Erratum: Origin plasticity during budding yeast DNA replication in vitro (The EMBO Journal (2014) 33(621-636) (DOI 10.1002/embj.201387278));Origin plasticity during budding yeast DNA replication in vitro

EMBO Journal

Volumn 33, Issue 6, 2014, Pages 621-636

  Gros, Julien ^a   Devbhandari, Sujan ^a,b   Remus, Dirk ^a  

^a MEMORIAL SLOAN KETTERING CANCER CENTER   (United States)

^b Weill Cornell Graduate School of Biomedical Sciences   (United States)

Author keywords

budding yeast; cell cycle; DNA replication; origin; pre RC

Indexed keywords

CELL DNA; INITIATION FACTOR; PLASMID DNA;

ARTICLE; BUDDING; CELL CYCLE S PHASE; CELL DIVISION; DNA REPLICATION; DNA REPLICATION ORIGIN; DNA SEQUENCE; NONHUMAN; PLASTICITY; PRIORITY JOURNAL; YEAST; YEAST CELL;

DEOXYRIBONUCLEASE I; DNA FOOTPRINTING; DNA PRIMERS; DNA REPLICATION; EPIGENESIS, GENETIC; ESCHERICHIA COLI; MINICHROMOSOME MAINTENANCE PROTEINS; MODELS, BIOLOGICAL; PLASMIDS; REPLICATION ORIGIN; SACCHAROMYCETALES;

EID: 84898641338     PISSN: 02614189     EISSN: 14602075     Source Type: Journal    
DOI: 10.15252/embj.201470070     Document Type: Erratum

References (76)

1. Aparicio OM, Stout AM, Bell SP, (1999) Differential assembly of Cdc45p and DNA polymerases at early and late origins of DNA replication. Proc Natl Acad Sci USA 96: 9130-9135 (Pubitemid 29374719)
2. Araki H, (2010) Cyclin-dependent kinase-dependent initiation of chromosomal DNA replication. Curr Opin Cell Biol 22: 766-771
3. Atanasiu C, Deng Z, Wiedmer A, Norseen J, Lieberman PM, (2006) ORC binding to TRF2 stimulates OriP replication. EMBO Rep 7: 716-721 (Pubitemid 43986269)
4. 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 (Pubitemid 36019633)
5. Bell SP, Stillman B, (1992) ATP-dependent recognition of eukaryotic origins of DNA replication by a multiprotein complex. Nature 357: 128-134
6. Blow JJ, Ge XQ, Jackson DA, (2011) How dormant origins promote complete genome replication. Trends Biochem Sci 36: 405-414
7. Boos D, Frigola J, Diffley JF, (2012) Activation of the replicative DNA helicase: breaking up is hard to do. Curr Opin Cell Biol 24: 423-430
8. Bowers JL, Randell JC, Chen S, Bell SP, (2004) ATP hydrolysis by ORC catalyzes reiterative Mcm2-7 assembly at a defined origin of replication. Mol Cell 16: 967-978 (Pubitemid 40018406)
9. Bramhill D, Kornberg A, (1988) Duplex opening by dnaA protein at novel sequences in initiation of replication at the origin of the E. coli chromosome. Cell 52: 743-755
10. Breier AM, Chatterji S, Cozzarelli NR, (2004) Prediction of Saccharomyces cerevisiae replication origins. Genome Biol 5: R22
11. Byun TS, Pacek M, Yee MC, Walter JC, Cimprich KA, (2005) Functional uncoupling of MCM helicase and DNA polymerase activities activates the ATR-dependent checkpoint. Genes Dev 19: 1040-1052 (Pubitemid 40632450)
12. Chen S, de Vries MA, Bell SP, (2007) Orc6 is required for dynamic recruitment of Cdt1 during repeated Mcm2-7 loading. Genes Dev 21: 2897-2907 (Pubitemid 350133438)
13. Chuang RY, Kelly TJ, (1999) The fission yeast homologue of Orc4p binds to replication origin DNA via multiple AT-hooks. Proc Natl Acad Sci USA 96: 2656-2661 (Pubitemid 29148773)
14. Clarey MG, Erzberger JP, Grob P, Leschziner AE, Berger JM, Nogales E, Botchan M, (2006) Nucleotide-dependent conformational changes in the DnaA-like core of the origin recognition complex. Nat Struct Mol Biol 13: 684-690 (Pubitemid 44175160)
15. Crevel G, Cotterill S, (2012) Forced binding of the origin of replication complex to chromosomal sites in Drosophila S2 cells creates an origin of replication. J Cell Sci 125: 965-972
16. Cuvier O, Stanojcic S, Lemaitre JM, Mechali M, (2008) A topoisomerase II-dependent mechanism for resetting replicons at the S-M-phase transition. Genes Dev 22: 860-865 (Pubitemid 351482838)
17. Deng Z, Norseen J, Wiedmer A, Riethman H, Lieberman PM, (2009) TERRA RNA binding to TRF2 facilitates heterochromatin formation and ORC recruitment at telomeres. Mol Cell 35: 403-413
18. Dershowitz A, Snyder M, Sbia M, Skurnick JH, Ong LY, Newlon CS, (2007) Linear derivatives of Saccharomyces cerevisiae chromosome III can be maintained in the absence of autonomously replicating sequence elements. Mol Cell Biol 27: 4652-4663 (Pubitemid 47016120)
19. van Deursen F, Sengupta S, De Piccoli G, Sanchez-Diaz A, Labib K, (2012) Mcm10 associates with the loaded DNA helicase at replication origins and defines a novel step in its activation. EMBO J 31: 2195-2206
20. Diffley JF, (2011) Quality control in the initiation of eukaryotic DNA replication. Philos Trans R Soc Lond B Biol Sci 366: 3545-3553
21. Diffley JF, Cocker JH, (1992) Protein-DNA interactions at a yeast replication origin. Nature 357: 169-172
22. Diffley JF, Cocker JH, Dowell SJ, Rowley A, (1994) Two steps in the assembly of complexes at yeast replication origins in vivo. Cell 78: 303-316 (Pubitemid 24241097)
23. Diffley JF, Stillman B, (1988) Purification of a yeast protein that binds to origins of DNA replication and a transcriptional silencer. Proc Natl Acad Sci USA 85: 2120-2124 (Pubitemid 24315840)
24. Donovan S, Harwood J, Drury LS, Diffley JF, (1997) Cdc6p-dependent loading of Mcm proteins onto pre-replicative chromatin in budding yeast. Proc Natl Acad Sci USA 94: 5611-5616 (Pubitemid 27241817)
25. Dubey DD, Davis LR, Greenfeder SA, Ong LY, Zhu JG, Broach JR, Newlon CS, Huberman JA, (1991) Evidence suggesting that the ARS elements associated with silencers of the yeast mating-type locus HML do not function as chromosomal DNA replication origins. Mol Cell Biol 11: 5346-5355 (Pubitemid 21895298)
26. Eaton ML, Galani K, Kang S, Bell SP, MacAlpine DM, (2010) Conserved nucleosome positioning defines replication origins. Genes Dev 24: 748-753
27. Erzberger JP, Berger JM, (2006) Evolutionary relationships and structural mechanisms of AAA+ proteins. Annu Rev Biophys Biomol Struct 35: 93-114 (Pubitemid 43877371)
28. Evrin C, Clarke P, Zech J, Lurz R, Sun J, Uhle S, Li H, Stillman B, Speck C, (2009) A double-hexameric MCM2-7 complex is loaded onto origin DNA during licensing of eukaryotic DNA replication. Proc Natl Acad Sci USA 106: 20240-20245
29. Fitzgerald-Hayes M, Clarke L, Carbon J, (1982) Nucleotide sequence comparisons and functional analysis of yeast centromere DNAs. Cell 29: 235-244 (Pubitemid 12027685)
30. Frigola J, Remus D, Mehanna A, Diffley JF, (2013) ATPase-dependent quality control of DNA replication origin licensing. Nature 495: 339-343
31. Fu YV, Yardimci H, Long DT, Ho TV, Guainazzi A, Bermudez VP, Hurwitz J, van Oijen A, Scharer OD, Walter JC, (2011) Selective bypass of a lagging strand roadblock by the eukaryotic replicative DNA helicase. Cell 146: 931-941
32. Gambus A, Khoudoli GA, Jones RC, Blow JJ, (2011) MCM2-7 form double hexamers at licensed origins in Xenopus egg extract. J Biol Chem 286: 11855-11864
33. Gilbert DM, (2004) In search of the holy replicator. Nat Rev Mol Cell Biol 5: 848-855 (Pubitemid 39336278)
34. Greenfeder SA, Newlon CS, (1992) A replication map of a 61-kb circular derivative of Saccharomyces cerevisiae chromosome III. Mol Biol Cell 3: 999-1013 (Pubitemid 23079772)
35. Harland RM, Laskey RA, (1980) Regulated replication of DNA microinjected into eggs of Xenopus laevis. Cell 21: 761-771 (Pubitemid 10022884)
36. Heller RC, Kang S, Lam WM, Chen S, Chan CS, Bell SP, (2011) Eukaryotic origin-dependent DNA replication in vitro reveals sequential action of DDK and S-CDK kinases. Cell 146: 80-91
37. Hua XH, Newport J, (1998) Identification of a preinitiation step in DNA replication that is independent of origin recognition complex and cdc6, but dependent on cdk2. J Cell Biol 140: 271-281 (Pubitemid 28078391)
38. Hyrien O, Maric C, Mechali M, (1995) Transition in specification of embryonic metazoan DNA replication origins. Science 270: 994-997
39. Ishimi Y, Ishida R, Andoh T, (1992) Effect of ICRF-193, a novel DNA topoisomerase II inhibitor, on simian virus 40 DNA and chromosome replication in vitro. Mol Cell Biol 12: 4007-4014
40. Kamimura Y, Tak YS, Sugino A, Araki H, (2001) Sld3, which interacts with Cdc45 (Sld4), functions for chromosomal DNA replication in Saccharomyces cerevisiae. EMBO J 20: 2097-2107 (Pubitemid 32397411)
41. Kanemaki M, Labib K, (2006) Distinct roles for Sld3 and GINS during establishment and progression of eukaryotic DNA replication forks. EMBO J 25: 1753-1763
42. Kipling D, Kearsey SE, (1990) Reversion of autonomously replicating sequence mutations in Saccharomyces cerevisiae: creation of a eucaryotic replication origin within procaryotic vector DNA. Mol Cell Biol 10: 265-272
43. Labib K, (2010) How do Cdc7 and cyclin-dependent kinases trigger the initiation of chromosome replication in eukaryotic cells? Genes Dev 24: 1208-1219
44. Lee DG, Bell SP, (1997) Architecture of the yeast origin recognition complex bound to origins of DNA replication. Mol Cell Biol 17: 7159-7168 (Pubitemid 27505946)
45. Marahrens Y, Stillman B, (1992) A yeast chromosomal origin of DNA replication defined by multiple functional elements. Science 255: 817-823
46. Masai H, Matsumoto S, You Z, Yoshizawa-Sugata N, Oda M, (2010) Eukaryotic chromosome DNA replication: where, when, and how? Annu Rev Biochem 79: 89-130
47. McGuffee SR, Smith DJ, Whitehouse I, (2013) Quantitative, genome-wide analysis of eukaryotic replication initiation and termination. Mol Cell 50: 123-135
48. Mechali M, Kearsey S, (1984) Lack of specific sequence requirement for DNA replication in Xenopus eggs compared with high sequence specificity in yeast. Cell 38: 55-64 (Pubitemid 15216535)
49. Mechali M, Yoshida K, Coulombe P, Pasero P, (2013) Genetic and epigenetic determinants of DNA replication origins, position and activation. Curr Opin Genet Dev 23: 124-131
50. Moyer SE, Lewis PW, Botchan MR, (2006) Isolation of the Cdc45/Mcm2-7/GINS (CMG) complex, a candidate for the eukaryotic DNA replication fork helicase. Proc Natl Acad Sci USA 103: 10236-10241 (Pubitemid 44051150)
51. Muramatsu S, Hirai K, Tak YS, Kamimura Y, Araki H, (2010) CDK-dependent complex formation between replication proteins Dpb11, Sld2, Pol (epsilon}, and GINS in budding yeast. Genes Dev 24: 602-612
52. Newlon CS, Theis JF, (1993) The structure and function of yeast ARS elements. Curr Opin Genet Dev 3: 752-758 (Pubitemid 23305048)
53. Nieduszynski CA, Knox Y, Donaldson AD, (2006) Genome-wide identification of replication origins in yeast by comparative genomics. Genes Dev 20: 1874-1879 (Pubitemid 44079324)
54. Pacek M, Tutter AV, Kubota Y, Takisawa H, Walter JC, (2006) Localization of MCM2-7, Cdc45, and GINS to the site of DNA unwinding during eukaryotic DNA replication. Mol Cell 21: 581-587 (Pubitemid 43228013)
55. Rao H, Stillman B, (1995) The origin recognition complex interacts with a bipartite DNA binding site within yeast replicators. Proc Natl Acad Sci USA 92: 2224-2228
56. Remus D, Beall EL, Botchan MR, (2004) DNA topology, not DNA sequence, is a critical determinant for Drosophila ORC-DNA binding. EMBO J 23: 897-907 (Pubitemid 38418756)
57. Remus D, Beuron F, Tolun G, Griffith JD, Morris EP, Diffley JF, (2009) Concerted loading of Mcm2-7 double hexamers around DNA during DNA replication origin licensing. Cell 139: 719-730
58. Ricke RM, Bielinsky AK, (2004) Mcm10 regulates the stability and chromatin association of DNA polymerase-alpha. Mol Cell 16: 173-185 (Pubitemid 39388833)
59. Rowles A, Tada S, Blow JJ, (1999) Changes in association of the Xenopus origin recognition complex with chromatin on licensing of replication origins. J Cell Sci 112 (Pt 12): 2011-2018 (Pubitemid 29338825)
60. Rowley A, Cocker JH, Harwood J, Diffley JF, (1995) Initiation complex assembly at budding yeast replication origins begins with the recognition of a bipartite sequence by limiting amounts of the initiator, ORC. EMBO J 14: 2631-2641
61. Schaarschmidt D, Baltin J, Stehle IM, Lipps HJ, Knippers R, (2004) An episomal mammalian replicon: sequence-independent binding of the origin recognition complex. EMBO J 23: 191-201 (Pubitemid 38165759)
62. Simpson RT, (1990) Nucleosome positioning can affect the function of a cis-acting DNA element in vivo. Nature 343: 387-389
63. Speck C, Chen Z, Li H, Stillman B, (2005) ATPase-dependent cooperative binding of ORC and Cdc6 to origin DNA. Nat Struct Mol Biol 12: 965-971
64. Spradling A, Orr-Weaver T, (1987) Regulation of DNA replication during Drosophila development. Annu Rev Genet 21: 373-403
65. Takeda DY, Shibata Y, Parvin JD, Dutta A, (2005) Recruitment of ORC or CDC6 to DNA is sufficient to create an artificial origin of replication in mammalian cells. Genes Dev 19: 2827-2836 (Pubitemid 41739968)
66. Tanaka S, Nakato R, Katou Y, Shirahige K, Araki H, (2011) Origin association of Sld3, Sld7, and Cdc45 proteins is a key step for determination of origin-firing timing. Curr Biol 21: 2055-2063
67. Tanaka S, Umemori T, Hirai K, Muramatsu S, Kamimura Y, Araki H, (2007) CDK-dependent phosphorylation of Sld2 and Sld3 initiates DNA replication in budding yeast. Nature 445: 328-332 (Pubitemid 46122821)
68. Tatsumi Y, Ezura K, Yoshida K, Yugawa T, Narisawa-Saito M, Kiyono T, Ohta S, Obuse C, Fujita M, (2008) Involvement of human ORC and TRF2 in pre-replication complex assembly at telomeres. Genes Cells 13: 1045-1059
69. Vashee S, Cvetic C, Lu W, Simancek P, Kelly TJ, Walter JC, (2003) Sequence-independent DNA binding and replication initiation by the human origin recognition complex. Genes Dev 17: 1894-1908 (Pubitemid 36944566)
70. Walter J, Newport J, (2000) Initiation of eukaryotic DNA replication: origin unwinding and sequential chromatin association of Cdc45, RPA, and DNA polymerase alpha. Mol Cell 5: 617-627
71. Wang JC, (2002) Cellular roles of DNA topoisomerases: a molecular perspective. Nat Rev Mol Cell Biol 3: 430-440 (Pubitemid 34685700)
72. Watase G, Takisawa H, Kanemaki MT, (2012) Mcm10 plays a role in functioning of the eukaryotic replicative DNA helicase, Cdc45-Mcm-GINS. Curr Biol 22: 343-349
73. Wilmes GM, Bell SP, (2002) The B2 element of the Saccharomyces cerevisiae ARS1 origin of replication requires specific sequences to facilitate pre-RC formation. Proc Natl Acad Sci USA 99: 101-106 (Pubitemid 34060323)
74. Xu W, Aparicio JG, Aparicio OM, Tavare S, (2006) Genome-wide mapping of ORC and Mcm2p binding sites on tiling arrays and identification of essential ARS consensus sequences in S. cerevisiae. BMC Genomics 7: 276
75. Yardimci H, Loveland AB, Habuchi S, van Oijen AM, Walter JC, (2010) Uncoupling of sister replisomes during eukaryotic DNA replication. Mol Cell 40: 834-840
76. Zegerman P, Diffley JF, (2007) Phosphorylation of Sld2 and Sld3 by cyclin-dependent kinases promotes DNA replication in budding yeast. Nature 445: 281-285 (Pubitemid 46122811)