메뉴 건너뛰기




Volumn 6, Issue , 2016, Pages

Deciphering DNA replication dynamics in eukaryotic cell populations in relation with their averaged chromatin conformations

Author keywords

[No Author keywords available]

Indexed keywords

CELL POPULATION; CHROMATIN; DNA REPLICATION; DNA REPLICATION ORIGIN; EUKARYOTE; EUKARYOTIC CELL; STOCHASTIC MODEL; CELL LINE; GENETICS; HUMAN; METABOLISM; PHYSIOLOGY; SACCHAROMYCES CEREVISIAE;

EID: 84960156863     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/srep22469     Document Type: Article
Times cited : (9)

References (54)
  • 2
    • 0027443434 scopus 로고
    • The structure and function of yeast ARS elements
    • Newlon, C. S. & Theis, J. F. The structure and function of yeast ARS elements. Curr. Opin. Genet. Dev. 3, 752-758 (1993).
    • (1993) Curr. Opin. Genet. Dev. , vol.3 , pp. 752-758
    • Newlon, C.S.1    Theis, J.F.2
  • 3
    • 84887404285 scopus 로고    scopus 로고
    • Bubble-seq analysis of the human genome reveals distinct chromatin-mediated mechanisms for regulating earlyand late-firing origins
    • Mesner, L. D. et al. Bubble-seq analysis of the human genome reveals distinct chromatin-mediated mechanisms for regulating earlyand late-firing origins. Genome Res. 23, 1774-1788 (2013).
    • (2013) Genome Res. , vol.23 , pp. 1774-1788
    • Mesner, L.D.1
  • 4
    • 84874693355 scopus 로고    scopus 로고
    • Regulating DNA replication in eukarya. Cold Spring Harb
    • Siddiqui, K., On, K. F. & Diffley, J. F. X. Regulating DNA replication in eukarya. Cold Spring Harb. Perspect. Biol. 5, a012930 (2013).
    • (2013) Perspect. Biol. , vol.5 , pp. a012930
    • Siddiqui, K.1    On, K.F.2    Diffley, J.F.X.3
  • 5
    • 0037319618 scopus 로고    scopus 로고
    • Paradoxes of eukaryotic DNA replication: MCM proteins and the random completion problem
    • Hyrien, O., Marheineke, K. & Goldar, A. Paradoxes of eukaryotic DNA replication: MCM proteins and the random completion problem. Bioessays 25, 116-125 (2003).
    • (2003) Bioessays , vol.25 , pp. 116-125
    • Hyrien, O.1    Marheineke, K.2    Goldar, A.3
  • 6
    • 0037031834 scopus 로고    scopus 로고
    • MCM2-7 complexes bind chromatin in a distributed pattern surrounding the origin recognition complex in xenopus egg extracts
    • Edwards, M. C. et al. MCM2-7 complexes bind chromatin in a distributed pattern surrounding the origin recognition complex in xenopus egg extracts. J. Biol. Chem. 277, 33049-33057 (2002).
    • (2002) J. Biol. Chem. , vol.277 , pp. 33049-33057
    • Edwards, M.C.1
  • 7
    • 0141557808 scopus 로고    scopus 로고
    • CpG methylation of DNA restricts prereplication complex assembly in xenopus egg extracts
    • Harvey, K. J. et al. CpG methylation of DNA restricts prereplication complex assembly in xenopus egg extracts. Mol. Cell. Biol. 23, 6769-6779 (2003).
    • (2003) Mol. Cell. Biol. , vol.23 , pp. 6769-6779
    • Harvey, K.J.1
  • 8
    • 0034711945 scopus 로고    scopus 로고
    • Mechanisms ensuring rapid and complete DNA replication despite random initiation in xenopus early embryos
    • Lucas, I., Chevrier-Miller, M., Sogo, J. M. & Hyrien, O. Mechanisms ensuring rapid and complete DNA replication despite random initiation in xenopus early embryos. J. Mol. Biol. 296, 769-786 (2000).
    • (2000) J. Mol. Biol. , vol.296 , pp. 769-786
    • Lucas, I.1    Chevrier-Miller, M.2    Sogo, J.M.3    Hyrien, O.4
  • 9
    • 64049108074 scopus 로고    scopus 로고
    • A model for DNA replication showing how dormant origins safeguard against replication fork failure
    • Blow, J. J. & Ge, X. Q. A model for DNA replication showing how dormant origins safeguard against replication fork failure. EMBO Rep. 10, 406-412 (2009).
    • (2009) EMBO Rep. , vol.10 , pp. 406-412
    • Blow, J.J.1    Ge, X.Q.2
  • 10
    • 84887401265 scopus 로고    scopus 로고
    • From simple bacterial and archaeal replicons to replication N/U-domains
    • Hyrien, O. et al. From simple bacterial and archaeal replicons to replication N/U-domains. J. Mol. Biol. 425, 4673-4689 (2013).
    • (2013) J. Mol. Biol. , vol.425 , pp. 4673-4689
    • Hyrien, O.1
  • 11
    • 84901605710 scopus 로고    scopus 로고
    • Temporal and spatial regulation of eukaryotic DNA replication: From regulated initiation to genome-scale timing program
    • Renard-Guillet, C., Kanoh, Y., Shirahige, K. & Masai, H. Temporal and spatial regulation of eukaryotic DNA replication: from regulated initiation to genome-scale timing program. Semin. Cell Dev. Biol. 30, 110-120 (2014).
    • (2014) Semin. Cell Dev. Biol. , vol.30 , pp. 110-120
    • Renard-Guillet, C.1    Kanoh, Y.2    Shirahige, K.3    Masai, H.4
  • 12
    • 0032558590 scopus 로고    scopus 로고
    • Replication conrol: Choreographing replication origins
    • Diffley, J. F. Replication conrol: choreographing replication origins. Curr. Biol. 8, R771-R773 (1998).
    • (1998) Curr. Biol. , vol.8 , pp. R771-R773
    • Diffley, J.F.1
  • 13
    • 0035812808 scopus 로고    scopus 로고
    • Replication dynamics of the yeast genome
    • Raghuraman, M. K. et al. Replication dynamics of the yeast genome. Science a, 115-121 (2001).
    • (2001) Science , vol.A , pp. 115-121
    • Raghuraman, M.K.1
  • 14
    • 36348988518 scopus 로고    scopus 로고
    • DNA combing reveals intrinsic temporal disorder in the replication of yeast chromosome VI
    • Czajkowsky, D. M., Liu, J., Hamlin, J. L. & Shao, Z. DNA combing reveals intrinsic temporal disorder in the replication of yeast chromosome VI. J. Mol. Biol. 375, 12-19 (2008).
    • (2008) J. Mol. Biol. , vol.375 , pp. 12-19
    • Czajkowsky, D.M.1    Liu, J.2    Hamlin, J.L.3    Shao, Z.4
  • 15
    • 84855272663 scopus 로고    scopus 로고
    • Evidence for sequential and increasing activation of replication origins along replication timing gradients in the human genome
    • Guilbaud, G. et al. Evidence for sequential and increasing activation of replication origins along replication timing gradients in the human genome. PLoS Comput. Biol. 7, e1002322 (2011).
    • (2011) PLoS Comput. Biol. , vol.7 , pp. e1002322
    • Guilbaud, G.1
  • 16
    • 77956253770 scopus 로고    scopus 로고
    • Modeling genome-wide replication kinetics reveals a mechanism for regulation of replication timing
    • Yang, S. C.-H., Rhind, N. & Bechhoefer, J. Modeling genome-wide replication kinetics reveals a mechanism for regulation of replication timing. Mol. Syst. Biol. 6, 404 (2010).
    • (2010) Mol. Syst. Biol. , vol.6 , pp. 404
    • Yang, S.C.-H.1    Rhind, N.2    Bechhoefer, J.3
  • 18
    • 0036306239 scopus 로고    scopus 로고
    • Kinetic model of DNA replication in eukaryotic organisms
    • Herrick, J., Jun, S., Bechhoefer, J. & Bensimon, A. Kinetic model of DNA replication in eukaryotic organisms. J. Mol. Biol. 320, 741-750 (2002).
    • (2002) J. Mol. Biol. , vol.320 , pp. 741-750
    • Herrick, J.1    Jun, S.2    Bechhoefer, J.3    Bensimon, A.4
  • 19
    • 51449101224 scopus 로고    scopus 로고
    • A dynamic stochastic model for DNA replication initiation in early embryos
    • Goldar, A., Labit, H., Marheineke, K. & Hyrien, O. A dynamic stochastic model for DNA replication initiation in early embryos. PLoS One 3, e2919 (2008).
    • (2008) PloS One , vol.3 , pp. e2919
    • Goldar, A.1    Labit, H.2    Marheineke, K.3    Hyrien, O.4
  • 20
    • 67651241789 scopus 로고    scopus 로고
    • Universal temporal profile of replication origin activation in eukaryotes
    • Goldar, A., Marsolier-Kergoat, M.-C. & Hyrien, O. Universal temporal profile of replication origin activation in eukaryotes. PLoS One 4, e5899 (2009).
    • (2009) PloS One , vol.4 , pp. e5899
    • Goldar, A.1    Marsolier-Kergoat, M.-C.2    Hyrien, O.3
  • 22
    • 84863219404 scopus 로고    scopus 로고
    • Inferring where and when replication initiates from genome-wide replication timing data
    • Baker, A., Audit, B., Yang, S. C.-H., Bechhoefer, J. & Arneodo, A. Inferring where and when replication initiates from genome-wide replication timing data. Phys. Rev. Lett. 108, 268101 (2012).
    • (2012) Phys. Rev. Lett. , vol.108 , pp. 268101
    • Baker, A.1    Audit, B.2    Yang, S.C.-H.3    Bechhoefer, J.4    Arneodo, A.5
  • 23
    • 65549146426 scopus 로고    scopus 로고
    • Control of DNA replication by anomalous reaction-diffusion kinetics
    • Gauthier, M. G. & Bechhoefer, J. Control of DNA replication by anomalous reaction-diffusion kinetics. Phys. Rev. Lett. 102, 158104 (2009).
    • (2009) Phys. Rev. Lett. , vol.102 , pp. 158104
    • Gauthier, M.G.1    Bechhoefer, J.2
  • 25
    • 84873044090 scopus 로고    scopus 로고
    • Location, location, location: It's all in the timing for replication origins
    • Aparicio, O. M. Location, location, location: it's all in the timing for replication origins. Genes Dev. 27, 117-128 (2013).
    • (2013) Genes Dev. , vol.27 , pp. 117-128
    • Aparicio, O.M.1
  • 26
    • 50449107544 scopus 로고    scopus 로고
    • Stochastic hybrid modeling of DNA replication across a complete genome
    • Lygeros, J. et al. Stochastic hybrid modeling of DNA replication across a complete genome. Proc. Natl. Acad. Sci. USA 105, 12295-12300 (2008).
    • (2008) Proc. Natl. Acad. Sci. USA , vol.105 , pp. 12295-12300
    • Lygeros, J.1
  • 27
    • 0030596416 scopus 로고    scopus 로고
    • Response theory for non-stationary ligand-receptor interaction and a solution to the growth signal firing problem
    • Matsson, L. Response theory for non-stationary ligand-receptor interaction and a solution to the growth signal firing problem. J. Theor. Biol. 180, 93-104 (1996).
    • (1996) J. Theor. Biol. , vol.180 , pp. 93-104
    • Matsson, L.1
  • 28
    • 70350751416 scopus 로고    scopus 로고
    • Concerted loading of MCM2-7 double hexamers around DNA during DNA replication origin licensing
    • Remus, D. et al. Concerted loading of MCM2-7 double hexamers around DNA during DNA replication origin licensing. Cell 139, 719-730 (2009).
    • (2009) Cell , vol.139 , pp. 719-730
    • Remus, D.1
  • 29
    • 78651492264 scopus 로고    scopus 로고
    • Multi-scale coding of genomic information: From DNA sequence to genome structure and function
    • Arneodo, A. et al. Multi-scale coding of genomic information: From DNA sequence to genome structure and function. Phys. Rep. 498, 45-188 (2011).
    • (2011) Phys. Rep. , vol.498 , pp. 45-188
    • Arneodo, A.1
  • 30
    • 36749112484 scopus 로고
    • Kinetics of diffusion controlled processes in dense polymer systems. I. Nonentangled regimes
    • De Gennes, P. Kinetics of diffusion controlled processes in dense polymer systems. I. Nonentangled regimes. J. Chem. Phys. 76, 3316 (1982).
    • (1982) J. Chem. Phys. , vol.76 , pp. 3316
    • De Gennes, P.1
  • 31
    • 30244438013 scopus 로고
    • Rate processes on fractals: Theory, simulations, and experiments
    • Kopelman, R. Rate processes on fractals: Theory, simulations, and experiments. J. Stat. Phys. 42, 185-200 (1986).
    • (1986) J. Stat. Phys. , vol.42 , pp. 185-200
    • Kopelman, R.1
  • 32
    • 0342869049 scopus 로고
    • Kinetics of phase change. I. General theory
    • Avrami, M. Kinetics of phase change. I. General theory. J. Chem. Phys. 7, 1103-1112 (1939).
    • (1939) J. Chem. Phys. , vol.7 , pp. 1103-1112
    • Avrami, M.1
  • 33
    • 55849108473 scopus 로고    scopus 로고
    • How xenopus laevis embryos replicate reliably: Investigating the random-completion problem
    • Yang, S. C.-H. & Bechhoefer, J. How xenopus laevis embryos replicate reliably: investigating the random-completion problem. Phys. Rev. E. Stat. Nonlin. Soft Matter Phys. 78, 041917 (2008).
    • (2008) Phys. Rev. E. Stat. Nonlin. Soft Matter Phys. , vol.78 , pp. 041917
    • Yang, S.C.-H.1    Bechhoefer, J.2
  • 34
    • 0035861492 scopus 로고    scopus 로고
    • Genome-wide distribution of ORC and MCM proteins in S. Cerevisiae: High-resolution mapping of replication origins
    • Wyrick, J. J. et al. Genome-wide distribution of ORC and MCM proteins in S. cerevisiae: high-resolution mapping of replication origins. Science 294, 2357-2360 (2001).
    • (2001) Science , vol.294 , pp. 2357-2360
    • Wyrick, J.J.1
  • 35
    • 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, J. G., Aparicio, O. M. & Tavar, S. 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).
    • (2006) BMC Genomics , vol.7 , pp. 276
    • Xu, W.1    Aparicio, J.G.2    Aparicio, O.M.3    Tavar, S.4
  • 36
    • 79952303535 scopus 로고    scopus 로고
    • CDC45 limits replicon usage from a low density of preRCS in mammalian cells
    • Wong, P. G. et al. CDC45 limits replicon usage from a low density of preRCS in mammalian cells. PLoS One 6, e17533 (2011).
    • (2011) PloS One , vol.6 , pp. e17533
    • Wong, P.G.1
  • 37
    • 23444434202 scopus 로고    scopus 로고
    • A genomic view of eukaryotic DNA replication
    • MacAlpine, D. M. & Bell, S. P. A genomic view of eukaryotic DNA replication. Chromosome Res. 13, 309-326 (2005).
    • (2005) Chromosome Res. , vol.13 , pp. 309-326
    • MacAlpine, D.M.1    Bell, S.P.2
  • 38
    • 84888432841 scopus 로고    scopus 로고
    • High-resolution replication profiles define the stochastic nature of genome replication initiation and termination
    • Hawkins, M. et al. High-resolution replication profiles define the stochastic nature of genome replication initiation and termination. Cell Rep. 5, 1132-1141 (2013).
    • (2013) Cell Rep. , vol.5 , pp. 1132-1141
    • Hawkins, M.1
  • 39
    • 84901599268 scopus 로고    scopus 로고
    • The spatiotemporal program of DNA replication is associated with specific combinations of chromatin marks in human cells
    • Picard, F. et al. The spatiotemporal program of DNA replication is associated with specific combinations of chromatin marks in human cells. PLoS Genet. 10, e1004282 (2014).
    • (2014) PLoS Genet. , vol.10 , pp. e1004282
    • Picard, F.1
  • 40
    • 77949368063 scopus 로고    scopus 로고
    • Gins motion reveals replication fork progression is remarkably uniform throughout the yeast genome
    • Sekedat, M. D. et al. Gins motion reveals replication fork progression is remarkably uniform throughout the yeast genome. Mol. Syst. Biol. 6, 353 (2010).
    • (2010) Mol. Syst. Biol. , vol.6 , pp. 353
    • Sekedat, M.D.1
  • 41
    • 0020498687 scopus 로고
    • Random walks on fractal structures and percolation clusters
    • Rammal, G., R. & Toulouse. Random walks on fractal structures and percolation clusters. J. Phys. Lett. 44, L13-L22 (1983).
    • (1983) J. Phys. Lett. , vol.44 , pp. L13-L22
    • Rammal, G.1    Toulouse, R.2
  • 43
    • 77952744854 scopus 로고    scopus 로고
    • A three-dimensional model of the yeast genome
    • Duan, Z. et al. A three-dimensional model of the yeast genome. Nature 465, 363-367 (2010).
    • (2010) Nature , vol.465 , pp. 363-367
    • Duan, Z.1
  • 44
    • 79952279926 scopus 로고    scopus 로고
    • The fractal globule as a model of chromatin architecture in the cell
    • Mirny, L. A. The fractal globule as a model of chromatin architecture in the cell. Chromosome Res. 19, 37-51 (2011).
    • (2011) Chromosome Res. , vol.19 , pp. 37-51
    • Mirny, L.A.1
  • 45
    • 70349873824 scopus 로고    scopus 로고
    • Comprehensive mapping of long-range interactions reveals folding principles of the human genome
    • Lieberman-Aiden, E. et al. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 326, 289-293 (2009).
    • (2009) Science , vol.326 , pp. 289-293
    • Lieberman-Aiden, E.1
  • 46
    • 14844331313 scopus 로고    scopus 로고
    • Anomalous subdiffusion is a measure for cytoplasmic crowding in living cells
    • Weiss, M., Elsner, M., Kartberg, F. & Nilsson, T. Anomalous subdiffusion is a measure for cytoplasmic crowding in living cells. Biophys. J. 87, 3518-3524 (2004).
    • (2004) Biophys. J. , vol.87 , pp. 3518-3524
    • Weiss, M.1    Elsner, M.2    Kartberg, F.3    Nilsson, T.4
  • 47
    • 27744475701 scopus 로고    scopus 로고
    • Anomalous diffusion of proteins due to molecular crowding
    • Banks, D. S. & Fradin, C. Anomalous diffusion of proteins due to molecular crowding. Biophys. J. 89, 2960-2971 (2005).
    • (2005) Biophys. J. , vol.89 , pp. 2960-2971
    • Banks, D.S.1    Fradin, C.2
  • 48
    • 84943360303 scopus 로고    scopus 로고
    • Structural organization of human replication timing domains
    • Boulos, R. E., Drillon, G., Argoul, F., Arneodo, A. & Audit, B. Structural organization of human replication timing domains. FEBS Lett. 589, 2944-2957 (2015).
    • (2015) FEBS Lett. , vol.589 , pp. 2944-2957
    • Boulos, R.E.1    Drillon, G.2    Argoul, F.3    Arneodo, A.4    Audit, B.5
  • 49
    • 84924386715 scopus 로고    scopus 로고
    • Embryonic stem cell specific "master" replication origins at the heart of the loss of pluripotency
    • Julienne, H., Audit, B. & Arneodo, A. Embryonic stem cell specific "master" replication origins at the heart of the loss of pluripotency. PLoS Comput. Biol. 11, e1003969 (2015).
    • (2015) PLoS Comput. Biol. , vol.11 , pp. e1003969
    • Julienne, H.1    Audit, B.2    Arneodo, A.3
  • 50
    • 84887271825 scopus 로고    scopus 로고
    • Human genome replication proceeds through four chromatin states
    • Julienne, H., Zoufir, A., Audit, B. & Arneodo, A. Human genome replication proceeds through four chromatin states. PLoS Comput. Biol. 9, e1003233 (2013).
    • (2013) PLoS Comput. Biol. , vol.9 , pp. e1003233
    • Julienne, H.1    Zoufir, A.2    Audit, B.3    Arneodo, A.4
  • 51
    • 84873375779 scopus 로고    scopus 로고
    • Constitutive nuclear lamina-genome interactions are highly conserved and associated with A/T-rich sequence
    • Meuleman, W. et al. Constitutive nuclear lamina-genome interactions are highly conserved and associated with A/T-rich sequence. Genome Res. 23, 270-280 (2013).
    • (2013) Genome Res. , vol.23 , pp. 270-280
    • Meuleman, W.1
  • 53
    • 84855289466 scopus 로고    scopus 로고
    • Do replication forks control late origin firing in saccharomyces cerevisiae?
    • Ma, E., Hyrien, O. & Goldar, A. Do replication forks control late origin firing in saccharomyces cerevisiae? Nucleic Acids Res. 40, 2010-2019 (2012).
    • (2012) Nucleic Acids Res. , vol.40 , pp. 2010-2019
    • Ma, E.1    Hyrien, O.2    Goldar, A.3
  • 54
    • 78651348651 scopus 로고    scopus 로고
    • Spectral dimensions of hierarchical scale-free networks with weighted shortcuts
    • Hwang, S., Yun, C.-K., Lee, D.-S., Kahng, B. & Kim, D. Spectral dimensions of hierarchical scale-free networks with weighted shortcuts. Phys. Rev. E 82, 056110 (2010).
    • (2010) Phys. Rev. E , vol.82 , pp. 056110
    • Hwang, S.1    Yun, C.-K.2    Lee, D.-S.3    Kahng, B.4    Kim, D.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.