메뉴 건너뛰기




Volumn 5, Issue , 2009, Pages

Global effects of DNA replication and DNA replication origin activity on eukaryotic gene expression

Author keywords

A higher order singular value decomposition (HOSVD); Cell cycle; DNA microarrays; DNA replication origin licensing and firing; mRNA expression

Indexed keywords

DNA; HISTONE; MESSENGER RNA; SACCHAROMYCES CEREVISIAE PROTEIN;

EID: 73149099424     PISSN: 17444292     EISSN: 17444292     Source Type: Journal    
DOI: 10.1038/msb.2009.70     Document Type: Article
Times cited : (34)

References (41)
  • 1
    • 33750808399 scopus 로고    scopus 로고
    • Discovery of principles of nature from mathematical modeling of DNA microarray data
    • Alter O (2006) Discovery of principles of nature from mathematical modeling of DNA microarray data. Proc Natl Acad Sci USA 103: 16063-16064
    • (2006) Proc Natl Acad Sci USA , vol.103 , pp. 16063-16064
    • Alter, O.1
  • 2
    • 0034730140 scopus 로고    scopus 로고
    • Singular value decomposition for genome-wide expression data processing and modeling
    • Alter O, Brown PO, Botstein D (2000) Singular value decomposition for genome-wide expression data processing and modeling. Proc Natl Acad Sci USA 97: 10101-10106
    • (2000) Proc Natl Acad Sci USA , vol.97 , pp. 10101-10106
    • Alter, O.1    Brown, P.O.2    Botstein, D.3
  • 3
    • 9344230857 scopus 로고    scopus 로고
    • Integrative analysis of genome-scale data by using pseudoinverse projection predicts novel correlation between DNA replication and RNA transcription
    • DOI 10.1073/pnas.0406767101
    • Alter O, Golub GH (2004) Integrative analysis of genome-scale data by using pseudoinverse projection predicts novel correlation between DNA replication and RNA transcription. Proc Natl Acad Sci USA 103: 16577-16582 (Pubitemid 39557755)
    • (2004) Proceedings of the National Academy of Sciences of the United States of America , vol.101 , Issue.47 , pp. 16577-16582
    • Alter, O.1    Golub, G.H.2
  • 4
    • 0017701049 scopus 로고
    • Characterization of the autoregulation of simian virus 40 gene A
    • Alwine JC, Reed SI, Stark GR (1977) Characterization of the autoregulation of simian virus 40 gene A. J Virol 24: 22-27
    • (1977) J Virol , vol.24 , pp. 22-27
    • Alwine, J.C.1    Reed, S.I.2    Stark, G.R.3
  • 5
    • 0024276903 scopus 로고
    • When polymerases collide: Replication and the transcriptional organization of the E. coli chromosome
    • Brewer BJ (1988) When polymerases collide: replication and the transcriptional organization of the E. coli chromosome. Cell 53: 679-686
    • (1988) Cell , vol.53 , pp. 679-686
    • Brewer, B.J.1
  • 7
    • 0015886745 scopus 로고
    • Relationship of replication and transcription of Simian Virus 40 DNA
    • Cowan K, Tegtmeyer P, Anthony DD (1973) Relationship of replication and transcription of Simian Virus 40 DNA. Proc Natl Acad Sci USA 70: 1927-1930
    • (1973) Proc Natl Acad Sci USA , vol.70 , pp. 1927-1930
    • Cowan, K.1    Tegtmeyer, P.2    Anthony, D.D.3
  • 8
    • 0023853757 scopus 로고
    • Transcriptional elements as components of eukaryotic origins of DNA replication
    • DePamphilis ML (1988) Transcriptional elements as components of eukaryotic origins of DNA replication. Cell 52: 635-638
    • (1988) Cell , vol.52 , pp. 635-638
    • Depamphilis, M.L.1
  • 9
    • 33749411934 scopus 로고    scopus 로고
    • Genome-wide hierarchy of replication origin usage in Saccharomyces cerevisiae
    • Donato JJ, Chung SC, Tye BK (2006) Genome-wide hierarchy of replication origin usage in Saccharomyces cerevisiae. PLoS Genet 2: e141
    • (2006) PLoS Genet , vol.2
    • Donato, J.J.1    Chung, S.C.2    Tye, B.K.3
  • 10
    • 33750431363 scopus 로고    scopus 로고
    • Natural isolates of Saccharomyces cerevisiae display complex genetic variation in sporulation efficiency
    • Gerke JP, Chen CT, Cohen BA (2006) Natural isolates of Saccharomyces cerevisiae display complex genetic variation in sporulation efficiency. Genetics 174: 985-997
    • (2006) Genetics , vol.174 , pp. 985-997
    • Gerke, J.P.1    Chen, C.T.2    Cohen, B.A.3
  • 11
    • 27644485122 scopus 로고    scopus 로고
    • Eukaryotic mRNA 30 processing: A common means to different ends
    • Gilmartin GM (2005) Eukaryotic mRNA 30 processing: a common means to different ends. Genes Dev 19: 2517-2521
    • (2005) Genes Dev , vol.19 , pp. 2517-2521
    • Gilmartin, G.M.1
  • 12
    • 0004236492 scopus 로고    scopus 로고
    • 3rd edn. Baltimore, Maryland, USA: Johns Hopkins University Press
    • Golub GH, Van Loan CF (1996) Matrix Computations, 3rd edn. Baltimore, Maryland, USA: Johns Hopkins University Press
    • (1996) Matrix Computations
    • Golub, G.H.1    Van Loan, C.F.2
  • 13
    • 0024325630 scopus 로고
    • Enhancement of bacteriophage T4 late transcription by components of the T4 DNA replication apparatus
    • Herendeen DR, Kassavetis GA, Barry J, Alberts BM, Geiduschek EP (1989) Enhancement of bacteriophage T4 late transcription by components of the T4 DNA replication apparatus. Science 245: 952-958
    • (1989) Science , vol.245 , pp. 952-958
    • Herendeen, D.R.1    Kassavetis, G.A.2    Barry, J.3    Alberts, B.M.4    Geiduschek, E.P.5
  • 14
    • 34247629588 scopus 로고    scopus 로고
    • Genetic reconstruction of a functional transcriptional regulatory network
    • Hu Z, Killion PJ, Iyer VR (2007) Genetic reconstruction of a functional transcriptional regulatory network. Nat Genet 39: 683-687
    • (2007) Nat Genet , vol.39 , pp. 683-687
    • Hu, Z.1    Killion, P.J.2    Iyer, V.R.3
  • 15
    • 0033573938 scopus 로고    scopus 로고
    • Global response of Saccharomyces cerevisiae to an alkylating agent
    • Jelinsky SA, Samson LD (1999) Global response of Saccharomyces cerevisiae to an alkylating agent. Proc Natl Acad Sci USA 96: 1486-1491
    • (1999) Proc Natl Acad Sci USA , vol.96 , pp. 1486-1491
    • Jelinsky, S.A.1    Samson, L.D.2
  • 16
    • 42649096299 scopus 로고    scopus 로고
    • Collective behavior in gene regulation: The cell is an oscillator, the cell cycle a developmental process
    • Klevecz RR, Li CM, Marcus I, Frankel PH (2008) Collective behavior in gene regulation: the cell is an oscillator, the cell cycle a developmental process. FEBS J 275: 2372-2384
    • (2008) FEBS J , vol.275 , pp. 2372-2384
    • Klevecz, R.R.1    Li, C.M.2    Marcus, I.3    Frankel, P.H.4
  • 17
    • 33750823409 scopus 로고    scopus 로고
    • A rapid genome-scale response of the transcriptional oscillator to perturbation reveals a period-doubling path to phenotypic change
    • Li CM, Klevecz RR (2006) A rapid genome-scale response of the transcriptional oscillator to perturbation reveals a period-doubling path to phenotypic change. Proc Natl Acad Sci USA 103: 16254-16259
    • (2006) Proc Natl Acad Sci USA , vol.103 , pp. 16254-16259
    • Li, C.M.1    Klevecz, R.R.2
  • 18
    • 0028908039 scopus 로고
    • Head-on collision between a DNA replication apparatus and RNA polymerase transcription complex
    • Liu B, Alberts BM (1995) Head-on collision between a DNA replication apparatus and RNA polymerase transcription complex. Science 267: 1131-1137
    • (1995) Science , vol.267 , pp. 1131-1137
    • Liu, B.1    Alberts, B.M.2
  • 19
    • 0023150161 scopus 로고
    • Role of transcriptional and posttranscriptional regulation in expression of histone genes in Saccharomyces cerevisiae
    • Lycan DE, Osley MA, Hereford LM (1987) Role of transcriptional and posttranscriptional regulation in expression of histone genes in Saccharomyces cerevisiae. Mol Cell Biol 7: 614-621
    • (1987) Mol Cell Biol , vol.7 , pp. 614-621
    • Lycan, D.E.1    Osley, M.A.2    Hereford, L.M.3
  • 20
    • 17844364938 scopus 로고    scopus 로고
    • The requirement of yeast replication origins for pre-replication complex proteins is modulated by transcription
    • Nieduszynski CA, Blow JJ, Donaldson AD (2005) The requirement of yeast replication origins for pre-replication complex proteins is modulated by transcription. Nucleic Acids Res 33: 2410-2420
    • (2005) Nucleic Acids Res , vol.33 , pp. 2410-2420
    • Nieduszynski, C.A.1    Blow, J.J.2    Donaldson, A.D.3
  • 23
    • 36749028922 scopus 로고    scopus 로고
    • Tensor higher-order singular value decomposition for integrative analysis of DNAmicroarray data from different studies
    • Omberg L, Golub GH, Alter O (2007) Tensor higher-order singular value decomposition for integrative analysis of DNAmicroarray data from different studies. Proc Natl Acad Sci USA 104: 18371-18376
    • (2007) Proc Natl Acad Sci USA , vol.104 , pp. 18371-18376
    • Omberg, L.1    Golub, G.H.2    Alter, O.3
  • 25
    • 0029082391 scopus 로고
    • Cdc6 is an unstable protein whose de novo synthesis in G1 is important for the onset of S phase and for preventing a 'reductional' anaphase in the budding yeast Saccharomyces cerevisiae
    • Piatti S, Lengauer C, Nasmyth K (1995) Cdc6 is an unstable protein whose de novo synthesis in G1 is important for the onset of S phase and for preventing a 'reductional' anaphase in the budding yeast Saccharomyces cerevisiae. EMBO J 14: 3788-3799
    • (1995) EMBO J , vol.14 , pp. 3788-3799
    • Piatti, S.1    Lengauer, C.2    Nasmyth, K.3
  • 26
    • 2342505693 scopus 로고    scopus 로고
    • New perspectives on connecting messenger RNA 30 end formation to transcription
    • Proudfoot N (2004) New perspectives on connecting messenger RNA 30 end formation to transcription. Curr Opin Cell Biol 16: 272-278
    • (2004) Curr Opin Cell Biol , vol.16 , pp. 272-278
    • Proudfoot, N.1
  • 27
    • 0017362144 scopus 로고
    • The control of SV40 transcription during a lytic infection: Late RNA synthesis in the presence of inhibitors of DNA replication
    • Rosenthal LJ, Brown M (1977) The control of SV40 transcription during a lytic infection: late RNA synthesis in the presence of inhibitors of DNA replication. Nucleic Acids Res 4: 551-565
    • (1977) Nucleic Acids Res , vol.4 , pp. 551-565
    • Rosenthal, L.J.1    Brown, M.2
  • 28
    • 33745178478 scopus 로고    scopus 로고
    • Terminating the transcript: Breaking up is hard to do
    • Rosonina E, Kaneko S, Manley JL (2006) Terminating the transcript: breaking up is hard to do. Genes Dev 20: 1050-1056
    • (2006) Genes Dev , vol.20 , pp. 1050-1056
    • Rosonina, E.1    Kaneko, S.2    Manley, J.L.3
  • 30
    • 0024009977 scopus 로고
    • Transcription interferes with elements important for chromosome maintenance in Saccharomyces cerevisiae
    • Snyder M, Sapolsky RJ, Davis RW (1988) Transcription interferes with elements important for chromosome maintenance in Saccharomyces cerevisiae. Mol Cell Biol 8: 2184-2194
    • (1988) Mol Cell Biol , vol.8 , pp. 2184-2194
    • Snyder, M.1    Sapolsky, R.J.2    Davis, R.W.3
  • 33
    • 0034595211 scopus 로고    scopus 로고
    • DNA synthesis at individual replication forks requires the essential initiation factor Cdc45p
    • Tercero JA, Labib K, Diffley JFX (2000) DNA synthesis at individual replication forks requires the essential initiation factor Cdc45p. EMBO J 19: 2082-2093
    • (2000) EMBO J , vol.19 , pp. 2082-2093
    • Tercero, J.A.1    Labib, K.2    Diffley, J.F.X.3
  • 34
    • 0019215848 scopus 로고
    • DNA replication and the early to late transition in adenovirus infection
    • Thomas GP, Mathews MB (1980) DNA replication and the early to late transition in adenovirus infection. Cell 22: 523-533
    • (1980) Cell , vol.22 , pp. 523-533
    • Thomas, G.P.1    Mathews, M.B.2
  • 35
    • 0026675743 scopus 로고
    • Adenovirus DNA replication facilitates binding of the MLTF/USF transcription factor to the viral major late promoter within infected cells
    • Toth M, Doerfler W, Shenk T (1992) Adenovirus DNA replication facilitates binding of the MLTF/USF transcription factor to the viral major late promoter within infected cells. Nucleic Acids Res 20: 5143-5148
    • (1992) Nucleic Acids Res , vol.20 , pp. 5143-5148
    • Toth, M.1    Doerfler, W.2    Shenk, T.3
  • 36
    • 0029133544 scopus 로고
    • Transcription-induced deletions in Escherichia coli plasmids
    • Vilette D, Ehrlich SD, Michel B (1995) Transcription-induced deletions in Escherichia coli plasmids. Mol Microbiol 17: 493-504
    • (1995) Mol Microbiol , vol.17 , pp. 493-504
    • Vilette, D.1    Ehrlich, S.D.2    Michel, B.3
  • 37
    • 26944433047 scopus 로고    scopus 로고
    • E Pluribus Unum: 30 end formation of polyadenylated mRNAs, histone mRNAs, and U snRNAs
    • Weiner AM (2005) E Pluribus Unum: 30 end formation of polyadenylated mRNAs, histone mRNAs, and U snRNAs. Mol Cell 20: 168-170
    • (2005) Mol Cell , vol.20 , pp. 168-170
    • Weiner, A.M.1
  • 38
    • 33645823661 scopus 로고    scopus 로고
    • Replication fork progression is impaired by transcription in hyperrecombinant yeast cells lacking a functional THO complex
    • Wellinger RE, Prado F, Aguilera A (2006) Replication fork progression is impaired by transcription in hyperrecombinant yeast cells lacking a functional THO complex. Mol Cell Biol 26: 3327-3334
    • (2006) Mol Cell Biol , vol.26 , pp. 3327-3334
    • Wellinger, R.E.1    Prado, F.2    Aguilera, A.3
  • 39
    • 0023026843 scopus 로고
    • DNA replication in vitro erases a Xenopus 5S RNA gene transcription complex
    • Wolffe AP, Brown DD (1986) DNA replication in vitro erases a Xenopus 5S RNA gene transcription complex. Cell 47: 217-227
    • (1986) Cell , vol.47 , pp. 217-227
    • Wolffe, A.P.1    Brown, D.D.2
  • 41
    • 34547236841 scopus 로고    scopus 로고
    • Genome-wide mapping of ORC and Mcm2p binding sites on tiling arrays and identification of essential ARS consensus sequences in S. cerevisiae
    • Xu W, Aparicio JG, Aparicio OM, Tavaré 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
    • (2006) BMC Genomics , vol.7 , pp. 276
    • Xu, W.1    Aparicio, J.G.2    Aparicio, O.M.3    Tavaré, S.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.