Nuclear transcription is essential for specification of mammalian replication origins

Genes to Cells

Volumn 11, Issue 7, 2006, Pages 829-844

  Dimitrova, Daniela S ^a,b  

^a UNIVERSITY AT BUFFALO   (United States)

^b BABRAHAM INSTITUTE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

4',6 DIAMIDINO 2 PHENYLINDOLE; CYCLOHEXIMIDE; DIHYDROFOLATE REDUCTASE; DNA; FLUOROURIDINE; SPACER DNA;

ANIMAL CELL; ARTICLE; CELL CYCLE G1 PHASE; CELL NUCLEUS; CHO CELL; CONTROLLED STUDY; DNA REPLICATION; DNA REPLICATION ORIGIN; EPIGENETICS; FEMALE; GENE EXPRESSION; GENE LOCUS; GENE MAPPING; GENETIC TRANSCRIPTION; IN VIVO STUDY; INHIBITION KINETICS; MAMMAL; NONHUMAN; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN SYNTHESIS; TRANSCRIPTION REGULATION; XENOPUS;

ANIMALS; CELL NUCLEUS; CHO CELLS; CRICETINAE; G1 PHASE; HUMANS; REPLICATION ORIGIN; RNA POLYMERASE II; TETRAHYDROFOLATE DEHYDROGENASE; TRANSCRIPTION, GENETIC;

CRICETULUS GRISEUS; MAMMALIA;

EID: 33745241143     PISSN: 13569597     EISSN: 13652443     Source Type: Journal    
DOI: 10.1111/j.1365-2443.2006.00981.x     Document Type: Article

References (60)

1. Ausubel, F.M., Brent, R., Kingston, R.E., et al. (eds) (2003) Current Protocols in Molecular Biology. New York: John Wiley & Sons, Inc.
2. Bendig, M.M. & Williams, J.G. (1983) Replication and expression of Xenopus laevis globin genes injected into fertilized Xenopus eggs. Proc. Natl. Acad. Sci. USA 80, 6197-6201.
3. Bernstein, E. & Allis, C.D. (2005) RNA meets chromatin. Genes Dev. 19, 1635-1655.
4. Boisvert, F.M., Hendzel, M.J. & Bazett-Jones, D.P. (2000) Promyelocytic leukemia (PML) nuclear bodies are protein structures that do not accumulate RNA. J. Cell Biol. 148, 283-292.
5. Chen, S., Reger, R., Miller, C. & Hyman, L.E. (1996) Transcriptional terminators of RNA polymerase II are associated with yeast replication origins. Nucleic Acids Res. 24, 2885-2893.
6. Chomczynski, P. & Sacchi, N. (1987) Single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction. Anal. Biochem. 162, 156-159.
7. Claverie, J.M. (2005) Fewer genes, more noncoding RNA. Science 309, 1529-1530.
8. Crouse, G.F., Leys, E.J., McEwan, R.N., Frayne, E.G. & Kellems, R.E. (1985) Analysis of the mouse dhfr promoter region: Existence of a divergently transcribed gene. Mol. Cell. Biol. 5, 1847-1858.
9. Custodio, N., Carmo-Fonseca, M., Geraghty, F., Pereira, H.S., Grosveld, F. & Antoniou, M. (1999) Inefficient processing impairs release of RNA from the site of transcription. EMBO J. 18, 2855-2866.
10. Danis, E., Brodolin, K., Menut, S., Maiorano, D., Girard-Reydet, C. & Mechali, M. (2004) Specification of a DNA replication origin by a transcription complex. Nat. Cell Biol. 6, 721-730.
11. DePamphilis, M.L. (1999) Replication origins in metazoan chromosomes: fact or fiction? Bioessays 21, 5-16.
12. Diffley, J.F., Cocker, J.H., Dowell, S.J., Harwood, J. & Rowley, A. (1995) Stepwise assembly of initiation complexes at budding yeast replication origins during the cell cycle. J. Cell Sci. Suppl. 19, 67-72.
13. Dimitrova, D.S. (2006) Single labelling of nascent DNA with halogenated thymidine analogues. In: Cell Biology Protocols (eds J.R. Harris, J.M. Graham & D. Rickwood), pp. 6.2. Chichester: John Wiley & Sons Ltd.
14. Dimitrova, D.S. & Berezney, R. (2002) The spatio-temporal organization of DNA replication sites is identical in primary, immortalized and transformed mammalian cells. J. Cell Sci. 115, 4037-4051.
15. Dimitrova, D.S. & Gilbert, D.M. (1998) Regulation of mammalian replication origin usage in Xenopus egg extract. J. Cell Sci. 111, 2989-2998.
16. Dimitrova, D.S. & Gilbert, D.M. (1999a) DNA replication and nuclear organization: Prospects for a soluble in vitro system. Crit. Rev. Eukaryot. Gene Expr. 9, 353-361.
17. Dimitrova, D.S. & Gilbert, D.M. (1999b) The spatial position and replication timing of chromosomal domains are both established in early G1 phase. Mol. Cell 4, 983-993.
18. Dimitrova, D.S., Prokhorova, T.A., Blow, J.J., Todorov, I.T. & Gilbert, D.M. (2002) Mammalian nuclei become licensed for DNA replication during late telophase. J. Cell Sci. 115, 51-59.
19. Dimitrova, D.S., Todorov, I.T., Melendy, T. & Gilbert, D.M. (1999) Mcm2, but not RPA, is a component of the mammalian early G1-phase prereplication complex. J. Cell Biol. 146, 709-722.
20. Gilbert, D.M., Miyazawa, H. & DePamphilis, M.L. (1995) Site-specific initiation of DNA replication in Xenopus egg extract requires nuclear structure. Mol. Cell. Biol. 15, 2942-2954.
21. Granick, D. (1975) Nucleolar necklaces in chick embryo fibroblast cells. I. Formation of necklaces by dichlororibobenzimidazole and other adenosine analogues that decrease RNA synthesis and degrade preribosomes. J. Cell Biol. 65, 398-417.
22. Gribnau, J., Diderich, K., Pruzina, S., Calzolari, R. & Fraser, P. (2000) Intergenic transcription and developmental remodeling of chromatin subdomains in the human β-globin locus. Mol. Cell 5, 377-386.
23. Haase, S.B., Heinzel, S.S. & Calos, M.P. (1994) Transcription inhibits the replication of autonomously replicating plasmids in human cells. Mol. Cell. Biol. 14, 2516-2524.
24. Hall, L.L., Byron, M., Sakai, K., Carrel, L., Willard, H.F. & Lawrence, J.B. (2002) An ectopic human XIST gene can induce chromosome inactivation in postdifferentiation human HT-1080 cells. Proc. Natl. Acad. Sci. USA 99, 8677-8682.
25. Iborra, F.J., Jackson, D.A. & Cook, P.R. (1998) The path of transcripts from extra-nucleolar synthetic sites to nuclear pores: transcripts in transit are concentrated in discrete structures containing SR proteins. J. Cell Sci. 111, 2269-2282.
26. Jackson, D.A., Hassan, A.B., Errington, R.J. & Cook, P.R. (1993) Visualization of focal sites of transcription within human nuclei. EMBO J. 12, 1059-1065.
27. Jackson, D.A., Iborra, F.J., Manders, E.M. & Cook, P.R. (1998) Numbers and organization of RNA polymerases, nascent transcripts, and transcription units in HeLa nuclei. Mol. Biol. Cell 9, 1523-1536.
28. Kedinger, C. & Simard, R. (1974) The action of α-amanitin on RNA synthesis in Chinese hamster ovary cells. Ultrastructural and biochemical studies. J. Cell Biol. 63, 831-842.
29. Keezer, S.M. & Gilbert, D.M. (2002) Sensitivity of the Origin Decision Point to specific inhibitors of cellular signaling and metabolism. Exp. Cell Res. 273, 54-64.
30. Kessler, O. & Chasin, L.A. (1996) Effects of nonsense mutations on nuclear and cytoplasmic adenine phosphoribosyltransferase RNA. Mol. Cell. Biol. 16, 4426-4435.
31. Kikyo, N., Wade, P.A., Guschin, D., Ge, H. & Wolffe, A.P. (2000) Active remodeling of somatic nuclei in egg cytoplasm by the nucleosomal ATPase ISWI. Science 289, 2360-2362.
32. Lawlis, S.J., Keezer, S.M., Wu, J.R. & Gilbert, D.M. (1996) Chromosome architecture can dictate site-specific initiation of DNA replication in Xenopus egg extracts. J. Cell Biol. 135, 1207-1218.
33. Le Panse, S., Masson, C., Heliot, L., Chassery, J.M., Junera, H.R. & Hernandez-Verdun, D. (1999) 3-D organization of ribosomal transcription units after DRB inhibition of RNA polymerase II transcription. J. Cell Sci. 112, 2145-2154.
34. Lee, Y., Kim, M., Han, J., et al. (2004) MicroRNA genes are transcribed by RNA polymerase II. EMBO J. 23, 4051-4060.
35. Li, R., Yu, D.S., Tanaka, M., Zheng, L., Berger, S.L. & Stillman, B. (1998) Activation of chromosomal DNA replication in Saccharomyces cerevisiae by acidic transcriptional activation domains. Mol. Cell. Biol. 18, 1296-1302.
36. Lindell, T.J., Weinberg, F., Morris, P.W., Roeder, R.G. & Rutter, W.J. (1970) Specific inhibition of nuclear RNA polymerase II by α-amanitin. Science 170, 447-449.
37. Maderious, A. & Chen-Kiang, S. (1984) Pausing and premature termination of human RNA polymerase II during transcription of adenovirus in vivo and in vitro. Proc. Natl. Acad. Sci. USA 81, 5931-5935.
38. Marshall, N.F. & Price, D.H. (1992) Control of formation of two distinct classes of RNA polymerase II elongation complexes. Mol. Cell. Biol. 12, 2078-2090.
39. Masson, C., Bouniol, C., Fomproix, N., Szollosi, M.S., Debey, P. & Hernandez-Verdun, D. (1996) Conditions favoring RNA polymerase I transcription in permeabilized cells. Exp. Cell Res. 226, 114-125.
40. Mechali, M. (2001) DNA replication origins: From sequence specificity to epigenetics. Nat. Rev. Genet. 2, 640-645.
41. Mesner, L.D. & Hamlin, J.L. (2005) Specific signals at the 3′ end of the DHFR gene define one boundary of the downstream origin of replication. Genes Dev. 19, 1053-1066.
42. Mitchell, P.J., Carothers, A.M., Han, J.H., et al. (1986) Multiple transcription start sites, DNase I-hypersensitive sites, and an opposite-strand exon in the 5′ region of the CHO dhfr gene. Mol. Cell. Biol. 6, 425-440.
43. Muller, M., Lucchini, R. & Sogo, J.M. (2000) Replication of yeast rDNA initiates downstream of transcriptionally active genes. Mol. Cell 5, 767-777.
44. Newport, J. & Kirschner, M. (1982) A major developmental transition in early Xenopus embryos: II. Control of the onset of transcription. Cell 30, 687-696.
45. Pemov, A., Bavykin, S. & Hamlin, J.L. (1998) Attachment to the nuclear matrix mediates specific alterations in chromatin structure. Proc. Natl. Acad. Sci. USA 95, 14757-14762.
46. Perry, R.P. & Kelley, D.E. (1970) Inhibition of RNA synthesis by actinomycin D: Characteristic dose-response of different RNA species. J. Cell Physiol. 76, 127-139.
47. Prescott, D.M. & Bender, M.A. (1962) Synthesis of RNA and protein during mitosis in mammalian tissue culture cells. Exp. Cell Res. 26, 260-268.
48. Prioleau, M.N., Huet, J., Sentenac, A. & Mechali, M. (1994) Competition between chromatin and transcription complex assembly regulates gene expression during early development. Cell 77, 439-449.
49. Rowles, A., Tada, S. & Blow, J.J. (1999) Changes in association of the Xenopus Origin Recognition Complex with chromatin on licensing of replication origins. J. Cell Sci. 112, 2011-2018.
50. Saha, S., Shan, Y., Mesner, L.D. & Hamlin, J.L. (2004) The promoter of the Chinese hamster ovary dihydrofolate reductase gene regulates the activity of the local origin and helps define its boundaries. Genes Dev. 18, 397-410.
51. Schubeler, D., MacAlpine, D.M., Scalzo, D., et al. (2004) The histone modification pattern of active genes revealed through genome-wide chromatin analysis of a higher eukaryote. Genes Dev. 18, 1263-1271.
52. Shabalina, S.A., Ogurtsov, A.Y., Kondrashov, V.A. & Kondrashov, A.S. (2001) Selective constraint in intergenic regions of human and mouse genomes. Trends Genet. 17, 373-376.
53. Sobell, H.M. (1985) Actinomycin and DNA transcription. Proc. Natl. Acad. Sci. USA 82, 5328-5331.
54. Storz, G. (2002) An expanding universe of noncoding RNAs. Science 296, 1260-1263.
55. Tamm, I., Hand, R. & Caliguiri, L.A. (1976) Action of dichlorobenzimidazole riboside on RNA synthesis in L-929 and HeLa cells. J. Cell Biol. 69, 229-240.
56. Tamm, I., Kikuchi, T., Darnell, J.E. Jr & Salditt-Georgieff, M. (1980) Short capped hnRNA precursor chains in HeLa cells: Continued synthesis in the presence of 5,6-dichloro-1-β-D-ribofuranosylbenzimidazole. Biochemistry 19, 2743-2748.
57. Wansink, D.G., Schul, W., van der Kraan, I., van Steensel, B., van Driel, R. & 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.
58. Wieland, T. & Faulstich, H. (1991) Fifty years of amanitin. Experientia 47, 1186-1193.
59. Woodland, H.R. & Pestell, R.Q. (1972) Determination of the nucleoside triphosphate contents of eggs and oocytes of Xenopus laevis. Biochem. J. 127, 597-605.
60. Wu, J.R. & Gilbert, D.M. (1996) A distinct G1 step required to specify the Chinese hamster DHFR replication origin. Science 271, 1270-1272.