Nongenic transcription, gene regulation and action at a distance

Journal of Cell Science

Volumn 116, Issue 22, 2003, Pages 4483-4491

  Cook, Peter R ^a  

^a UNIVERSITY OF OXFORD   (United Kingdom)

Author keywords

Barrier; Enhancer; Heterochromatin; Locus control region; Position effect; Silencer

Indexed keywords

BETA GLOBIN; DNA;

BASE PAIRING; CHROMOSOME; ENHANCER REGION; EUKARYOTE; FLY; GENE CONTROL; GENETIC TRANSCRIPTION; HEAT SHOCK; HETEROCHROMATIN; HYPOTHESIS; INTRON; MOLECULAR INTERACTION; NONHUMAN; PRIORITY JOURNAL; REGULATOR GENE; REVIEW; SILENCER GENE; TRANSCRIPTION REGULATION;

ANIMALS; DROSOPHILA; ENHANCER ELEMENTS (GENETICS); GENE EXPRESSION REGULATION; GLOBINS; HETEROCHROMATIN; HUMANS; LOCUS CONTROL REGION; MODELS, MOLECULAR; NUCLEOSOMES; REGULATORY SEQUENCES, NUCLEIC ACID; SACCHAROMYCES CEREVISIAE; TRANSCRIPTION FACTORS; TRANSCRIPTION, GENETIC;

EUKARYOTA;

EID: 0344897665     PISSN: 00219533     EISSN: None     Source Type: Journal    
DOI: 10.1242/jcs.00819     Document Type: Review

References (74)

1. Abranches, R., Beven, A. F., Aragon-Alcaide, L. and Shaw, P. J. (1998). Transcription sites are not correlated with chromosome territories in wheat nuclei. J. Cell Biol. 143, 5-12.
2. Adachi, N. and Lieber, M. R. (2002). Bidirectional gene organization: a common architectural feature of the human genome. Cell 109, 807-809.
3. Ashe, H. L., Monks, J., Wijgerde, M., Fraser, P. and Proudfoot, N. J. (1997). Intergenic transcription and transinduction of the human beta-globin locus. Genes Dev. 11, 2494-2509.
4. Avramova, Z. and Tikhonov, A. (1999). Are scs and scs' 'neutral' chromatin domain boundaries of the locus? Trends Genet. 15, 138-139.
5. Baker, W. K. (1968). Position-effect variegation. Adv. Genetics 14, 133-169.
6. Belmont, A. S. (2002). Mitotic chromosome scaffold structure: new approaches to an old controversy. Proc. Natl. Acad. Sci. USA 99, 15855-15857.
7. Bender, W. and Fitzgerald, D. P. (2002). Transcription activates repressed domains in the Drosophila bithorax complex. Development 129, 4923-4930.
8. Bi, X. and Broach, J. R. (1999). UASrpg can function as a heterochromatin boundary element in yeast. Genes Dev. 13, 1089-1101.
9. Blanton, J., Gaszner, M. and Schedl, P. (2003). Protein:protein interactions and the pairing of boundary elements in vivo. Genes Dev. 17, 664-675.
10. Bolton, E. C. and Boeke, J. D. (2003). Transcriptional interactions between yeast tRNA genes, flanking genes and Ty elements: a genomic point of view. Genome Res. 13, 254-263.
11. Burgess-Beusse, B., Farrell, C., Gaszner, M., Litt, M., Mutskov, V., Recillas-Targa, F., Simpson, M., West, A. and Felsenfeld, G. (2002). The insulation of genes from external enhancers and silencing chromatin. Proc. Natl. Acad. Sci. USA 99 (Suppl. 4), 16433-16437.
12. Carter, D., Chakalova, L., Osborne, C. S., Dal, Y.-f. and Fraser, P. (2002). Long-range chromatin regulatory interactions in vivo. Nat. Genet. 32, 623-626.
13. Cheng, T. H. and Gartenberg, M. R. (2000). Yeast heterochromatin is a dynamic structure that requires silencers continuously. Genes Dev. 14, 452-463.
14. Cockell, M. and Gasser, S. M. (1999). Nuclear compartments and gene regulation. Curr Opin. Genet. Dev. 9, 199-205.
15. Cook, P. R. (1999). The organization of replication and transcription. Science 284, 1790-1795.
16. Cook, P. R. (2001). Principles of nuclear structure and function. New York: J. Wiley.
17. Cook, P. R. (2002). Predicting three-dimensional genome structure from transcriptional activity. Nat. Genet. 32, 347-352.
18. Dekker, J., Rippe, K., Dekker, M. and Kleckner, N. (2002). Capturing chromosome conformation. Science 295, 1306-1311.
19. Donze, D. and Kamakaka, R. T. (2001). RNA polymerase III and RNA polymerase II promoter complexes are heterochromatin barriers in Saccharomyces cerevisiae. EMBO J. 20, 520-531.
20. Donze, D. and Kamakaka, R. T. (2002). Braking the silence: how heterochromatic gene repression is stopped in its tracks. Bioessays 24, 344-349.
21. Drewell, R. A., Bae, E., Burr, J. and Lewis, E. B. (2002a). Transcription defines the embryonic domains of cis-regulatory activity at the Drosophila bithorax complex. Proc. Natl. Acad. Sci. USA 99, 16853-16858.
22. Drewell, R. A., Arney, K. L., Arima, T., Barton, S. C., Brenton, J. D. and Surani, M. A. (2002b). Novel conserved elements upstream of the H19 gene are transcribed and act as mesodermal enhancers. Development 129, 1205-1213.
23. Emerman, M. and Temin, H. M. (1986). Quantitative analysis of gene suppression in integrated virus vectors. Mol. Cell. Biol. 6, 792-800.
24. Galy, V., Olivo-Marin, J. C., Scherthan, H., Doye, V., Rascalou, N. and Nehrbass, U. (2000). Nuclear pore complexes in the organization of silent telomeric chromatin. Nature 403, 108-112.
25. Gerasimova, T. I. and Corces, V. G. (2001). Chromatin insulators and boundaries: effects on transcription and nuclear organization. Annu. Rev. Genet. 35, 193-208.
26. Gottesman, S. (2002). Stealth regulation: biological circuits with small RNA switches. Genes Dev. 16, 2829-2842.
27. Grunstein, M. (1990). Histone function in transcription. Annu. Rev. Cell Biol. 6, 643-678.
28. Hertel, K. J., Lynch, K. W. and Maniatis, T. (1997). Common themes in the function of transcription and splicing enhancers. Curr. Opin. Cell Biol. 9, 350-357.
29. Hirotsune, S., Yoshida, N., Chen, A., Garrett, L., Sugiyama, F., Takahashi, S., Yagami, K., Wynshaw-Boris, A. and Yoshiki, A. (2003). An expressed pseudogene regulates the messenger-RNA stability of its homologous coding gene. Nature 423, 91-96.
30. Hogga, I. and Karch, E. (2002). Transcription through the iab-7 cis-regulatory domain of the bithorax complex interferes with maintenance of Polycomb-mediated silencing. Development 129, 4915-4922.
31. Iborra, F. J., Pombo, A., McManus, J., Jackson, D. A. and Cook, P. R. (1996). The topology of transcription by immobilized polymerases. Exp. Cell Res. 229, 167-173.
32. Iborra, F. J., Jackson, D. A. and Cook, P. R. (2001). Coupled transcription and translation within nuclei of mammalian cells. Science 293, 1139-1142.
33. Ivarie, R. D., Schacter, B. S. and O'Farrell, P. H. (1983). The level of expression of the rat growth hormone gene in liver tumour cells is at least eight orders of magnitude less than that in anterior pituitary cells. Mol. Cell. Biol. 3, 1460-1467.
34. Jackson, D. A. and Cook, P. R. (1993). Transcriptionally-active minichromosomes are attached transiently in nuclei through transcription units. J. Cell Sci. 105, 1143-1150.
35. Jackson, D. A., McCready, S. J. and Cook, P. R. (1984). Replication and transcription depend on attachment of DNA to the nuclear cage. J. Cell Sci. (Suppl. 1), 59-79.
36. Jackson, D. A., Dickinson, P. and Cook, P. R. (1990). The size of chromatin loops in HeLa cells. EMBO J. 9, 567-571.
37. Jackson, D. A., Bartlett, J. and Cook, P. R. (1996). Sequences attaching loops of nuclear and mitochondrial DNA to underlying structures in human cells: the role of transcription units. Nucleic Acids Res. 24, 1212-1219.
38. Jenuwein, T. and Allis, C. D. (2001). Translating the histone code. Science 293, 1074-1080.
39. Johnson, K. D., Christensen, H. M., Zhao, B. and Bresnick, E. H. (2001). Distinct mechanisms control RNA polymerase II recruitment to a tissue-specific locus control region and a downstream promoter. Mol. Cell 8, 465-471.
40. Kapranov, P., Cawley, S. E., Drenkow, J., Bekiranov, S., Strausberg, R. L., Fodor, S. P. and Gingeras, T. R. (2002). Large-scale transcriptional activity in chromosomes 21 and 22. Science 296, 916-919.
41. Kellum, R. and Schedl, P. (1991). A position-effect assay for boundaries of higher order chromosomal domains. Cell 64, 941-950.
42. 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.
43. 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.
44. Kurdistani, S. K. and Grunstein, M. (2003). Histone acetylation and deacetylation in yeast. Nat. Rev. Mol. Cell. Biol. 4, 276-284.
45. Labrador, M. and Corces, V. G. (2002). Setting the boundaries of chromatin domains and nuclear organization. Cell 111, 151-154.
46. Li, Q., Peterson, K. R., Fang, X. and Stamatoyannopoulos, G. (2002). Locus control regions. Blood 100, 3077-3086.
47. Lindsley, D. L., Edington, C. W. and von Halle, E. S. (1960). Sex-linked recessive lethals in Drosophila whose expression is suppressed by the Y-chromosome. Genetics 45, 1649-1670.
48. Litt, M. D., Simpson, M., Gaszner, M., Allis, C. D. and Felsenfeld, G. (2001). Correlation between histone lysine methylation and developmental changes at the chicken beta-globin locus. Science 293, 2453-2455.
49. Martin, C. H., Mayeda, C. A., Davis, C. A., Ericsson, C. L., Knafels, J. D., Mathog, D. R., Celniker, S. E., Lewis, E. B. and Palazzolo, M. J. (1995). Complete sequence of the bithorax complex of Drosophila. Proc. Natl. Acad. Sci. USA 92, 8398-8402.
50. Merika, M. and Thanos, D. (2001). Enhanceosomes. Curr. Opin. Genet. Dev. 11, 205-208.
51. Misteli, T. (2001). The concept of self-organization in cellular architecture. J. Cell Biol. 155, 181-185.
52. Partridge, J. F., Borgstrom, B. and Allshire, R. C. (2000). Distinct protein interaction domains and protein spreading in a complex centromere. Genes Dev. 14, 783-791.
53. Plath, K., Mlynarczyk-Evans, S., Nusinow, D. A. and Panning, B. (2002). Xist RNA and the mechanism of x chromosome inactivation. Anna. Rev. Genet. 36, 233-278.
54. Polioudaki, H., Kourmouli, N., Drosou, V., Bakou, A., Theodoropoulos, P, A., Singh, P. B., Giannakouros, T. and Georgatos, S. D. (2001). Histones H3/H4 form a tight complex with the inner nuclear membrane protein LBR and heterochromatin protein 1. EMBO Rep. 2, 920-925.
55. Pombo, A., Cuello, P., Schul, W., Yoon, J.-B., Roeder, R. G., Cook, P. R. and Murphy, S. (1998). Regional and temporal specialization in the nucleus: a transcriptionally-active nuclear domain rich in PTF, Oct1 and PIKA antigens associates with specific chromosomes early in the cell cycle. EMBO J. 17, 1768-1778.
56. 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.
57. 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.
58. Richards, E. J. and Elgin, S. C. (2002). Epigenetic codes for heterochromatin formation and silencing: rounding up the usual suspects. Cell 108, 489-500.
59. Routledge, S. J. and Proudfoot, N. J. (2002). Definition of transcriptional promoters in the human beta globin locus control region. J Mol. Biol. 323, 601-611.
60. Schedl, P. and Broach, J. R. (2003). Making good neighbors: the right fence for the right job. Nat. Struct. Biol. 10, 241-243.
61. Shendure, J. and Church, G. M. (2002). Computational discovery of sense-antisense transcription in the human and mouse genomes. Genome Biol. 3, RESEARCH0044.
62. Skaletsky, H., Kuroda-Kawaguchi, T., Minx, P. J., Cordum, H. S., Hillier, L., Brown, L. G., Repping, S., Pyntikova, T., Ali, J., Bieri, T. et al. (2003). The male-specific region of the human Y chromosome is a mosaic of discrete sequence classes. Nature, 423, 825-837.
63. Snow, M. H. L. and Callan, H. G. (1969). Evidence for a polarized movement of the lateral loops of newt lampbrush chromosomes during oogenesis. J. Cell Sci. 5, 1-25.
64. Spector, D. L. (2003). The dynamics of chromosome organization and gene regulation. Annu. Rev. Biochem. 72, 573-608.
65. Storz, G. (2002). An expanding universe of noncoding RNAs. Science 296, 1260-1263.
66. Sturtevant, A. H. and Beadle, G. W. (1962). An introduction to Genetics. New York: Dover Publications.
67. Sudbrak, R., Wieczorek, G., Nuber, U. A., Mann, W., Kirchner, R., Erdogan, F., Brown, C. J., Wohrle, D., Sterk, P., Kalscheuer, V. M. et al. (2001). X chromosome-specific cDNA arrays: identification of genes that escape from X-inactivation and other applications. Hum. Mol. Genet. 10, 77-83.
68. Sutter, N. B., Scalzo, D., Fiering, S., Groudine, M. and Martin, D. L. (2003). Chromatin insulation by a transcriptional activator. Proc. Natl. Acad. Sci. USA 100, 1105-1110.
69. Tanimoto, K., Liu, Q., Bungert, J. and Engel, J. D. (1999). Effects of altered gene order or orientation of the locus control region on human beta-globin gene expression in mice. Nature 398, 344-348.
70. 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.
71. Volpe, T. A., Kidner, C., Hall, I. M., Teng, G., Grewal, S. I. and Martienssen, R. A. (2002). Regulation of heterochromatic silencing and histone H3 lysine-9 methylation by RNAi. Science 297, 1833-1837.
72. West, A. G., Gaszner, M. and Felsenfeld, G. (2002). Insulators: many functions, many mechanisms. Genes Dev. 16, 271-288.
73. Willoughby, D. A., Vilalta, A. and Oshima, R. G. (2000). An Alu element from the K18 gene confers position-independent expression in transgenic mice. J. Biol. Chem. 275, 759-768.
74. Wyrick, J. J., Holstege, F. C., Jennings, E. G., Causton, H. C., Shore, D., Grunstein, M., Lander, E. S. and Young, R. A. (1999). Chromosomal landscape of nucleosome-dependent gene expression and silencing in yeast. Nature 402, 418-421.