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Volumn 12, Issue 1, 2005, Pages 46-53

Rapid spontaneous accessibility of nucleosomal DNA

Author keywords

[No Author keywords available]

Indexed keywords

DNA; HISTONE; LEXA PROTEIN; RNA POLYMERASE;

EID: 11444262202     PISSN: 15459993     EISSN: None     Source Type: Journal    
DOI: 10.1038/nsmb869     Document Type: Article
Times cited : (538)

References (42)
  • 1
    • 0008242366 scopus 로고    scopus 로고
    • Nucleosome and chromatin structure
    • (eds. Eligin, S.C.R. & Workman, J.L.) Oxford Univ. Press, Oxford
    • Richmond, T. & Widom, J. Nucleosome and chromatin structure. In Chromatin Structure and Gene Expression (eds. Eligin, S.C.R. & Workman, J.L.) (Oxford Univ. Press, Oxford. 2000).
    • (2000) Chromatin Structure and Gene Expression
    • Richmond, T.1    Widom, J.2
  • 2
    • 0037992395 scopus 로고    scopus 로고
    • The structure of DNA in the nucleosome core
    • Richmond, T.J. & Davey, C.A. The structure of DNA in the nucleosome core. Nature 423, 145-150 (2003).
    • (2003) Nature , vol.423 , pp. 145-150
    • Richmond, T.J.1    Davey, C.A.2
  • 3
    • 0033529565 scopus 로고    scopus 로고
    • Twenty-five years of the nucleosome, fundamental particle of the eukaryote chromosome
    • Kornberg, R.D. & Lorch, Y. Twenty-five years of the nucleosome, fundamental particle of the eukaryote chromosome. Cell 98, 285-294 (1999).
    • (1999) Cell , vol.98 , pp. 285-294
    • Kornberg, R.D.1    Lorch, Y.2
  • 4
    • 85015069067 scopus 로고    scopus 로고
    • Controlling the double helix
    • Felsenfeld, G. & Groudine, M. Controlling the double helix. Nature 421, 448-453 (2003).
    • (2003) Nature , vol.421 , pp. 448-453
    • Felsenfeld, G.1    Groudine, M.2
  • 5
    • 0030581149 scopus 로고    scopus 로고
    • Chromatin unfolds
    • Felsenfeld, G. Chromatin unfolds. Cell 86, 13-19 (1996).
    • (1996) Cell , vol.86 , pp. 13-19
    • Felsenfeld, G.1
  • 6
    • 0842324785 scopus 로고    scopus 로고
    • The nucleosome: From genomic organization to genomic regulation
    • Khorasanizadeh, S. The nucleosome: from genomic organization to genomic regulation. Cell 116, 259-272 (2004).
    • (2004) Cell , vol.116 , pp. 259-272
    • Khorasanizadeh, S.1
  • 7
    • 1542328273 scopus 로고    scopus 로고
    • Nucleosome remodeling: One mechanism, many phenomena?
    • Langst, G. & Becker, P.B. Nucleosome remodeling: one mechanism, many phenomena? Biochim. Biophys. Acta 1677, 58-63 (2004).
    • (2004) Biochim. Biophys. Acta , vol.1677 , pp. 58-63
    • Langst, G.1    Becker, P.B.2
  • 8
    • 0032742874 scopus 로고    scopus 로고
    • ATP-dependent chromatin remodelling: SWI/SNF and Co. are on the job
    • Muchardt, C. & Yaniv, M. ATP-dependent chromatin remodelling: SWI/SNF and Co. are on the job. J. Mol. Biol. 293, 187-198 (1999).
    • (1999) J. Mol. Biol. , vol.293 , pp. 187-198
    • Muchardt, C.1    Yaniv, M.2
  • 9
    • 0037154963 scopus 로고    scopus 로고
    • Cooperation between complexes that regulate chromatin structure and transcription
    • Narlikar, G.J., Fan, H.Y. & Kingston, R.E. Cooperation between complexes that regulate chromatin structure and transcription. Cell 108, 475-487 (2002).
    • (2002) Cell , vol.108 , pp. 475-487
    • Narlikar, G.J.1    Fan, H.Y.2    Kingston, R.E.3
  • 10
    • 0034131012 scopus 로고    scopus 로고
    • Recruitment of chromatin remodeling machines
    • Peterson, C.L. & Logie, C. Recruitment of chromatin remodeling machines. J. Cell. Biochem. 78, 179-185 (2000).
    • (2000) J. Cell. Biochem. , vol.78 , pp. 179-185
    • Peterson, C.L.1    Logie, C.2
  • 11
    • 0028791330 scopus 로고
    • Mechanism of protein access to specific DNA sequences in chromatin: A dynamic equilibrium model for gene regulation
    • Polach, K.J. & Widom, J. Mechanism of protein access to specific DNA sequences in chromatin: a dynamic equilibrium model for gene regulation. J. Mol. Biol. 254, 130-149 (1995).
    • (1995) J. Mol. Biol. , vol.254 , pp. 130-149
    • Polach, K.J.1    Widom, J.2
  • 12
    • 0034598944 scopus 로고    scopus 로고
    • Sequence and position-dependence of the equilibrium accessibility of nucleosomal DNA target sites
    • Anderson, J.D. & Widom, J. Sequence and position-dependence of the equilibrium accessibility of nucleosomal DNA target sites. J. Mol. Biol. 296, 979-987 (2000).
    • (2000) J. Mol. Biol. , vol.296 , pp. 979-987
    • Anderson, J.D.1    Widom, J.2
  • 13
    • 0026687952 scopus 로고
    • Fluorescence resonance energy transfer and nucleic acids
    • Clegg, R.M. Fluorescence resonance energy transfer and nucleic acids. Methods Enzymol. 211, 353-388 (1992).
    • (1992) Methods Enzymol. , vol.211 , pp. 353-388
    • Clegg, R.M.1
  • 14
    • 3542998667 scopus 로고    scopus 로고
    • Nucleosomes facilitate their own invasion
    • Li, G. & Widom, J. Nucleosomes facilitate their own invasion. Nat. Struct. Mol. Biol. 11, 763-769 (2004).
    • (2004) Nat. Struct. Mol. Biol. , vol.11 , pp. 763-769
    • Li, G.1    Widom, J.2
  • 16
    • 0037512311 scopus 로고    scopus 로고
    • Distinct strategies to make nucleosomal DNA accessible
    • Fan, H.Y., He, X., Kingston, R.E. & Narlikar, G.J. Distinct strategies to make nucleosomal DNA accessible. Mol. Cell 11, 1311-1322 (2003).
    • (2003) Mol. Cell , vol.11 , pp. 1311-1322
    • Fan, H.Y.1    He, X.2    Kingston, R.E.3    Narlikar, G.J.4
  • 18
    • 0031578809 scopus 로고    scopus 로고
    • Coupled-enzymatic assays for the rate and mechanism of DNA site exposure in a nucleosome
    • Protacio, R.U., Polach, K.J. & Widom, J. Coupled-enzymatic assays for the rate and mechanism of DNA site exposure in a nucleosome. J. Mol. Biol. 274, 708-721 (1997).
    • (1997) J. Mol. Biol. , vol.274 , pp. 708-721
    • Protacio, R.U.1    Polach, K.J.2    Widom, J.3
  • 19
    • 0032555119 scopus 로고    scopus 로고
    • Kinetics of conformational fluctuations in DNA hairpin-loops
    • Bonnet, G., Krichevsky, O. & Libchaber, A. Kinetics of conformational fluctuations in DNA hairpin-loops. Proc. Natl. Acad. Sci. USA 95, 8602-8606 (1998).
    • (1998) Proc. Natl. Acad. Sci. USA , vol.95 , pp. 8602-8606
    • Bonnet, G.1    Krichevsky, O.2    Libchaber, A.3
  • 20
    • 0037154114 scopus 로고    scopus 로고
    • Biological and chemical applications of fluorescence correlation spectroscopy: A review
    • Hess, S.T., Huang, S., Heikal, A.A. & Webb, W.W. Biological and chemical applications of fluorescence correlation spectroscopy: a review. Biochemistry 41, 697-705 (2002).
    • (2002) Biochemistry , vol.41 , pp. 697-705
    • Hess, S.T.1    Huang, S.2    Heikal, A.A.3    Webb, W.W.4
  • 21
    • 0036175642 scopus 로고    scopus 로고
    • Fluorescence correlation spectroscopy: The technique and its applications
    • Krichevsky, O. & Bonnet, G. Fluorescence correlation spectroscopy: the technique and its applications. Rep. Prog. Phys. 65, 251-297 (2002).
    • (2002) Rep. Prog. Phys. , vol.65 , pp. 251-297
    • Krichevsky, O.1    Bonnet, G.2
  • 22
    • 0037057630 scopus 로고    scopus 로고
    • Initiation and re-initiation of DNA unwinding by the Escherichia coli Rep helicase
    • Ha, T. et al. Initiation and re-initiation of DNA unwinding by the Escherichia coli Rep helicase. Nature 419, 638-641 (2002).
    • (2002) Nature , vol.419 , pp. 638-641
    • Ha, T.1
  • 23
    • 3042579602 scopus 로고    scopus 로고
    • How do site-specific DNA-binding proteins find their targets?
    • Halford, S.E. & Marko, J.F. How do site-specific DNA-binding proteins find their targets? Nucleic Acids Res. 32, 3040-3052 (2004).
    • (2004) Nucleic Acids Res. , vol.32 , pp. 3040-3052
    • Halford, S.E.1    Marko, J.F.2
  • 24
    • 0024531901 scopus 로고
    • Facilitated target location in biological systems
    • von Hippel, P.H. & Berg, O.G. Facilitated target location in biological systems. J. Biol. Chem. 264, 675-678 (1989).
    • (1989) J. Biol. Chem. , vol.264 , pp. 675-678
    • Von Hippel, P.H.1    Berg, O.G.2
  • 25
    • 0029841339 scopus 로고    scopus 로고
    • Remodeling the chromatin structure of a nucleosome array by transcription factor-targeted trans-displacement of histones
    • Owen-Hughes, T. & Workman, J.L. Remodeling the chromatin structure of a nucleosome array by transcription factor-targeted trans-displacement of histones. EMBO J. 15, 4702-4712 (1996).
    • (1996) EMBO J. , vol.15 , pp. 4702-4712
    • Owen-Hughes, T.1    Workman, J.L.2
  • 26
    • 0029826906 scopus 로고    scopus 로고
    • Persistent site-specific remodeling of a nucleosome array by transient action of the SWI/SNF complex
    • Owen-Hughes, T., Utley, R.T., Cote, J., Peterson, C.L. & Workman, J.L. Persistent site-specific remodeling of a nucleosome array by transient action of the SWI/SNF complex. Science 273, 513-516 (1996).
    • (1996) Science , vol.273 , pp. 513-516
    • Owen-Hughes, T.1    Utley, R.T.2    Cote, J.3    Peterson, C.L.4    Workman, J.L.5
  • 27
    • 0030782468 scopus 로고    scopus 로고
    • Catalytic activity of the yeast SWI/SNF complex on reconstituted nucleosome arrays
    • Logie, C. & Peterson, C.L. Catalytic activity of the yeast SWI/SNF complex on reconstituted nucleosome arrays. EMBO J. 16, 6772-6782 (1997).
    • (1997) EMBO J. , vol.16 , pp. 6772-6782
    • Logie, C.1    Peterson, C.L.2
  • 28
    • 0035093560 scopus 로고    scopus 로고
    • Computational modeling predicts the structure and dynamics of chromatin fiber
    • Beard, D.A. & Schlick, T. Computational modeling predicts the structure and dynamics of chromatin fiber. Structure 9, 105-114 (2001).
    • (2001) Structure , vol.9 , pp. 105-114
    • Beard, D.A.1    Schlick, T.2
  • 29
    • 0031831516 scopus 로고    scopus 로고
    • Structure, dynamics, and function of chromatin in vitro
    • Widom, J. Structure, dynamics, and function of chromatin in vitro. Annu. Rev. Biophys. Biomol. Struct. 27, 285-327 (1998).
    • (1998) Annu. Rev. Biophys. Biomol. Struct. , vol.27 , pp. 285-327
    • Widom, J.1
  • 30
    • 0032488030 scopus 로고    scopus 로고
    • Chromatin structure: Linking structure to function with histone H1
    • Widom, J. Chromatin structure: linking structure to function with histone H1. Curr. Biol. 8, R788-R791 (1998).
    • (1998) Curr. Biol. , vol.8
    • Widom, J.1
  • 31
    • 0024489155 scopus 로고
    • Toward a unified model of chromatin folding
    • Widom, J. Toward a unified model of chromatin folding. Annu. Rev. Biophys. Biophys. Chem. 18, 365-395 (1989).
    • (1989) Annu. Rev. Biophys. Biophys. Chem. , vol.18 , pp. 365-395
    • Widom, J.1
  • 32
    • 0030726678 scopus 로고    scopus 로고
    • Gene activation at a distance and telomeric silencing are not affected by yeast histone H1
    • Escher, D. & Schaffner, W. Gene activation at a distance and telomeric silencing are not affected by yeast histone H1. Mol. Gen. Genet. 256, 456-461 (1997).
    • (1997) Mol. Gen. Genet. , vol.256 , pp. 456-461
    • Escher, D.1    Schaffner, W.2
  • 33
    • 0032571258 scopus 로고    scopus 로고
    • The biochemical and phenotypic characterization of Hho1p, the putative linker histone H1 of Saccharomyces cerevisiae
    • Patterton, H.G., Landel, C.C., Landsman, D., Peterson, C.L. & Simpson, R.T. The biochemical and phenotypic characterization of Hho1p, the putative linker histone H1 of Saccharomyces cerevisiae. J. Biol. Chem. 273, 7268-7276 (1998).
    • (1998) J. Biol. Chem. , vol.273 , pp. 7268-7276
    • Patterton, H.G.1    Landel, C.C.2    Landsman, D.3    Peterson, C.L.4    Simpson, R.T.5
  • 34
    • 0035477211 scopus 로고    scopus 로고
    • Specific distribution of the Saccharomyces cerevisiae linker histone homolog HHO1p in the chromatin
    • Freidkin, I. & Katcoff, D.J. Specific distribution of the Saccharomyces cerevisiae linker histone homolog HHO1p in the chromatin. Nucleic Acids Res. 29, 4043-4051 (2001).
    • (2001) Nucleic Acids Res. , vol.29 , pp. 4043-4051
    • Freidkin, I.1    Katcoff, D.J.2
  • 35
    • 2342518189 scopus 로고    scopus 로고
    • Spontaneous sharp bending of double-stranded DNA
    • Cloutier, T.E. & Widom, J. Spontaneous sharp bending of double-stranded DNA. Mol. Cell 14, 355-362 (2004).
    • (2004) Mol. Cell , vol.14 , pp. 355-362
    • Cloutier, T.E.1    Widom, J.2
  • 36
    • 0035691979 scopus 로고    scopus 로고
    • Generation and interconversion of multiple distinct nucleosomal states as a mechanism for catalyzing chromatin fluidity
    • Narlikar, G.J., Phelan, M.L. & Kingston, R.E. Generation and interconversion of multiple distinct nucleosomal states as a mechanism for catalyzing chromatin fluidity. Mol. Cell 8, 1219-1230 (2001).
    • (2001) Mol. Cell , vol.8 , pp. 1219-1230
    • Narlikar, G.J.1    Phelan, M.L.2    Kingston, R.E.3
  • 37
    • 0026006495 scopus 로고
    • Progression of the cell cycle through mitosis leads to abortion of nascent transcripts
    • Shermoen, A.W. & O'Farrell, P.H. Progression of the cell cycle through mitosis leads to abortion of nascent transcripts. Cell 67, 303-310 (1991).
    • (1991) Cell , vol.67 , pp. 303-310
    • Shermoen, A.W.1    O'Farrell, P.H.2
  • 38
    • 1942489758 scopus 로고    scopus 로고
    • Nucleosomal locations of dominant DNA sequence motifs for histone-DNA interactions and nucleosome positioning
    • Thastrom, A., Bingham, L.M. & Widom, J. Nucleosomal locations of dominant DNA sequence motifs for histone-DNA interactions and nucleosome positioning. J. Mol. Biol. 338, 695-709 (2004).
    • (2004) J. Mol. Biol. , vol.338 , pp. 695-709
    • Thastrom, A.1    Bingham, L.M.2    Widom, J.3
  • 39
    • 0028672846 scopus 로고
    • Cleavage of LexA repressor
    • Little, J.W. et al. Cleavage of LexA repressor. Methods Enzymol. 244, 266-284 (1994).
    • (1994) Methods Enzymol. , vol.244 , pp. 266-284
    • Little, J.W.1
  • 40
    • 0026528848 scopus 로고
    • Dimerization of a specific DNA-binding protein on the DNA
    • Kim, B. & Little, J.W. Dimerization of a specific DNA-binding protein on the DNA. Science 255, 203-206 (1992).
    • (1992) Science , vol.255 , pp. 203-206
    • Kim, B.1    Little, J.W.2
  • 41
    • 0039313256 scopus 로고
    • Investigation of rates and mechanisms of reactions
    • Wiley, New York
    • th edn. Vol. VI (Wiley, New York, 1986).
    • (1986) th Edn. , vol.6
    • Bernasconi, C.F.1
  • 42
    • 0042660353 scopus 로고    scopus 로고
    • Conceptual basis of fluorescence correlation spectroscopy and related techniques as tools in bioscience
    • eds. Zander, C., Enderlein, J. & Keller, R.A. Wiley-VCH, Berlin
    • Widengren, J. & Mets, U. Conceptual basis of fluorescence correlation spectroscopy and related techniques as tools in bioscience. In Single Molecule Detection in Solution (eds. Zander, C., Enderlein, J. & Keller, R.A.) 69-120 (Wiley-VCH, Berlin, 2002).
    • (2002) Single Molecule Detection in Solution , pp. 69-120
    • Widengren, J.1    Mets, U.2


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