The amazing complexity of transcription factories

Briefings in Functional Genomics and Proteomics

Volumn 4, Issue 2, 2005, Pages 143-157

  Jackson, Dean A ^a  

^a UNIVERSITY OF MANCHESTER   (United Kingdom)

Author keywords

Chromatin; DNA integrity; Dynamics; Gene expression; Nuclear structure; Protein protein interactions; RNA polymerase II; Systems biology; Transcription factories

Indexed keywords

BETA GLOBIN; BRCA1 PROTEIN; DNA DIRECTED RNA POLYMERASE; ERYTHROID KRUPPEL LIKE FACTOR; IMMUNOGLOBULIN HEAVY CHAIN; IMMUNOGLOBULIN KAPPA CHAIN; MESSENGER RNA; PROTEIN MLH1; PROTEIN MSH2; RIBOSOME DNA; RIBOSOME RNA; RNA POLYMERASE II; SMALL NUCLEOLAR RNA; TATA BINDING PROTEIN; TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR GATA 1; TRANSCRIPTION FACTOR RUNX1; TRANSCRIPTION FACTOR RUNX2; TRANSFER RNA;

B LYMPHOCYTE; CELL CYCLE S PHASE; CELL MATURATION; CELL NUCLEUS; CELL NUCLEUS MATRIX; CELL PROLIFERATION; CELL SURVIVAL; CHROMATIN STRUCTURE; CHROMOSOME STRUCTURE; CYTOPLASM; DNA DAMAGE; DNA MODIFICATION; DNA REPAIR; DNA REPLICATION; DNA SYNTHESIS; ENHANCER REGION; EUKARYOTE; FLUORESCENCE IN SITU HYBRIDIZATION; GENE CLUSTER; GENE EXPRESSION; GENE EXPRESSION REGULATION; GENETIC TRANSCRIPTION; GENOME ANALYSIS; GENOMIC INSTABILITY; HUMAN; MAMMAL CELL; NONHUMAN; NUCLEOLUS; PROTEIN FUNCTION; PROTEIN PURIFICATION; PROTEIN RNA BINDING; PROTEOMICS; REVIEW; RNA METABOLISM; RNA SYNTHESIS; SIGNAL TRANSDUCTION;

ANIMALS; CELL NUCLEUS; CELL PROLIFERATION; CYTOPLASM; DNA; DNA REPAIR; DNA REPLICATION; GENE EXPRESSION REGULATION; HUMANS; MULTIGENE FAMILY; PROTEOMICS; RNA; TRANSCRIPTION, GENETIC;

EUKARYOTA; MAMMALIA;

EID: 23844469094     PISSN: 14739550     EISSN: None     Source Type: Journal    
DOI: 10.1093/bfgp/4.2.143     Document Type: Review

References (79)

1. Emerson, B. M. (2002), 'Specificity of gene regulation', Cell, Vol. 109, pp. 267-270.
2. Maniatis, T. and Reed, R. (2002), 'An extensive network of coupling among gene expression machines', Nature, Vol, 416, pp. 499-506.
3. Jenuwein, T. and Allis, C. D. (2001), 'Translating the histone code', Science, Vol. 293, pp. 1074-1080.
4. Fischle, W., Wang, Y. M. and Allis, C. D. (2003), 'Histone and chromatin cross-talk', Curr. Opin. Cell Biol., Vol. 15, pp. 172-183.
5. Jackson, D. A. (2003), 'The principles of nuclear structure', Chromosome Res., Vol. 11, pp. 387-401.
6. Jackson, D. A. (2003), 'The anatomy of transcription sites', Curr. Opin. Cell Biol., Vol. 15, pp. 311-317.
7. Cremer, T. and Cremer, C. (2001), 'Chromosome territories, nuclear architecture and gene regulation in mammalian cells', Nat. Rev. Genet., Vol. 2, pp. 292-301.
8. Kosak, S. T. and Groudine, M. (2004), 'Gene order and dynamic domains', Science, Vol. 306, pp. 644-647.
9. Kosak, S. T. and Groudine, M. (2004), 'Form follows function: The genomic organization of cellular differentiation', Genes Dev., Vol. 18, pp. 1371-1384.
10. Bickmore, W. A. and Chubb, J. R. (2003), 'Chromosome position: Now, where was I?', Curr. Biol., Vol. 13, pp. R357-R359.
11. Kosak, S. T., Skok, J. A., Medina, K. L. et al. (2002), 'Subnuclear compartmentalization of immunoglobulin loci during lymphocyte development', Science, Vol. 296, pp. 158-162.
12. Shaw, P. and Doonan J. (2005), 'The nucleolus - Playing by different rules?', Cell Cycle, Vol. 4, pp. 102-105.
13. Koberna, K., Malinsky, J., Pliss, A., et al. (2002), 'Ribosomal genes in focus: New transcripts label the dense fibrillar components and form clusters indicative of "Christmas trees" in situ', J. Cell Biol., Vol. 157, pp. 743-748.
14. Dundr, M., Hoffmann-Rohrer, U., Hu, Q. Y. et al. (2002), 'A kinetic framework for a mammalian RNA polymerase in vivo', Science, Vol. 298, pp. 1623-1626.
15. Martin, S. and Pombo, A. (2003), 'Transcription factories: Quantitative studies of nanostructures in the mammalian nucleus', Chromosome Res., Vol. 11, pp. 461-470.
16. Jackson, D. A., Iborra, F. J., Manders, E. M. M. et al. (1998), 'Numbers and organization of RNA polymerases, nascent transcripts, and transcription units in HeLa nuclei', Mol. Biol. Cell, Vol. 9, pp. 1523-1536.
17. Pombo, A., Jackson, D. A., Hollinshead, M. et al. (1999), 'Regional specialization inhuman nuclei: Visualization of discrete sites of transcription by RNA polymerase III', EMBO J., Vol. 18, pp. 2241-2253.
18. Elbi, C., Misteli, T. and Hager, G. L. (2002), 'Recruitment of dioxin receptor to active transcription sites', Mol. Cell. Biol., Vol. 13, pp. 2001-2015.
19. Chen, D. Y., Dundr, M., Wang, C. et al. (2005), 'Condensed mitotic chromatin is accessible to transcription factors and chromatin structural proteins', J. Cell Biol., Vol. 168, pp. 41-54.
20. Jackson, D. A., Hassan, A. B., Errington, R. J. et al. (1993), 'Visualization of focal sites of transcription within human nuclei', EMBO J., Vol. 12, pp. 1059-1065.
21. Cook, P. R. (1999), 'The organization of replication and transcription', Science, Vol. 284, pp. 1790-1795.
22. Cook, P. R. (2002), 'Predicting three-dimensional genome structure from transcriptional activity', Nat. Genet., Vol. 32, pp. 347-352.
23. Femme, A., Fay, F. S., Fogarty, K. et al. (1998), 'Visualization of single RNA transcripts in situ', Science, Vol. 280, pp. 585-590.
24. Jackson, D. A. and Cook, P. R. (1985), 'Transcription occurs at a nucleoskeleton', EMBO J., Vol. 4, pp. 919-925.
25. Mahy, N. L., Perry, P. E., Gilchrist, S. et al. (2002), 'Spatial organization of active and inactive genes and noncoding DNA within chromosome territories', J. Cell Biol., Vol. 157, pp. 579-589.
26. Jackson, D. A., Pombo, A. and Iborra, F. (2000), 'The balance sheet for transcription: An analysis of nuclear RNA metabolism in mammalian cells', FASEB J, Vol. 14, pp. 242-254.
27. Kimura, H., Tao, Y., Roeder, R. G. et al. (1999), 'Quantitation of RNA polymerase II and its transcription factors in a HeLa cell: Little soluble holoenzyme but significant amounts of polymerases attached to the nuclear substructure', Mol. Cell. Biol., Vol. 19, pp. 5383-5392.
28. Kimura, H., Sugaya, K. and Cook, P. R. (2002), 'The transcription cycle of RNA polymerase II in living cells', J. Cell Biol., Vol. 159, pp. 777-782.
29. McNally, J. G., Muller, W. G., Walker, D. et al. (2000), 'The glucocorticoid receptor: Rapid exchange with regulatory sites in living cells', Science, Vol. 287, pp. 1262-1265.
30. Chen, D. Y., Hinkley, C. S., Henry, R. W. et al. (2002), 'TBP dynamics in living human cells: Constitutive association of TBP with mitotic chromosomes', Mol. Biol. Cell, Vol. 13, pp. 276-284.
31. Grosveld, F. (1999), 'Activation by locus control regions?', Curr. Opin. Genet. Dev., Vol. 9, pp. 152-157.
32. Wijgerde, M., Grosveld, F. and Fraser, P. (1995), 'Transcription complex stability and chromatin dynamics in vivo', Nature, Vol. 377, pp. 209-213.
33. West, A. G., Huang, S. M., Gaszner, M. et al. (2004), 'Recruitment of histione modifications by USF proteins at a vertebrate barrier element', Mol. Cell, Vol. 16, pp. 453-463.
34. Brand, M., Ranish, J. A., Kummer, N. T. et al. (2004), 'Dynamic changes in transcription factor complexes during erythroid differentiation revealed by quantitative proteomics', Nat. Struct. Mol. Biol., Vol. 11, pp. 73-80.
35. Bender, M. A., Bulger, M., Close, J. et al. (2000), 'Beta-globin gene switching and DNase I sensitivity of the endogenous beta-globin locus in mice do not require the locus control region', Mol. Cell, Vol. 5, pp. 387-393.
36. Tolhuis, B., Palstra, R. J., Splinter, E. et al. (2002), 'Looping and interaction between hypersensitive sites in the active beta-globin locus', Mol. Cell, Vol. 10, pp. 1453-1465.
37. Patrinos, G. P., de Krom, M., de Boer, E. et al. (2004), 'Multiple interactions between regulatory regions are required to stabilize an active chromatin hub', Genes Dev., Vol. 18, pp. 1495-1509.
38. Drissen, R., Palstra, R. J., Gillemans, N. et al. (2004), 'The active spatial organization of the beta-globin locus requires the transcription factor EKLF', Genes Dev., Vol. 18, pp. 2485-2490.
39. Vakoc, C.R., Letting, D. L., Gheldof, N. et al. (2005), 'Proximity among distant regulatory elements at the beta-globin locus requires GATA-1 and FOG-1', Mol. Cell, Vol. 17, pp. 453-462.
40. Osborne, C. S., Chakalova, L., Brown, K. E. et al. (2004), 'Active genes dynamically colocalize to shared sites of ongoing transcription', Nat. Genet., Vol. 36, pp. 1065-1071.
41. Reed, R. (2003), 'Coupling transcription, splicing and mRNA export', Curr. Opin. Cell Biol., Vol. 15, pp. 326-331.
42. Vinciguerra, P. and Stutz, F. (2004), 'MRNA export: An assembly line from genes to nuclear pores', Curr. Opin. Cell Biol., Vol. 16, pp. 285-292.
43. Sims, J., Belotserkovskaya, R. and Reinberg, D. (2004), 'Elongation by RNA polymerase II: The short and long of it', Genes Dev., Vol. 18, pp.2437-2468.
44. McCracken, S., Fong, N., Yankulov, K. et al. (1997), 'The C-terminal domain of RNA polymerase II couples mRNA processing to transcription', Nature, Vol. 385, pp. 357-361.
45. Hirose, Y. and Manley, J. L. (1998), 'RNA polymerase II is an essential mRNA polyadenylation factor', Nature, Vol. 395, pp. 93-96.
46. Shuman, S. (1997), 'Origins of mRNA identity: Capping enzymes bind to the phosphorylated C-terminal domain of the RNA polymerase II', Proc. Natl. Acad. Sci. USA, Vol. 94, pp. 12758-12760.
47. Hieronymus, H. and Silver, P. A. (2004), 'A systems view of mRNP biology', Genes Dev., Vol. 18, pp. 2845-2860.
48. Iborra, F. J., Jackson, D. A. and Cook, P. R. (2004), 'The case for nuclear translation', J. Cell Sci., Vol. 117, pp. 5713-5720.
49. Buhler, M., Wilkinson, M. F. and Muhlemann, O. (2002), 'Intranuclear degradation of nonsense codon-containing mRNA', EMBO Rep., Vol. 3, pp. 646-651.
50. Visa, N. (2005), 'Transcription in action', EMBO Rep., Vol. 6, pp. 218-219.
51. Thomsen, R., Libri, D., Boulay, J. et al. (2003), 'Localization of nuclear retained mRNAs in Saccharomyces cerevisiae', RNA, Vol. 9, pp. 1049-1057.
52. Hieronymus, H., Yu, M. C. and Silver, P. A. (2004), 'Genome-wide mRNA surveillance is coupled to mRNA export', Genes Dev., Vol. 18, pp. 2652-2662.
53. Choi, J. Y., Pratap, J., Javed, A. et al. (2001), 'Subnuclear targeting of Runx/Cbfa/AML factors is essential for tissue-specific differentiation during embryonic development', Proc. Natl. Acad. Sci. USA, Vol. 98, pp. 8650-8655.
54. Harrington, K. S., Javed, A., Drissi, H. et al. (2002), 'Transcription factors RUNX1/AML1 and RUNX2/Cbfa1 dynamically associate with stationary subnuclear domains', J. Cell Sci., Vol. 115, pp. 4167-4176.
55. Zaidi, S. K., Sullivan, A. J., van Wijnen, A.J. et al. (2002), 'Integration of Runx and Smad regulatory signals at transcriptionally active subnuclear sites', Proc. Natl. Acad. Sci. USA, Vol. 99, pp. 8048-8053.
56. Ljungman, M. and Lane, D. P. (2004), 'Transcription - Guarding the genome by sensing DNA damage', Nat. Rev. Cancer, Vol. 4, pp. 727-737.
57. Ljungman, M. and Zhang, F. F. (1996), 'Blockage of RNA polymerase as a possible trigger for UV light-induced apoptosis', Oncogene, Vol. 13, pp. 823-831.
58. Yamaizumi, M. and Sugano, T. (1994), 'UV-induced nuclear accumulation of p53 is evoked through DNA damage of actively transcribed genes independent of the cell cycle', Oncogene, Vol. 9, pp. 2775-2784.
59. McGlynn, P. and Lloyd, R. G. (2002), 'Recombinational repair and restart of damaged replication forks', Nat. Rev. Mol. Cell Biol., Vol. 3, pp. 859-870.
60. Barnes, D. E. and Lindahl, T. (2004), 'Repair and genetic consequences of endogenous DNA base damage in mammalian cells', Ann. Rev. Genet., Vol. 38, pp. 445-476.
61. Kamiuchi, S., Saijo, M., Citterio, E. et al. (2002), 'Translocation of Cockayne syndrome group A protein to the nuclear matrix: Possible relevance to transcnption-coupled DNA repair', Proc. Natl. Acad. Sci. USA, Vol. 99, pp. 201-206.
62. Scully, R., Anderson, S. F., Chao, D. M. et al. (1997), 'BRCA1 is a component of the RNA polymerase II holoenzyme', Proc. Natl. Acad. Sci. USA, Vol. 94, pp. 5605-5610.
63. Krum, S. A., Miranda, G. A., Lin, C. W. et al. (2003), 'BRCA1 associates with processive RNA polymerase II', J. Biol. Chem., Vol. 278, pp. 52012-52020.
64. Mone, M. J., Volker, M., Nikaido, O. et al. (2001), 'Local UV induced DNA damage in cell nuclei results in local transcription inhibition', EMBO Rep., Vol. 2, pp. 1013-1017.
65. Sporbert, A., Gahl, A., Ankerhold, R. et al. (2002), 'DNA polymerase clamp shows little turnover at established replication sites but sequential de novo assembly at adjacent origin clusters', Mol. Cell, Vol. 10, pp. 1355-1365.
66. Gilbert, D. M. (2002), 'Replication timing and transcriptional control: Beyond cause and effect', Curr. Opin. Cell Biol., Vol. 14, pp. 377-383.
67. Pliss, A., Koberna, K., Vecerova, J. et al. (2005), 'Spatio-temporal dynamics at rDNA foci: Global switching between DNA replication and transcription', J. Cell. Biochem., Vol. 94, pp. 554-565.
68. Cohen, B. A., Mitra, R. D., Hughes, J. D. et al. (2000), 'A computational analysis of whole-genome expression data reveals chromosomal domains of gene expression', Nat. Genet., Vol. 26, pp. 183-186.
69. Caron, H., van Schaik, B., van der Mee, M. et al. (2001), 'The human transcriptome map: Clustering of highly expressed genes in chromosomal domains', Science, Vol. 291, pp 1289-1292.
70. 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., Vol. 31, pp. 180-183.
71. Roy, P. J., Stuart, J. M., Lund, J. et al. (2002), 'Chromosomal clustering of muscle-expressed genes in Caenorhabditis elegans', Nature, Vol. 418, pp. 975-979.
72. Spellman, P. T. and Rubin, G. M. (2002), 'Evidence for large domains of similarly expressed genes in the Drosophila genome', J. Biol. 1:5 (http://jbiol.com/1/1/5).
73. Thompson, M., Haeusler, R. A., Good, P. D. et al. (2003), 'Nucleolar clustering of dispersed tRNA genes', Science, Vol. 302, pp. 1399-1401.
74. Jeronimo, C., Langelier, M. F., Zeghouf, M. et al. (2004), 'RPAP1, a novel human RNA polymerase II-associated protein affinity purified with recombinant wild-type and mutated polymerase subunits', Mol. Cell. Biol., Vol. 24, pp. 7043-7058.
75. Xia, Y., Yu, H. Y., Jansen, R. et al. (2004), 'Analyzing cellular biochemistry in terms of molecular networks', Ann. Rev. Biochem., Vol. 73, pp. 1051-1087.
76. Gavin, A. C., Bosche, M., Krause, R. et al. (2002), 'Functional organization of the yeast proteome by systematic analysis of protein complexes', Nature, Vol. 415, pp. 141-147.
77. Li, S. M., Armstrong, C. M., Bertin, N. et al. (2004), 'A map of the interactome network of the metazoan C. elegans', Science, Vol. 303, pp. 540-543.
78. Coulombe, B., Jeronimo, C., Langelier, M. F. et al. (2004), 'Interaction networks of the molecular machines that decode, replicate, and maintain the integrity of the human genome', Mol. Cell. Proteomics, Vol. 3, pp. 851-856.
79. Gasser, S. M. (2002), 'Nuclear architecture - Visualizing chromatin dynamics in interphase nuclei', Science, Vol. 296, pp. 1412-1416.