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Volumn 7, Issue 9, 2012, Pages

Asymmetry Indices for Analysis and Prediction of Replication Origins in Eukaryotic Genomes

Author keywords

[No Author keywords available]

Indexed keywords

ADENINE; CYTOSINE; DNA; GUANINE; THYMINE;

EID: 84866943596     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0045050     Document Type: Article
Times cited : (12)

References (36)
  • 1
    • 0028956546 scopus 로고
    • Properties of a general model of DNA evolution under no-strand-bias conditions
    • Lobry JR, (1995) Properties of a general model of DNA evolution under no-strand-bias conditions. J Mol Evol 40: 326-330.
    • (1995) J Mol Evol , vol.40 , pp. 326-330
    • Lobry, J.R.1
  • 2
    • 0028922156 scopus 로고
    • Intrastrand parity rules of DNA base composition and usage biases of synonymous codons
    • Sueoka N, (1995) Intrastrand parity rules of DNA base composition and usage biases of synonymous codons. J Mol Evol 40: 318-325.
    • (1995) J Mol Evol , vol.40 , pp. 318-325
    • Sueoka, N.1
  • 3
    • 0036345594 scopus 로고    scopus 로고
    • Yeast origins establish a strand bias for replicational mutagenesis
    • Pavlov YI, Newlon CS, Kunkel TA, (2002) Yeast origins establish a strand bias for replicational mutagenesis. Mol Cell 10: 207-213.
    • (2002) Mol Cell , vol.10 , pp. 207-213
    • Pavlov, Y.I.1    Newlon, C.S.2    Kunkel, T.A.3
  • 4
    • 0028013058 scopus 로고
    • Mispair-, site-, and strand-specific error rates during simian virus 40 origin-dependent replication in vitro with excess deoxythymidine triphosphate
    • Roberts JD, Izuta S, Thomas DC, Kunkel TA, (1994) Mispair-, site-, and strand-specific error rates during simian virus 40 origin-dependent replication in vitro with excess deoxythymidine triphosphate. J Biol Chem 269: 1711-1717.
    • (1994) J Biol Chem , vol.269 , pp. 1711-1717
    • Roberts, J.D.1    Izuta, S.2    Thomas, D.C.3    Kunkel, T.A.4
  • 5
    • 33845289433 scopus 로고    scopus 로고
    • Similar compositional biases are caused by very different mutational effects
    • Rocha EP, Touchon M, Feil EJ, (2006) Similar compositional biases are caused by very different mutational effects. Genome Res 16: 1537-1547.
    • (2006) Genome Res , vol.16 , pp. 1537-1547
    • Rocha, E.P.1    Touchon, M.2    Feil, E.J.3
  • 6
    • 0029985398 scopus 로고    scopus 로고
    • Asymmetric substitution patterns in the two DNA strands of bacteria
    • Lobry JR, (1996) Asymmetric substitution patterns in the two DNA strands of bacteria. Mol Biol Evol 13: 660-665.
    • (1996) Mol Biol Evol , vol.13 , pp. 660-665
    • Lobry, J.R.1
  • 7
    • 0032417093 scopus 로고    scopus 로고
    • Base composition skews, replication orientation, and gene orientation in 12 prokaryote genomes
    • McLean MJ, Wolfe KH, Devine KM, (1998) Base composition skews, replication orientation, and gene orientation in 12 prokaryote genomes. J Mol Evol 47: 691-696.
    • (1998) J Mol Evol , vol.47 , pp. 691-696
    • McLean, M.J.1    Wolfe, K.H.2    Devine, K.M.3
  • 8
    • 0032584101 scopus 로고    scopus 로고
    • Strand compositional asymmetry in bacterial and large viral genomes
    • Mrazek J, Karlin S, (1998) Strand compositional asymmetry in bacterial and large viral genomes. Proc Natl Acad Sci U S A 95: 3720-3725.
    • (1998) Proc Natl Acad Sci U S A , vol.95 , pp. 3720-3725
    • Mrazek, J.1    Karlin, S.2
  • 9
    • 0032524384 scopus 로고    scopus 로고
    • Analyzing genomes with cumulative skew diagrams
    • Grigoriev A, (1998) Analyzing genomes with cumulative skew diagrams. Nucleic Acids Res 26: 2286-2290.
    • (1998) Nucleic Acids Res , vol.26 , pp. 2286-2290
    • Grigoriev, A.1
  • 10
    • 0029938912 scopus 로고    scopus 로고
    • Origin of replication of Mycoplasma genitalium
    • Lobry JR, (1996) Origin of replication of Mycoplasma genitalium. Science 272: 745-746.
    • (1996) Science , vol.272 , pp. 745-746
    • Lobry, J.R.1
  • 11
    • 33947231236 scopus 로고    scopus 로고
    • Mutational bias suggests that replication termination occurs near the dif site, not at Ter sites
    • Hendrickson H, Lawrence JG, (2007) Mutational bias suggests that replication termination occurs near the dif site, not at Ter sites. Mol Microbiol 64: 42-56.
    • (2007) Mol Microbiol , vol.64 , pp. 42-56
    • Hendrickson, H.1    Lawrence, J.G.2
  • 12
    • 62049085766 scopus 로고    scopus 로고
    • Termination structures in the Escherichia coli chromosome replication fork trap
    • Duggin IG, Bell SD, (2009) Termination structures in the Escherichia coli chromosome replication fork trap. J Mol Biol 387: 532-539.
    • (2009) J Mol Biol , vol.387 , pp. 532-539
    • Duggin, I.G.1    Bell, S.D.2
  • 13
    • 33751520767 scopus 로고    scopus 로고
    • DNA replication timing: random thoughts about origin firing
    • Rhind N, (2006) DNA replication timing: random thoughts about origin firing. Nat Cell Biol 8: 1313-1316.
    • (2006) Nat Cell Biol , vol.8 , pp. 1313-1316
    • Rhind, N.1
  • 14
    • 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: 667-678.
    • (1997) Genes Cells , vol.2 , pp. 667-678
    • Friedman, K.L.1    Brewer, B.J.2    Fangman, W.L.3
  • 16
    • 34548396264 scopus 로고    scopus 로고
    • Human gene organization driven by the coordination of replication and transcription
    • Huvet M, Nicolay S, Touchon M, Audit B, d'Aubenton-Carafa Y, et al. (2007) Human gene organization driven by the coordination of replication and transcription. Genome Res 17: 1278-1285.
    • (2007) Genome Res , vol.17 , pp. 1278-1285
    • Huvet, M.1    Nicolay, S.2    Touchon, M.3    Audit, B.4    d'Aubenton-Carafa, Y.5
  • 18
    • 84857216671 scopus 로고    scopus 로고
    • The mutational profile of the yeast genome is shaped by replication
    • Agier N, Fischer G (2012) The mutational profile of the yeast genome is shaped by replication. Mol Biol Evol.
    • (2012) Mol Biol Evol
    • Agier, N.1    Fischer, G.2
  • 19
    • 84857198915 scopus 로고    scopus 로고
    • DNA replication induces compositional biases in yeast
    • Marsolier-Kergoat MC, Goldar A, (2012) DNA replication induces compositional biases in yeast. Mol Biol Evol 29: 893-904.
    • (2012) Mol Biol Evol , vol.29 , pp. 893-904
    • Marsolier-Kergoat, M.C.1    Goldar, A.2
  • 20
    • 77957337127 scopus 로고    scopus 로고
    • Epigenetically-inherited centromere and neocentromere DNA replicates earliest in S-phase
    • Koren A, Tsai HJ, Tirosh I, Burrack LS, Barkai N, et al. (2010) Epigenetically-inherited centromere and neocentromere DNA replicates earliest in S-phase. PLoS Genet 6: e1001068.
    • (2010) PLoS Genet , vol.6
    • Koren, A.1    Tsai, H.J.2    Tirosh, I.3    Burrack, L.S.4    Barkai, N.5
  • 23
    • 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: 781-789.
    • (2002) Genes Cells , vol.7 , pp. 781-789
    • Yabuki, N.1    Terashima, H.2    Kitada, K.3
  • 24
    • 77956253770 scopus 로고    scopus 로고
    • Modeling genome-wide replication kinetics reveals a mechanism for regulation of replication timing
    • Yang SC, Rhind N, Bechhoefer J, (2010) Modeling genome-wide replication kinetics reveals a mechanism for regulation of replication timing. Mol Syst Biol 6: 404.
    • (2010) Mol Syst Biol , vol.6 , pp. 404
    • Yang, S.C.1    Rhind, N.2    Bechhoefer, J.3
  • 25
    • 0242391986 scopus 로고    scopus 로고
    • Codon adaptation index as a measure of dominating codon bias
    • Carbone A, Zinovyev A, Kepes F, (2003) Codon adaptation index as a measure of dominating codon bias. Bioinformatics 19: 2005-2015.
    • (2003) Bioinformatics , vol.19 , pp. 2005-2015
    • Carbone, A.1    Zinovyev, A.2    Kepes, F.3
  • 26
    • 5344244656 scopus 로고    scopus 로고
    • R Development Core Team, Vienna, Austria: R Foundation for Statistical Computing
    • R Development Core Team (2008) R: A language and environment for statistical computing. Vienna, Austria: R Foundation for Statistical Computing.
    • (2008) R: A language and environment for statistical computing
  • 28
    • 0021166345 scopus 로고
    • Structural requirements for the function of a yeast chromosomal replicator
    • Kearsey S, (1984) Structural requirements for the function of a yeast chromosomal replicator. Cell 37: 299-307.
    • (1984) Cell , vol.37 , pp. 299-307
    • Kearsey, S.1
  • 29
    • 0642365324 scopus 로고
    • DNA sequences that allow the replication and segregation of yeast chromosomes
    • Stinchcomb DT, Mann C, Selker E, Davis RW, (1981) DNA sequences that allow the replication and segregation of yeast chromosomes. ICN-UCLA Symp Mol Cell Biol 22: 473-488.
    • (1981) ICN-UCLA Symp Mol Cell Biol , vol.22 , pp. 473-488
    • Stinchcomb, D.T.1    Mann, C.2    Selker, E.3    Davis, R.W.4
  • 30
    • 15244359893 scopus 로고    scopus 로고
    • Independence of replisomes in Escherichia coli chromosomal replication
    • Breier AM, Weier HU, Cozzarelli NR, (2005) Independence of replisomes in Escherichia coli chromosomal replication. Proc Natl Acad Sci U S A 102: 3942-3947.
    • (2005) Proc Natl Acad Sci U S A , vol.102 , pp. 3942-3947
    • Breier, A.M.1    Weier, H.U.2    Cozzarelli, N.R.3
  • 32
    • 33746101049 scopus 로고    scopus 로고
    • Genome-wide identification of replication origins in yeast by comparative genomics
    • Nieduszynski CA, Knox Y, Donaldson AD, (2006) Genome-wide identification of replication origins in yeast by comparative genomics. Genes Dev 20: 1874-1879.
    • (2006) Genes Dev , vol.20 , pp. 1874-1879
    • Nieduszynski, C.A.1    Knox, Y.2    Donaldson, A.D.3
  • 33
    • 77955997707 scopus 로고    scopus 로고
    • Replication termination at eukaryotic chromosomes is mediated by Top2 and occurs at genomic loci containing pausing elements
    • Fachinetti D, Bermejo R, Cocito A, Minardi S, Katou Y, et al. (2010) Replication termination at eukaryotic chromosomes is mediated by Top2 and occurs at genomic loci containing pausing elements. Mol Cell 39: 595-605.
    • (2010) Mol Cell , vol.39 , pp. 595-605
    • Fachinetti, D.1    Bermejo, R.2    Cocito, A.3    Minardi, S.4    Katou, Y.5
  • 34
    • 78651492264 scopus 로고    scopus 로고
    • Multi-scale coding of genomic information: From DNA sequence to genome structure and function
    • Arneodo A, Vaillant C, Audit B, Argoul F, d'Aubenton-Carafa Y, et al. (2011) Multi-scale coding of genomic information: From DNA sequence to genome structure and function. Physics Reports 498: 45-188.
    • (2011) Physics Reports , vol.498 , pp. 45-188
    • Arneodo, A.1    Vaillant, C.2    Audit, B.3    Argoul, F.4    d'Aubenton-Carafa, Y.5
  • 35
    • 41149138003 scopus 로고    scopus 로고
    • From GC skews to wavelets: a gentle guide to the analysis of compositional asymmetries in genomic data
    • Touchon M, Rocha EP, (2008) From GC skews to wavelets: a gentle guide to the analysis of compositional asymmetries in genomic data. Biochimie 90: 648-659.
    • (2008) Biochimie , vol.90 , pp. 648-659
    • Touchon, M.1    Rocha, E.P.2
  • 36
    • 0034695920 scopus 로고    scopus 로고
    • Is there replication-associated mutational pressure in the Saccharomyces cerevisiae genome?
    • Gierlik A, Kowalczuk M, Mackiewicz P, Dudek MR, Cebrat S, (2000) Is there replication-associated mutational pressure in the Saccharomyces cerevisiae genome? J Theor Biol 202: 305-314.
    • (2000) J Theor Biol , vol.202 , pp. 305-314
    • Gierlik, A.1    Kowalczuk, M.2    Mackiewicz, P.3    Dudek, M.R.4    Cebrat, S.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.