References

  1. Jacob F, Brenner S, Cuzin F: On the regulation of DNA replication in bacteria.

    Cold Spring Harb Symp Quant Biol 1963, 28:329-438. OpenURL

  2. Newlon CS, Collins I, Dershowitz A, Deshpande AM, Greenfeder SA, Ong LY, Theis JF: Analysis of replication origin function on chromosome III of Saccharomyces cerevisiae.

    Cold Spring Harb Symp Quant Biol 1993, 58:415-423. PubMed Abstract OpenURL

  3. Stinchcomb DT, Struhl K, Davis RW: Isolation and characterisation of a yeast chromosomal replicator.

    Nature 1979, 282:39-43. PubMed Abstract OpenURL

  4. Brewer BJ, Fangman WL: The localization of replication origins on ARS plasmids in S. cerevisiae.

    Cell 1987, 51:463-471. PubMed Abstract OpenURL

  5. Huberman JA, Spotila LD, Nawotka KA, el-Assouli SM, Davis LR: The in vivo replication origin of the yeast 2 microns plasmid.

    Cell 1987, 51:473-481. PubMed Abstract OpenURL

  6. Theis JF, Newlon CS: The ARS309 chromosomal replicator of Saccharomyces cerevisiae depends on an exceptional ARS consensus sequence.

    Proc Natl Acad Sci USA 1997, 94:10786-10791. PubMed Abstract | Publisher Full Text OpenURL

  7. Diffley JF, Cocker JH: Protein-DNA interactions at a yeast replication origin.

    Nature 1992, 357:169-172. PubMed Abstract | Publisher Full Text OpenURL

  8. Bell SP, Stillman B: ATP-dependent recognition of eukaryotic origins of DNA replication by a multiprotein complex.

    Nature 1992, 357:128-134. PubMed Abstract | Publisher Full Text OpenURL

  9. Chesnokov I, Remus D, Botchan M: Functional analysis of mutant and wild-type Drosophila origin recognition complex.

    Proc Natl Acad Sci USA 2001, 98:11997-12002. PubMed Abstract | Publisher Full Text OpenURL

  10. Gavin KA, Hidaka M, Stillman B: Conserved initiator proteins in eukaryotes.

    Science 1995, 270:1667-1671. PubMed Abstract OpenURL

  11. Foss M, McNally FJ, Laurenson P, Rine J: Origin recognition complex (ORC) in transcriptional silencing and DNA replication in S. cerevisiae.

    Science 1993, 262:1838-1844. PubMed Abstract OpenURL

  12. Pak DT, Pflumm M, Chesnokov I, Huang DW, Kellum R, Marr J, Romanowski P, Botchan MR: Association of the origin recognition complex with heterochromatin and HP1 in higher eukaryotes.

    Cell 1997, 91:311-323. PubMed Abstract | Publisher Full Text OpenURL

  13. Chesnokov IN, Chesnokova ON, Botchan M: A cytokinetic function of Drosophila ORC6 protein resides in a domain distinct from its replication activity.

    Proc Natl Acad Sci USA 2003, 100:9150-9155. PubMed Abstract | Publisher Full Text OpenURL

  14. Prasanth SG, Prasanth KV, Stillman B: Orc6 involved in DNA replication, chromosome segregation, and cytokinesis.

    Science 2002, 297:1026-1031. PubMed Abstract | Publisher Full Text OpenURL

  15. Aparicio OM, Weinstein DM, Bell SP: Components and dynamics of DNA replication complexes in S. cerevisiae: redistribution of MCM proteins and Cdc45p during S phase.

    Cell 1997, 91:59-69. PubMed Abstract | Publisher Full Text OpenURL

  16. Celniker SE, Sweder K, Srienc F, Bailey JE, Campbell JL: Deletion mutations affecting autonomously replicating sequence ARS1 of Saccharomyces cerevisiae.

    Mol Cell Biol 1984, 4:2455-2466. PubMed Abstract OpenURL

  17. Newlon CS, Theis JF: The structure and function of yeast ARS elements.

    Curr Opin Genet Dev 1993, 3:752-758. PubMed Abstract OpenURL

  18. Wilmes GM, Bell SP: The B2 element of the Saccharomyces cerevisiae ARS1 origin of replication requires specific sequences to facilitate pre-RC formation.

    Proc Natl Acad Sci USA 2002, 99:101-106. PubMed Abstract | Publisher Full Text OpenURL

  19. Zou L, Stillman B: Assembly of a complex containing Cdc45p, replication protein A, and Mcm2p at replication origins controlled by S-phase cyclin-dependent kinases and Cdc7p-Dbf4p kinase.

    Mol Cell Biol 2000, 20:3086-3096. PubMed Abstract | Publisher Full Text OpenURL

  20. Matsumoto K, Ishimi Y: Single-stranded-DNA-binding protein-dependent DNA unwinding of the yeast ARS1 region.

    Mol Cell Biol 1994, 14:4624-4632. PubMed Abstract OpenURL

  21. Natale DA, Umek RM, Kowalski D: Ease of DNA unwinding is a conserved property of yeast replication origins.

    Nucleic Acids Res 1993, 21:555-560. PubMed Abstract OpenURL

  22. Lipford JR, Bell SP: Nucleosomes positioned by ORC facilitate the initiation of DNA replication.

    Mol Cell 2001, 7:21-30. PubMed Abstract | Publisher Full Text OpenURL

  23. Sharma K, Weinberger M, Huberman JA: Roles for internal and flanking sequences in regulating the activity of mating-type-silencer-associated replication origins in Saccharomyces cerevisiae.

    Genetics 2001, 159:35-45. PubMed Abstract | Publisher Full Text OpenURL

  24. Walker SS, Francesconi SC, Eisenberg S: A DNA replication enhancer in Saccharomyces cerevisiae.

    Proc Natl Acad Sci USA 1990, 87:4665-4669. PubMed Abstract | Publisher Full Text OpenURL

  25. Raychaudhuri S, Byers R, Upton T, Eisenberg S: Functional analysis of a replication origin from Saccharomyces cerevisiae: identification of a new replication enhancer.

    Nucleic Acids Res 1997, 25:5057-5064. PubMed Abstract | Publisher Full Text OpenURL

  26. Chang VK, Fitch MJ, Donato JJ, Christensen TW, Merchant AM, Tye BK: Mcm1 binds replication origins.

    J Biol Chem 2003, 278:6093-6100. PubMed Abstract | Publisher Full Text OpenURL

  27. Raghuraman MK, Winzeler EA, Collingwood D, Hunt S, Wodicka L, Conway A, Lockhart DJ, Davis RW, Brewer BJ, Fangman WL: Replication dynamics of the yeast genome.

    Science 2001, 294:115-121. PubMed Abstract | Publisher Full Text OpenURL

  28. Wyrick JJ, Aparicio JG, Chen T, Barnett JD, Jennings EG, Young RA, Bell SP, Aparicio OM: Genome-wide distribution of ORC and MCM proteins in S. cerevisiae: high-resolution mapping of replication origins.

    Science 2001, 294:2357-2360. PubMed Abstract | Publisher Full Text OpenURL

  29. Yabuki N, Terashima H, Kitada K: Mapping of early firing origins on a replication profile of budding yeast.

    Genes Cells 2002, 7:781-789. PubMed Abstract | Publisher Full Text OpenURL

  30. Bielinsky AK, Gerbi SA: Discrete start sites for DNA synthesis in the yeast ARS1 origin.

    Science 1998, 279:95-98. PubMed Abstract | Publisher Full Text OpenURL

  31. Schneider TD, Stormo GD, Gold L, Ehrenfeucht A: Information content of binding sites on nucleotide sequences.

    J Mol Biol 1986, 188:415-431. PubMed Abstract OpenURL

  32. Theis JF, Newlon CS: Domain B of ARS307 contains two functional elements and contributes to chromosomal replication origin function.

    Mol Cell Biol 1994, 14:7652-7659. PubMed Abstract OpenURL

  33. Shirahige K, Iwasaki T, Rashid MB, Ogasawara N, Yoshikawa H: Location and characterization of autonomously replicating sequences from chromosome VI of Saccharomyces cerevisiae.

    Mol Cell Biol 1993, 13:5043-5056. PubMed Abstract OpenURL

  34. Shero JH, Koval M, Spencer F, Palmer RE, Hieter P, Koshland D: Analysis of chromosome segregation in Saccharomyces cerevisiae.

    Methods Enzymol 1991, 194:749-773. PubMed Abstract OpenURL

  35. Kellis M, Patterson N, Endrizzi M, Birren B, Lander ES: Sequencing and comparison of yeast species to identify genes and regulatory elements.

    Nature 2003, 423:241-254. PubMed Abstract | Publisher Full Text OpenURL

  36. Cliften P, Sudarsanam P, Desikan A, Fulton L, Fulton B, Majors J, Waterston R, Cohen BA, Johnston M: Finding functional features in Saccharomyces genomes by phylogenetic footprinting.

    Science 2003, 301:71-76. PubMed Abstract | Publisher Full Text OpenURL

  37. Notredame C, Higgins DG, Heringa J: T-Coffee: a novel method for fast and accurate multiple sequence alignment.

    J Mol Biol 2000, 302:205-217. PubMed Abstract | Publisher Full Text OpenURL

  38. Durbin R, Eddy S, Krogh A, Mitchison G:

    Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids Cambridge, UK: Cambridge University Press 1998. OpenURL

  39. Natale DA, Schubert AE, Kowalski D: DNA helical stability accounts for mutational defects in a yeast replication origin.

    Proc Natl Acad Sci USA 1992, 89:2654-2658. PubMed Abstract | Publisher Full Text OpenURL

  40. Allawi HT, SantaLucia J Jr: Thermodynamics and NMR of internal G•T mismatches in DNA.

    Biochemistry 1997, 36:10581-10594. PubMed Abstract | Publisher Full Text OpenURL

  41. Ohler U, Liao GC, Niemann H, Rubin GM: Computational analysis of core promoters in the Drosophila genome.

    Genome Biol 2002, 3:research0087.1-0087.12. PubMed Abstract | BioMed Central Full Text OpenURL

  42. Reese MG: Application of a time-delay neural network to promoter annotation in the Drosophila melanogaster genome.

    Comput Chem 2001, 26:51-56. PubMed Abstract | Publisher Full Text OpenURL

  43. Bielinsky AK, Gerbi SA: Chromosomal ARS1 has a single leading strand start site.

    Mol Cell 1999, 3:477-486. PubMed Abstract | Publisher Full Text OpenURL

  44. Kornberg A, Baker T:

    DNA Replication New York: WH Freeman and Company 1992. OpenURL

  45. Kowalski D, Eddy MJ: The DNA unwinding element: a novel, cis-acting component that facilitates opening of the Escherichia coli replication origin.

    EMBO J 1989, 8:4335-4344. PubMed Abstract OpenURL

  46. Shimizu M, Mori T, Sakurai T, Shindo H: Destabilization of nucleosomes by an unusual DNA conformation adopted by poly(dA)•poly(dT) tracts in vivo.

    EMBO J 2000, 19:3358-3365. PubMed Abstract | Publisher Full Text OpenURL

  47. Suter B, Schnappauf G, Thoma F: Poly(dA•dT) sequences exist as rigid DNA structures in nucleosome-free yeast promoters in vivo.

    Nucleic Acids Res 2000, 28:4083-4089. PubMed Abstract | Publisher Full Text OpenURL

  48. Marahrens Y, Stillman B: A yeast chromosomal origin of DNA replication defined by multiple functional elements.

    Science 1992, 255:817-823. PubMed Abstract OpenURL

  49. Huang RY, Kowalski D: Multiple DNA elements in ARS305 determine replication origin activity in a yeast chromosome.

    Nucleic Acids Res 1996, 24:816-823. PubMed Abstract | Publisher Full Text OpenURL

  50. Bailey TL, Elkan C: Fitting a mixture model by expectation maximization to discover motifs in biopolymers.

    Proc Int Conf Intell Syst Mol Biol 1994, 2:28-36. PubMed Abstract OpenURL

  51. Hardison RC: Conserved noncoding sequences are reliable guides to regulatory elements.

    Trends Genet 2000, 16:369-372. PubMed Abstract | Publisher Full Text OpenURL

  52. Moses AM, Chiang DY, Kellis M, Lander ES, Eisen MB: Position specific variation in the rate of evolution in transcription factor binding sites.

    BMC Evol Biol 2003, 3:19. PubMed Abstract | BioMed Central Full Text OpenURL

  53. Ehrenhofer-Murray AE, Kamakaka RT, Rine J: A role for the replication proteins PCNA, RF-C, polymerase epsilon and Cdc45 in transcriptional silencing in Saccharomyces cerevisiae.

    Genetics 1999, 153:1171-1182. PubMed Abstract | Publisher Full Text OpenURL

  54. Austin RJ, Orr-Weaver TL, Bell SP: Drosophila ORC specifically binds to ACE3, an origin of DNA replication control element.

    Genes Dev 1999, 13:2639-2649. PubMed Abstract | Publisher Full Text OpenURL

  55. Ladenburger EM, Keller C, Knippers R: Identification of a binding region for human origin recognition complex proteins 1 and 2 that coincides with an origin of DNA replication.

    Mol Cell Biol 2002, 22:1036-1048. PubMed Abstract | Publisher Full Text OpenURL

  56. Spradling AC: ORC binding, gene amplification, and the nature of metazoan replication origins.

    Genes Dev 1999, 13:2619-2623. PubMed Abstract | Publisher Full Text OpenURL

  57. Theis JF, Newlon CS: Two compound replication origins in Saccharomyces cerevisiae contain redundant origin recognition complex binding sites.

    Mol Cell Biol 2001, 21:2790-2801. PubMed Abstract | Publisher Full Text OpenURL

  58. The R Project for Statistical Computing [http://www.r-project.org]
  59. methodbook.net [http://www.methodbook.net/pcr/pcrmut.html]
  60. Gietz RD, Woods RA: Transformation of yeast by the lithium acetate/single-stranded carrier DNA/polyethylene glycol method.

    Methods Enzymol 2002, 350:87-96. PubMed Abstract OpenURL

  61. Cliften PF, Hillier LW, Fulton L, Graves T, Miner T, Gish WR, Waterston RH, Johnston M: Surveying Saccharomyces genomes to identify functional elements by comparative DNA sequence analysis.

    Genome Res 2001, 11:1175-1186. PubMed Abstract | Publisher Full Text OpenURL

  62. Dimock K, James AP, Seligy VL: Molecular cloning of the ADE1 gene of Saccharomyces cerevisiae and stability of the transformants.

    Gene 1984, 27:233-237. PubMed Abstract | Publisher Full Text OpenURL

  63. Bouton AH, Smith MM: Fine-structure analysis of the DNA sequence requirements for autonomous replication of Saccharomyces cerevisiae plasmids.

    Mol Cell Biol 1986, 6:2354-2363. PubMed Abstract OpenURL

  64. Button LL, Astell CR: The Saccharomyces cerevisiae chromosome III left telomere has a type X, but not a type Y', ARS region.

    Mol Cell Biol 1986, 6:1352-1356. PubMed Abstract OpenURL

  65. Newlon CS, Lipchitz LR, Collins I, Deshpande A, Devenish RJ, Green RP, Klein HL, Palzkill TG, Ren RB, Synn S, et al.: Analysis of a circular derivative of Saccharomyces cerevisiae chromosome III: a physical map and identification and location of ARS elements.

    Genetics 1991, 129:343-357. PubMed Abstract | Publisher Full Text OpenURL

  66. Vujcic M, Miller CA, Kowalski D: Activation of silent replication origins at autonomously replicating sequence elements near the HML locus in budding yeast.

    Mol Cell Biol 1999, 19:6098-6109. PubMed Abstract | Publisher Full Text OpenURL

  67. Theis JF, Yang C, Schaefer CB, Newlon CS: DNA sequence and functional analysis of homologous ARS elements of Saccharomyces cerevisiae and S. carlsbergensis.

    Genetics 1999, 152:943-952. PubMed Abstract | Publisher Full Text OpenURL

  68. Van Houten JV, Newlon CS: Mutational analysis of the consensus sequence of a replication origin from yeast chromosome III.

    Mol Cell Biol 1990, 10:3917-3925. PubMed Abstract OpenURL

  69. Poloumienko A, Dershowitz A, De J, Newlon CS: Completion of replication map of Saccharomyces cerevisiae chromosome III.

    Mol Biol Cell 2001, 12:3317-3327. PubMed Abstract | Publisher Full Text OpenURL

  70. Brand AH, Micklem G, Nasmyth K: A yeast silencer contains sequences that can promote autonomous plasmid replication and transcriptional activation.

    Cell 1987, 51:709-719. PubMed Abstract OpenURL

  71. Rivier DH, Ekena JL, Rine J: HMR-I is an origin of replication and a silencer in Saccharomyces cerevisiae.

    Genetics 1999, 151:521-529. PubMed Abstract | Publisher Full Text OpenURL

  72. Kearsey S: Structural requirements for the function of a yeast chromosomal replicator.

    Cell 1984, 37:299-307. PubMed Abstract OpenURL

  73. Celniker SE, Campbell JL: Yeast DNA replication in vitro: initiation and elongation events mimic in vivo processes.

    Cell 1982, 31:201-213. PubMed Abstract OpenURL

  74. Tanaka S, Tanaka Y, Isono K: Systematic mapping of autonomously replicating sequences on chromosome V of Saccharomyces cerevisiae using a novel strategy.

    Yeast 1996, 12:101-113. PubMed Abstract | Publisher Full Text OpenURL

  75. Feldmann H, Olah J, Friedenreich H: Sequence of a yeast DNA fragment containing a chromosomal replicator and a tRNA Glu 3 gene.

    Nucleic Acids Res 1981, 9:2949-2959. PubMed Abstract OpenURL

  76. Ferguson BM, Brewer BJ, Reynolds AE, Fangman WL: A yeast origin of replication is activated late in S phase.

    Cell 1991, 65:507-515. PubMed Abstract OpenURL

  77. Eisenberg S, Civalier C, Tye BK: Specific interaction between a Saccharomyces cerevisiae protein and a DNA element associated with certain autonomously replicating sequences.

    Proc Natl Acad Sci USA 1988, 85:743-746. PubMed Abstract OpenURL

  78. Friedman KL, Brewer BJ, Fangman WL: Replication profile of Saccharomyces cerevisiae chromosome VI.

    Genes Cells 1997, 2:667-678. PubMed Abstract | Publisher Full Text OpenURL

  79. Iraqui I, Vissers S, Cartiaux M, Urrestarazu A: Characterisation of Saccharomyces cerevisiae ARO8 and ARO9 genes encoding aromatic aminotransferases I and II reveals a new aminotransferase subfamily.

    Mol Gen Genet 1998, 257:238-248. PubMed Abstract | Publisher Full Text OpenURL

  80. Chan SMC: Chromosome structure of yeast: replication origins and telomeres.

    PhD thesis Ithaca: Cornell University 1985. OpenURL

  81. Atcheson C: Meiosis-specific regulation of the SPO11 gene of the yeast Saccharomyces cerevisiae.

    PhD thesis Chicago: University of Chicago 1991. OpenURL

  82. Hsiao CL, Carbon J: Characterization of a yeast replication origin (ars2) and construction of stable minichromosomes containing cloned yeast centromere DNA (CEN3).

    Gene 1981, 15:157-166. PubMed Abstract | Publisher Full Text OpenURL

  83. Walker SS, Francesconi SC, Tye BK, Eisenberg S: The OBF1 protein and its DNA-binding site are important for the function of an autonomously replicating sequence in Saccharomyces cerevisiae.

    Mol Cell Biol 1989, 9:2914-2921. PubMed Abstract OpenURL

  84. Friedman KL, Diller JD, Ferguson BM, Nyland SV, Brewer BJ, Fangman WL: Multiple determinants controlling activation of yeast replication origins late in S phase.

    Genes Dev 1996, 10:1595-1607. PubMed Abstract OpenURL

  85. Sasnauskas KV, Giadvilaite AA, Ianulaitis AA: [Cloning of the ADE2 gene of Saccharomyces cerevisiae and localization of the ARS-sequence].

    Genetika 1987, 23:1141-1148. PubMed Abstract OpenURL