메뉴 건너뛰기




Volumn 27, Issue 6, 2015, Pages

The viscoelastic properties of chromatin and the nucleoplasm revealed by scale-dependent protein mobility

Author keywords

chromatin access; diffusion; nuclear organization; protein transport; target search

Indexed keywords

CHROMOSOMES; DIFFUSION; DIFFUSION IN LIQUIDS; FRACTAL DIMENSION; PROTEINS;

EID: 84921718963     PISSN: 09538984     EISSN: 1361648X     Source Type: Journal    
DOI: 10.1088/0953-8984/27/6/064115     Document Type: Article
Times cited : (37)

References (55)
  • 1
    • 72449204595 scopus 로고    scopus 로고
    • Molecular crowding affects diffusion and binding of nuclear proteins in heterochromatin and reveals the fractal organization of chromatin
    • Bancaud A, Huet S, Daigle N, Mozziconacci J, Beaudouin J and Ellenberg J 2009 Molecular crowding affects diffusion and binding of nuclear proteins in heterochromatin and reveals the fractal organization of chromatin EMBO J. 28 3785-98
    • (2009) EMBO J. , vol.28 , pp. 3785-3798
    • Bancaud, A.1    Huet, S.2    Daigle, N.3    Mozziconacci, J.4    Beaudouin, J.5    Ellenberg, J.6
  • 2
    • 84867498711 scopus 로고    scopus 로고
    • A fractal model for nuclear organization: Current evidence and biological implications
    • Bancaud A, Lavelle C, Huet S and Ellenberg J 2012 A fractal model for nuclear organization: current evidence and biological implications Nucleic Acids Res. 40 8783-92
    • (2012) Nucleic Acids Res. , vol.40 , pp. 8783-8792
    • Bancaud, A.1    Lavelle, C.2    Huet, S.3    Ellenberg, J.4
  • 3
    • 84859891208 scopus 로고    scopus 로고
    • A brief review of elasticity and viscoelasticity for solids
    • Banks H T, Hu S H and Kenz Z R 2011 A brief review of elasticity and viscoelasticity for solids Adv. Appl. Math. Mech. 3 1-51
    • (2011) Adv. Appl. Math. Mech. , vol.3 , pp. 1-51
    • Banks, H.T.1    Hu, S.H.2    Kenz, Z.R.3
  • 5
    • 84905042146 scopus 로고    scopus 로고
    • Retrieving the intracellular topology from multi-scale protein mobility mapping in living cells
    • Baum M, Erdel F, Wachsmuth M and Rippe K 2014 Retrieving the intracellular topology from multi-scale protein mobility mapping in living cells Nat. Commun. 5 4494
    • (2014) Nat. Commun. , vol.5 , pp. 4494
    • Baum, M.1    Erdel, F.2    Wachsmuth, M.3    Rippe, K.4
  • 7
    • 84884333270 scopus 로고    scopus 로고
    • Nonspecific bridging-induced attraction drives clustering of DNA-binding proteins and genome organization
    • Brackley C A, Taylor S, Papantonis A, Cook P R and Marenduzzo D 2013 Nonspecific bridging-induced attraction drives clustering of DNA-binding proteins and genome organization Proc. Natl Acad. Sci. USA 110 E3605-11
    • (2013) Proc. Natl Acad. Sci. USA , vol.110 , pp. 3605-E3611
    • Brackley, C.A.1    Taylor, S.2    Papantonis, A.3    Cook, P.R.4    Marenduzzo, D.5
  • 10
    • 0030251350 scopus 로고    scopus 로고
    • Heterogeneity of the pore and solid volume of soil: Distinguishing a fractal space from its non-fractal complement
    • Crawford J W and Matsui N 1996 Heterogeneity of the pore and solid volume of soil: distinguishing a fractal space from its non-fractal complement Geoderma 73 183-95
    • (1996) Geoderma , vol.73 , pp. 183-195
    • Crawford, J.W.1    Matsui, N.2
  • 11
    • 84878011578 scopus 로고    scopus 로고
    • Exploring the three-dimensional organization of genomes: Interpreting chromatin interaction data
    • Dekker J, Marti-Renom M A and Mirny L A 2013 Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data Nat. Rev. Genet. 14 390-403
    • (2013) Nat. Rev. Genet. , vol.14 , pp. 390-403
    • Dekker, J.1    Marti-Renom, M.A.2    Mirny, L.A.3
  • 14
  • 15
    • 84898744376 scopus 로고    scopus 로고
    • Probing the type of anomalous diffusion with single-particle tracking
    • Ernst D, Kohler J and Weiss M 2014 Probing the type of anomalous diffusion with single-particle tracking Phys. Chem. Chem. Phys. 16 7686-91
    • (2014) Phys. Chem. Chem. Phys. , vol.16 , pp. 7686-7691
    • Ernst, D.1    Kohler, J.2    Weiss, M.3
  • 17
    • 77955723803 scopus 로고    scopus 로고
    • Anomalous diffusion in the interphase cell nucleus: The effect of spatial correlations of chromatin
    • Fritsch C C and Langowski J 2010 Anomalous diffusion in the interphase cell nucleus: the effect of spatial correlations of chromatin J. Chem. Phys. 133 025101
    • (2010) J. Chem. Phys. , vol.133
    • Fritsch, C.C.1    Langowski, J.2
  • 18
    • 79952282147 scopus 로고    scopus 로고
    • Chromosome dynamics, molecular crowding, and diffusion in the interphase cell nucleus: A Monte Carlo lattice simulation study
    • Fritsch C C and Langowski J 2011 Chromosome dynamics, molecular crowding, and diffusion in the interphase cell nucleus: a Monte Carlo lattice simulation study Chromosome Res. 19 63-81
    • (2011) Chromosome Res. , vol.19 , pp. 63-81
    • Fritsch, C.C.1    Langowski, J.2
  • 20
    • 34447263750 scopus 로고    scopus 로고
    • Probing the nanoscale viscoelasticity of intracellular fluids in living cells
    • Guigas G, Kalla C and Weiss M 2007 Probing the nanoscale viscoelasticity of intracellular fluids in living cells Biophys. J. 93 316-23
    • (2007) Biophys. J. , vol.93 , pp. 316-323
    • Guigas, G.1    Kalla, C.2    Weiss, M.3
  • 21
    • 37749053173 scopus 로고    scopus 로고
    • Sampling the cell with anomalous diffusion - The discovery of slowness
    • Guigas G and Weiss M 2008 Sampling the cell with anomalous diffusion - the discovery of slowness Biophys. J. 94 90-4
    • (2008) Biophys. J. , vol.94 , pp. 90-94
    • Guigas, G.1    Weiss, M.2
  • 22
    • 67651180530 scopus 로고    scopus 로고
    • Analysis of protein mobilities and interactions in living cells by multifocal fluorescence fluctuation microscopy
    • Heuvelman G, Erdel F, Wachsmuth M and Rippe K 2009 Analysis of protein mobilities and interactions in living cells by multifocal fluorescence fluctuation microscopy Eur. Biophys. J. 38 813-28
    • (2009) Eur. Biophys. J. , vol.38 , pp. 813-828
    • Heuvelman, G.1    Erdel, F.2    Wachsmuth, M.3    Rippe, K.4
  • 23
    • 84875951973 scopus 로고    scopus 로고
    • Anomalous transport in the crowded world of biological cells
    • Hofling F and Franosch T 2013 Anomalous transport in the crowded world of biological cells Rep. Prog. Phys. 76 046602
    • (2013) Rep. Prog. Phys. , vol.76 , Issue.4
    • Hofling, F.1    Franosch, T.2
  • 24
    • 84876402853 scopus 로고    scopus 로고
    • Space exploration by the promoter of a long human gene during one transcription cycle
    • Larkin J D, Papantonis A, Cook P R and Marenduzzo D 2013 Space exploration by the promoter of a long human gene during one transcription cycle Nucleic Acids Res. 41 2216-27
    • (2013) Nucleic Acids Res. , vol.41 , pp. 2216-2227
    • Larkin, J.D.1    Papantonis, A.2    Cook, P.R.3    Marenduzzo, D.4
  • 26
    • 70349873824 scopus 로고    scopus 로고
    • Comprehensive mapping of long-range interactions reveals folding principles of the human genome
    • Lieberman-Aiden E et al 2009 Comprehensive mapping of long-range interactions reveals folding principles of the human genome Science 326 289-93
    • (2009) Science , vol.326 , pp. 289-293
    • Lieberman-Aiden, E.1
  • 27
    • 84873702707 scopus 로고    scopus 로고
    • A novel approach to interpretation of the time-dependent self-diffusion coefficient as a probe of porous media geometry
    • Loskutov V V and Sevriugin V A 2013 A novel approach to interpretation of the time-dependent self-diffusion coefficient as a probe of porous media geometry J. Magn. Reson. 230C 1-9
    • (2013) J. Magn. Reson. , vol.230 , pp. 1-9
    • Loskutov, V.V.1    Sevriugin, V.A.2
  • 28
    • 84904567038 scopus 로고    scopus 로고
    • 3D Trajectories adopted by coding and regulatory dna elements: First-passage times for genomic interactions
    • Lucas J S, Zhang Y, Dudko O K and Murre C 2014 3D Trajectories adopted by coding and regulatory dna elements: first-passage times for genomic interactions Cell 158 339-52
    • (2014) Cell , vol.158 , pp. 339-352
    • Lucas, J.S.1    Zhang, Y.2    Dudko, O.K.3    Murre, C.4
  • 30
    • 79953687408 scopus 로고    scopus 로고
    • Creep, relaxation and viscosity properties for basic fractional models in rheology
    • Mainardi F and Spada G 2011 Creep, relaxation and viscosity properties for basic fractional models in rheology Eur. Phys. J. Spec. Top. 193 133-60
    • (2011) Eur. Phys. J. Spec. Top. , vol.193 , pp. 133-160
    • Mainardi, F.1    Spada, G.2
  • 32
    • 11944256524 scopus 로고
    • Optical measurements of frequency-dependent linear viscoelastic moduli of complex fluids
    • Mason T G and Weitz D A 1995 Optical measurements of frequency-dependent linear viscoelastic moduli of complex fluids Phys. Rev. Lett. 74 1250-3
    • (1995) Phys. Rev. Lett. , vol.74 , pp. 1250-1253
    • Mason, T.G.1    Weitz, D.A.2
  • 33
    • 75649085702 scopus 로고    scopus 로고
    • Fractal geometry in the nucleus
    • McNally J G and Mazza D 2010 Fractal geometry in the nucleus EMBO J 29 2-3
    • (2010) EMBO J , vol.29 , pp. 2-3
    • McNally, J.G.1    Mazza, D.2
  • 34
    • 79952279926 scopus 로고    scopus 로고
    • The fractal globule as a model of chromatin architecture in the cell
    • Mirny L A 2011 The fractal globule as a model of chromatin architecture in the cell Chromosome Res. 19 37-51
    • (2011) Chromosome Res. , vol.19 , pp. 37-51
    • Mirny, L.A.1
  • 35
    • 26544475690 scopus 로고
    • Short-time behavior of the diffusion coefficient as a geometrical probe of porous media
    • Mitra P P, Sen P N and Schwartz L M 1993 Short-time behavior of the diffusion coefficient as a geometrical probe of porous media Phys. Rev. B 47 8565-74
    • (1993) Phys. Rev. , vol.47 , pp. 8565-8574
    • Mitra, P.P.1    Sen, P.N.2    Schwartz, L.M.3
  • 39
    • 33751229633 scopus 로고    scopus 로고
    • Microenvironment and effect of energy depletion in the nucleus analyzed by mobility of multiple oligomeric EGFPs
    • Pack C, Saito K, Tamura M and Kinjo M 2006 Microenvironment and effect of energy depletion in the nucleus analyzed by mobility of multiple oligomeric EGFPs Biophys. J. 91 3921-36
    • (2006) Biophys. J. , vol.91 , pp. 3921-3936
    • Pack, C.1    Saito, K.2    Tamura, M.3    Kinjo, M.4
  • 40
    • 38149020517 scopus 로고    scopus 로고
    • Transcription-dependent gene looping of the HIV-1 provirus is dictated by recognition of pre-mRNA processing signals
    • Perkins K J, Lusic M, Mitar I, Giacca M and Proudfoot N J 2008 Transcription-dependent gene looping of the HIV-1 provirus is dictated by recognition of pre-mRNA processing signals Mol. Cell 29 56-68
    • (2008) Mol. Cell , vol.29 , pp. 56-68
    • Perkins, K.J.1    Lusic, M.2    Mitar, I.3    Giacca, M.4    Proudfoot, N.J.5
  • 41
    • 84887065048 scopus 로고    scopus 로고
    • Brownian motion in a viscoelastic medium modelled by a Jeffreys fluid
    • Raikher Y L, Rusakov V V and Perzynski R 2013 Brownian motion in a viscoelastic medium modelled by a Jeffreys fluid Soft Matter 9 10857-65
    • (2013) Soft Matter , vol.9 , pp. 10857-10865
    • Raikher, Y.L.1    Rusakov, V.V.2    Perzynski, R.3
  • 42
    • 0023237919 scopus 로고
    • The shapes of random-walks
    • Rudnick J and Gaspari G 1987 The shapes of random-walks Science 237 384-9
    • (1987) Science , vol.237 , pp. 384-389
    • Rudnick, J.1    Gaspari, G.2
  • 43
    • 0027163092 scopus 로고
    • Lateral diffusion in an archipelago dependence on tracer size
    • Saxton M J 1993 Lateral diffusion in an archipelago dependence on tracer size Biophys. J. 64 1053-62
    • (1993) Biophys. J. , vol.64 , pp. 1053-1062
    • Saxton, M.J.1
  • 44
    • 0028140412 scopus 로고
    • Anomalous diffusion due to obstacles: A Monte Carlo study
    • Saxton M J 1994 Anomalous diffusion due to obstacles: a Monte Carlo study Biophys. J. 66 394-401
    • (1994) Biophys. J. , vol.66 , pp. 394-401
    • Saxton, M.J.1
  • 45
    • 0030050141 scopus 로고    scopus 로고
    • Anomalous diffusion due to binding: A Monte Carlo study
    • Saxton M J 1996 Anomalous diffusion due to binding: a Monte Carlo study Biophys. J. 70 1250-62
    • (1996) Biophys. J. , vol.70 , pp. 1250-1262
    • Saxton, M.J.1
  • 46
    • 18444369287 scopus 로고    scopus 로고
    • Time-dependent diffusion coefficient as a probe of geometry
    • Sen P N 2004 Time-dependent diffusion coefficient as a probe of geometry Concepts Magn. Reson. Part A 23A 1-21
    • (2004) Concepts Magn. Reson. Part , vol.23 , pp. 1-21
    • Sen, P.N.1
  • 47
    • 80051714809 scopus 로고    scopus 로고
    • Integrated gene regulatory circuits: Celebrating the 50(th) anniversary of the operon model
    • Tajbakhsh S, Cavalli G and Richet E 2011 Integrated gene regulatory circuits: celebrating the 50(th) anniversary of the operon model Mol. Cell 43 505-14
    • (2011) Mol. Cell , vol.43 , pp. 505-514
    • Tajbakhsh, S.1    Cavalli, G.2    Richet, E.3
  • 48
    • 42449140588 scopus 로고    scopus 로고
    • Dynamic interactions between the promoter and terminator regions of the mammalian BRCA1 gene
    • Tan-Wong S M, French J D, Proudfoot N J and Brown M A 2008 Dynamic interactions between the promoter and terminator regions of the mammalian BRCA1 gene Proc. Natl Acad. Sci. USA 105 5160-5
    • (2008) Proc. Natl Acad. Sci. USA , vol.105 , pp. 5160-5165
    • Tan-Wong, S.M.1    French, J.D.2    Proudfoot, N.J.3    Brown, M.A.4
  • 50
    • 0034640133 scopus 로고    scopus 로고
    • Anomalous diffusion of fluorescent probes inside living cell nuclei investigated by spatially-resolved fluorescence correlation spectroscopy
    • Wachsmuth M, Waldeck W and Langowski J 2000 Anomalous diffusion of fluorescent probes inside living cell nuclei investigated by spatially-resolved fluorescence correlation spectroscopy J. Mol. Biol. 298 677-89
    • (2000) J. Mol. Biol. , vol.298 , pp. 677-689
    • Wachsmuth, M.1    Waldeck, W.2    Langowski, J.3
  • 51
    • 14844331313 scopus 로고    scopus 로고
    • Anomalous subdiffusion is a measure for cytoplasmic crowding in living cells
    • Weiss M, Elsner M, Kartberg F and Nilsson T 2004 Anomalous subdiffusion is a measure for cytoplasmic crowding in living cells Biophys. J. 87 3518-24
    • (2004) Biophys. J. , vol.87 , pp. 3518-3524
    • Weiss, M.1    Elsner, M.2    Kartberg, F.3    Nilsson, T.4
  • 52
    • 48249107073 scopus 로고    scopus 로고
    • Out-of-equilibrium microrheology inside living cells
    • Wilhelm C 2008 Out-of-equilibrium microrheology inside living cells Phys. Rev. Lett. 101
    • (2008) Phys. Rev. Lett. , vol.101
    • Wilhelm, C.1
  • 53
    • 22444455915 scopus 로고    scopus 로고
    • Polymer solutions: A geometric introduction
    • Witten T A 1998 Polymer solutions: a geometric introduction Rev. Mod. Phys. 70 1531-44
    • (1998) Rev. Mod. Phys. , vol.70 , pp. 1531-1544
    • Witten, T.A.1
  • 54
    • 84903373858 scopus 로고    scopus 로고
    • Geometry of the nucleus: A perspective on gene expression regulation
    • Woringer M, Darzacq X and Izeddin I 2014 Geometry of the nucleus: a perspective on gene expression regulation Curr. Opin. Chem. Biol. 20C 112-9
    • (2014) Curr. Opin. Chem. Biol. , vol.20 , pp. 112-119
    • Woringer, M.1    Darzacq, X.2    Izeddin, I.3
  • 55
    • 36849141559 scopus 로고
    • Dynamics of polymer molecules in dilute solution: Viscoelasticity, flow birefringence and dielectric loss
    • Zimm B H 1956 Dynamics of polymer molecules in dilute solution: viscoelasticity, flow birefringence and dielectric loss J. Chem. Phys. 24 269-78
    • (1956) J. Chem. Phys. , vol.24 , pp. 269-278
    • Zimm, B.H.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.