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Volumn 110, Issue 14, 2013, Pages 5719-5724

Toward a unified physical model of nucleosome patterns flanking transcription start sites

Author keywords

Chromatin structure; Nucleosome maps; Quantitative biology

Indexed keywords

CELL NUCLEUS DNA; HISTONE;

EID: 84875873326     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1214048110     Document Type: Article
Times cited : (34)

References (33)
  • 1
    • 0037083376 scopus 로고    scopus 로고
    • Capturing chromosome conformation
    • Dekker J, Rippe K, Dekker M, Kleckner N (2002) Capturing chromosome conformation. Science 295(5558):1306-1311.
    • (2002) Science , vol.295 , Issue.5558 , pp. 1306-1311
    • Dekker, J.1    Rippe, K.2    Dekker, M.3    Kleckner, N.4
  • 2
    • 22744432660 scopus 로고    scopus 로고
    • Genome-scale identification of nucleosome positions in S. cerevisiae
    • Yuan GC, et al. (2005) Genome-scale identification of nucleosome positions in S. cerevisiae. Science 309(5734):626-630.
    • (2005) Science , vol.309 , Issue.5734 , pp. 626-630
    • Yuan, G.C.1
  • 3
    • 68349125112 scopus 로고    scopus 로고
    • What controls nucleosome positions?
    • Segal E, Widom J (2009) What controls nucleosome positions? Trends Genet 25(8): 335-343.
    • (2009) Trends Genet , vol.25 , Issue.8 , pp. 335-343
    • Segal, E.1    Widom, J.2
  • 4
    • 60349089645 scopus 로고    scopus 로고
    • Nucleosome positioning and gene regulation: Advances through genomics
    • Jiang C, Pugh BF (2009) Nucleosome positioning and gene regulation: Advances through genomics. Nat Rev Genet 10(3):161-172.
    • (2009) Nat Rev Genet , vol.10 , Issue.3 , pp. 161-172
    • Jiang, C.1    Pugh, B.F.2
  • 5
    • 76949093375 scopus 로고    scopus 로고
    • Nucleosome positioning: How is it established, and why does it matter?
    • Radman-LivajaM, Rando OJ (2010) Nucleosome positioning: How is it established, and why does it matter? Dev Biol 339(2):258-266.
    • (2010) Dev Biol , vol.339 , Issue.2 , pp. 258-266
    • Radman-Livaja, M.1    Rando, O.J.2
  • 6
    • 77955045449 scopus 로고    scopus 로고
    • The role of nucleosome positioning in the evolution of gene regulation
    • Tsankov AM, Thompson DA, Socha A, Regev A, Rando OJ (2010) The role of nucleosome positioning in the evolution of gene regulation. PLoS Biol 8(7):e1000414.
    • (2010) PLoS Biol , vol.8 , Issue.7
    • Tsankov, A.M.1    Thompson, D.A.2    Socha, A.3    Regev, A.4    Rando, O.J.5
  • 8
    • 78049434489 scopus 로고    scopus 로고
    • Quantitative test of the barrier nucleosome model for statistical positioning of nucleosomes up- and downstream of transcription start sites
    • Möbius W, Gerland U (2010) Quantitative test of the barrier nucleosome model for statistical positioning of nucleosomes up- and downstream of transcription start sites. PLOS Comput Biol 6(8):e1000891.
    • (2010) PLOS Comput Biol , vol.6 , Issue.8
    • Möbius, W.1    Gerland, U.2
  • 9
    • 46449112319 scopus 로고    scopus 로고
    • A barrier nucleosome model for statistical positioning of nucleosomes throughout the yeast genome
    • Mavrich TN, et al. (2008) A barrier nucleosome model for statistical positioning of nucleosomes throughout the yeast genome. Genome Res 18(7):1073-1083.
    • (2008) Genome Res , vol.18 , Issue.7 , pp. 1073-1083
    • Mavrich, T.N.1
  • 10
    • 0023777538 scopus 로고
    • Statistical distributions of nucleosomes: Nonrandom locations by a stochastic mechanism
    • Kornberg RD, Stryer L (1988) Statistical distributions of nucleosomes: Nonrandom locations by a stochastic mechanism. Nucleic Acids Res 16(14A):6677-6690.
    • (1988) Nucleic Acids Res , vol.16 , Issue.14 A , pp. 6677-6690
    • Kornberg, R.D.1    Stryer, L.2
  • 11
    • 36149012094 scopus 로고
    • The complete equation of state of one, two and three-dimensional gases of hard elastic spheres
    • Tonks L (1936) The complete equation of state of one, two and three-dimensional gases of hard elastic spheres. Phys Rev 50:955-963.
    • (1936) Phys Rev , vol.50 , pp. 955-963
    • Tonks, L.1
  • 13
    • 79956316470 scopus 로고    scopus 로고
    • A packing mechanism for nucleosome organization reconstituted across a eukaryotic genome
    • Zhang Z, et al. (2011) A packing mechanism for nucleosome organization reconstituted across a eukaryotic genome. Science 332(6032):977-980.
    • (2011) Science , vol.332 , Issue.6032 , pp. 977-980
    • Zhang, Z.1
  • 14
    • 80053140931 scopus 로고    scopus 로고
    • A role for Snf2-related nucleosome-spacing enzymes in genome-wide nucleosome organization
    • Gkikopoulos T, et al. (2011) A role for Snf2-related nucleosome-spacing enzymes in genome-wide nucleosome organization. Science 333(6050):1758-1760.
    • (2011) Science , vol.333 , Issue.6050 , pp. 1758-1760
    • Gkikopoulos, T.1
  • 15
    • 79959811626 scopus 로고    scopus 로고
    • Substantial histone reduction modulates genomewide nucleosomal occupancy and global transcriptional output
    • Celona B, et al. (2011) Substantial histone reduction modulates genomewide nucleosomal occupancy and global transcriptional output. PLoS Biol 9(6):e1001086.
    • (2011) PLoS Biol , vol.9 , Issue.6
    • Celona, B.1
  • 16
    • 0028791330 scopus 로고
    • Mechanism of protein access to specific DNA sequences in chromatin: A dynamic equilibrium model for gene regulation
    • Polach KJ, Widom J (1995) Mechanism of protein access to specific DNA sequences in chromatin: A dynamic equilibrium model for gene regulation. J Mol Biol 254(2): 130-149.
    • (1995) J Mol Biol , vol.254 , Issue.2 , pp. 130-149
    • Polach, K.J.1    Widom, J.2
  • 17
    • 44149119036 scopus 로고    scopus 로고
    • Spontaneous access to DNA target sites in folded chromatin fibers
    • Poirier MG, Bussiek M, Langowski J, Widom J (2008) Spontaneous access to DNA target sites in folded chromatin fibers. J Mol Biol 379(4):772-786.
    • (2008) J Mol Biol , vol.379 , Issue.4 , pp. 772-786
    • Poirier, M.G.1    Bussiek, M.2    Langowski, J.3    Widom, J.4
  • 18
    • 79960717668 scopus 로고    scopus 로고
    • Dynamics of nucleosome invasion by DNA binding proteins
    • Tims HS, Gurunathan K, Levitus M, Widom J (2011) Dynamics of nucleosome invasion by DNA binding proteins. J Mol Biol 411(2):430-448.
    • (2011) J Mol Biol , vol.411 , Issue.2 , pp. 430-448
    • Tims, H.S.1    Gurunathan, K.2    Levitus, M.3    Widom, J.4
  • 19
    • 33750998762 scopus 로고    scopus 로고
    • Kinetic accessibility of buried DNA sites in nucleosomes
    • Möbius W, Neher RA, Gerland U (2006) Kinetic accessibility of buried DNA sites in nucleosomes. Phys Rev Lett 97(20):208102.
    • (2006) Phys Rev Lett , vol.97 , Issue.20 , pp. 208102
    • Möbius, W.1    Neher, R.A.2    Gerland, U.3
  • 20
    • 68949085807 scopus 로고    scopus 로고
    • SpFRET using alternating excitation and FCS reveals progressive DNA unwrapping in nucleosomes
    • Koopmans WJA, Buning R, Schmidt T, van Noort J (2009) spFRET using alternating excitation and FCS reveals progressive DNA unwrapping in nucleosomes. Biophys J 97(1):195-204.
    • (2009) Biophys J , vol.97 , Issue.1 , pp. 195-204
    • Koopmans, W.J.A.1    Buning, R.2    Schmidt, T.3    Van Noort, J.4
  • 21
    • 1842411320 scopus 로고    scopus 로고
    • Crystal structure of the nucleosome core particle at 2.8 Å resolution
    • Luger K, Mäder AW, Richmond RK, Sargent DF, Richmond TJ (1997) Crystal structure of the nucleosome core particle at 2.8 Å resolution. Nature 389(6648):251-260.
    • (1997) Nature , vol.389 , Issue.6648 , pp. 251-260
    • Luger, K.1    Mäder, A.W.2    Richmond, R.K.3    Sargent, D.F.4    Richmond, T.J.5
  • 22
    • 79956351217 scopus 로고    scopus 로고
    • Nucleosome positioning in a model of active chromatin remodeling enzymes
    • Padinhateeri R, Marko JF (2011) Nucleosome positioning in a model of active chromatin remodeling enzymes. Proc Natl Acad Sci USA 108(19):7799-7803.
    • (2011) Proc Natl Acad Sci USA , vol.108 , Issue.19 , pp. 7799-7803
    • Padinhateeri, R.1    Marko, J.F.2
  • 23
    • 0027180551 scopus 로고
    • The nucleosome repeat length of Kluyveromyces lactis is 16 bp longer than that of Saccharomyces cerevisiae
    • Heus JJ, Zonneveld BJ, Bloom KS, de Steensma HY, van den Berg JA (1993) The nucleosome repeat length of Kluyveromyces lactis is 16 bp longer than that of Saccharomyces cerevisiae. Nucleic Acids Res 21(9):2247-2248.
    • (1993) Nucleic Acids Res , vol.21 , Issue.9 , pp. 2247-2248
    • Heus, J.J.1    Zonneveld, B.J.2    Bloom, K.S.3    De Steensma, H.Y.4    Van Den Berg, J.A.5
  • 24
    • 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
  • 25
    • 78049343481 scopus 로고    scopus 로고
    • A lattice model for transcription factor access to nucleosomal DNA
    • Teif VB, Ettig R, Rippe K (2010) A lattice model for transcription factor access to nucleosomal DNA. Biophys J 99(8):2597-2607.
    • (2010) Biophys J , vol.99 , Issue.8 , pp. 2597-2607
    • Teif, V.B.1    Ettig, R.2    Rippe, K.3
  • 26
    • 66349114864 scopus 로고    scopus 로고
    • Modeling interactions between adjacent nucleosomes improves genome-wide predictions of nucleosome occupancy
    • Lubliner S, Segal E (2009) Modeling interactions between adjacent nucleosomes improves genome-wide predictions of nucleosome occupancy. Bioinformatics 25(12): i348-i355.
    • (2009) Bioinformatics , vol.25 , Issue.12
    • Lubliner, S.1    Segal, E.2
  • 27
    • 0034598944 scopus 로고    scopus 로고
    • Sequence and position-dependence of the equilibrium accessibility of nucleosomal DNA target sites
    • Anderson JD, Widom J (2000) Sequence and position-dependence of the equilibrium accessibility of nucleosomal DNA target sites. J Mol Biol 296(4):979-987.
    • (2000) J Mol Biol , vol.296 , Issue.4 , pp. 979-987
    • Anderson, J.D.1    Widom, J.2
  • 29
    • 67650725820 scopus 로고    scopus 로고
    • The biology of chromatin remodeling complexes
    • Clapier CR, Cairns BR (2009) The biology of chromatin remodeling complexes. Annu Rev Biochem 78:273-304.
    • (2009) Annu Rev Biochem , vol.78 , pp. 273-304
    • Clapier, C.R.1    Cairns, B.R.2
  • 30
    • 79955547248 scopus 로고    scopus 로고
    • Structure and mechanism of the chromatin remodelling factor ISW1a
    • Yamada K, et al. (2011) Structure and mechanism of the chromatin remodelling factor ISW1a. Nature 472(7344):448-453.
    • (2011) Nature , vol.472 , Issue.7344 , pp. 448-453
    • Yamada, K.1
  • 31
    • 0029085907 scopus 로고
    • Electrostatic mechanism of nucleosome spacing
    • Blank TA, Becker PB (1995) Electrostatic mechanism of nucleosome spacing. J Mol Biol 252(3):305-313.
    • (1995) J Mol Biol , vol.252 , Issue.3 , pp. 305-313
    • Blank, T.A.1    Becker, P.B.2
  • 32
    • 68349128355 scopus 로고    scopus 로고
    • The physics behind the larger scale organization of DNA in eukaryotes
    • Emanuel M, Radja NH, Henriksson A, Schiessel H (2009) The physics behind the larger scale organization of DNA in eukaryotes. Phys Biol 6(2):025008.
    • (2009) Phys Biol , vol.6 , Issue.2 , pp. 025008
    • Emanuel, M.1    Radja, N.H.2    Henriksson, A.3    Schiessel, H.4
  • 33
    • 79960984132 scopus 로고    scopus 로고
    • Statistical mechanics of nucleosomes constrained by higher-order chromatin structure
    • Chereji RV, Morozov AV (2011) Statistical mechanics of nucleosomes constrained by higher-order chromatin structure. J Stat Phys 144(2):379-404.
    • (2011) J Stat Phys , vol.144 , Issue.2 , pp. 379-404
    • Chereji, R.V.1    Morozov, A.V.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.