Transcription factories

Frontiers in Genetics

Volumn 3, Issue OCT, 2012, Pages

  Rieder, Dietmar ^a   Trajanoski, Zlatko ^a   McNally, James G ^b  

^a INNSBRUCK MEDICAL UNIVERSITY   (Austria)

^b NATIONAL CANCER INSTITUTE   (United States)

Author keywords

Factory; Gene clustering; Nucleus; RNA polymerase II; Transcription; Transcription factories

Indexed keywords

EID: 84876112711     PISSN: None     EISSN: 16648021     Source Type: Journal    
DOI: 10.3389/fgene.2012.00221     Document Type: Article

References (92)

1. Becker, M., Baumann, C, John, S., Walker, D. A., Vigneron, M., McNally, J. G., et al. (2002). Dynamic behavior of transcription factors on a natural promoter in living cells. EMBO Rep. 3,1188-1194.
2. Brown, J. M., Green, J., das Neves, R. P., Wallace, H. A. C, Smith, A. J. H., Hughes, J., et al. (2008). Association between active genes occurs at nuclear speckles and is modulated by chromatin environment. j. Cell Biol. 182,1083-1097.
3. Brown, J. M., Leach, J., Reittie, J. E., Atzberger, A., Lee-Prudhoe, J., Wood, W. G., et al. (2006). Coregulated human globin genes are frequently in spatial proximity when active. j. Cell Biol. 172,177-187.
4. Carter, D., Chakalova, L., Osborne, C. S., Dai, Y., and Fraser, P. (2002). Long-range chromatin regulatory interactions in vivo. Nat. Genet. 32, 623-626.
5. Chodosh, L. A., Fire, A., Samuels, M., and Sharp, P. A. (1989). 5, 6-Dichloro-l-beta-D-ribofuranosylbenzimidazole inhibits transcription elongation by RNA polymerase II in vitro. j. Biol. Chem. 264, 2250-2257.
6. Chubb, J. R., Trcek, T., Shenoy, S. M., and Singer, R. H. (2006). Transcriptional pulsing of a developmental gene. Curr. Biol. 16, 1018-1025.
7. Cook, P. R. (2002). Predicting three-dimensional genome structure from transcriptional activity. Nat. Genet. 32,347-352.
8. Cook, P. R. (2010). A model for all genomes: the role of transcription factories. j. Mol. Biol. 395,1-10.
9. Cowell, I. G., Sondka, Z., Smith, K., Lee, K. C, Manville, C. M., Sidorczuk-Lesthuruge, M., et al. (2012). Model for MLL translocations in therapy-related leukemia involving topoisomerase IIβ-mediated DNA strand breaks and gene proximity. Proc. Natl. Acad. Sci. U.S.A. 109, 8989-8994.
10. Darzacq, X., Shav-Tal, Y., Turris, V., de Brody, Y, Shenoy, S. M., Phair, R. D., et al. (2007). In vivo dynamics of RNA polymerase II transcription. Nat. Struct. Mol. Biol. 14, 796-806.
11. Dekker, J., Rippe, K., Dekker, M., and Kleckner, N. (2002). Capturing chromosome conformation. Science 295, 1306-1311.
12. Donnert, G., Keller, J., Medda, R., Andrei, M. A., Rizzoli, S. O., Liihrmann, R., et al. (2006). Macromolecular-scale resolution in biological fluorescence microscopy. Proc. Nail. Acad. Sci. U.S.A. 103, 11440-11445.
13. Dundr, M. (2012). Nuclear bodies: multifunctional companions of the genome. Curr. Opin. Cell Biol. 24, 415-422.
14. Dundr, M., and Misteli, T. (2010). Biogenesis of nuclear bodies. Cold Spring Hark Perspect. Biol. 2, a000711.
15. Eskiw, C. H., and Fraser, P. (2011). Ultrastructural study of transcription factories in mouse erythroblasts. j. Cell Sci. 124, 3676-3683.
16. Eskiw, C. H., Rapp, A., Carter, D. R. E, and Cook, P. R. (2008). RNA poly-merase II activity is located on the surface of protein-rich transcription factories. j. Cell Sci. 121, 1999-2007.
17. Fay, F. S., Taneja, K. L., Shenoy, S., Lif-shitz, L., and Singer, R. H. (1997). Quantitative digital analysis of diffuse and concentrated nuclear distributions of nascent transcripts, SC35 and poly(A). Exp. Cell Res. 231, 27-37.
18. Fedorova, E., and Zink, D. (2009). Nuclear genome organization: common themes and individual patterns. Curr. Opin. Genet. Dev. 19, 166-171.
19. Ferrai, C.,Xie, S. Q.,Luraghi,R, Munari, D., Ramirez, F., Branco, M. R., et al. (2010). Poised transcription factories prime silent uPA gene prior to activation. PLoS Biol. 8, el000270. doi: 10.1371/joumal.pbio.l000270
20. Flicek, P., Amode, M. R., Barrell, D., Beal, K., Brent, S., Carvalho-Silva, D., et al. (2012). Ensembl 2012. Nucleic Acids Res. 40, D84-D90.
21. Gavrilov, A. A., Zukher, I. S., Philo-nenko,E. S., Razin, S.V.,andIarovaia, O. V. (2010). Mapping of the nuclear matrix-bound chromatin hubs by a new M3C experimental procedure. Nucleic Acids Res. 38,8051-8060.
22. Grande, M. A., van der Kraan, I., de Jong, L., and van Driel, R. (1997). Nuclear distribution of transcription factors in relation to sites of transcription and RNA polymerase II. j. CellSci. 110(Pt 15), 1781-1791.
23. Guthold, M., Zhu, X., Rivetti, C, Yang, G., Thomson, N. H., Kasas, S., et al. (1999). Direct observation of one-dimensional diffusion and transcription by Escherichia coli RNA polymerase. Biophys. J. 77, 2284-2294.
24. Hakim, O., Resch, W., Yamane, A., Klein, I., Kieffer-Kwon, K.-R., Jankovic, M., et al. (2012). DNA damage defines sites of recurrent chromosomal translocations in B lymphocytes. Nature 484, 69-74.
25. Hakim, O., Sung, M.-H., Voss, T. C, Splinter, E., John, S., Sabo, P. J., et al. (2011). Diverse gene reprogramming events occur in the same spatial clusters of distal regulatory elements. Genome Res. 21,697-706.
26. Harada, Y., Funatsu, T., Murakami, K., Nonoyama, Y, Ishihama, A., and Yanagida, T. (1999). Single-molecule imaging of RNA polymerase-DNA interactions in real time. Biophys. J. 76, 709-715.
27. Hell, S. W., and Wichmann, J. (1994). Breaking the diffraction reso-lution limit by stimulated emission: stimulated-emission-depletion fluorescence microscopy. Opt. Lett. 19, 780-782.
28. Herbert, K. M., Greenleaf, W. J., and Block, S. M. (2008). Single-molecule studies of RNA polymerase: motoring along. Annu. Rev. Biochem. 77, 149-176.
29. Hieda, M., Winstanley, H., Maini, P., Iborra, F. J., and Cook, P. R. (2005). Different populations of RNA polymerase II in living mammalian cells. Chromosome Res. 13, 135-144.
30. Hozak, P., Cook, P. R., Schofer, C, Mos-goller, W., and Wachtler, F. (1994). Site of transcription of ribosomal RNA and intranucleolar structure in HeLa cells. j. Cell Sci. 107(Pt 2), 639-648.
31. Hozak, P., Hassan, A. B., Jackson, D. A., and Co ok, P. R. (1993). Visualization of replication factories attached to nucleoskeleton. Cell 73, 361-373.
32. Iborra, F. J., Pombo, A., Jackson, D. A., and Cook, P. R. (1996). Active RNA polymerases are localized within discrete transcription "factories" in human nuclei. j. Cell Sci. 109(Pt 6), 1427-1436.
33. Jackson, D. A. (1997). Chromatin domains and nuclear compartments: establishing sites of gene expression in eukaryotic nuclei. Mol Biol. Rep. 24,209-220.
34. Jackson, D. A., and Cook, P. R. (1985). Transcription occurs at a nucleoskeleton. EMBOJ. 4, 919-925.
35. Jackson, D. A., Cook, P. R., and Patel, S. B. (1984a). Attachment of repeated sequences to the nuclear cage. Nucleic Acids Res. 12, 6709-6726.
36. Jackson, D. A., McCready, S. J., and Cook, P. R. (1984b). Replication and transcription depend on attachment of DNA to the nuclear cage. j. Cell Sci. Suppl. 1, 59-79.
37. Jackson, D. A., Dickinson, P., and Cook, P. R. (1990). Attachment of DNA to the nucleoskeleton of HeLa cells examined using physiological conditions. Nucleic Acids Res. 18, 4385-4393.
38. Jackson, D. A., Hassan, A. B., Errington, R. J., and Cook, P. R. (1993). Visualization of focal sites of transcription within human nuclei. EMBO J. 12, 1059-1065.
39. Jackson, D. A., Iborra, F. J., Man-ders, E. M., and Cook, P. R. (1998). Numbers and organization of RNA polymerases, nascent transcripts, and transcription units in HeLa nuclei. Mol. Biol. Cell 9,1523-1536.
40. Jackson, D. A., McCready, S. J., and Cook, P. R. (1981). RNA is synthesized at the nuclear cage. Nature 292, 552-555.
41. Jackson, D. A., Yuan, J., and Cook, P. R. (1988). A gentle method for preparing cyto- and nucleo-skeletons and associated chromatin. j. Cell Sci. 90(Pt 3), 365-378.
42. Jin, D. J., and Cabrera, J. E. (2006). Coupling the distribution of RNA polymerase to global gene regulation and the dynamic structure of the bacterial nucleoid in Escherichia coli. J. Struct. Biol. 156,284-291.
43. Kabata, H., Kurosawa, O., Arai, I., Washizu, M., Margarson, S. A., Glass, R. E., et al. (1993). Visualization of single molecules of RNA polymerase sliding along DNA. Science 262, 1561-1563.
44. Kimura, H., Sugaya, K., and Cook, P. R. (2002). The transcription cycle of RNA polymerase II in living cells. j. Cell Biol. 159,777-782.
45. Kocanova, S., Kerr, E. A., Rafique, S., Boyle, S., Katz, E., Caze-Subra, S., et al. (2010). Activation of estrogen-responsive genes does not require their nuclear co-localization. PLoS Genet. 6,el000922. doi: 10.1371/journal.pgen.l000922
46. Lin, S., Coutinho-Mansfield, G., Wang, D., Pandit, S., and Fu, X.-D. (2008). The splicing factor SC35 has an active role in transcriptional elongation. Nat. Struct. Mol. Biol. 15, 819-826.
47. Lindquist, S. (1986). The heat-shock response. Annu. Rev. Biochem. 55, 1151-1191.
48. Lis, J., and Wu, C. (1993). Protein traffic on the heat shock promoter: parking, stalling, and trucking along. Cell 74, 1-4.
49. Marenduzzo, D., Faro-Trindade, I., and Cook, P. R. (2007). What are the molecular ties that maintain genomic loops? Trends Genet. 23, 126-133.
50. Marenduzzo, D., Finan, K., and Cook, P. R. (2006a). The depletion attraction: an underappreciated force driving cellular organization. j. Cell Biol. 175,681-686.
51. Marenduzzo, D., Micheletti, C, and Cook, P. R. (2006b). Entropy-driven genome organization. Biophys. J. 90, 3712-3721.
52. Marshall, N. E, and Price, D. H. (1992). Control of formation of two distinct classes of RNA polymerase II elongation complexes. Mol. Cell. Biol. 12, 2078-2090.
53. Martin, S., and Pombo, A. (2003). Transcription factories: quantitative studies of nanostructures in the mammalian nucleus. Chromosome Res. 11, 461-470.
54. Mehta, I. S., Amira, M., Harvey, A. J., and Bridger, J. M. (2010). Rapid chromosome territory relocation by nuclear motor activity in response to serum removal in primary human fibroblasts. Genome Biol. 11, R5.
55. Melnik, S., Deng, B., Papantonis, A., Baboo, S., Carr, I. M., and Cook, P. R. (2011). The proteomes of transcription factories containing RNA polymerases I, II or III. Nat. Methods 8, 963-968.
56. Misteli, T. (2007). Beyond the sequence: cellular organization of genome function. Cell 128, 787-800.
57. Mitchell, J. A., and Fraser, P. (2008). Transcription factories are nuclear subcompartments that remain in the absence of transcription. Genes Dev. 22,20-25.
58. Morgan, G. T. (2002). Lampbrush chromosomes and associated bodies: new insights into principles of nuclear structure and function. Chromosome Res. 10,177-200.
59. Mosgoeller, W, Schofer, C, Steiner, M., Sylvester, J. E., and Hozak, P. (2001). Arrangement of ribosomal genes in nucleolar domains revealed by detection of "Christmas tree" components. Histochem. Cell Biol. 116,495-505.
60. Miiller, W. G., Rieder, D., Karpova, T. S., John, S., Trajanoski, Z., and McNally, J. G. (2007). Organization of chromatin and histone modifications at a transcription site. j. Cell Biol. 177, 957-967.
61. Nakamura, H., Morita, T., and Sato, C. (1986). Structural organizations of replicon domains during DNA synthetic phase in the mammalian nucleus. Exp. Cell Res. 165, 291-297.
62. Nakayasu, H., and Berezney, R. (1989). Mapping replicational sites in the eucaryotic cell nucleus. j. Cell Biol. 108,1-11.
63. Osborne, C. S., Chakalova, L., Brown, K. E., Carter, D., Horton, A., Debrand, E., et al. (2004). Active genes dynamically colocalize to shared sites of ongoing transcription. Nat. Genet. 36,1065-1071.
64. Osborne, C. S., Chakalova, L., Mitchell, J. A., Horton, A., Wood, A. L., Bolland, D. J., et al. (2007). Myc dynamically and preferentially relocates to a transcription factory occupied by Igh. PLoS Biol. 5, el92. doi: 10.1371/joumal.pbio.0050192
65. Palstra, R.-J., Simonis, M., Klous, P., Brasset, E., Eijkelkamp, B., and de Laat, W. (2008). Maintenance of long-range DNA interactions after inhibition of ongoing RNA polymerase II transcription. PLoS ONE 3, el661. doi: 10.1371/jour-nal.pone.0001661
66. Papantonis, A., and Cook, P. R. (2011). Fixing the model for transcription: the DNA moves, not the polymerase. Transcription 2, 41-44.
67. Papantonis, A., Larkin, J. D., Wada, Y., Ohta, Y., Ihara, S., Kodama, T., et al. (2010). Active RNA polymerases: mobile or immobile molecular machines? PLoS Biol 8, el000419. doi: 10.1371/joumal.pbio. 1000419
68. Pederson, T. (2000). Half a century of "the nuclear matrix". Mol. Biol. Cell 11,799-805.
69. Pombo, A., Jackson, D. A., Hollinshead, M., Wang, Z., Roeder, R. G., and Cook, P. R. (1999). Regional specialization in human nuclei: visualization of discrete sites of transcription by RNA polymerase III. EMBO J.. 18, 2241-2253.
70. Ragoczy, T., Bender, M. A., Telling, A., Byron, R., and 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.
71. Raj, A., Peskin, C. S., Tranchina, D., Vargas, D. Y, and Tyagi, S. (2006). Stochastic mRNA synthesis in mammalian cells. PLoS Biol. 4, e309. doi: 10.1371/joumal.pbio.0040309
72. Roix, J. J., McQueen, P. G., Munson, P. J., Parada, L. A., and Misteli, T. (2003). Spatial proximity of translocation-prone gene loci in human lym-phomas. Nat. Genet. 34,287-291.
73. Saitoh, N., Sakamoto, C, Hagi-wara, M., Agredano-Moreno, L. T., Jimenez-Garcia, L. E, and Nakao, M. (2012). The distribution of phospho-rylated SR proteins and alternative splicing are regulated by RANBP2. Mol. Biol. Cell 23, 1115-1128.
74. Schermelleh, L., Heintzmann, R., and Leonhardt, H. (2010). A guide to super-resolution fluorescence microscopy. j. Cell Biol. 190, 165-175.
75. Schoenfelder, S., Sexton, T., Chakalova, L., Cope, N. F., Horton, A., Andrews, S., et al. (2010). Preferential associations between co-regulated genes reveal a transcriptional interactome in erythroid cells. Nat. Genet. 42, 53-61.
76. Schiibeler, D., Francastel, C, Cimb-ora, D. M., Reik, A., Martin, D. I., and Groudine, M. (2000). Nuclear localization and histone acetylation: a pathway for chromatin opening and transcriptional activation of the human beta-globin locus. Genes Dev. 14,940-950.
77. Sexton, T., Umlauf, D., Kurukuti, S., and Fraser, P. (2007). The role of transcription factories in large-scale structure and dynamics of interphase chromatin. Semin. Cell Dev. Biol. 18, 691-697.
78. Shopland, L. S., Johnson, C. V., Byron, M., McNeil, J., and Lawrence, J. B. (2003). Clustering of multiple specific genes and gene-rich R-bands around SC-35 domains: evidence for local euchromatic neighborhoods. j. Cell Biol. 162,981-990.
79. Simonis, M., Klous, P., Splinter, E., Moshkin, Y, Willemsen, R, de Wit, E., et al. (2006). Nuclear organization of active and inactive chromatin domains uncovered by chromosome conformation capture-on-chip (4C). Nat. Genet. 38, 1348-1354.
80. Simonis, M., and de Laat, W. (2008). FISH-eyed and genome-wide views on the spatial organisation of gene expression. Biochim. Biophys. Ada 1783,2052-2060.
81. Spilianakis, C. G., and Flavell, R. A. (2004). Long-range intrachromoso-mal interactions in the T helper type 2 cytokine locus. Nat. Immunol. 5, 1017-1027.
82. Szczerbal, I., and Bridger, J. M. (2010). Association of adipogenic genes with SC-35 domains during porcine adi-pogenesis. Chromosome Res. 18, 887-895.
83. Taddei, A., Schober, H., and Gasser, S. M. (2010). The budding yeast nucleus. Cold Spring Harb. Perspect. Biol. 2,a000612.
84. Takizawa, T., Gudla, P. R., Guo, L., Lockett, S., and Misteli, T. (2008). Allele-specific nuclear positioning of the monoallelically expressed astro-cyte marker GFAP. Genes Dev. 22, 489-498.
85. Tang, C. W., Maya-Mendoza, A., Martin, C, Zeng, K., Chen, S., Feret, D., et al. (2008). The integrity of a lamin-Bl-dependent nucleoskeleton is a fundamental determinant of RNA synthesis in human cells. j. Cell Sci. 121, 1014-1024.
86. Tokunaga, M., Imamoto, N., and Sakata-Sogawa, K. (2008). Highly inclined thin illumination enables clear single-molecule imaging in cells. Nat. Methods 5,159-161.
87. Tolhuis, B., Palstra, R. J., Splinter, E., Grosveld, F., and de Laat, W. (2002). Looping and interaction between hypersensitive sites in the active beta-globin locus. Mol. Cell 10, 1453-1465.
88. Wang, M. D., Schnitzer, M. J., Yin, H., Landick, R, Gelles, J., and Block, S.M. (1998). Force and velocity measured for single molecules of RNA polymerase. Science 282, 902-907.
89. Wang, Z., Gerstein, M., and Snyder, M. (2009). RNA-Seq: a revolutionary tool for transcriptomics. Nat. Rev. Genet. 10, 57-63.
90. Wansink, D. G., Schul, W., van der Kraan, I., van Steensel, B., van Driel, R, and 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.
91. Xu, M., and Cook, P. R. (2008). Similar active genes cluster in specialized transcription factories. j. Cell Biol. 181,615-623.
92. Yao, J., Ardehali, M. B., Fecko, C. J., Webb, W W, and Lis, J. T. (2007). Intranuclear distribution and local dynamics of RNA polymerase II during transcription activation. Mol. Cell 28,978-990.