Sequence and context effects on origin function in mammalian cells

Journal of Cellular Biochemistry

Volumn 62, Issue 2, 1996, Pages 210-222

  Dijkwel, Pieter A ^a   Hamlin, Joyce L ^a  

^a UNIVERSITY OF VIRGINIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DIHYDROFOLATE REDUCTASE;

CELL NUCLEUS; CHO CELL; CHROMOSOME STRUCTURE; DNA DETERMINATION; DNA REPLICATION; GENE LOCUS; GENE REPLICATION; GENE SEQUENCE; HUMAN; MAMMAL; NONHUMAN; PRIORITY JOURNAL; REVIEW;

ANIMALS; CHO CELLS; CRICETINAE; DNA REPLICATION; MAMMALS; MODELS, GENETIC; REPLICATION ORIGIN; TETRAHYDROFOLATE DEHYDROGENASE;

EUKARYOTA; MAMMALIA; PROKARYOTA;

EID: 0029848056     PISSN: 07302312     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1097-4644(199608)62:2<210::AID-JCB9>3.0.CO;2-V     Document Type: Review

References (85)

1. Adachi Y, Laemmli UK (1994): Study of the cell cycle-dependent assembly of the DNA pre-replication centres in Xenopus egg extracts. EMBO J 13:4153-4164.
2. Amati B, Gasser SM (1988): Chromosomal ARS and CEN elements bind specifically to the yeast nuclear scaffold. Cell 54:967-978.
3. Amati B, Gasser SM (1990): Drosophila scaffold-attached regions bind nuclear scaffolds and can function as ARS elements in both budding and fission yeasts. Mol Cell Biol 10:5442-5454.
4. Belgrader P, Siegel AJ, Berezney R (1991): A comprehensive study on the isolation and characterization of the HeLa S3 nuclear matrix. J Cell Sci 98:281-291.
5. Bell SP, Kobayashi R, Stillman B (1993): Yeast origin recognition complex functions in transcription silencing and DNA replication [see comments]. Science 262:1844-1849.
6. Berezney R (1984): Organization and functions of the nuclear matrix. In: Anonymous Chromosomal Nonhistone Proteins. Boca Raton, FL: CRC Press, pp 119-130.
7. Berezney R, Coffey DS (1974): Identification of nuclear protein matrix. Biochem Biophys Res Commun 60:1410-1417.
8. Biedler JL, Spengler, BA (1976): Metaphase chromosome anomaly: Association with drug-resistance and cell-specific products. Science 191:185-187.
9. Blow JJ, Dilworth SM, Dingwall C, Mills AD, Laskey RA (1987): Chromosome replication in cell-free systems from Xenopus eggs. Philos Trans R Soc Lond B Biol Sci 317:483-494.
10. Brewer BJ, Fangman WL (1987): The localization of replication origins on ARS plasmids in S. cerevisiae. Cell 51:463-471.
11. Brewer BJ, Fangman WL (1991): Mapping replication origins in yeast chromosomes. Bioessays 13:317-322.
12. Brewer BJ, Fangman WL (1993): Initiation at closely spaced replication origins in a yeast chromosome. Science 262: 1728-1731.
13. Burhans WC, Vassilev LT, Caddle MS, Heintz NH, De-Pamphilis ML (1990): Identification of an origin of bidirectional DNA replication in mammalian chromosomes. Cell 62:955-965.
14. Burhans WC, Vassilev LT, Wu J, Sogo JM, Nallaseth FS, DePamphilis ML (1991): Emetine allows identification of origins of mammalian DNA replication by imbalanced DNA synthesis, not through conservative nucleosome segregation. EMBO J 10:4351-4360.
15. Carroll SM, DeRose ML, Kolman JL, Nonet GH, Kelly RE, Wahl GM (1993): Localization of a bidirectional DNA replication origin in the native locus and in episomally amplified murine adenosine deaminase loci. Mol Cell Biol 13:2971-2981.
16. Chan CS, Tye BK (1980): Autonomously replicating sequences in Saccharomyces cerevisiae. Proc Natl Acad Sci USA 77:6329-6333.
17. Dijkwel PA, Hamlin JL (1988): Matrix attachment regions are positioned near replication initiation sites, genes, and an interamplicon junction in the amplified dihydrofolate reductase domain of Chinese hamster ovary cells. Mol Cell Biol 8:5398-5409.
18. Dijkwel PA, Hamlin JL (1992): Initiation of DNA replication in the dihydrofolate reductase locus is confined to the early S period in CHO cells synchronized with the plant amino acid mimosine. Mol Cell Biol 12:3715-3722.
19. Dijkwel PA, Hamlin JL (1995): The Chinese hamster dihydrofolate reductase origin consists of multiple potential nascent-strand start sites. Mol Cell Biol 15:3023-3031.
20. Dijkwel PA, Wenink PW, Poddighe J (1986): Permanent attachment of replication origins to the nuclear matrix in BHK-cells. Nucleic Acids Res 14:3241-3249.
21. Dijkwel PA, Vaughn JP, Hamlin JL (1991): Mapping of replication initiation sites in mammalian genomes by two-dimensional gel analysis: Stabilization and enrichment of replication intermediates by isolation on the nuclear matrix. Mol Cell Biol 11:3850-3859.
22. Ferguson BM, Brewer BJ, Fangman WL (1991): Temporal control of DNA replication in yeast. Cold Spring Harbor Symp Quant Biol 56:293-302.
23. Fishel BR, Sperry AO, Garrard WT (1993): Yeast calmodulin and a conserved nuclear protein participate in the in vivo binding of a matrix association region. Proc Natl Acad Sci USA 90:5623-5627.
24. Frappier L, Zannis-Hadjopoulos M (1987): Autonomous replication of plasmids bearing monkey DNA origin-enriched sequences. Proc Natl Acad Sci USA 84:6668-6672.
25. Gerace L, Blobel G (1980): The nuclear envelope lamina is reversibly depolymerized during mitosis. Cell 19:277-287.
26. Gilbert DM, Miyazawa H, DePamphilis ML (1995): Site-specific initiation of DNA replication in Xenopus egg extract requires nuclear structure. Mol Cell Biol 15:2942-2954.
27. Goldman MA, Holmquist GP, Gray MC, Caston LA, Nag A (1984): Replication timing of genes and middle repetitive sequences. Science 224:686-692.
28. Gray JW, Lucas JN, Pinkel D, Awa A (1992): Structural chromosome analysis by whole chromosome painting for assessment of radiation-induced genetic damage. J Radiat Res (Tokyo) 33(Suppl):80-6.
29. Handeli S, Klar A, Meuth M, Cedar H (1989): Mapping replication units in animal cells. Cell 57:909-920.
30. Hassan AB, Errington RJ, White NS, Jackson DA, Cook PR (1994): Replication and transcription sites are colocalized in human cells. J Cell Science 107:425-434.
31. Heintz NH, Hamlin JL (1982): An amplified chromosomal sequence that includes the gene for dihydrofolate reductase initiates replication within specific restriction fragments. Proc Natl Acad Sci USA 79:4083-4087.
32. Heinzel SS, Krysan PJ, Tran CT, Calos MP (1991): Autonomous DNA replication in human cells is affected by the size and the source of the DNA. Mol Cell Biol 11:2263-2272.
33. Holmquist GP (1987): Role of replication time in the control of tissue-specific gene expression. Am J Hum Genet 40: 151-173.
34. Huberman JA, Riggs AD (1968): On the mechanism of DNA replication in mammalian chromosomes. J Mol Biol 32: 327-341.
35. Jackson DA, Hassan AB, Errington RJ, Cook PR (1993): Visualization of focal sites of transcription within human nuclei. EMBO J 12:1059-1065.
36. Jacob F, Brenner S (1963): Sur la Regulation de la synthese du DNA chez les bacteriers: l'Hypothese du replicon. Comp Rendu Acad Sci 246:298-300.
37. Kaguni JM, Kornberg A (1984): Replication initiated at the origin (oriC) of the E. coli chromosome reconstituted with purified enzymes. Cell 38:183-190.
38. Kas E, Poljak L, Adachi Y, Laemmli UK (1993): A model for chromatin opening: Stimulation of topoisomerase II and restriction enzyme cleavage of chromatin by distamycin. EMBO J 12:115-126.
39. Kaufmann SH, Coffey DS, Shaper JH (1981): Considerations in the isolation of rat liver nuclear matrix, nuclear envelope, and pore complex lamina. Exp Cell Res 132:105-123.
40. Kellum R, Schedl P (1991): A position-effect assay for boundaries of higher order chromosomal domains. Cell 64:941-950.
41. Kelly RE, DeRose ML, Draper BW, Wahl GM (1995): Identification of an origin of bidirectional DNA replication in the ubiquitously expressed mammalian CAD gene. Mol Cell Biol 15:4136-4148.
42. Klehr D, Maass K, Bode J (1991): Scaffold-attached regions from the human interferon beta domain can be used to enhance the stable expression of genes under the control of various promoters. Biochemistry 30:1264-1270.
43. Kornberg A, Baker TA (1992) DNA Replication. New York: W.H. Freeman.
44. Krysan PJ, Calos MP (1991): Replication initiates at multiple locations on an autonomously replicating plasmid in human cells. Mol Cell Biol 11:1464-1472.
45. Krysan PJ, Haase SB, Calos MP (1989): Isolation of human sequences that replicate autonomously in human cells. Mol Cell Biol 9:1026-1033.
46. Lee MS, Garrard WT (1991): Transcription-induced nucleosome "splitting": An underlying structure for DNase I sensitive chromatin. EMBO J 10:607-615.
47. Lengauer C, Riethman H, Cremer T (1990): Painting of human chromosomes with probes generated from hybrid cell lines by PCR with Alu and L1 primers. Hum Genet 86:1-6.
48. Leu TH, Hamlin JL (1989): High-resolution mapping of replication fork movement through the amplified dihydrofolate reductase domain in CHO cells by in-gel renaturation analysis. Mol Cell Biol 9:523-531.
49. Li JJ, Kelly TJ (1984): Simian virus 40 DNA replication in vitro. Proc Natl Acad Sci USA 81:6973-6977.
50. Lichter P, Cremer T, Tang CJ, Watkins PC, Manuelidis L, Ward DC (1988): Rapid detection of human chromosome 21 aberrations by in situ hybridization. Proc Natl Acad Sci USA 85:9664-9668.
51. Little RD, Platt TH, Schildkraut CL (1993): Initiation and termination of DNA replication in human rRNA genes. Mol Cell Biol 13:6600-6613.
52. Liu LF, Wang JC (1987): Supercoiling of the DNA template during transcription. Proc Natl Acad Sci USA 84:7024-7027.
53. Loc PV, Stratling WH (1988): The matrix attachment regions of the chicken lysozyme gene co-map with the boundaries of the chromatin domain. EMBO J 7:655-664.
54. Looney JE, Hamlin JL (1987): Isolation of the amplified dihydrofolate reductase domain from methotrexate-resistant Chinese hamster ovary cells. Mol Cell Biol 7:569-577.
55. Ma C, Leu TH, Hamlin JL (1990): Multiple origins of replication in the dihydrofolate reductase amplicons of a methotrexate-resistant chinese hamster cell line. Mol Cell Biol 10:1338-1346.
56. Mah DC, Dijkwel PA, Todd A, Klein V, Price GB, Zannis-Hadjopoulos M (1993): ors 12, a mammalian autonomously replicating DNA sequence, associates with the nuclear matrix in a cell cycle-dependent manner. J Cell Science 105:807-818.
57. McWhinney C, Leffak M (1990): Autonomous replication of a DNA fragment containing the chromosomal replication origin of the human c-myc gene. Nucleic Acids Res 18: 1233-1242.
58. Meier J, Campbell KH, Ford CC, Stick R, Hutchison CJ (1991): The role of lamin LIII in nuclear assembly and DNA replication, in cell-free extracts of Xenopus eggs. J Cell Sci 98:271-279.
59. Milbrandt JD, Heintz NH, White WC, Rothman SM, Hamlin JL (1981): Methotrexate-resistant Chinese hamster ovary cells have amplified a 135-kilobase-pair region that includes the dihydrofolate reductase gene. Proc Natl Acad Sci USA 78:6043-6047.
60. Mirkositch J, Mirault ME, Laemmli UK (1986): Organization of the higher order of chromatin loop: Specific DNA attachment sites on the nuclear scaffold. Cell 38:223-232.
61. Nakamura H, Morita T, 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, Berezney R (1989): Mapping replicational sites in the eucaryotic cell nucleus. J Cell Biol 108:1-11.
63. Natale DA, Umek RM, Kowalski D (1993): Ease of DNA unwinding is a conserved property of yeast replication origins. Nucleic Acids Res 21:555-560.
64. Nawotka KA, Huberman JA (1988): Two-dimensional gel electrophoretic method for mapping DNA replicons. Mol Cell Biol 8:1408-1413.
65. Newlon CS, Theis JF (1993): The structure and function of yeast autonomously replicating sequences. Curr Opin Genet Dev 3:752-758.
66. Newport J (1987): Nuclear reconstitution in vitro: Stages of assembly around protein-free DNA. Cell 48:205-217.
67. Newport JW, Wilson KL, Dunphy WG (1990): A lamin-independent pathway for nuclear envelope assembly. J Cell Biol 111:2247-59.
68. Pienta KJ, Getzenberg RH, Coffey DS (1991): Cell structure and DNA organization. Crit Rev Eukaryot Gene Exp 1:355-385.
69. Razin SV, Kekelidze MG, Lukanidin EM, Scherrer K, Georgiev GP (1986): Replication origins are attached to the nuclear skeleton. Nucleic Acids Res 14:8189-8207.
70. Roufa DJ, Marchionni MA (1982): Nucleosome segregation at a defined mammalian chromosomal site. Proc Natl Acad Sci USA 79:1810-1814.
71. Shinomiya T, Ina S (1991): Analysis of chromosomal replicons in early embryos of Drosophila melanogaster by two-dimensional gel electrophoresis. Nucleic Acids Res 19:3935-3941.
72. Shinomiya T, Ina S (1993): DNA replication of histone gene repeats in Drosophila melanogaster tissue culture cells: Multiple initiation sites and replication pause sites. Mol Cell Biol 13:4098-4106.
73. Spector DL (1990): Higher order nuclear organization: Three-dimensional distribution of small nuclear ribonucleoprotein particles [published erratum appears in Proc Natl Acad Sci USA 1990, 87:2384]. Proc Natl Acad Sci USA 87:147-151.
74. Stief A, Winter DM, Stratling WH, Sippel AE (1989): A nuclear DNA attachment element mediates elevated and position-independent gene activity. Nature 341:343-345.
75. Stinchcomb DT, Thomas M, Kelly J, Selker E, Davis RW (1980): Eukaryotic DNA segments capable of autonomous replication in yeast. Proc Natl Acad Sci USA 77:4559-4563.
76. Sudo K, Ogata M, Sato Y, Iguchi AS, Ariga H (1990): Cloned origin of DNA replication in c-myc gene can function and be transmitted in transgenic mice in an episomal state. Nucleic Acids Res 18:5425-5432.
77. Trask BJ, Hamlin JL (1989): Early dihydrofolate reductase gene amplification events in CHO cells usually occur on the same chromosome arm as the original locus. Genes Dev 3:1913-1925.
78. Valenzuela MS, Mueller GC, Dasgupta S (1983): Nuclear matrix-DNA complex resulting from EcoR1 digestion of HeLa nucleoids is enriched for DNA replicating forks. Nucleic Acids Res 11:2155-2164.
79. Vassilev L, Johnson EM (1989): Mapping initiation sites of DNA replication in vivo using polymerase chain reaction amplification of nascent strand segments. Nucleic Acids Res 17:7693-7705.
80. Vassilev LT, Burhans WC, DePamphilis ML (1990): Mapping an origin of DNA replication at a single-copy locus in exponentially proliferating mammalian cells. Mol Cell Biol 10:4685-4689.
81. Vaughn JP, Dijkwel PA, Hamlin JL (1990): Replication initiates in a broad zone in the amplified CHO dihydrofolate reductase domain. Cell 61:1075-1087.
82. Yan H, Newport J (1995): An analysis of the regulation of DNA synthesis by cdk2, Cip1, and licensing factor. J Cell Biol 129:1-15.
83. Yoon Y, Sanchez JA, Brun C, Huberman JA (1995): Mapping of replication initiation sites in human ribosomal DNA by nascent-strand abundance analysis. Mol Cell Biol 15:2482-2489.
84. Zannis-Hadjopoulos M, Kaufmann G, Wang SS, Lechner RL, Karawya E, Hesse J, Martin RG (1985): Properties of some monkey DNA sequences obtained by a procedure that enriches for DNA replication origins. Mol Cell Biol 5:1621-1629.
85. Zhao K, Kas E, Gonzalez E, Laemmli UK (1993): SAR-dependent mobilization of histone H1 by HMG-I/Y in vitro: HMG-I/Y is enriched in H1-depleted chromatin. EMBO J 12:3237-3247.