메뉴 건너뛰기




Volumn 295, Issue 1, 2000, Pages 29-40

Pulling chromatin fibers: Computer simulations of direct physical micromanipulations

Author keywords

Chromatin fiber; Monte Carlo simulations; Single fiber stretching

Indexed keywords

DNA;

EID: 0034614436     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1999.3021     Document Type: Article
Times cited : (83)

References (38)
  • 1
    • 0029583420 scopus 로고
    • Chromatin conformation and salt-induced compaction: Three-dimensional structural information from cryoelectron microscopy
    • Bednar J., Horowitz R. A., Dubochet J., Woodcock C. L. Chromatin conformation and salt-induced compaction: three-dimensional structural information from cryoelectron microscopy. J. Cell Biol. 131:1995;1365-1376.
    • (1995) J. Cell Biol. , vol.131 , pp. 1365-1376
    • Bednar, J.1    Horowitz, R.A.2    Dubochet, J.3    Woodcock, C.L.4
  • 3
    • 0022565962 scopus 로고
    • The superstructure of chromatin and its condensation mechanism. II. Theoretical analysis of the X-ray scattering patterns and model calculations
    • Bordas J., Perez-Grau L., Koch M. H. J., Vega M. C., Nave C. The superstructure of chromatin and its condensation mechanism. II. Theoretical analysis of the X-ray scattering patterns and model calculations. Eur. Biophys. J. 13:1986;175-185.
    • (1986) Eur. Biophys. J. , vol.13 , pp. 175-185
    • Bordas, J.1    Perez-Grau, L.2    Koch, M.H.J.3    Vega, M.C.4    Nave, C.5
  • 6
    • 0019130753 scopus 로고
    • Changes in chromatin folding in solution
    • Butler P. J., Thomas J. O. Changes in chromatin folding in solution. J. Mol. Biol. 140:1980;505-529.
    • (1980) J. Mol. Biol. , vol.140 , pp. 505-529
    • Butler, P.J.1    Thomas, J.O.2
  • 7
    • 85031642189 scopus 로고    scopus 로고
    • Pulling a single chromatin fiber reveals the forces that maintain its higher-order structure
    • Cui Y., Bustamante C. Pulling a single chromatin fiber reveals the forces that maintain its higher-order structure. Proc. Natl Acad. Sci. USA. in the press:1999.
    • (1999) Proc. Natl Acad. Sci. USA
    • Cui, Y.1    Bustamante, C.2
  • 8
    • 0030916931 scopus 로고    scopus 로고
    • A Brownian dynamics model for the chromatin fiber
    • Ehrlich L., Münkel C., Chirico G., Langowski J. A Brownian dynamics model for the chromatin fiber. CABIOS. 13:1997;271-279.
    • (1997) CABIOS , vol.13 , pp. 271-279
    • Ehrlich, L.1    Münkel, C.2    Chirico, G.3    Langowski, J.4
  • 9
    • 0023447159 scopus 로고
    • Chromatin higher order structure studied by neutron scattering and scanning transmission electron microscopy
    • Gerchman S. E., Ramakrishnan V. Chromatin higher order structure studied by neutron scattering and scanning transmission electron microscopy. Proc. Natl Acad. Sci. USA. 84:1987;7802-7806.
    • (1987) Proc. Natl Acad. Sci. USA , vol.84 , pp. 7802-7806
    • Gerchman, S.E.1    Ramakrishnan, V.2
  • 10
    • 0028931709 scopus 로고
    • B-DNA twisting correlates with base-pair morphology
    • Gorin A. A., Zhurkin V. B., Olson W. K. B-DNA twisting correlates with base-pair morphology. J. Mol. Biol. 247:1995;34-48.
    • (1995) J. Mol. Biol. , vol.247 , pp. 34-48
    • Gorin, A.A.1    Zhurkin, V.B.2    Olson, W.K.3
  • 13
    • 0028221098 scopus 로고
    • The three-dimensional architecture of chromatin in situ: Electron tomography reveals fibers composed of a continuously variable zig-zag nucleosomal ribbon
    • Horowitz R. A., Agard D. A., Sedat J. W., Woodcock C. L. The three-dimensional architecture of chromatin in situ: electron tomography reveals fibers composed of a continuously variable zig-zag nucleosomal ribbon. J. Cell. Biol. 125:1994;1-10.
    • (1994) J. Cell. Biol. , vol.125 , pp. 1-10
    • Horowitz, R.A.1    Agard, D.A.2    Sedat, J.W.3    Woodcock, C.L.4
  • 14
    • 0031422137 scopus 로고    scopus 로고
    • Automated electron microscope tomography of frozen-hydrated chromatin: The irregular three-dimensional zigzag architecture persists in compact, isolated fibers
    • Horowitz R. A., Koster A. J., Walz J., Woodcock C. L. Automated electron microscope tomography of frozen-hydrated chromatin: the irregular three-dimensional zigzag architecture persists in compact, isolated fibers. J. Struct. Biol. 120:1997;353-362.
    • (1997) J. Struct. Biol. , vol.120 , pp. 353-362
    • Horowitz, R.A.1    Koster, A.J.2    Walz, J.3    Woodcock, C.L.4
  • 15
    • 0031048190 scopus 로고    scopus 로고
    • The effect of intrinsic curvature on conformational properties of circular DNA
    • Katritch V., Vologodskii A. V. The effect of intrinsic curvature on conformational properties of circular DNA. Biophys. J. 72:1997;1070-1079.
    • (1997) Biophys. J. , vol.72 , pp. 1070-1079
    • Katritch, V.1    Vologodskii, A.V.2
  • 16
    • 0032484098 scopus 로고    scopus 로고
    • Requirement of RSF and FACT for transcription of chromatin templates in vitro
    • LeRoy G., Orphanides G., Lane W. S., Reinberg D. Requirement of RSF and FACT for transcription of chromatin templates in vitro. Science. 282:1998;1900-1904.
    • (1998) Science , vol.282 , pp. 1900-1904
    • Leroy, G.1    Orphanides, G.2    Lane, W.S.3    Reinberg, D.4
  • 18
    • 0031835671 scopus 로고    scopus 로고
    • Linker histone tails and N-tails of histone H3 are redundant: Scanning force microscopy studies of reconstituted fibers
    • Leuba S. H., Bustamante C., Zlatanova J., van Holde K. Linker histone tails and N-tails of histone H3 are redundant: scanning force microscopy studies of reconstituted fibers. Biophys. J. 74:1998a;2830-2839.
    • (1998) Biophys. J. , vol.74 , pp. 2830-2839
    • Leuba, S.H.1    Bustamante, C.2    Zlatanova, J.3    Van Holde, K.4
  • 19
    • 0031806540 scopus 로고    scopus 로고
    • Contributions of linker histones and histone H3 to chromatin structure: Scanning force microscopy studies on trypsinized fibers
    • Leuba S. H., Bustamante C., Zlatanova J., van Holde K. Contributions of linker histones and histone H3 to chromatin structure: scanning force microscopy studies on trypsinized fibers. Biophys. J. 74:1998b;2823-2829.
    • (1998) Biophys. J. , vol.74 , pp. 2823-2829
    • Leuba, S.H.1    Bustamante, C.2    Zlatanova, J.3    Van Holde, K.4
  • 21
    • 1842411320 scopus 로고    scopus 로고
    • Crystal structure of the nucleosome core particle at 2.8 Å resolution
    • Luger K., Mader A. W., Richmond R. K., Sargent D. F., Richmond T. J. Crystal structure of the nucleosome core particle at 2.8 Å resolution. Nature. 389:1997;251-260.
    • (1997) Nature , vol.389 , pp. 251-260
    • Luger, K.1    Mader, A.W.2    Richmond, R.K.3    Sargent, D.F.4    Richmond, T.J.5
  • 22
    • 84886640511 scopus 로고
    • The effect of histone H1 on the compaction of oligonucleosomes. A quasielastic light scattering study
    • Marion C., Hesse-Bezot C., Bezot P., Marion M. J., Roux B., Bernengo J. C. The effect of histone H1 on the compaction of oligonucleosomes. A quasielastic light scattering study. Biophys. Chem. 22:1985;53-64.
    • (1985) Biophys. Chem. , vol.22 , pp. 53-64
    • Marion, C.1    Hesse-Bezot, C.2    Bezot, P.3    Marion, M.J.4    Roux, B.5    Bernengo, J.C.6
  • 24
    • 0032530555 scopus 로고    scopus 로고
    • DNA sequence-dependent deformability deduced from protein-DNA crystal complexes
    • Olson W. K., Gorin A. A., Lu X.-J., Hock L. M., Zhurkin V. B. DNA sequence-dependent deformability deduced from protein-DNA crystal complexes. Proc. Natl Acad. Sci. USA. 95:1998;11163-11168.
    • (1998) Proc. Natl Acad. Sci. USA , vol.95 , pp. 11163-11168
    • Olson, W.K.1    Gorin, A.A.2    Lu, X.-J.3    Hock, L.M.4    Zhurkin, V.B.5
  • 25
    • 0023001414 scopus 로고
    • Sequence periodicities in chicken nucleosome core DNA
    • Satchwell S. C., Drew H. R., Travers A. A. Sequence periodicities in chicken nucleosome core DNA. J. Mol. Biol. 191:1986;659-675.
    • (1986) J. Mol. Biol. , vol.191 , pp. 659-675
    • Satchwell, S.C.1    Drew, H.R.2    Travers, A.A.3
  • 26
    • 0018266771 scopus 로고
    • Structure of the chromatosome, a chromatin particle containing 160 bp of DNA and all the histones
    • Simpson R. T. Structure of the chromatosome, a chromatin particle containing 160 bp of DNA and all the histones. Biochemistry. 17:1978;5524-5531.
    • (1978) Biochemistry , vol.17 , pp. 5524-5531
    • Simpson, R.T.1
  • 27
    • 0026495432 scopus 로고
    • Direct mechanical measurements of the elasticity of single DNA molecules by using magnetic beads
    • Smith S. B., Finzi L., Bustamante C. Direct mechanical measurements of the elasticity of single DNA molecules by using magnetic beads. Science. 258:1992;1122-1126.
    • (1992) Science , vol.258 , pp. 1122-1126
    • Smith, S.B.1    Finzi, L.2    Bustamante, C.3
  • 28
    • 0018581187 scopus 로고
    • Involvement of the histone H1 in the organization of chromatin and the salt-dependent superstructures of chromatin
    • Thoma F., Koller T., Klug A. Involvement of the histone H1 in the organization of chromatin and the salt-dependent superstructures of chromatin. J. Cell. Biol. 83:1979;403-427.
    • (1979) J. Cell. Biol. , vol.83 , pp. 403-427
    • Thoma, F.1    Koller, T.2    Klug, A.3
  • 29
    • 0003903126 scopus 로고
    • New York: Springer-Verlag
    • van Holde K. E. Chromatin. 1988;Springer-Verlag, New York.
    • (1988) Chromatin
    • Van Holde, K.E.1
  • 30
    • 0028495164 scopus 로고
    • DNA extension under the action of an external force
    • Vologodskii A. V. DNA extension under the action of an external force. Macromolecules. 27:1994;5623-5625.
    • (1994) Macromolecules , vol.27 , pp. 5623-5625
    • Vologodskii, A.V.1
  • 32
    • 0033080794 scopus 로고    scopus 로고
    • Chromatin disruption and modification
    • Wolffe A. P., Hayes J. J. Chromatin disruption and modification. Nucl. Acids Res. 27:1999;711-720.
    • (1999) Nucl. Acids Res. , vol.27 , pp. 711-720
    • Wolffe, A.P.1    Hayes, J.J.2
  • 33
    • 0028207905 scopus 로고
    • Chromatin fibers observed in situ in frozen hydrated sections. Native fiber diameter is not correlated with nucleosome repeat length
    • Woodcock C. L. Chromatin fibers observed in situ in frozen hydrated sections. Native fiber diameter is not correlated with nucleosome repeat length. J. Cell Biol. 125:1994;11-19.
    • (1994) J. Cell Biol. , vol.125 , pp. 11-19
    • Woodcock, C.L.1
  • 34
    • 0031972528 scopus 로고    scopus 로고
    • Electron microscopy imaging of chromatin with nucleosome resolution
    • Woodcock C. L., Horowitz R. A. Electron microscopy imaging of chromatin with nucleosome resolution. Methods Cell Biol. 53:1998;167-186.
    • (1998) Methods Cell Biol. , vol.53 , pp. 167-186
    • Woodcock, C.L.1    Horowitz, R.A.2
  • 35
    • 0027517831 scopus 로고
    • A chromatin folding model that incorporates linker variability generates fibers resembling native structures
    • Woodcock C. L., Grigoryev S. A., Horowitz R. A., Whitaker N. A chromatin folding model that incorporates linker variability generates fibers resembling native structures. Proc. Natl Acad. Sci. USA. 90:1993;9021-9025.
    • (1993) Proc. Natl Acad. Sci. USA , vol.90 , pp. 9021-9025
    • Woodcock, C.L.1    Grigoryev, S.A.2    Horowitz, R.A.3    Whitaker, N.4
  • 36
    • 0031707751 scopus 로고    scopus 로고
    • Alteration of nucleosome structure as a mechanism of transcriptional regulation
    • Workman J. L., Kingston R. E. Alteration of nucleosome structure as a mechanism of transcriptional regulation. Annu. Rev. Biochem. 67:1998;545-579.
    • (1998) Annu. Rev. Biochem. , vol.67 , pp. 545-579
    • Workman, J.L.1    Kingston, R.E.2
  • 38
    • 0017885231 scopus 로고
    • Different families of double-stranded conformations of DNA revealed by computer calculations
    • Zhurkin V. B., Lysov Y. P., Ivanov V. I. Different families of double-stranded conformations of DNA revealed by computer calculations. Biopolymers. 17:1978;377-412.
    • (1978) Biopolymers , vol.17 , pp. 377-412
    • Zhurkin, V.B.1    Lysov, Y.P.2    Ivanov, V.I.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.