Prediction of Saccharomyces cerevisiae replication origins

Genome Biology

Volumn 5, Issue 4, 2004, Pages

  Breier, Adam M ^a   Chatterji, Sourav ^a   Cozzarelli, Nicholas R ^b  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b University of California Berkeley   (United States)

Author keywords

Additional Data File; Array Origin; Autonomously Replicate Sequence; Conservative Mutation; Origin Recognition Complex

Indexed keywords

DNA BINDING PROTEIN; FUNGAL DNA; ORIGIN RECOGNITION COMPLEX;

ALGORITHM; ARTICLE; BINDING SITE; CHEMISTRY; CHROMOSOME; CHROMOSOME MAP; COMPARATIVE STUDY; COMPUTER PROGRAM; DNA BASE COMPOSITION; DNA REPLICATION; DNA REPLICATION ORIGIN; DNA SEQUENCE; EVALUATION; GENETICS; METHODOLOGY; MOLECULAR EVOLUTION; NUCLEOTIDE SEQUENCE; PREDICTION AND FORECASTING; SACCHAROMYCES CEREVISIAE; THERMODYNAMICS;

ALGORITHMS; BASE COMPOSITION; BINDING SITES; CHROMOSOME MAPPING; CHROMOSOMES, FUNGAL; CONSERVED SEQUENCE; DNA REPLICATION; DNA, FUNGAL; DNA-BINDING PROTEINS; EVALUATION STUDIES; EVOLUTION, MOLECULAR; ORIGIN RECOGNITION COMPLEX; PREDICTIVE VALUE OF TESTS; REPLICATION ORIGIN; SACCHAROMYCES CEREVISIAE; SEQUENCE ANALYSIS, DNA; SOFTWARE; SOFTWARE DESIGN; THERMODYNAMICS;

EID: 3042717854     PISSN: 14747596     EISSN: 1474760X     Source Type: Journal    
DOI: 10.1186/gb-2004-5-4-r22     Document Type: Article

References (85)

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. DOI: 10.1101/SQB.1963.028.01.048
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. DOI: 10.1101/SQB.1993.058.01.048
3. Stinchcomb DT, Struhl K, Davis RW: Isolation and characterisation of a yeast chromosomal replicator. Nature 1979, 282:39–43. DOI: 10.1038/282039a0
4. Brewer BJ, Fangman WL: The localization of replication origins on ARS plasmids in S. cerevisiae. Cell 1987, 51:463–471. DOI: 10.1016/0092-8674(87)90642-8
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. DOI: 10.1016/0092-8674(87)90643-X
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. DOI: 10.1073/pnas.94.20.10786
7. Diffley JF, Cocker JH: Protein-DNA interactions at a yeast replication origin. Nature 1992, 357:169–172. DOI: 10.1038/357169a0
8. Bell SP, Stillman B: ATP-dependent recognition of eukaryotic origins of DNA replication by a multiprotein complex. Nature 1992, 357:128–134. DOI: 10.1038/357128a0
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. DOI: 10.1073/pnas.211342798
10. Gavin KA, Hidaka M, Stillman B: Conserved initiator proteins in eukaryotes. Science 1995, 270:1667–1671. DOI: 10.1126/science.270.5242.1667
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. DOI: 10.1126/science.8266071
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. DOI: 10.1016/S0092-8674(00)80415-8
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. DOI: 10.1073/pnas.1633580100
14. Prasanth SG, Prasanth KV, Stillman B: Orc6 involved in DNA replication, chromosome segregation, and cytokinesis. Science 2002, 297:1026–1031. DOI: 10.1126/science.1072802
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. DOI: 10.1016/S0092-8674(01)80009-X
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. DOI: 10.1128/MCB.4.11.2455
17. Newlon CS, Theis JF: The structure and function of yeast ARS elements. Curr Opin Genet Dev 1993, 3:752–758. DOI: 10.1016/S0959-437X(05)80094-2
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. DOI: 10.1073/pnas.012578499
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. DOI: 10.1128/MCB.20.9.3086-3096.2000
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. DOI: 10.1128/MCB.14.7.4624
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. DOI: 10.1093/nar/21.3.555
22. Lipford JR, Bell SP: Nucleosomes positioned by ORC facilitate the initiation of DNA replication. Mol Cell 2001, 7:21–30. DOI: 10.1016/S1097-2765(01)00151-4
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.
24. Walker SS, Francesconi SC, Eisenberg S: A DNA replication enhancer in Saccharomyces cerevisiae. Proc Natl Acad Sci USA 1990, 87:4665–4669. DOI: 10.1073/pnas.87.12.4665
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. DOI: 10.1093/nar/25.24.5057
26. Chang VK, Fitch MJ, Donato JJ, Christensen TW, Merchant AM, Tye BK: Mcm1 binds replication origins. J Biol Chem 2003, 278:6093–6100. DOI: 10.1074/jbc.M209827200
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. DOI: 10.1126/science.294.5540.115
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. DOI: 10.1126/science.1066101
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. DOI: 10.1046/j.1365-2443.2002.00559.x
30. Bielinsky AK, Gerbi SA: Discrete start sites for DNA synthesis in the yeast ARS1 origin. Science 1998, 279:95–98. DOI: 10.1126/science.279.5347.95
31. Schneider TD, Stormo GD, Gold L, Ehrenfeucht A: Information content of binding sites on nucleotide sequences. J Mol Biol 1986, 188:415–431. DOI: 10.1016/0022-2836(86)90165-8
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. DOI: 10.1128/MCB.14.11.7652
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. DOI: 10.1128/MCB.13.8.5043
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. DOI: 10.1016/0076-6879(91)94057-J
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. DOI: 10.1038/nature01644
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. DOI: 10.1126/science.1084337
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. DOI: 10.1006/jmbi.2000.4042
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. DOI: 10.1017/CBO9780511790492
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. DOI: 10.1073/pnas.89.7.2654
40. Allawi HT, SantaLucia J Jr: Thermodynamics and NMR of internal G•T mismatches in DNA. Biochemistry 1997, 36:10581–10594. DOI: 10.1021/bi962590c
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. DOI: 10.1186/gb-2002-3-12-research0087
42. Reese MG: Application of a time-delay neural network to promoter annotation in the Drosophila melanogaster genome. Comput Chem 2001, 26:51–56. DOI: 10.1016/S0097-8485(01)00099-7
43. Bielinsky AK, Gerbi SA: Chromosomal ARS1 has a single leading strand start site. Mol Cell 1999, 3:477–486. DOI: 10.1016/S1097-2765(00)80475-X
44. Kornberg A, Baker T: DNA Replication New York: WH Freeman and Company 1992.
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.
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. DOI: 10.1093/emboj/19.13.3358
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. DOI: 10.1093/nar/28.21.4083
48. Marahrens Y, Stillman B: A yeast chromosomal origin of DNA replication defined by multiple functional elements. Science 1992, 255:817–823. DOI: 10.1126/science.1536007
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. DOI: 10.1093/nar/24.5.816
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.
51. Hardison RC: Conserved noncoding sequences are reliable guides to regulatory elements. Trends Genet 2000, 16:369–372. DOI: 10.1016/S0168-9525(00)02081-3
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. DOI: 10.1186/1471-2148-3-19
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.
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. DOI: 10.1101/gad.13.20.2639
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. DOI: 10.1128/MCB.22.4.1036-1048.2002
56. Spradling AC: ORC binding, gene amplification, and the nature of metazoan replication origins. Genes Dev 1999, 13:2619–2623. DOI: 10.1101/gad.13.20.2619
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. DOI: 10.1128/MCB.21.8.2790-2801.2001
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. DOI: 10.1016/S0076-6879(02)50957-5
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. DOI: 10.1101/gr.182901
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. DOI: 10.1016/0378-1119(84)90144-6
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. DOI: 10.1128/MCB.6.7.2354
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. DOI: 10.1128/MCB.6.4.1352
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.
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. DOI: 10.1128/MCB.19.9.6098
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.
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. DOI: 10.1128/MCB.10.8.3917
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. DOI: 10.1091/mbc.12.11.3317
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. DOI: 10.1016/0092-8674(87)90094-8
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.
72. Kearsey S: Structural requirements for the function of a yeast chromosomal replicator. Cell 1984, 37:299–307. DOI: 10.1016/0092-8674(84)90326-X
73. Celniker SE, Campbell JL: Yeast DNA replication in vitro: initiation and elongation events mimic in vivo processes. Cell 1982, 31:201–213. DOI: 10.1016/0092-8674(82)90420-2
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. DOI: 10.1002/(SICI)1097-0061(199602)12:2<101::AID-YEA885>3.0.CO;2-2
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. DOI: 10.1093/nar/9.12.2949
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. DOI: 10.1016/0092-8674(91)90468-E
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. DOI: 10.1073/pnas.85.3.743
78. Friedman KL, Brewer BJ, Fangman WL: Replication profile of Saccharomyces cerevisiae chromosome VI. Genes Cells 1997, 2:667–678. DOI: 10.1046/j.1365-2443.1997.1520350.x
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. DOI: 10.1007/s004380050644
80. Chan SMC: Chromosome structure of yeast: replication origins and telomeres. PhD thesis Ithaca: Cornell University 1985.
81. Atcheson C: Meiosis-specific regulation of the SPO11 gene of the yeast Saccharomyces cerevisiae. PhD thesis Chicago: University of Chicago 1991.
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. DOI: 10.1016/0378-1119(81)90125-6
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. DOI: 10.1128/MCB.9.7.2914
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. DOI: 10.1101/gad.10.13.1595
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.