Remodeling of chromatin loops does not account for specification of replication origins during Xenopus development

Chromosoma

Volumn 107, Issue 3, 1998, Pages 155-165

  Marie, Chrystelle ^a   Hyrien, Olivier ^a  

^a ECOLE NORMALE SUPÉRIEURE   (France)

Author keywords

[No Author keywords available]

Indexed keywords

RIBOSOME DNA; SPACER DNA;

ANIMAL TISSUE; ARTICLE; BLASTULA; CELL NUCLEUS MATRIX; CHROMATIN STRUCTURE; DEVELOPMENTAL GENETICS; DNA REPLICATION ORIGIN; EMBRYO; EMBRYO DEVELOPMENT; GASTRULA; GENE CLUSTER; NONHUMAN; REPLICON; XENOPUS;

ANIMALS; BINDING SITES; CELL FRACTIONATION; CHROMATIN; DNA; DNA PROBES; DNA, RIBOSOMAL; ELECTROPHORESIS, AGAR GEL; NUCLEAR MATRIX; NUCLEIC ACID CONFORMATION; PROTEIN BINDING; REPLICATION ORIGIN; RESTRICTION MAPPING; XENOPUS;

ANIMALIA; VERTEBRATA;

EID: 0031903512     PISSN: 00095915     EISSN: None     Source Type: Journal    
DOI: 10.1007/s004120050292     Document Type: Article

References (70)

1. Aelen JM, Opstelten RJ, Wanka F (1983) Organization of DNA replication in Physarum polycephalum. Attachment of origins of replicons and replication forks to the nuclear matrix. Nucleic Acids Res 11:1181-1195
2. 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
3. Amati B, Pick L, Laroche T, Gasser SM (1990) Nuclear scaffold attachment stimulates, but is not essential for ARS activity in Saccharomyces cerevisiae: analysis of the Drosophila ftz SAR. EMBO J 9:4007-4016
4. Ariizumi K, Ghosh MR, Tucker PW (1993) Elements in the immunoglobulin heavy-chain enhancer directly regulate simian virus 40 ori-dependent DNA replication. Mol Cell Biol 13:5629-5636
5. Bakken A, Morgan G, Sollner-Webb B, Roan J, Busby S, Reeder RH (1982) Mapping of transcription initiation and termination signals on Xenopus laevis ribosomal DNA. Proc Natl Acad Sci USA 79:56-60
6. Berezney R, Coffey DS (1974) Identification of a nuclear protein matrix. Biochem Biophys Res Commun 60:1410-1417
7. Berezney R, Coffey DS (1975) Nuclear protein matrix: association with newly synthesized DNA. Science 189:291-293
8. Bickmore WA, Oghene K (1996) Visualizing the spatial relationships between defined DNA sequences and the axial region of extracted metaphase chromosomes. Cell 84:95-104
9. Blumenthal AB, Kriegstein HJ, Hogness DS (1974) The units of DNA replication in Drosophila melanogaster chromosomes. Cold Spring Harb Symp Quant Biol 38:205-223
10. Buongiorno-Nardelli M, Micheli G, Carri MT, Marilley M (1982) A relationship between replicon size and supercoiled loop domains in the eukaryotic genome. Nature 298:100-102
11. Carpenter PB, Mueller PR, Dunphy WG ( 1996) Role for a Xenopus Orc-2-related protein in controlling DNA replication. Nature 379:357-360
12. Carri MT, Micheli G, Graziano E, Pace T, Buogiorno-Nardelli M (1986) The relationship between chromosomal origins of replication and the nuclear matrix during the cell cycle. Exp Cell Res 164:426-436
13. Cockerill PN (1990) Nuclear matrix attachment occurs in several regions of the IgH locus. Nucleic Acids Res 18:2643-2648
14. Cockerill PN, Garrard WT (1986) Chromosomal loop anchorage of the kappa immunoglobulin gene occurs next to the enhancer in a region containing topoisomerase II sites. Cell 44:273-282
15. Coleman TR, Carpenter PB, Dunphy WG (1996) The Xenopus Cdc6 protein is essential for the initiation of a single round of DNA replication in cell-free extracts. Cell 87:53-63
16. Cook PR (1991) The nucleoskeleton and the topology of replication. Cell 66:627-635
17. Dijkwel PA (1992) DNA replication: the search few support. Cell Biol Int Rep 16:725-737
18. Dijkwel PA, Hamlin JL (1988) Matrix attachment regions are positioned near replication initiation sites, genes, and an inter-amplicon junction in the amplified dihydrofolate reductase domain of Chinese hamster ovary cells. Mol Cell Biol 8:5398-5409
19. 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
20. Dijkwel PA, Hamlin JL (1995) Origins of replication and the nuclear matrix: the DHFR domain as a paradigm. Int Rev Cytol 162A:455-484
21. 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
22. Dingman CW (1974) Bidirectional chromosome replication: some topological considerations. J Theor Biol 43:187-195
23. Farache G, Razin SV, Rzeszowska-Wolny J, Moreau J, Targa FR, Scherrer K (1990) Mapping of structural and transcription-related matrix attachment sites in the alpha-globin gene domain of avian erythroblasts and erythrocytes. Mol Cell Biol 10:5349-5358
24. Frederick DL, Andrews MT (1994) Cell cycle remodeling requires cell-cell interactions in developing Xenopus embryos. J Exp Zool 270:410-416
25. Gasser SM, Laemmli UK (1986) Cohabitation of scaffold binding regions with upstream/enhancer elements of three developmentally regulated genes of D. melanogaster. Cell 46:521-530
26. Gasser SM, Amati BB, Cardenas ME, Hofmann JF (1989) Studies on scaffold attachment sites and their relation to genome function, Int Rev Cytol 119:57-96
27. Gencheva M, Anachkova B, Russev G (1996) Mapping the sites of initiation of DNA replication in rat and human rRNA genes. J Biol Chem 271:2608-2614
28. Gerdes MG, Carter KC, Moen PT Jr, Lawrence JB (1994) Dynamic changes in the higher-level chromatin organization of specific sequences revealed by in situ hybridization to nuclear halos. J Cell Biol 126:289-304
29. 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
30. Hamlin JL; Dijkwel PA (1995) On the nature of replication origins in higher eukaryotes. Curr Opin Genet Dev 5:153-161
31. Hyrien O, Méchali M (1992) Plasmid replication in Xenopus eggs and egg extracts: a 2D gel electrophoretic analysis. Nucleic Acids Res 20:1463-3469
32. Hyrien O. Méchali M (1993) Chromosomal replication initiates and terminates at random sequences but at regular intervals in the ribosomal DNA of Xenopus early embroys. EMBO J 12: 4511-4520
33. Hyrien O, Marie C, Méchali M (1995) Transition in specification of embryonic metazoan DNA replication origins. Science 270: 994-997
34. Hyrien O, Marie C, Lucas I (1997) Role of nuclear architecture in the initiation of eukaryotic DNA replication. Biochimie 79: 541-548
35. Izaurralde E, Mirkovitch J, Laemmli UK (1988) Interaction of DNA with nuclear scaffolds in vitro. J Mol Biol 200:11-125
36. Jackson DA, Cook PR (1986) Replication occurs at a nucleoskeleton. EMBO J 5:1403-1410
37. Jarman AP, Higgs DR (1988) Nuclear scaffold attachment sites in the human globin gene complexes. EMBO J 7:3337-3344
38. Keppel F (1986) Transcribed human ribosomal RNA genes are attached to the nuclear matrix. J Mol Biol 187:15-21
39. Kitsberg D, Selig S, Keshet I, Cedar H (1993) Replication structure of the human beta-globin gene domain. Nature 366:588-590
40. Laemmli UK. Kas E, Poljak L, Adachi Y (1992) Scaffold-associated regions: cis-acting determinants of chromatin structural loops and functional domains. Curr Opin Genet Dev 2:275-285
41. Little RD, Platt TH, Schildkraut CL (1993) Initiation and termination of DNA replication in human rRNA genes. Mol Cell Biol 13:6600-6613
42. Lucchini R, Sogo JM (1992) Different chromatin structures along the spacers flanking active and inactive Xenopus rRNA genes. Mol Cell Biol 12:4288-4296
43. Man DC, Dijkwel PA, Todd A, Klein V, Price GB, Zannis-Hajopoulos M (1993) ors12, a mammalian autonomously replicating DNA sequence, associates with the nuclear matrix in a cell cycle-dependent manner. J Cell Sci 105:807-818
44. Mahbubani HM, Paull T, Elder JK, Blow JJ (1992) DNA replication initiates at multiple sites on plasmid DNA in Xenopus egg extracts. Nucleic Acids Res 20:1457-1462
45. Marilley M, Gassend-Bonnet G (1989) Supercoiled loop organization of genomic DNA: a close relationship between loop domains, expression units, and replicon organization in rDNA from Xenopus laevis. Exp Cell Res 180:475-489
46. Micheli G, Luzzatto AR, Carri MT, de Capoa A, Pelliccia F (1993) Chromosome length and DNA loop size during early embryonic development of Xenopus laevis. Chromosoma 102:478-483
47. Mills AD, Blow JJ, White JG, Amos WB, Wilcock D, Laskey RA (1989) Replication occurs at discrete foci spaced throughout nuclei replicating in vitro. J Cell Sci 94:471-474
48. Mirkovitch J, Mirault ME, Laemmli UK (1984) Organization of the higher-order chromatin loop: specific DNA attachment sites on nuclear scaffold. Cell 39:223-232
49. Mirkovitch J, Gasser SM, Laemmli UK (1988) Scaffold attachment of DNA loops in metaphase chromosomes. J Mol Biol 200:101-109
50. 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
51. Nakayasu H, Berezney R (1989) Mapping replicational sites in the eucaryotic cell nucleus. J Cell Biol 108:1-11
52. Newport J, Kirschner M (1982) A major developmental transition in early Xenopus embryos: I. characterization and timing of cellular changes at the midblastula stage. Cell 30:675-686
53. Newport J, Yan H (1996) Organization of DNA into foci during replication. Curr Opin Cell Biol 8:365-368
54. Paulson JR, Laemmli UK (1977) The structure of histone-depleted metaphase chromosomes. Cell 12:817-828
55. Romanowski P, Madine MA, Rowles A, Blow JJ, Laskey RA (1996) The Xenopus origin recognition complex is essentia for DNA replication and MCM binding to chromatin. Curr Biol 6:1416-1425
56. Rowles A, Chong JP, Brown L, Howell M, Evan GI, Blow JJ (1996) Interaction between the origin recognition complex and the replication licensing system in Xenopus. Cell 87:287-296
57. Shinomiya T, Ina S (1991) Analysis of chromosomal replicons in early embryos of Drosophila melanogaster by two-dimensiona gel electrophoresis. Nucleic Acids Res 19:3935-3941
58. Shinomiya T, Ina S (1993) DNA replication of histone gene repeat in Drosophila melanogaster tissue culture cells: multiple initia tion sites and replication pause sites. Mol Cell Biol 13:4098 4106
59. Shiodkawa K, Misumi Y, Yamana K (1981) Demonstration of rRNA synthesis in pre-gastrular embryos of Xenopus laevis. Dev Growth Diff 23:579-587
60. Spann TP, Moir RD. Goldman AE, Stick R, Goldman RD (1997) Disruption of nuclear lamin organization alters the distribution of replication factors and inhibits DNA synthesis. J Cell Biol 136:1201-1212
61. van den Engh G, Sachs R, Trask BJ (1992) Estimating genomic distance from DNA sequence location in cell nuclei by a random walk model. Science 257:1410-1412
62. Vaughn JP, Dijkwel PA, Hamlin JL (1990)a) Replication initiates in a broad zone in the amplified CHO dihydrofolate reductase domain. Cell 61:1075-1087
63. Vaughn JP, Dijkwel PA, Mullenders LH, Hamlin JL (1990b) Replication forks are associated with the nuclear matrix. Nucleic Acids Res 18:1965-1969
64. Verbovaia L, Razin SV (1995) Analysis of the replication direction trough the domain of alpha-globin-encoding chicken genes. Gene 166:255-259
65. Vogelstein B, Pardoll DM, Coffey DS (1980) Supercoiled loops and eucaryotic DNA replication. Cell 22:79-85
66. Walter J, Newport JW (1997) Regulation of replicon size in Xenopus egg extracts. Science 275:993-995
67. Westley B, Knowland J (1978) An estrogen receptor from Xenopus laevis liver possibly connected with vitellogenin synthesis. Cell 15:367-374
68. Wu JR, Gilbert DM (1996) A distinct G1 step required to specify the Chinese hamster DHFR replication origin. Science 271: 1270-1272
69. Wu JR, Gilbert DM (1997) The replication origin decision point is a mitogen-independent, 2-aminopurine-sensitive, G1-phase event that precedes restriction point control. Mol Cell Biol 17: 4312-1321
70. 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