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Volumn 37, Issue 10, 2015, Pages 1067-1073

Replication dynamics in fission and budding yeasts through DNA polymerase tracking

Author keywords

DNA polymerases; DNA replication; Genome instability; Nucleosomes; Replication origin

Indexed keywords

DNA POLYMERASE; FUNGAL ENZYME; OKAZAKI FRAGMENT; RIBONUCLEOTIDE; DNA; DNA DIRECTED DNA POLYMERASE; FUNGAL DNA; OKAZAKI FRAGMENTS;

EID: 84942832860     PISSN: 02659247     EISSN: 15211878     Source Type: Journal    
DOI: 10.1002/bies.201500072     Document Type: Article
Times cited : (3)

References (49)
  • 1
    • 84876490667 scopus 로고    scopus 로고
    • Structure and evolutionary origins of the CMG complex
    • Onesti S, MacNeill SA. 2013. Structure and evolutionary origins of the CMG complex. Chromosoma 122: 47-53.
    • (2013) Chromosoma , vol.122 , pp. 47-53
    • Onesti, S.1    MacNeill, S.A.2
  • 2
  • 3
    • 84898637956 scopus 로고    scopus 로고
    • Prereplicative complexes assembled in vitro support origin-dependent and independent DNA replication
    • On KF, Beuron F, Frith D, Snijders AP, et al. 2014. Prereplicative complexes assembled in vitro support origin-dependent and independent DNA replication. EMBO J 33: 605-20.
    • (2014) EMBO J , vol.33 , pp. 605-620
    • On, K.F.1    Beuron, F.2    Frith, D.3    Snijders, A.P.4
  • 4
    • 84898641338 scopus 로고    scopus 로고
    • Origin plasticity during budding yeast DNA replication in vitro
    • Gros J, Devbhandari S, Remus D. 2014. Origin plasticity during budding yeast DNA replication in vitro. EMBO J 33: 621-36.
    • (2014) EMBO J , vol.33 , pp. 621-636
    • Gros, J.1    Devbhandari, S.2    Remus, D.3
  • 5
    • 84925813600 scopus 로고    scopus 로고
    • Regulated eukaryotic DNA replication origin firing with purified proteins
    • Yeeles JTP, Deegan TD, Janska A, Early A, et al. 2015. Regulated eukaryotic DNA replication origin firing with purified proteins. Nature 519: 431-5.
    • (2015) Nature , vol.519 , pp. 431-435
    • Yeeles, J.T.P.1    Deegan, T.D.2    Janska, A.3    Early, A.4
  • 6
    • 84906101503 scopus 로고    scopus 로고
    • Mechanism of asymmetric polymerase assembly at the eukaryotic replication fork
    • Georgescu RE, Langston L, Yao NY, Yurieva O, et al. 2014. Mechanism of asymmetric polymerase assembly at the eukaryotic replication fork. Nat Struct Mol Biol 21: 664-70.
    • (2014) Nat Struct Mol Biol , vol.21 , pp. 664-670
    • Georgescu, R.E.1    Langston, L.2    Yao, N.Y.3    Yurieva, O.4
  • 7
    • 77956879643 scopus 로고    scopus 로고
    • Evaluating genome-scale approaches to eukaryotic DNA replication
    • Gilbert DM. 2010. Evaluating genome-scale approaches to eukaryotic DNA replication. Nat Rev Genet 11: 673-84.
    • (2010) Nat Rev Genet , vol.11 , pp. 673-684
    • Gilbert, D.M.1
  • 8
    • 84921799659 scopus 로고    scopus 로고
    • Peaks cloaked in the mist: the landscape of mammalian replication origins
    • Hyrien O. 2015. Peaks cloaked in the mist: the landscape of mammalian replication origins. J Cell Biol 208: 147-60.
    • (2015) J Cell Biol , vol.208 , pp. 147-160
    • Hyrien, O.1
  • 9
    • 84924565490 scopus 로고    scopus 로고
    • The hunt for origins of DNA replication in multicellular eukaryotes
    • Urban JM, Foulk MS, Casella C, Gerbi SA. 2015. The hunt for origins of DNA replication in multicellular eukaryotes. F1000Prime Rep 7: 30.
    • (2015) F1000Prime Rep , vol.7 , pp. 30
    • Urban, J.M.1    Foulk, M.S.2    Casella, C.3    Gerbi, S.A.4
  • 10
    • 84924180985 scopus 로고    scopus 로고
    • Tracking replication enzymology in vivo by genome-wide mapping of ribonucleotide incorporation
    • Clausen AR, Lujan SA, Burkholder AB, Orebaugh CD, et al. 2015. Tracking replication enzymology in vivo by genome-wide mapping of ribonucleotide incorporation. Nat Struct Mol Biol 22: 185-91.
    • (2015) Nat Struct Mol Biol , vol.22 , pp. 185-191
    • Clausen, A.R.1    Lujan, S.A.2    Burkholder, A.B.3    Orebaugh, C.D.4
  • 11
    • 84923844518 scopus 로고    scopus 로고
    • Ribose-seq: global mapping of ribonucleotides embedded in genomic DNA
    • Koh KD, Balachander S, Hesselberth JR, Storici F. 2015. Ribose-seq: global mapping of ribonucleotides embedded in genomic DNA. Nat Methods 12: 251-7.
    • (2015) Nat Methods , vol.12 , pp. 251-257
    • Koh, K.D.1    Balachander, S.2    Hesselberth, J.R.3    Storici, F.4
  • 12
    • 84924072858 scopus 로고    scopus 로고
    • Lagging-strand replication shapes the mutational landscape of the genome
    • Reijns MAM, Kemp H, Ding J, de Procé SM, et al. 2015. Lagging-strand replication shapes the mutational landscape of the genome. Nature 518: 502-6.
    • (2015) Nature , vol.518 , pp. 502-506
    • Reijns, M.A.M.1    Kemp, H.2    Ding, J.3    de Procé, S.M.4
  • 14
    • 84862776917 scopus 로고    scopus 로고
    • Intrinsic coupling of lagging-strand synthesis to chromatin assembly
    • Smith DJ, Whitehouse I. 2012. Intrinsic coupling of lagging-strand synthesis to chromatin assembly. Nature 483: 434-8.
    • (2012) Nature , vol.483 , pp. 434-438
    • Smith, D.J.1    Whitehouse, I.2
  • 15
    • 84876073691 scopus 로고    scopus 로고
    • Quantitative, genome-wide analysis of eukaryotic replication initiation and termination
    • McGuffee SR, Smith DJ, Whitehouse I. 2013. Quantitative, genome-wide analysis of eukaryotic replication initiation and termination. Mol Cell 50: 123-35.
    • (2013) Mol Cell , vol.50 , pp. 123-135
    • McGuffee, S.R.1    Smith, D.J.2    Whitehouse, I.3
  • 16
    • 0022371530 scopus 로고
    • Isolation of the gene encoding yeast DNA polymerase I
    • Johnson LM, Snyder M, Chang LMS, Davis RW, et al. 1985. Isolation of the gene encoding yeast DNA polymerase I. Cell 43: 369-77.
    • (1985) Cell , vol.43 , pp. 369-377
    • Johnson, L.M.1    Snyder, M.2    Chang, L.M.S.3    Davis, R.W.4
  • 17
    • 0025054609 scopus 로고
    • A third essential DNA polymerase in S. cerevisiae
    • Morrison A, Araki H, Clark AB, Hamatake RK, et al. 1990. A third essential DNA polymerase in S. cerevisiae. Cell 62: 1143-51.
    • (1990) Cell , vol.62 , pp. 1143-1151
    • Morrison, A.1    Araki, H.2    Clark, A.B.3    Hamatake, R.K.4
  • 18
    • 0024977355 scopus 로고
    • DNA polymerase III, a second essential DNA polymerase, is encoded by the S. cerevisiae CDC2 gene
    • Sitney KC, Budd ME, Campbell JL. 1989. DNA polymerase III, a second essential DNA polymerase, is encoded by the S. cerevisiae CDC2 gene. Cell 56: 599-605.
    • (1989) Cell , vol.56 , pp. 599-605
    • Sitney, K.C.1    Budd, M.E.2    Campbell, J.L.3
  • 20
    • 77950406088 scopus 로고    scopus 로고
    • Abundant ribonucleotide incorporation into DNA by yeast replicative polymerases
    • Nick McElhinny SA, Watts BE, Kumar D, Watt DL, et al. 2010. Abundant ribonucleotide incorporation into DNA by yeast replicative polymerases. Proc Natl Acad Sci USA 107: 4949-54.
    • (2010) Proc Natl Acad Sci USA , vol.107 , pp. 4949-4954
    • Nick McElhinny, S.A.1    Watts, B.E.2    Kumar, D.3    Watt, D.L.4
  • 21
    • 84861578543 scopus 로고    scopus 로고
    • Enzymatic removal of ribonucleotides from DNA is essential for mammalian genome integrity and development
    • Reijns MAM, Rabe B, Rigby RE, Mill P, et al. 2012. Enzymatic removal of ribonucleotides from DNA is essential for mammalian genome integrity and development. Cell 149: 1008-22.
    • (2012) Cell , vol.149 , pp. 1008-1022
    • Reijns, M.A.M.1    Rabe, B.2    Rigby, R.E.3    Mill, P.4
  • 22
    • 84902074659 scopus 로고    scopus 로고
    • Ribonucleotides in DNA: origins, repair and consequences
    • Williams JS, Kunkel TA. 2014. Ribonucleotides in DNA: origins, repair and consequences. DNA Repair (Amst) 19: 27-37.
    • (2014) DNA Repair (Amst) , vol.19 , pp. 27-37
    • Williams, J.S.1    Kunkel, T.A.2
  • 23
  • 24
    • 84887156806 scopus 로고    scopus 로고
    • Ribonucleotides are signals for mismatch repair of leading-strand replication errors
    • Lujan SA, Williams JS, Clausen AR, Clark AB, et al. 2013. Ribonucleotides are signals for mismatch repair of leading-strand replication errors. Mol Cell 50: 437-43.
    • (2013) Mol Cell , vol.50 , pp. 437-443
    • Lujan, S.A.1    Williams, J.S.2    Clausen, A.R.3    Clark, A.B.4
  • 25
    • 36348988518 scopus 로고    scopus 로고
    • DNA combing reveals intrinsic temporal disorder in the replication of yeast chromosome VI
    • 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: 12-9.
    • (2008) J. Mol. Biol. , vol.375 , pp. 12-19
    • Czajkowsky, D.M.1    Liu, J.2    Hamlin, J.L.3    Shao, Z.4
  • 26
    • 84923920881 scopus 로고    scopus 로고
    • The spatial and temporal organization of origin firing during the S-phase of fission yeast
    • Kaykov A, Nurse P. 2015. The spatial and temporal organization of origin firing during the S-phase of fission yeast. Genome Res 25: 391-401.
    • (2015) Genome Res , vol.25 , pp. 391-401
    • Kaykov, A.1    Nurse, P.2
  • 28
    • 0035861492 scopus 로고    scopus 로고
    • Genome-wide distribution of ORC and MCM proteins in S. cerevisiae: high-resolution mapping of replication origins
    • Wyrick JJ, Aparicio JG, Chen T, Barnett JD, et al. 2001. Genome-wide distribution of ORC and MCM proteins in S. cerevisiae: high-resolution mapping of replication origins. Science 294: 2357-60.
    • (2001) Science , vol.294 , pp. 2357-2360
    • Wyrick, J.J.1    Aparicio, J.G.2    Chen, T.3    Barnett, J.D.4
  • 29
    • 0036668464 scopus 로고    scopus 로고
    • Mapping of early firing origins on a replication profile of budding yeast
    • Yabuki N, Terashima H, Kitada K. 2002. Mapping of early firing origins on a replication profile of budding yeast. Genes Cells 7: 781-9.
    • (2002) Genes Cells , vol.7 , pp. 781-789
    • Yabuki, N.1    Terashima, H.2    Kitada, K.3
  • 30
    • 33645152790 scopus 로고    scopus 로고
    • Genomic mapping of single-stranded DNA in hydroxyurea-challenged yeasts identifies origins of replication
    • Feng W, Collingwood D, Boeck ME, Fox LA, et al. 2006. Genomic mapping of single-stranded DNA in hydroxyurea-challenged yeasts identifies origins of replication. Nat Cell Biol 8: 148-55.
    • (2006) Nat Cell Biol , vol.8 , pp. 148-155
    • Feng, W.1    Collingwood, D.2    Boeck, M.E.3    Fox, L.A.4
  • 32
    • 0031265756 scopus 로고    scopus 로고
    • Replication profile of Saccharomyces cerevisiae chromosome VI
    • Friedman KL, Brewer BJ, Fangman WL. 1997. Replication profile of Saccharomyces cerevisiae chromosome VI. Genes Cells 2: 667-78.
    • (1997) Genes Cells , vol.2 , pp. 667-678
    • Friedman, K.L.1    Brewer, B.J.2    Fangman, W.L.3
  • 33
    • 0031261584 scopus 로고    scopus 로고
    • The efficiency and timing of initiation of replication of multiple replicons of Saccharomyces cerevisiae chromosome VI
    • Yamashita M, Hori Y, Shinomiya T, Obuse C, et al. 1997. The efficiency and timing of initiation of replication of multiple replicons of Saccharomyces cerevisiae chromosome VI. Genes Cells 2: 655-65.
    • (1997) Genes Cells , vol.2 , pp. 655-665
    • Yamashita, M.1    Hori, Y.2    Shinomiya, T.3    Obuse, C.4
  • 34
    • 77649320197 scopus 로고    scopus 로고
    • Structural diversity and dynamics of genomic replication origins in Schizosaccharomyces pombe
    • Cotobal C, Segurado M, Antequera F. 2010. Structural diversity and dynamics of genomic replication origins in Schizosaccharomyces pombe. EMBO J 29: 934-42.
    • (2010) EMBO J , vol.29 , pp. 934-942
    • Cotobal, C.1    Segurado, M.2    Antequera, F.3
  • 35
    • 0346873031 scopus 로고    scopus 로고
    • Genome-wide distribution of DNA replication origins at A+T-rich islands in Schizosaccharomyces pombe
    • Segurado M, de Luis A, Antequera F. 2003. Genome-wide distribution of DNA replication origins at A+T-rich islands in Schizosaccharomyces pombe. EMBO Rep 4: 1048-53.
    • (2003) EMBO Rep , vol.4 , pp. 1048-1053
    • Segurado, M.1    de Luis, A.2    Antequera, F.3
  • 36
    • 84887403248 scopus 로고    scopus 로고
    • Specification of DNA replication origins and genomic base composition in fission yeasts
    • Mojardín L, Vázquez E, Antequera F. 2013. Specification of DNA replication origins and genomic base composition in fission yeasts. J. Mol. Biol. 425: 4706-13.
    • (2013) J. Mol. Biol. , vol.425 , pp. 4706-4713
    • Mojardín, L.1    Vázquez, E.2    Antequera, F.3
  • 37
    • 33750438774 scopus 로고    scopus 로고
    • Genome-wide characterization of fission yeast DNA replication origins
    • Heichinger C, Penkett CJ, Bähler J, Nurse P. 2006. Genome-wide characterization of fission yeast DNA replication origins. EMBO J 25: 5171-9.
    • (2006) EMBO J , vol.25 , pp. 5171-5179
    • Heichinger, C.1    Penkett, C.J.2    Bähler, J.3    Nurse, P.4
  • 38
    • 33947110984 scopus 로고    scopus 로고
    • Genome-wide localization of pre-RC sites and identification of replication origins in fission yeast
    • Hayashi M, Katou Y, Itoh T, Tazumi A, et al. 2007. Genome-wide localization of pre-RC sites and identification of replication origins in fission yeast. EMBO J 26: 1327-39.
    • (2007) EMBO J , vol.26 , pp. 1327-1339
    • Hayashi, M.1    Katou, Y.2    Itoh, T.3    Tazumi, A.4
  • 39
    • 84859927986 scopus 로고    scopus 로고
    • Genome-wide identification and characterization of replication origins by deep sequencing
    • Xu J, Yanagisawa Y, Tsankov AM, Hart C, et al. 2012. Genome-wide identification and characterization of replication origins by deep sequencing. Genome Biol 13: R27.
    • (2012) Genome Biol , vol.13
    • Xu, J.1    Yanagisawa, Y.2    Tsankov, A.M.3    Hart, C.4
  • 40
    • 0035923508 scopus 로고    scopus 로고
    • The Schizosaccharomyces pombe origin recognition complex interacts with multiple AT-rich regions of the replication origin DNA by means of the AT-hook domains of the spOrc4 protein
    • Lee JK, Moon KY, Jiang Y, Hurwitz J. 2001. The Schizosaccharomyces pombe origin recognition complex interacts with multiple AT-rich regions of the replication origin DNA by means of the AT-hook domains of the spOrc4 protein. Proc Natl Acad Sci USA 98: 13589-94.
    • (2001) Proc Natl Acad Sci USA , vol.98 , pp. 13589-13594
    • Lee, J.K.1    Moon, K.Y.2    Jiang, Y.3    Hurwitz, J.4
  • 41
    • 59649112972 scopus 로고    scopus 로고
    • High-resolution dynamic mapping of histone-DNA interactions in a nucleosome
    • Hall MA, Shundrovsky A, Bai L, Fulbright RM, et al. 2009. High-resolution dynamic mapping of histone-DNA interactions in a nucleosome. Nat Struct Mol Biol 16: 124-9.
    • (2009) Nat Struct Mol Biol , vol.16 , pp. 124-129
    • Hall, M.A.1    Shundrovsky, A.2    Bai, L.3    Fulbright, R.M.4
  • 42
    • 56649089682 scopus 로고    scopus 로고
    • Evolutionary footprints of nucleosome positions in yeast
    • Washietl S, Machné R, Goldman N. 2008. Evolutionary footprints of nucleosome positions in yeast. Trends Genet 24: 583-7.
    • (2008) Trends Genet , vol.24 , pp. 583-587
    • Washietl, S.1    Machné, R.2    Goldman, N.3
  • 43
    • 80555156662 scopus 로고    scopus 로고
    • Widespread signatures of recent selection linked to nucleosome positioning in the human lineage
    • Prendergast JGD, Semple CAM. 2011. Widespread signatures of recent selection linked to nucleosome positioning in the human lineage. Genome Res 21: 1777-87.
    • (2011) Genome Res , vol.21 , pp. 1777-1787
    • Prendergast, J.G.D.1    Semple, C.A.M.2
  • 44
    • 58449116917 scopus 로고    scopus 로고
    • Chromatin-associated periodicity in genetic variation downstream of transcriptional start sites
    • Sasaki S, Mello CC, Shimada A, Nakatani Y, et al. 2009. Chromatin-associated periodicity in genetic variation downstream of transcriptional start sites. Science 323: 401-4.
    • (2009) Science , vol.323 , pp. 401-404
    • Sasaki, S.1    Mello, C.C.2    Shimada, A.3    Nakatani, Y.4
  • 45
    • 56049115800 scopus 로고    scopus 로고
    • A novel DNA sequence periodicity decodes nucleosome positioning
    • Chen K, Meng Q, Ma L, Liu Q, et al. 2008. A novel DNA sequence periodicity decodes nucleosome positioning. Nucleic Acids Res 36: 6228-36.
    • (2008) Nucleic Acids Res , vol.36 , pp. 6228-6236
    • Chen, K.1    Meng, Q.2    Ma, L.3    Liu, Q.4
  • 46
    • 84890280929 scopus 로고    scopus 로고
    • Chemical map of Schizosaccharomyces pombe reveals species-specific features in nucleosome positioning
    • Moyle-Heyrman G, Zaichuk T, Xi L, Zhang Q, et al. 2013. Chemical map of Schizosaccharomyces pombe reveals species-specific features in nucleosome positioning. Proc Natl Acad Sci USA 110: 20158-63.
    • (2013) Proc Natl Acad Sci USA , vol.110 , pp. 20158-20163
    • Moyle-Heyrman, G.1    Zaichuk, T.2    Xi, L.3    Zhang, Q.4
  • 47
    • 75149135277 scopus 로고    scopus 로고
    • G+C content dominates intrinsic nucleosome occupancy
    • Tillo D, Hughes TR. 2009. G+C content dominates intrinsic nucleosome occupancy. BMC Bioinformatics 10: 442.
    • (2009) BMC Bioinformatics , vol.10 , pp. 442
    • Tillo, D.1    Hughes, T.R.2
  • 48
    • 84934966303 scopus 로고    scopus 로고
    • A species-specific nucleosomal signature defines a periodic distribution of amino acids in proteins
    • Quintales L, Soriano I, Vázquez E, Segurado M, et al. 2015. A species-specific nucleosomal signature defines a periodic distribution of amino acids in proteins. Open Biol 5: 140218.
    • (2015) Open Biol , vol.5 , pp. 140218
    • Quintales, L.1    Soriano, I.2    Vázquez, E.3    Segurado, M.4
  • 49
    • 84907910826 scopus 로고    scopus 로고
    • Different nucleosomal architectures at early and late replicating origins in Saccharomyces cerevisiae
    • Soriano I, Morafraile EC, Vázquez E, Antequera F, et al. 2014. Different nucleosomal architectures at early and late replicating origins in Saccharomyces cerevisiae. BMC Genomics 15: 791.
    • (2014) BMC Genomics , vol.15 , pp. 791
    • Soriano, I.1    Morafraile, E.C.2    Vázquez, E.3    Antequera, F.4


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