Predicting three-dimensional genome structure from transcriptional activity

Nature Genetics

Volumn 32, Issue 3, 2002, Pages 347-352

  Cook, Peter R ^a  

^a UNIVERSITY OF OXFORD   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; DNA POLYMERASE; RNA POLYMERASE;

GENE STRUCTURE; GENETIC TRANSCRIPTION; PREDICTION; PRIORITY JOURNAL; REVIEW; SEQUENCE HOMOLOGY; STRUCTURE ANALYSIS;

BASE SEQUENCE; CHROMOSOMES; DNA-DIRECTED DNA POLYMERASE; ESCHERICHIA COLI; GENES, BACTERIAL; GENOME; GREEN FLUORESCENT PROTEINS; HETEROCHROMATIN; LUMINESCENT PROTEINS; MICROSCOPY, ELECTRON; MODELS, BIOLOGICAL; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; PROTEIN BINDING; PROTEIN CONFORMATION; RIBONUCLEASES; TRANSCRIPTION, GENETIC;

BACTERIA (MICROORGANISMS);

EID: 0036842123     PISSN: 10614036     EISSN: None     Source Type: Journal    
DOI: 10.1038/ng1102-347     Document Type: Review

References (52)

1. Jackson. D.A., Dickinson. P. & Cook. P.R. The size of chromatin loops in HeLa cells. EMBO J. 9, 567-571 (1990).
2. Pettijohn, D.E. in Escherichia Coli and Salmonella Typhimurium: Cellular and Molecular Biology (eds Neidhardt. F.C., Curtiss, R., Ingraham, J.L., Lin. E.C.C., Low, K.B., Magasanik, B., Reznifoff, W.S., Riley, M., Schaechter, M. & Umbarger, H.E.) 158-166 (ASM Press, Washington, 1996).
3. Cook, P.R. Principles of Nuclear Structure and Function (Wiley, New York, 2001).
4. Sachs, R.K., van den Engh, G., Trask, B., Yokota, H. & Hearst, J.E. A random-walk/giant-loop model for interphase chromosomes. Proc. Natl Acad. Sci. USA 92, 2710-2714 (1995).
5. Sedat, J. & Manuelidis, L. A direct approach to the structure of eukaryotic chromosomes. Cold Spring Harb. Symp. Quant. Biol. 42, 331-350 (1978).
6. Saitoh, Y. & Laemmli, U.K. From the chromosomal loops and the scaffold to the classic bands of metaphase chromosomes. Cold Spring Harb. Symp. Quant. Biol. 58, 755-765 (1978).
7. Cook, P.R. A chromomeric model for nuclear and chromosome structure. J. Cell. Sci. 108, 2927-2935 (1995).
8. Manuelidis, L. A view of interphase chromosomes. Science. 250, 1533-1540 (1990).
9. Li, G., Sudlow, G. & Belmont, A.S. Interphase cell cycle dynamics of a late-replicating, heterochromatic homogeneously staining region: Precise choreography of condensation/decondensation and nuclear positioning. J. Cell. Biol. 140, 975-989 (1998).
10. Jackson, D.A., McCready, S.J. & Cook, P.R. Replication and transcription depend on attachment of DNA to the nuclear cage. J. Cell. Sci. Suppl. 1, 59-79 (1984).
11. McManus, J. et al. Unusual chromosome structure of fission yeast DNA in mouse cells. J. Cell. Sci. 107, 469-486 (1994).
12. Misteli, T. The concept of self-organization in cellular architecture. J. Cell. Biol. 155, 181-185 (2001).
13. Nedelec, F., Surrey, T., Maggs, A.C. & Leibler, S. Self-organization of microtubules and motors. Nature. 389, 305-308 (1997).
14. Minton, A.R The influence of macromolecular crowding and macromolecular confinement on biochemical reactions in physiological media. J. Biol. Chem. 256, 10577-10580 (2001).
15. Ishihama, A. Subunit of assembly of Escherichia coli RNA polymerase. Adv. Biophys. 14, 1-35 (1981).
16. Minsky, A., Shimoni, E. & Frenkiel-Krispin, D. Stress, order and survival. Nature. Rev. Mol. Cell. Biol. 3, 50-60 (2002).
17. Mascarenhas, J., Weber, M.H. & Graumann, P.L. Specific polar localization of ribosomes in Bacillus subtilis depends on active transcription. EMBO Rep. 2, 685-689 (2001).
18. Haaf, T. & Ward, D.C. Inhibition of RNA polymerase II transcription causes chromatin decondensation, loss of nucleolar structure, and dispersion of chromosomal domains. Exp. Cell. Res. 224, 163-173 (1996).
19. Chubb, J.R., Boyle, S., Perry, P. & Bickmore, W.A. Chromatin motion is constrained by association with nuclear compartments in human cells. Curr. Biol. 12, 439-445 (2002).
20. Cook, P.R. The organization of replication and transcription. Science. 284, 1790-1795 (1999).
21. Gelles, J. & Landick, R. RNA polymerase as a molecular motor. Cell. 93, 13-16 (1998).
22. Maniatis, T. & Reed, R. An extensive network of coupling among gene expression machines. Nature. 416, 499-506 (2002).
23. Lewis, P.J., Thaker, S.D. & Errington, J. Compartmentalization of transcription and translation in Bacillus subtilis. EMBO J. 19, 710-718 (2000).
24. Bremer, H. & Dennis, P.P. in Escherichia coli and Salmonella typhimurium: Cellular and Molecular Biology (eds Neidhardt, F.C., Curtiss, R., Ingraham, J.L., Lin, E.C.C., Low, K.8., Magasanik, B., Reznifoff, W.S., Riley, M., Schaechter, M. & Umbarger, H.E.) 1553-1569 (ASM Press, Washington, 1996).
25. Shaw, P.J. & Jordan, E.G. The nucleolus. Ann. Rev. Cell. Dev. Biol. 11, 93-121 (1995).
26. Jackson, D.A., Iborra, F.J., Manders, E.M.M. & Cook, P.R. Numbers and organization of RNA polymerases, nascent transcripts and transcription units in HeLa nuclei. Mol. Biol. Cell. 9, 1523-1536 (1998).
27. Lemon, K.P. & Grossman, A.D. The extrusion-capture model for chromosome partitioning in bacteria. Genes. Dev. 15, 2031-2041 (2001).
28. Pombo, A. et al. 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 (1998).
29. Frey, M.R., Bailey, A.D., Weiner, A.M. & Matera, A.G. Association of snRNA genes with coiled bodies is mediated by nascent snRNA transcripts. Curr. Biol. 9, 126-135 (1999).
30. Cook, P.R. The transcriptional basis of chromosome pairing. J. Cell. Sci. 110, 1033-1040 (1997).
31. McKee, B.D., Habera, L. & Vrana, J.A. Evidence that intergenic spacer repeats of Drosophila melanogaster rRNA genes function as X-Y pairing sites in male meiosis, and a general model for achiasmatic pairing. Genetics. 132, 529-544 (1992).
32. Hiraoka, Y. et al. The onset of homologous chromosome pairing during Drosophila melanogaster embryogenesis. J. Cell. Biol. 120, 591-600 (1993).
33. Henikoff, 5. Heterochromatin function in complex genomes. Biochim. Biophys. Acta. 1470, 1-8 (2000).
34. Kurz, A. et al. Active and inactive genes localize preferentially in the periphery of chromosome territories. J. Cell. Biol. 135, 1195-1205 (1996).
35. Abranches, R., Beven, A.F., Aragon-Alcaide, L. & Shaw, P.J. Transcription sites are not correlated with chromosome territories in wheat nuclei. J. Cell. Biol. 143, 5-12 (1998).
36. Sudbrak, R. et al. X chromosome-specific cDNA arrays: Identification of genes that escape from X-inactivation and other applications. Hum. Mol. Genet. 10, 77-83 (2001).
37. Jenuwein, T. & Allis, C.D. Translating the histone code. Science. 201, 1074-1080 (2001).
38. Pederson, T. Half a century of 'the nuclear matrix'. Mol. Biol. Cell. 11, 799-805 (2000).
39. Jackson, D.A., Bartlett, J. & Cook, P.R. 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 (1996).
40. Christensen, M.O. et al. Dynamics of human DNA topoisomerases IIα and IIβ in living cells. J. Cell. Biol. 157, 31-44 (2002).
41. Gribnau, J., Diderich, K., Pruzina, S., Calzolari, R. & Fraser, R Intergenic transcription and developmental remodeling of chromatin subdomains in the human β-globin locus. Mol. Cell. 5, 377-386 (2000).
42. Glover, D.M., Leibowitz, M.H., McLean, D.A. & Parry, H. Mutations in aurora prevent centrosome separation leading to the formation of monopolar spindles. Cell. 81, 95-105 (1995).
43. Nickerson, J.A. Experimental observations of a nuclear matrix. J. Cell. Sci. 114, 463-474 (2001).
44. Manders, E.M.M., Kimura, H. & Cook, RR. Direct imaging of DNA in living cells reveals the dynamics of chromosome formation. J. Cell. Biol. 144, 813-822 (1999).
45. Sugaya, K., Vigneron, M. & Cook, RR. Mammalian cell lines expressing functional RNA polymerase II tagged with the green fluorescent protein. J. Cell. Sci. 113, 2679-2683 (2000).
46. Gustafsson, M.G. Extended resolution fluorescence microscopy. Curr. Opin. Struct. Biol. 9, 627-634 (1999).
47. Dekker, J., Rippe, K., Dekker, M. & Kleckner, N. Capturing chromosome conformation. Science. 295, 1306-1311 (2002).
48. Levsky, J.M., Shenoy, S.M., Pezo, R.C. & Singer, R.H. Single-cell gene expression profiling. Science. 297, 836-840 (2002).
49. Pombo, A. et al. Regional specialization in human nuclei: visualization of discrete sites of transcription by RNA polymerase III. EMBO J. 18, 2241-2253 (1999).
50. Lercher, M.J., Urrutia, A.O. & Hurst, L.D. Clustering of housekeeping genes provides a unified model of gene order in the human genome. Nat. Genet. 31, 180-183 (2002).
51. Marshall, W.F. et al. Interphase chromosomes undergo constrained diffusional motion in living cells. Curr. Biol. 7, 930-939 (1997).
52. Liu, L.F. & Wang, J.C. Supercoiling of the DNA template during transcription. Proc. Natl. Acad. Sci. USA 84, 7024-7027 (1987).