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Volumn 87, Issue 5, 2004, Pages 3372-3387

A statistical thermodynamic model applied to experimental AFM population and location data is able to quantify DNA-histone binding strength and internucleosomal interaction differences between acetylated and unacetylated nucleosomal arrays

Author keywords

[No Author keywords available]

Indexed keywords

RIBOSOME DNA; DNA; HISTONE;

EID: 16644363134     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1529/biophysj.103.034744     Document Type: Article
Times cited : (29)

References (42)
  • 1
    • 0033710367 scopus 로고    scopus 로고
    • Role of histone acetylation in the assembly and modulation of chromatin structures
    • Annunziato, A. T., and J. C. Hansen. 2000. Role of histone acetylation in the assembly and modulation of chromatin structures. Gene Expr. 9:37-61.
    • (2000) Gene Expr. , vol.9 , pp. 37-61
    • Annunziato, A.T.1    Hansen, J.C.2
  • 2
    • 0035930512 scopus 로고    scopus 로고
    • Population analysis of subsaturated 172-12 nucleosomal arrays by atomic force microscopy detects nonrandom behavior that is favored by histone acetylation and short repeat length
    • Bash, R. C., J. Yodh, Y. Lyubchenko, N. Woodbury, and D. Lohr. 2001. Population analysis of subsaturated 172-12 nucleosomal arrays by atomic force microscopy detects nonrandom behavior that is favored by histone acetylation and short repeat length. J. Biol. Chem. 276:48362-48370.
    • (2001) J. Biol. Chem. , vol.276 , pp. 48362-48370
    • Bash, R.C.1    Yodh, J.2    Lyubchenko, Y.3    Woodbury, N.4    Lohr, D.5
  • 3
    • 0037472112 scopus 로고    scopus 로고
    • Nucleosomal arrays can be salt-reconstituted on a single-copy MMTV promoter DNA template: Their properties differ in several ways from those of comparable 5S concatameric arrays
    • Bash, R., H. Wang, J. Yodh, G. Hager, S. M. Lindsay, and D. Lohr. 2003. Nucleosomal arrays can be salt-reconstituted on a single-copy MMTV promoter DNA template: their properties differ in several ways from those of comparable 5S concatameric arrays. Biochemistry. 42:4681-4690.
    • (2003) Biochemistry , vol.42 , pp. 4681-4690
    • Bash, R.1    Wang, H.2    Yodh, J.3    Hager, G.4    Lindsay, S.M.5    Lohr, D.6
  • 5
    • 0033067219 scopus 로고    scopus 로고
    • Assembly of defined nucleosomal and chromatin arrays from pure components
    • Carruthers, L. M., C. Tse, K. P. Walker, and J. C. Hansen. 1999. Assembly of defined nucleosomal and chromatin arrays from pure components. Chromatin Meth. Enzymol. 304:19-35.
    • (1999) Chromatin Meth. Enzymol. , vol.304 , pp. 19-35
    • Carruthers, L.M.1    Tse, C.2    Walker, K.P.3    Hansen, J.C.4
  • 6
    • 0038456227 scopus 로고    scopus 로고
    • An exact theory of histone-DNA adsorption and wrapping
    • Chou, T. 2003. An exact theory of histone-DNA adsorption and wrapping. Europhys. Lett. 62:753-759.
    • (2003) Europhys. Lett. , vol.62 , pp. 753-759
    • Chou, T.1
  • 7
    • 0036307707 scopus 로고    scopus 로고
    • Solvent-mediated interactions in the structure of the nucleosome core particle at 1.9 Å resolution
    • Davey, C. A., D. F. Sargent, K. Luger, A. W. Maeder, and T. J. Richmond. 2002. Solvent-mediated interactions in the structure of the nucleosome core particle at 1.9 Å resolution. J. Mol. Biol. 319:1097-1113.
    • (2002) J. Mol. Biol. , vol.319 , pp. 1097-1113
    • Davey, C.A.1    Sargent, D.F.2    Luger, K.3    Maeder, A.W.4    Richmond, T.J.5
  • 8
    • 0025311114 scopus 로고
    • DNA and protein determinants of nucleosome positioning on sea urchin 5S rRNA gene sequences in vitro
    • Dong, F., J. Hansen, and K. van Holde. 1990. DNA and protein determinants of nucleosome positioning on sea urchin 5S rRNA gene sequences in vitro. Proc. Natl. Acad. Sci. USA. 87:5724-5728.
    • (1990) Proc. Natl. Acad. Sci. USA , vol.87 , pp. 5724-5728
    • Dong, F.1    Hansen, J.2    Van Holde, K.3
  • 9
    • 0022398241 scopus 로고
    • Effects of sequence alterations in a DNA segment containing the 5S RNA gene from Lytechinus variegatus on positioning of a nucleosome core particle in vitro
    • Fitzgerald, P. C., and R. T. Simpson. 1985. Effects of sequence alterations in a DNA segment containing the 5S RNA gene from Lytechinus variegatus on positioning of a nucleosome core particle in vitro. J. Biol. Chem. 260:15318-15324.
    • (1985) J. Biol. Chem. , vol.260 , pp. 15318-15324
    • Fitzgerald, P.C.1    Simpson, R.T.2
  • 10
    • 0029815618 scopus 로고    scopus 로고
    • The nucleosomal array: Structure/function relationships
    • Fletcher, T. M., and J. C. Hansen. 1996. The nucleosomal array: structure/ function relationships. Crit. Rev. Eukaryote Gene Expr. 6:149-188.
    • (1996) Crit. Rev. Eukaryote Gene Expr. , vol.6 , pp. 149-188
    • Fletcher, T.M.1    Hansen, J.C.2
  • 11
    • 0029046603 scopus 로고
    • Modulation of chromatin folding by histone acetylation
    • Garcia-Ramirez, M., C. Rochini, and J. Ausio. 1995. Modulation of chromatin folding by histone acetylation. J. Biol. Chem. 270:17923-17928.
    • (1995) J. Biol. Chem. , vol.270 , pp. 17923-17928
    • Garcia-Ramirez, M.1    Rochini, C.2    Ausio, J.3
  • 12
    • 0035909076 scopus 로고    scopus 로고
    • Energetics and affinity of the histone octamer for defined DNA sequences
    • Gottesfeld, J. M., and K. Luger. 2001. Energetics and affinity of the histone octamer for defined DNA sequences. Biochemistry. 40:10927-10933.
    • (2001) Biochemistry , vol.40 , pp. 10927-10933
    • Gottesfeld, J.M.1    Luger, K.2
  • 13
    • 0030798245 scopus 로고    scopus 로고
    • Histone acetylation in chromatin structure and transcription
    • Grunstein, M. 1997. Histone acetylation in chromatin structure and transcription. Nature. 389:349-352.
    • (1997) Nature , vol.389 , pp. 349-352
    • Grunstein, M.1
  • 14
    • 0025736538 scopus 로고
    • The mechanism of nucleosome assembly onto oligomers of the sea urchin 5S DNA positioning sequence
    • Hansen, J. C., K. E. Van Holde, and D. Lohr. 1991. The mechanism of nucleosome assembly onto oligomers of the sea urchin 5S DNA positioning sequence. J. Biol. Chem. 266:4276-4282.
    • (1991) J. Biol. Chem. , vol.266 , pp. 4276-4282
    • Hansen, J.C.1    Van Holde, K.E.2    Lohr, D.3
  • 15
    • 0027412701 scopus 로고
    • Assembly and structural properties of subsaturated chromatin arrays
    • Hansen, J. C., and D. Lohr. 1993. Assembly and structural properties of subsaturated chromatin arrays. J. Biol. Chem. 268:5840-5848.
    • (1993) J. Biol. Chem. , vol.268 , pp. 5840-5848
    • Hansen, J.C.1    Lohr, D.2
  • 16
    • 0032558998 scopus 로고    scopus 로고
    • Structure and function of the core histone N-termini: More than meets the eye
    • Hansen, J. C., C. Tse, and A. P. Wolffe. 1998. Structure and function of the core histone N-termini: more than meets the eye. Biochemistry. 37:17637-17641.
    • (1998) Biochemistry , vol.37 , pp. 17637-17641
    • Hansen, J.C.1    Tse, C.2    Wolffe, A.P.3
  • 17
    • 0036089388 scopus 로고    scopus 로고
    • Conformational dynamics of the chromatin fiber in solution: Determinants, mechanisms, and functions
    • Hansen, J. C. 2002. Conformational dynamics of the chromatin fiber in solution: determinants, mechanisms, and functions. Annu. Rev. Biophys. Biomol. Struct. 31:361-392.
    • (2002) Annu. Rev. Biophys. Biomol. Struct. , vol.31 , pp. 361-392
    • Hansen, J.C.1
  • 18
    • 0034310582 scopus 로고    scopus 로고
    • Salt-induced DNA-histone complexation
    • Kunze, K.-K., and R. R. Netz. 2000. Salt-induced DNA-histone complexation. Phys. Rev. Lett. 85:4389-4392.
    • (2000) Phys. Rev. Lett. , vol.85 , pp. 4389-4392
    • Kunze, K.-K.1    Netz, R.R.2
  • 19
    • 0031579664 scopus 로고    scopus 로고
    • Mechanisms of stabilizing nucleosome structure. Study of dissociation of histone octamer from DNA
    • Khrapunov, S. N., A. I. Dragan, A. V. Sivolob, and A. M. Zagariya. 1997. Mechanisms of stabilizing nucleosome structure. Study of dissociation of histone octamer from DNA. Biochim. Biophys. Acta. 1351:213-222.
    • (1997) Biochim. Biophys. Acta , vol.1351 , pp. 213-222
    • Khrapunov, S.N.1    Dragan, A.I.2    Sivolob, A.V.3    Zagariya, A.M.4
  • 20
    • 0021768552 scopus 로고
    • Reconstitution of mononucleosomes-characterization of distinct particles that differ in the position of the histone core
    • Linxweiler, W., and W. Horz. 1984. Reconstitution of mononucleosomes- characterization of distinct particles that differ in the position of the histone core. Nucleic Acids Res. 12:9395-9413.
    • (1984) Nucleic Acids Res. , vol.12 , pp. 9395-9413
    • Linxweiler, W.1    Horz, W.2
  • 21
    • 0022998739 scopus 로고
    • The salt dependence of chicken and yeast chromatin structure-effects on internucleosomal organization and relation to active chromatin
    • Lohr, D. 1986. The salt dependence of chicken and yeast chromatin structure-effects on internucleosomal organization and relation to active chromatin. J. Biol. Chem. 261:9904-9919.
    • (1986) J. Biol. Chem. , vol.261 , pp. 9904-9919
    • Lohr, D.1
  • 22
    • 0031585394 scopus 로고    scopus 로고
    • Nucleosome transactions on the promoters of the yeast GAL and PHO genes
    • Lohr, D. 1997. Nucleosome transactions on the promoters of the yeast GAL and PHO genes. J. Biol. Chem. 272:26795-26798.
    • (1997) J. Biol. Chem. , vol.272 , pp. 26795-26798
    • Lohr, D.1
  • 23
    • 0024300805 scopus 로고
    • Structure of the chromosomal copy of yeast ARS1
    • Lohr, D., and T. Torchia. 1988. Structure of the chromosomal copy of yeast ARS1. Biochemistry. 27:3961-3965.
    • (1988) Biochemistry , vol.27 , pp. 3961-3965
    • Lohr, D.1    Torchia, T.2
  • 24
    • 1842411320 scopus 로고    scopus 로고
    • Crystal structure of the nucleosome core particle at 2.8 Å resolution
    • Luger, K., A. W. Mader, R. K. Richmond, D. F. Sargent, and T. J. Richmond. 1997. Crystal structure of the nucleosome core particle at 2.8 Å resolution. Nature. 389:251-260.
    • (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
  • 25
    • 0033039285 scopus 로고    scopus 로고
    • Preparation of NCPs from recombinant histones
    • Luger, K., T. J. Rechsteiner, and T. Richmond. 1999. Preparation of NCPs from recombinant histones. Meth. Enzymol. 304:3-19.
    • (1999) Meth. Enzymol. , vol.304 , pp. 3-19
    • Luger, K.1    Rechsteiner, T.J.2    Richmond, T.3
  • 26
    • 0033562039 scopus 로고    scopus 로고
    • Overcharging of a spherical macroion by an oppositely charged polyelectrolyte
    • Mateescu, E. M., C. Jeppesen, and P. Pincus. 1999. Overcharging of a spherical macroion by an oppositely charged polyelectrolyte. Europhys. Lett. 46:493-498.
    • (1999) Europhys. Lett. , vol.46 , pp. 493-498
    • Mateescu, E.M.1    Jeppesen, C.2    Pincus, P.3
  • 27
    • 0016175370 scopus 로고
    • Theoretical aspects of DNA-protein interactions: Cooperative and non-cooperative binding of large ligands to a one-dimensional homogeneous lattice
    • McGhee, J. D., and P. H. von Hippel. 1974. Theoretical aspects of DNA-protein interactions: cooperative and non-cooperative binding of large ligands to a one-dimensional homogeneous lattice. J. Mol. Biol. 86:469-489.
    • (1974) J. Mol. Biol. , vol.86 , pp. 469-489
    • McGhee, J.D.1    Von Hippel, P.H.2
  • 28
    • 0025916330 scopus 로고
    • Chromatosome positioning on assembled long chromatin linker histones affect nucleosome placement on 5-S-RDNA
    • Meerseman, G., S. Pennings, and E. Bradbury. 1991. Chromatosome positioning on assembled long chromatin linker histones affect nucleosome placement on 5-S-RDNA. J. Mol. Biol. 220:89-100.
    • (1991) J. Mol. Biol. , vol.220 , pp. 89-100
    • Meerseman, G.1    Pennings, S.2    Bradbury, E.3
  • 29
    • 0028791330 scopus 로고
    • Mechanism of protein access to specific DNA sequences in chromatin: A dynamic equilibrium model for gene regulation
    • Polach, K. J., and J. Widom. 1995. Mechanism of protein access to specific DNA sequences in chromatin: a dynamic equilibrium model for gene regulation. J. Mol. Biol. 254:130-149.
    • (1995) J. Mol. Biol. , vol.254 , pp. 130-149
    • Polach, K.J.1    Widom, J.2
  • 31
    • 0001079085 scopus 로고
    • Artificial nucleosome positioning sequences
    • Shrader, T., and D. Crothers. 1989. Artificial nucleosome positioning sequences. Proc. Natl. Acad. Sci. USA. 86:7418-7422.
    • (1989) Proc. Natl. Acad. Sci. USA , vol.86 , pp. 7418-7422
    • Shrader, T.1    Crothers, D.2
  • 32
    • 0020695571 scopus 로고
    • Structural features of a phased nucleosome core particle
    • Simpson, R., and D. Stafford. 1983. Structural features of a phased nucleosome core particle. Proc. Natl. Acad. Sci. USA. 80:51-55.
    • (1983) Proc. Natl. Acad. Sci. USA , vol.80 , pp. 51-55
    • Simpson, R.1    Stafford, D.2
  • 33
    • 0022234831 scopus 로고
    • Chromatin reconstituted from tandemly repeated cloned DNA fragments and core histones: A model system for study of higher order structure
    • Simpson, R. T., F. Thoma, and J. M. Brubaker. 1985. Chromatin reconstituted from tandemly repeated cloned DNA fragments and core histones: a model system for study of higher order structure. Cell. 42:799-808.
    • (1985) Cell , vol.42 , pp. 799-808
    • Simpson, R.T.1    Thoma, F.2    Brubaker, J.M.3
  • 34
    • 0022457421 scopus 로고
    • Structure of the replicating SV40 minichromosomes: The replication fork, core histone segregation and terminal structures
    • Sogo, J. M., H. Stahl, T. Koller, and R. Knippers. 1986. Structure of the replicating SV40 minichromosomes: the replication fork, core histone segregation and terminal structures. J. Mol. Biol. 189:189-206.
    • (1986) J. Mol. Biol. , vol.189 , pp. 189-206
    • Sogo, J.M.1    Stahl, H.2    Koller, T.3    Knippers, R.4
  • 35
    • 0032516927 scopus 로고    scopus 로고
    • Functionally relevant histone-DNA interactions extend beyond the classically defined nucleosome core region
    • Thiriet, C., and J. Hayes. 1998. Functionally relevant histone-DNA interactions extend beyond the classically defined nucleosome core region. J. Biol. Chem. 273:21352-21358.
    • (1998) J. Biol. Chem. , vol.273 , pp. 21352-21358
    • Thiriet, C.1    Hayes, J.2
  • 36
    • 0033200347 scopus 로고    scopus 로고
    • The nucleosome core particle: Does it have structural and physiologic relevance?
    • Van Holde, K., and J. Zlatanova. 1999. The nucleosome core particle: does it have structural and physiologic relevance? Bioessays. 21:776-780.
    • (1999) Bioessays , vol.21 , pp. 776-780
    • Van Holde, K.1    Zlatanova, J.2
  • 37
    • 0002362439 scopus 로고
    • Elements of chromatin structure: Histones, nucleosomes, fibers
    • S.C.R. Elgin, editor. Oxford Press, New York
    • Van Holde, K., J. Zlatanova, G. Arents, and E. Moudrianakis. 1995. Elements of chromatin structure: histones, nucleosomes, fibers. In Chromatin Structure and Gene Expression. S.C.R. Elgin, editor. Oxford Press, New York. 1-21.
    • (1995) Chromatin Structure and Gene Expression , pp. 1-21
    • Van Holde, K.1    Zlatanova, J.2    Arents, G.3    Moudrianakis, E.4
  • 38
    • 0003903126 scopus 로고
    • Springer Series in Molecular Biology. Springer-Verlag, New York
    • Van Holde, K. E. 1989. Chromatin. Springer Series in Molecular Biology. Springer-Verlag, New York.
    • (1989) Chromatin
    • Van Holde, K.E.1
  • 39
    • 0034603742 scopus 로고    scopus 로고
    • DNA sequence-dependent contributions of core histone tails to nucleosome stability: Differential effects of acetylation and proteolytic tail removal
    • Widlund, H., J. Vitolo, C. Thiriet, and J. Hayes. 2000. DNA sequence-dependent contributions of core histone tails to nucleosome stability: differential effects of acetylation and proteolytic tail removal. Biochemistry. 39:3835-3841.
    • (2000) Biochemistry , vol.39 , pp. 3835-3841
    • Widlund, H.1    Vitolo, J.2    Thiriet, C.3    Hayes, J.4
  • 40
    • 0033080794 scopus 로고    scopus 로고
    • Chromatin disruption and modification
    • Wolffe, A. P., and J. J. Hayes. 1999. Chromatin disruption and modification. Nucl. Acids Res. 27:711-720.
    • (1999) Nucl. Acids Res. , vol.27 , pp. 711-720
    • Wolffe, A.P.1    Hayes, J.J.2
  • 41
    • 0033619736 scopus 로고    scopus 로고
    • Evidence for nonrandom behavior in 208-12 subsaturated nucleosomal array populations analyzed by AFM
    • Yodh, J. G., Y. L. Lyubchenko, L. S. Shlyakhtenko, N. Woodbury, and D. Lohr. 1999. Evidence for nonrandom behavior in 208-12 subsaturated nucleosomal array populations analyzed by AFM. Biochemistry. 38:15756-15763.
    • (1999) Biochemistry , vol.38 , pp. 15756-15763
    • Yodh, J.G.1    Lyubchenko, Y.L.2    Shlyakhtenko, L.S.3    Woodbury, N.4    Lohr, D.5
  • 42
    • 0037133515 scopus 로고    scopus 로고
    • Mapping nucleosome locations on the 208-12 by AFM provides clear evidence for cooperativity in array occupation
    • Yodh, J. G., N. Woodbury, L. S. Shlyakhtenko, Y. L. Lyubchenko, and D. Lohr. 2002. Mapping nucleosome locations on the 208-12 by AFM provides clear evidence for cooperativity in array occupation. Biochemistry. 41:3565-3574.
    • (2002) Biochemistry , vol.41 , pp. 3565-3574
    • Yodh, J.G.1    Woodbury, N.2    Shlyakhtenko, L.S.3    Lyubchenko, Y.L.4    Lohr, D.5


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