A revisionist replicon model for higher eukaryotic genomes

Journal of Cellular Biochemistry

Volumn 105, Issue 2, 2008, Pages 321-329

  Hamlin, J L ^a   Mesner, L D ^a   Lar, O ^a   Torres, R ^a   Chodaparambil, S V ^a   Wang, L ^a  

^a UNIVERSITY OF VIRGINIA   (United States)

Author keywords

Chromatin; Origin; Replicator; Replicon; Transcription

Indexed keywords

CHROMATIN; EPIGENETICS; EUKARYOTE; GENE EXPRESSION; GENE MAPPING; GENE REPLICATION; GENE SEQUENCE; GENOME; HUMAN; MICROARRAY ANALYSIS; NONHUMAN; PRIORITY JOURNAL; REPLICON; REVIEW; SACCHAROMYCES CEREVISIAE; SCHIZOSACCHAROMYCES POMBE;

EUKARYOTIC CELLS; GENOME; MODELS, GENETIC; REPLICATION ORIGIN; REPLICON;

EUKARYOTA; MAMMALIA; SACCHAROMYCES CEREVISIAE; SCHIZOSACCHAROMYCES POMBE;

EID: 54849417379     PISSN: 07302312     EISSN: 10974644     Source Type: Journal    
DOI: 10.1002/jcb.21828     Document Type: Review

References (81)

1. Abdurashidova G, Deganuto M, Klima R, Riva S, Biamonti G, Giacca M, Falaschi A. 2000. Start sites of bidirectional DNA synthesis at the human lamin B2 origin. Science 287:2023-2026.
2. Aladjem MI, Groudine M, Brody LL, Dieken ES, Fournier RE, Wahl GM, Epner EM. 1995. Participation of the human beta-globin locus control region in initiation of DNA replication. Science 270:815-819.
3. Aladjem MI, Rodewald LW, Kolman JL, Wahl GM. 1998. Genetic dissection of a mammalian replicator in the human beta-globin locus. Science 281:1005-1009.
4. Aladjem MI, Falaschi A, Kowalski D. 2006. Eukaryotic DNA replication origins. DePamphilis M, editor. DNA replication and human disease. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press. pp 31-62.
5. Altman AL, Fanning E. 2004. Defined sequence modules and an architectural element cooperate to promote initiation at an ectopic mammalian chromosomal replication origin. Mol Cell Biol 24:4138-4150.
6. Anglana M, Apiou F, Bensimon A, Debatisse M. 2003. Dynamics of DNA replication in mammalian somatic cells: Nucleotide pool modulates origin choice and interorigin spacing. Cell 114:385-394.
7. Beall EL, Manak JR, Zhou S, Bell M, Lipsick JS, Botchan MR. 2002. Role for a Drosophila Myb-containing protein complex in site-specific DNA replication. Nature 420:833-837.
8. Bell SP, Dutta A. 2002. DNA replication in eukaryotic cells. Annu Rev Biochem 71:333-374.
9. Bell SP, Stillman B. 1992. ATP-dependent recognition of eukaryotic origins of DNA replication by a multiprotein complex. Nature 357:128-134.
10. Benard M, Lagnel C, Pierron G. 1995. Site-specific initiation of DNA replication within the non-transcribed spacer of Physarum rDNA. Nucl Acids Res 23:1447-1453.
11. Benard M, Lagnel C, Pallotta D, Pierron G. 1996. Mapping of a replication origin within the promoter region of two unlinked, abundantly transcribed actin genes of Physarum polycephalum. Mol Cell Biol 16:968-976.
12. 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.
13. Bodmer-Glavas M, Edler K, Barberis A. 2001. RNA polymerase II and III transcription factors can stimulate DNA replication by modifying origin chromatin structures. Nucl Acids Res 29:4570-4580.
14. Bosco G, Du W, Orr-Weaver TL. 2001. DNA replication control through interaction of E2F-RB and the origin recognition complex. Nat Cell Biol 3:289-295.
15. Brewer BJ, Fangman WL. 1987. The localization of replication origins on ARS plasmids in S cerevisiae. Cell 51:463-471.
16. Brewer BJ, Fangman WL. 1993. Initiation at closely spaced replication origins in a yeast chromosome. Science 262:1728-1731.
17. Buongiorno-Nardelli M, Amaldi F, Lava-Sanchez PA. 1976. Electron microscope analysis of amplifying ribosomal DNA from Xenopus laevis. Exp Cell Res 98:95-103.
18. Burhans WC, Vassilev LT, Caddle MS, Heintz NH, DePamphilis ML. 1990. Identification of an origin of bidirectional replication in mammalian chromosomes. Cell 62:955-965.
19. Caddle MS, Calos MP. 1992. Analysis of the autonomous replication behavior in human cells of the dihydrofolate reductase putative chromosomal origin of replication. Nucl Acids Res 20:5971-5978.
20. Chan CS, Tye BK. 1980. Autonomously replicating sequences in Saccharomyces cerevisiae. Proc Natl Acad Sci USA 77:6329-6333.
21. Czajkowsky DM, Liu J, Hamlin JL, Shao Z. 2008. DNA combing reveals intrinsic temporal disorder in the replication of yeast chromosome VI. J Mol Biol 375:12-19.
22. Dai J, Chuang RY, Kelly TJ. 2005. DNA replication origins in the Schizosaccharomyces pombe genome. Proc Natl Acad Sci USA 102:337-342.
23. 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.
24. Delgado S, Gomez M, Bird A, Antequera F. 1998. Initiation of DNA replication at CpG islands in mammalian chromosomes. EMBO J 17:2426-2435.
25. Delidakis C, Kafatos FC. 1987. Amplification of a chorion gene cluster in Drosophila is subject to multiple cis-regulatory elements and to long-range position effects. J Mol Biol 197:11-26.
26. 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.
27. Dijkwel PA, Hamlin JL. 1996. Sequence and context effects on origin function in mammalian cells. J Cell Biochem 62:210-222.
28. Dijkwel PA, Wang S, Hamlin JL. 2002. Initiation sites are distributed at frequent intervals in the Chinese hamster dihydrofolate reductase origin of replication but are used with very different efficiencies. Mol Cell Biol 22:3053-3065.
29. Ferguson BM, Fangman WL. 1992. A position effect on the time of replication origin activation in yeast. Cell 68:333-339.
30. Ghosh M, Liu G, Randall G, Bevington J, Leffak M. 2004. Transcription factor binding and induced transcription alter chromosomal c-myc replicator activity. Mol Cell Biol 24:10193-10207.
31. Giacca M, Zentilin L, Norio P, Diviacco S, Dimitrova D, Contreas G, Biamonti G, Perini G, Weighardt F, Riva S. 1994. Fine mapping of a replication origin of human DNA. Proc Natl Acad Sci USA 91:7119-7123.
32. Gilbert DM. 2004. In search of the holy replicator. Nat Rev Mol Cell Biol 5:848-855.
33. Goldman MA, Holmquist GP, Gray MC, Caston LA, Nag A. 1984. Replication timing of genes and middle repetitive sequences. Science 224:686-692.
34. Gomez M, Antequera F. 1999. Organization of DNA replication origins in the fission yeast genome. EMBO J 18:5683-5690.
35. Gray SJ, Liu G, Altman AL, Small LE, Fanning E. 2007. Discrete functional elements required for initiation activity of the Chinese hamster dihydrofolate reductase origin beta at ectopic chromosomal sites. Exp Cell Res 313:109-120.
36. Haase SB, Heinzel SS, Calos MP. 1994. Transcription inhibits the replication of autonomously replicating plasmids in human cells. Mol Cell Biol 14:2516-2524.
37. Hamlin JL. 1992. Mammalian origins of replication. Bioessays 14:651-659.
38. Handeli S, Klar A, Meuth M, Cedar H. 1989. Mapping replication units in animal cells. Cell 57:909-920.
39. Harland RM, Laskey RA. 1980. Regulated replication of DNA microinjected into eggs of Xenopus laevis. Cell 20:761-771.
40. Heck MM, Spradling AC. 1990. Multiple replication origins are used during Drosophila chorion gene amplification. J Cell Biol 110:903-914.
41. Holmquist GP. 1987. Role of replication time in the control of tissue-specific gene expression. Am J Hum Genet 40:151-173.
42. Huberman JA, Riggs AD. 1968. On the mechanism of DNA replication in mammalian chromosomes. J Mol Biol 32:327-341.
43. Hyrien O, Maric C, Mechali M. 1995. Transition in specification of embryonic metazoan DNA replication origins. Science 270:994-997.
44. 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.
45. Jeon Y, Bekiranov S, Karnani N, Kapranov P, Ghosh S, MacAlpine D, Lee C, Hwang DS, Gingeras TR, Dutta A. 2005. Temporal profile of replication of human chromosomes. Proc Natl Acad Sci USA 102:6419-6424.
46. Kalejta RF, Li X, Mesner LD, Dijkwel PA, Lin HB, Hamlin JL. 1998. Distal sequences, but not ori-beta/OBR-1, are essential for initiation of DNA replication in the Chinese hamster DHFR origin. Mol Cell 2:797-806.
47. Keezer SM, Gilbert DM. 2002. Sensitivity of the origin decision point to specific inhibitors of cellular signaling and metabolism. Exp Cell Res 273:54-64.
48. Kim SM, Huberman JA. 2001. Regulation of replication timing in fission yeast. EMBO J 20:6115-6126.
49. Kitsberg D, Selig S, Keshet I, Cedar H. 1993. Replication structure of the human beta-globin gene domain. Nature 366:588-590.
50. Krysan PJ, Haase SB, Calos MP. 1989. Isolation of human sequences that replicate autonomously in human cells. Mol Cell Biol 9:1026-1033.
51. Lande-Diner L, Cedar H. 2005. Silence of the genes-Mechanisms of longterm repression. Nat Rev Genet 6:648-654.
52. Larner JM, Lee H, Little RD, Dijkwel PA, Schildkraut CL, Hamlin JL. 1999. Radiation down-regulates replication origin activity throughout the S phase in mammalian cells. Nucl Acids Res 27:803-809.
53. 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.
54. Lin HB, Dijkwel PA, Hamlin JL. 2005. Promiscuous initiation on mammalian chromosomal DNA templates and its possible suppression by transcription. Exp Cell Res 308:53-64.
55. Liu G, Malott M, Leffak M. 2003. Multiple functional elements comprise a Mammalian chromosomal replicator. Mol Cell Biol 23:1832-1842.
56. MacAlpine DM, Bell SP. 2005. A genomic view of eukaryotic DNA replication. Chromosome Res 13:309-326.
57. MacAlpine DM, Rodriguez HK, Bell SP. 2004. Coordination of replication and transcription along a Drosophila chromosome. Genes Dev 18:3094-3105.
58. Mesner LD, Hamlin JL. 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.
59. Mesner LD, Hamlin JL, Dijkwel PA. 2003a. The matrix attachment region in the Chinese hamster dihydrofolate reductase origin of replication may be required for local chromatid separation. Proc Natl Acad Sci USA 100:3281-3286.
60. Mesner LD, Li X, Dijkwel PA, Hamlin JL. 2003b. The dihydrofolate reductase origin of replication does not contain any nonredundant genetic elements required for origin activity. Mol Cell Biol 23:804-814.
61. Mesner LD, Crawford EL, Hamlin JL. 2006. Isolating apparently pure libraries of replication origins from complex genomes. Mol Cell 21:719-726.
62. Nawotka KA, Huberman JA. 1988. Two-dimensional gel electrophoretic method for mapping DNA replicons. Mol Cell Biol 8:1408-1413.
63. Newlon CS, Petes TD, Hereford LM, Fangman WL. 1974. Replication of yeast chromosomal DNA. Nature 247:32-35.
64. Norio P, Kosiyatrakul S, Yang Q, Guan Z, Brown NM, Thomas S, Riblet R, Schildkraut CL. 2005. Progressive activation of DNA replication initiation in large domains of the immunoglobulin heavy chain locus during B cell development. Mol Cell 20:575-587.
65. Paixao S, Colaluca IN, Cubells M, Peverali FA, Destro A, Giadrossi S, Giacca M, Falaschi A, Riva S, Biamonti G. 2004. Modular structure of the human lamin B2 replicator. Mol Cell Biol 24:2958-2967.
66. Pasero P, Bensimon A, Schwob E. 2002. Single-molecule analysis reveals clustering and epigenetic regulation of replication origins at the yeast rDNA locus. Genes Dev 16:2479-2484.
67. Pattenden SG, Chandy MJ, Gutierrez JL, Workman JL. 2005. Chromatin dynamics rule the genome. Genome Biol 6:355.
68. Raghuraman MK, Winzeler EA, Collingwood D, Hunt S, Wodicka L, Conway A, Lockhart DJ, Davis RW, Brewer BJ, Fangman WL. 2001. Replication dynamics of the yeast genome. Science 294:115-121.
69. Razin SV, Kekelidze MG, Lukanidin EM, Scherrer K, Georgiev GP. 1986. Replication origins are attached to the nuclear skeleton. Nucl Acids Res 14:8189-8207.
70. Saha S, Shan Y, Mesner LD, Hamlin JL. 2004. The promoter of the CHO dihydrofolate reductase gene regulates the activity of the local origin and helps define its boundaries. Genes Dev 18:397-410.
71. Schubeler D, MacAlpine DM, Scalzo D, Wirbelauer C, Kooperberg C, van Leeuwen F, Gottschling DE, O'neill LP, Turner BM, Delrow J, Bell SP, Groudine M. 2004. The histone modification pattern of active genes revealed through genome-wide chromatin analysis of a higher eukaryote. Genes Dev 18:1263-1271.
72. Segurado M, de Luis A, Antequera F. 2003. Genome-wide distribution of DNA replication origins at ART-rich islands in Schizosaccharomyces pombe. EMBO Rep 4:1048-1053.
73. Snyder M, Sapolsky RJ, Davis RW. 1988. Transcription interferes with elements important for chromosome maintenance in Saccharomyces cerevisiae. Mol Cell Biol 8:2184-2194.
74. Stinchcomb DT, Struhl K, Davis RW. 1979. Isolation and characterisation of a yeast chromosomal replicator. Nature 282:39-43.
75. Todorovic V, Giadrossi S, Pelizon C, Mendoza-Maldonado R, Masai H, Giacca M. 2005. Human origins of DNA replication selected from a library of nascent DNA. Mol Cell 19:567-575.
76. Toledo F, Baron B, Fernandez MA, Lachages AM, Mayau V, Buttin G, Debatisse M. 1998. oriGNA I3: A narrow zone of preferential replication initiation in mammalian cells identified by 2D gel and competitive PCR replicon mapping techniques. Nucl Acids Res 26:2313-2321.
77. Vogelauer M, Rubbi L, Lucas I, Brewer BJ, Grunstein M. 2002. Histone acetylation regulates the time of replication origin firing. Mol Cell 10:1223-1233.
78. Wright AP, Maundrell K, Shall S. 1986. Transformation of Schizosaccharomyces pombe by non-homologous, unstable integration of plasmids in the genome. Curr Genet 10:503-508.
79. Zhang J, Xu F, Hashimshony T, Keshet I, Cedar H. 2002. Establishment of transcriptional competence in early and late S phase. Nature 420:198-202.
80. Zhou J, Chau C, Deng Z, Stedman W, Lieberman PM. 2005. Epigenetic control of replication origins. Cell Cycle 4:889-892.
81. Zhou J, Chau CM, Deng Z, Shiekhattar R, Spindler MP, Schepers A, Lieberman PM. 2006. Cell cycle regulation of chromatin at an origin of DNA replication. EMBO J 24:1406-1417.