYOTA;

EID: 0242287927     PISSN: 00219533     EISSN: None     Source Type: Journal    
DOI: 10.1242/jcs.00779     Document Type: Review

References (123)

1. Ahmad, K. and Henikoff, S. (2002). Histone H3 variants specify modes of chromatin assembly. Proc. Natl. Acad. Sci. USA 99, 16477-16484.
2. Andrulis, E. D., Neiman, A. M., Zappulla, D. C. and Sternglanz, R. (1998). Perinuclear localization of chromatin facilitates transcriptional silencing. Nature 394, 592-595.
3. Bannister, A. J., Schneider, R. and Kouzarides, T. (2002). Histone methylation: Dynamic or static? Cell 109, 801-806.
4. Belmont, A. S. (2001). Visualizing chromosome dynamics with GFP. Trends Cell Biol. 11, 250-257.
5. Berman, B. P., Nibu, Y., Pfeiffer, B. D., Tomancak, P., Celniker, S. E., Levine, M., Rubin, G. M. and Eisen, M. B. (2002). Exploiting transcription factor binding site clustering to identify cis-regulatory modules involved in pattern formation in the Drosophila genome. Proc. Natl. Acad. Sci. USA 99, 757-762.
6. Blanton, J., Gaszner, M. and Schedl, P. (2003). Protein:protein interactions and the pairing of boundary elements in vivo. Gene Dev. 17, 664-675.
7. Boutanaev, A. M., Kalmykova, A. L, Shevelyou, Y. Y. and Nurminsky, D. I. (2002). Large clusters of co-expressed genes in the Drosophila genome. Nature 420, 666-669.
8. Brown, K. E., Guest, S. S., Smale, S. T., Hahm, K., Merkenschlager, M. and Fisher, A. G. (1997). Association of transcriptionally silent genes with Ikaros complexes at centromeric heterochromatin. Cell 91, 845-854.
9. Brown, K. E., Amoils, S., Horn, J. M., Buckle, V. J., Higgs, D. R., Merkenschlager, M. and 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.
10. Buck, S. W., Sandmeier, J. J. and Smith, J. S. (2002). RNA polymerase I propagates unidirectional spreading of rDNA silent chromatin. Cell 111, 1003-1014.
11. Cao, R., Wang, L. J., Wang, H. B., Xia, L., Erdjument Bromage, H., Tempst, P., Jones, R. S. and Zhang, Y. (2002). Role of histone H3 lysine 27 methylation in polycomb-group silencing. Science 298, 1039-1043.
12. CarmoFonseca, M. (2002). The contribution of nuclear compartmentalization to gene regulation. Cell 108, 513-521.
13. 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. et al. (2001). The human transcriptome map: clustering of highly expressed genes in chromosomal domains. Science 291, 1289-1292.
14. Cmarko, D., Verschure, P. J., Martin, T. E., Dahmus, M. E., Krause, S., Fu, X. D., van Driel, R. and Fakan, S. (1999). Ultrastructural analysis of transcription and splicing in the cell nucleus after bromo-UTP microinjection. Mol. Biol. Cell 10, 211-223.
15. Cmarko, D., Verschure, P. J., Otte, A. P., van Driel, R. and Fakan, S. (2003). Polycomb group gene silencing proteins are concentrated in the perichromatin compartment of the mammalian nucleus. J. Cell Sci. 16, 335-343.
16. Corona, D. F. V., Clapier, C. R., Becker, P. B. and Tamkun, J. W. (2002). Modulation of ISWI function by site-specific histone acetylation. EMBO Rep. 3, 242-247.
17. Cremer, T. and Cremer, C. (2001). Chromosome territories, nuclear architecture and gene regulation in mammalian cells. Nat. Rev. Genet. 2, 292-301.
18. Cremer, M., vonHase, J., Volm, T., Brero, A., Kreth, G., Walter, J., Fischer, C., Solovei, I., Cremer, C. and Cremer, T. (2001). Non-random radial higher-order chromatin arrangements in nuclei of diploid human cells. Chromosome Res. 9, 541-567.
19. Csink, A. K. and Henikoff, S. (1996). Genetic modification of heterochromatic association and nuclear organization in Drosophila. Nature 381, 529-531.
20. Cuvier, O., Hart, C. M., Kas, E. and Laemmli, U. K. (2002). Identification of a multicopy chromatin boundary element at the borders of silenced chromosomal domains. Chromosoma 110, 519-531.
21. Dillon, N. and Sabbattini, P. (2000). Functional gene expression domains: defining the functional unit of eukaryotic gene regulation. BioEssays 22, 657-665.
22. Dreesen, T. D., Henikoff, S. and Loughney, K. (1991). A pairing-sensitive element that mediates trans-inactivation is associated with the Drosophila brown gene. Genes Dev. 5, 331-340.
23. Duncan, I. W. (2002). Transvection effects in Drosophila. Annu. Rev. Genet. 36, 521-556.
24. Eberharter, A. and Becker, P. B. (2002). Histone acetylation: a switch between repressive and permissive chromatin - Second in review series on chromatin dynamics. EMBO Rep. 3, 224-229.
25. Esa, A., Edelmann, P., Kreth, G., Trakhtenbrot, L., Amariglio, N., Rechavi, G., Hausmann, M. and Cremer, C. (2000). Three-dimensional spectral precision distance microscopy of chromatin nanostructures after triple-colour DNA labelling: a study of the BCR region on chromosome 22 and the Philadelphia chromosome. J. Microsc. Oxford 199, 96-105.
26. Fakan, S. (1994). Perichromatin Fibrils are In Situ Forms of Nascent Transcripts. Trends Cell Biol. 4, 86-90.
27. Farrell, C. M., West, A. G. and Felsenfeld, G. (2002). Conserved CTCF insulator elements flank the mouse and human beta-globin loci. Mol. Cell. Biol. 22, 3820-3831.
28. Festenstein, R. and Kioussis, D. (2000). Locus control regions and epigenetic chromatin modifiers. Curr. Opin. Genet. Dev. 10, 199-203.
29. Fisher, A. G. and Merkenschlager, M. (2002). Gene silencing, cell fate and nuclear organisation. Curr. Opin. Genet. Dev. 12, 193-197.
30. Forsberg, E. C. and Bresnick, E. H. (2001). Histone acetylation beyond promoters: long-range acetylation patterns in the chromatin world. BioEssays 23, 820-830.
31. Francastel, C., Walters, M. C., Groudine, M. and Martin, D. I. (1999). A functional enhancer suppresses silencing of a transgene and prevents its localization close to centrometric heterochromatin. Cell 99, 259-269.
32. Francastel, C., Schubeler, D., Martin, D. I. K. and Groudine, M. (2000). Nuclear compartmentalization and gene activity. Nat. Rev. Mol. Cell. Biol. 1, 137-143.
33. Fransz, P., de Jong, J. H., Lysak, M., Castiglione, M. R. and Schubert, I. (2002). Interphase chromosomes in Arabidopsis are organized as well defined chromocenters from which euchromatin loops emanate. Proc. Natl. Acad. Sci. USA 99, 14584-14589.
34. Fung, J. C., Marshall, W. F., Dernburg, A., Agard, D. A. and Sedat, J. W. (1998). Homologous chromosome pairing in Drosophila melanogaster proceeds through multiple independent initiations. J. Cell Biol. 141, 5-20.
35. Gasser, S. M. (2002). Nuclear architecture - Visualizing chromatin dynamics in interphase nuclei. Science 296, 1412-1416.
36. Geiman, T. M. and Robertson, K. D. (2002). Chromatin remodeling, histone modifications, and DNA methylation - How does it all fit together? J. Cell. Biochem. 87, 117-125.
37. Gerasimova, T. I. and Corces, V. G. (2001). Chromatin insulators and boundaries: Effects on transcription and nuclear organization. Annu. Rev. Genet. 35, 193-208.
38. Grandjean, V., O'Neill, L., Sado, T., Turner, B. and Ferguson-Smith, A. (2001). Relationship between DNA methylation, histone H4 acetylation and gene expression in the mouse imprinted Igf2-H19 domain. FEBS Lett. 488, 165-169.
39. Gregory, P. D., Wagner, K. and Horz, W. (2001a). Histone acetylation and chromatin remodeling. Exp. Cell Res. 265, 195-202.
40. Gregory, R. I., Randall, T. E., Johnson, C. A., Khosla, S., Hatada, I., O'Neill, L. P., Turner, B. M. and Feil, R. (2001b). DNA methylation is linked to deacetylation of histone H3, but not H4, on the imprinted genes Snrpn and U2af1-rs1. Mol. Cell. Biol. 21, 5426-5436.
41. Grewal, S. I. S. and Elgin, S. C. (2002). Heterochromatin: new possibilities for the inheritance of structure. Curr. Opin. Genet. Dev. 12, 178-187.
42. Gribnau, J., Diderich, K., Pruzina, S., Calzolari, R. and Fraser, P. (2000). Intergenic transcription and developmental remodeling of chromatin subdomains in the human beta-globin locus. Mol. Cell 5, 377-386.
43. Hall, I. M., Shankaranarayana, G. D., Noma, K. I., Ayoub, N., Cohen, A. and Grewal, S. I. S. (2002). Establishment and maintenance of a heterochromatin domain. Science 297, 2232-2237.
44. Hardison, R. C. (2000). Conserved noncoding sequences are reliable guides to regulatory elements. Trends Genet. 16, 369-372.
45. Hendzel, M. J., Kruhlak, M. J., MacLean, N. A. B., Boisvert, F. M., Lever, M. A. and Bazett-Jones, D. P. (2001). Compartmentalization of regulatory proteins in the cell nucleus. J. Steroid Biochem. Mol. Biol. 76, 9-21.
46. Ho, Y. G., Elefant, F., Cooke, N. and Liebhaber, S. (2002). A defined locus control region determinant links chromatin domain acetylation with long-range gene activation. Mol. Cell 9, 291-302.
47. Horn, P. J., Carruthers, L. M., Logie, C., Hill, D. A., Solomon, M. J., Wade, P. A., Imbalzano, A. N., Hansen, J. C. and Peterson, C. L. (2002). Phosphorylation of linker histones regulates ATP-dependent chromatin remodeling enzymes. Nat. Struct. Biol. 9, 263-267.
48. Im, H., Grass, J. A., Christensen, H. M., Perkins, A. and Bresnick, E. H. (2002). Histone deacetylase-dependent establishment and maintenance of broad low-level histone acetylation within a tissue-specific chromatin domain. Biochemistry 41, 15152-15160.
49. Jackson, J. P., Lindroth, A. M., Cao, X. F. and Jacobsen, S. E. (2002). Control of CpNpG DNA methylation by the KRYPTONITE histone H3 methyltransferase. Nature 416, 556-560.
50. Jenuwein, T. and Allis, C. D. (2001). Translating the histone code. Science 293, 1074-1080.
51. Johnson, L. M., Cao, X. F. and Jacobsen, S. E. (2002). Interplay between two epigenetic marks: DNA methylation and histone H3 lysine 9 methylation. Curr. Biol. 12, 1360-1367.
52. Kano, H., Jakobs, S., Nagorni, M. and Hell, S. W. (2002). Dual-color 4Pi-confocal microscopy with 3D-resolution in the 100 nm range. Ultramicroscopy 90, 207-213.
53. KatanKhaykovich, Y. and Struhl, K. (2002). Dynamics of global histone acetylation and deacetylation in vivo: rapid restoration of normal histone acetylation status upon removal of activators and repressors. Gene Dev. 16, 743-752.
54. Kimura, H. and Cook, P. R. (2001). Kinetics of core histones in living human cells: Little exchange of H3 and H4 and some rapid exchange of H2B. J. Cell Biol. 153, 1341-1353.
55. Kouzarides, T. (2002). Histone methylation in transcriptional control. Curr. Opin. Genet. Dev. 12, 198-209.
56. Labrador, M. and Corces, V. G. (2002). Setting the boundaries of chromatin domains and nuclear organization. Cell 111, 151-154.
57. Lachner, M. and Jenuwein, T. (2002). The many faces of histone lysine methylation. Curr. Opin. Cell Biol. 14, 286-298.
58. Lachner, M., O'Sullivan, R. J. and Jenuwein, T. (2003). An epigenetic road map for histone lysine methylation. J. Cell Sci. 116, 2117-2124.
59. Langst, G. and Becker, P. B. (2001). Nucleosome mobilization and positioning by ISWI-containing chromatin-remodeling factors. J. Cell Sci. 114, 2561-2568.
60. Lercher, M. J., Urrutia, A. O. and Hurst, L. D. (2002). Clustering of housekeeping genes provides a unified model of gene order in the human genome. Nat. Genet. 31, 180-183.
61. Levings, P. P. and Bungert, J. (2002). The human beta-globin locus control region - A center of attraction. Eur. J. Biochem. 269, 1589-1599.
62. Li, Q. L., Harju, S. and Peterson, K. R. (1999). Locus control regions - coming of age at a decade plus. Trends Genet. 15, 403-408.
63. Li, Q. L., Peterson, K. R., Fang, X. D. and Stamatoyannopoulos, G. (2002). Locus control regions. Blood 100, 3077-3086.
64. Mahy, N. L., Perry, P. E. and 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.
65. Mahy, N. L., Perry, P. E., Gilchrist, S., Baldock, R. A. and Bickmore, W. A. (2002b). Spatial organization of active and inactive genes and noncoding DNA within chromosome territories. J. Cell Biol. 157, 579-589.
66. Manders, E. M. M., Visser, A. E., Koppen, A., de Leeuw, W. C., van Liere, R., Brakenhoff, G. J. and van Driel, R. (2003). Four-dimensional imaging of chromatin dynamics during the assembly of the interphase nucleus. Chrom. Res. (in press).
67. Maniatis, T. and Reed, R. (2002). An extensive network of coupling among gene expression machines. Nature 416, 499-506.
68. Marker, C., Zemann, A., Terhorst, T., Kiefmann, M., Kastenmayer, J. P., Green, P., Bachellerie, J. P., Brosius, J. and Huttenhofer, A. (2002). Experimental RNomics: Identification of 140 candidates for small non-messenger RNAs in the plant Arabidopsis thaliana. Curr. Biol. 12, 2002-2013.
69. McPherson, J. D., Marra, M., Hillier, L., Waterston, R. H., Chinwalla, A., Wallis, J., Sekhon, M., Wylie, K., Mardis, E. R., Wilson, R. K. et al. (2001). A physical map of the human genome. Nature 409, 934-941.
70. Memedula, S. and Belmont, A. S. (2003). Sequential Recruitment of HAT and SWI/SNF Components to Condensed Chromatin by VP16. Curr. Biol. 13, 241-246.
71. Meneghini, M. D., Wu, M. and Madhani, H. D. (2003). Conserved histone variant H2A.Z protects euchromatin from the ectopic spread of silent heterochromatin. Cell 112, 725-736.
72. Mishra, R. K. and Karch, F. (1999). Boundaries that demarcate structural and functional domains of chromatin. J. Biosci. 24, 377-399.
73. Mizuguchi, G., Vassilev, A., Tsukiyama, T., Nakatani, Y. and Wu, C. (2001). ATP-dependent nucleosome remodeling and histone hyperacetylation synergistically facilitate transcription of chromatin. J. Biol. Chem. 276, 14773-14783.
74. Muller, J., Hart, C. M., Francis, N. J., Vargas, M. L., Sengupta, A., Wild, B., Miller, E. L., O'Connor, M. B., Kingston, R. E. and Simon, J. A. (2002). Histone methyltransferase activity of a Drosophila polycomb group repressor complex. Cell 111, 197-208.
75. Mural, R. J., Adams, M. D., Myers, E. W., Smith, H. O, Miklos, G. L. G., Wides, R., Halpern, A., Li, P. W., Sutton, G. G., Nadeau, J. et al. (2002). A comparison of whole-genome shotgun-derived mouse chromosome 16 and the human genome. Science 296, 1661-1671.
76. Neely, K. E. and Workman, J. L. (2002). Histone acetylation and chromatin remodeling: which comes first? Mol. Genet. Metab. 76, 1-5.
77. Ng, H. H. and Bird, A. (2000). Histone deacetylases: silencers for hire. Trends Biochem. Sci. 25, 121-126.
78. Nickerson, J. A. (2001). Experimental observations of a nuclear matrix. J. Cell Sci. 114, 463-474.
79. Noma, K., Allis, C. D. and Grewal, S. I. (2001). Transitions in distinct histone H3 methylation patterns at the heterochromatin domain boundaries. Science 293, 1150-1155.
80. Nye, A. C., Rajendran, R. R., Stenoien, D. L., Mancini, M. A., Katzenellenbogen, B. S. and Belmont, A. S. (2002). Alteration of large-scale chromatin structure by estrogen receptor. Mol. Cell. Biol. 22, 3437-3449.
81. O'Brien, T. P., Bult, C. J., Cremer, C., Grunze, M., Knowles, B. B., Langowski, J., McNally, J., Pederson, T., Politz, J. C., Pombo, A. et al. (2003). Genome function and nuclear architecture: from gene expression to nanoscience. Genome Res. 13, 1029-1041.
82. Oliver, B., Parisi, M. and Clark, D. (2002). Gene expression neighborhoods. J. Biol. 1, 4.
83. Pederson, T. (2000). Half a century of 'The nuclear matrix'. Mol. Biol. Cell 11, 799-805.
84. Pederson, T. and Politz, J. C. (2000). The nucleolus and the four ribonucleoproteins of translation. J. Cell Biol. 148, 1091-1095.
85. Peterson, C. L. (2002). Chromatin remodeling enzymes: taming the machines. EMBO Rep. 3, 319-322.
86. Peterson, C. L. (2003). Transcriptional activation: Getting a grip on condensed chromatin. Curr. Biol. 13, R195-R197.
87. Pirrotta, V. (1999). Transvection and chromosomal trans-interaction effects. Biochim. Biophysica Acta Rev. Cancer 1424, M1-M8.
88. Plant, K. E., Routledge, S. J. E. and Proudfoot, N. J. (2001). Intergenic transcription in the human beta-globin gene cluster. Mol. Cell. Biol. 21, 6507-6514.
89. Politz, J. C., Tuft, R. A., Pederson, T. and Singer, R. H. (1999). Movement of nuclear poly(A) RNA throughout the interchromatin space in living cells. Curr. Biol. 9, 285-291.
90. Rank, G., Prestel, M. and Paro, R. (2002). Transcription through intergenic chromosomal memory elements of the Drosophila bithorax complex correlates with an epigenetic switch. Mol. Cell. Biol. 22, 8026-8034.
91. RecillasTarga, F., Pikaart, M. J., BurgessBeusse, B., Bell, A. C., Litt, M. D., West, A. G., Gaszner, M. and Felsenfeld, G. (2002). Position-effect protection and enhancer blocking by the chicken beta- globin insulator are separable activities. Proc. Natl. Acad. Sci. USA 99, 6883-6888.
92. Ridgway, P. and Almouzni, G. (2001). Chromatin assembly and organization. J. Cell Sci. 114, 2711-2712.
93. Roth, S. Y., Denu, J. M. and Allis, C. D. (2001). Histone acetyltransferases. Annu. Rev. Biochem. 70, 81-120.
94. Roy, P. J., Stuart, J. M., Lund, J. and Kim, S. K. (2002). Chromosomal clustering of muscle-expressed genes in Caenorhabditis elegans. Nature 418, 975-979.
95. SantosRosa, H., Schneider, R., Bannister, A. J., Sherriff, J., Bernstein, B. E., Emre, N. C. T., Schreiber, S. L., Mellor, J. and Kouzarides, T. (2002). Active genes are tri-methylated at K4 of histone H3. Nature 419, 407-411.
96. Sass, G. L. and Henikoff, S. (1999). Pairing-dependent mislocalization of a Drosophila brown gene reporter to a heterochromatic environment. Genetics 152, 595-604.
97. Satoh, A., Toyota, M., Itoh, F., Kikuchi, T., Obata, T., Sasaki, Y., Suzuki, H., Yawata, A., Kusano, M., Fujita, M. et al. (2002). DNA methylation and histone deacetylation associated with silencing DAP kinase gene expression in colorectal and gastric cancers. Brit. J. Cancer 86, 1817-1823.
98. Schedl, P. and Broach, J. R. (2003). Making good neighbors: The right fence for the right job. Nat. Struct. Biol. 10, 241-243.
99. Sewalt, R. G. A. B., Lachner, M., Vargas, M., Hamer, K. M., denBlaauwen, J. L., Hendrix, T., Melcher, M., Schweizer, D., Jenuwein, T. and Otte, A. P. (2002). Selective interactions between vertebrate polycomb homologs and the SUV39H1 histone lysine methyltransferase suggest that histone H3-K9 methylation contributes to chromosomal targeting of Polycomb group proteins. Mol. Cell. Biol. 22, 5539-5553.
100. Shabalina, S. A., Ogurtsov, A. Y., Kondrashov, V. A. and Kondrashov, A. S. (2001). Selective constraint in intergenic regions of human and mouse genomes. Trends Genet. 17, 373-376.
101. Soppe, W. J., Jasencakova, Z., Houben, A., Kakutani, T., Meister, A., Huang, M. S., Jacobsen, S. E., Schubert, I. and Fransz, P. F. (2002). DNA methylation controls histone H3 lysine 9 methylation and heterochromatin assembly in Arabidopsis. EMBO J. 21, 6549-6559.
102. Spector, D. L. (2001). Nuclear domains. J. Cell Sci. 114, 2891-2893.
103. Spellman, P. T. and Rubin, G. M. (2002). Evidence for large domains of similarly expressed genes in the Drosophila genome. J. Biol. 1, 5.
104. Strahl, B. D. and Allis, C. D. (2000). The language of covalent histone modifications. Nature 403, 41-45.
105. Surralles, J., Ramirez, M. J., Marcos, R., Natarajan, A. T. and Mullenders, L. H. F. (2002). Clusters of transcription-coupled repair in the human genome. Proc. Natl. Acad. Sci. USA 99, 10571-10574.
106. Tamaru, H. and Selker, E. U. (2001). A histone H3 methyltransferase controls DNA methylation in Neurospora crassa. Nature 414, 277-283.
107. Tanabe, H., Muller, S., Neusser, M., vonHase, J., Calcagno, E., Cremer, M., Solovei, I., Cremer, C. and Cremer, T. (2002). Evolutionary conservation of chromosome territory arrangements in cell nuclei from higher primates. Proc. Natl. Acad. Sci. USA 99, 4424-4429.
108. Tie, F., Furuyama, T., Prasad-Sinha, J., Jane, E. and Harte, P. J. (2001). The Drosophila Polycomb Group proteins ESC and E(Z) are present in a complex containing the histone-binding protein p55 and the histone deacetylase RPD3. Development 128, 275-286.
109. Tumbar, T., Sudlow, G. and Belmont, A. S. (1999). Large-scale chromatin unfolding and remodeling induced by VP16 acidic activation domain. J. Cell Biol. 145, 1341-1354.
110. Turner, B. M. (2002). Cellular memory and the histone code. Cell 111, 285-291.
111. Udvardy, A. (1999). Dividing the empire: boundary chromatin elements delimit the territory of enhancers. EMBO J. 18, 1-8.
112. Ureta Vidal, A., Ettwiller, L. and Birney, E. (2003). Comparative genomics: Genome-wide analysis in metazoan eukaryotes. Nat. Rev. Genet. 4, 251-262.
113. Van der Vlag, J., den Blaauwen, J. L., Sewall, R. G. A. B., van Driel, R. and Otte, A. P. (2000). Transcriptional repression mediated by polycomb group proteins and other chromatin-associated repressors is selectively blocked by insulators. J. Biol. Chem. 275, 697-704.
114. Venter, J. C., Adams, M. D., Myers, E. W., Li, P. W., Mural, R. J., Sutton, G. G., Smith, H. O., Yandell, M., Evans, C. A., Holt, R. A. et al. (2001). The sequence of the human genome. Science 291, 1304-1351.
115. Verschure, P. J., van der Kraan, I., Manders, E. M. and van Driel, R. (1999). Spatial relationship between transcription sites and chromosome territories. J. Cell Biol. 147, 13-24.
116. Verschure, P. J., van Der Kraan, I., Enserink, J. M., Mone, M. J., Manders, E. M. and van Driel, R. (2002). Large-scale chromatin organization and the localization of proteins involved in gene expression in human cells. J. Histochem. Cytochem. 50, 1303-1312.
117. Visser, A. E., Jaunin, F., Fakan, S. and Aten, J. A. (2000). High resolution analysis of interphase chromosome domains. J. Cell Sci. 113, 2585-2593.
118. Volpi, E. V., Chevret, E., Jones, T., Vatcheva, R., Williamson, J., Beck, S., Campbell, R. D., Goldsworthy, M., Powis, S. H., Ragoussis, J. et al. (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.
119. Vyas, P., Vickers, M. A., Simmons, D. L., Ayyub, H., Craddock, C. F. and Higgs, D. R. (1992). Cis-acting sequences regulating expression of the human alpha-globin cluster lie within constitutively open chromatin. Cell 69, 781-793.
120. West, A. G., Gaszner, M. and Felsenfeld, G. (2002). Insulators: many functions, many mechanisms. Gene Dev. 16, 271-288.
121. Wu, C. T. and Morris, J. R. (1999). Transvection and other homology effects. Curr. Opin. Genet. Dev. 9, 237-246.
122. Ye, Q. N., Hu, Y. F., Zhong, H. J., Nye, A. C., Belmont, A. S. and Li, R. (2001). BRCA1-induced large-scale chromatin unfolding and allele-specific effects of cancer-predisposing mutations. J. Cell Biol. 155, 911-921.
123. Zegerman, P., Canas, B., Pappin, D. and Kouzarides, T. (2002). Histone H3 lysine 4 methylation disrupts binding of nucleosome remodeling and deacetylase (NuRD) repressor complex. J. Biol. Chem. 277, 11621-11624.