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Volumn 106, Issue 32, 2009, Pages 13317-13322

Evidence for heteromorphic chromatin fibers from analysis of nucleosome interactions

Author keywords

Chromatin structure; Electron microscopy; Linker histone; Mesoscopic modeling; Monte carlo simulations

Indexed keywords

CURVED DNA; DIVALENT CATION; HISTONE; LINK PROTEIN; MONOVALENT CATION;

EID: 69449098842     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.0903280106     Document Type: Article
Times cited : (205)

References (54)
  • 1
    • 85015069067 scopus 로고    scopus 로고
    • Controlling the double helix
    • Felsenfeld G, Groudine M (2003) Controlling the double helix. Nature 421:448-453.
    • (2003) Nature , vol.421 , pp. 448-453
    • Felsenfeld, G.1    Groudine, M.2
  • 2
    • 0037992395 scopus 로고    scopus 로고
    • The structure of DNA in the nucleosome core
    • Richmond TJ, Davey CA (2003) The structure of DNA in the nucleosome core. Nature 423:145-150.
    • (2003) Nature , vol.423 , pp. 145-150
    • Richmond, T.J.1    Davey, C.A.2
  • 4
    • 17044365726 scopus 로고    scopus 로고
    • Nucleosome and chromatin fiberdynamics
    • Luger K, Hansen JC (2005) Nucleosome and chromatin fiberdynamics. Curr Opin Struct Biol 15:188-196.
    • (2005) Curr Opin Struct Biol , vol.15 , pp. 188-196
    • Luger, K.1    Hansen, J.C.2
  • 5
    • 33847106524 scopus 로고    scopus 로고
    • Higher-order structures of chromatin: The elusive 30 nm fiber
    • Tremethick DJ (2007) Higher-order structures of chromatin: The elusive 30 nm fiber. Cell 128:651-654.
    • (2007) Cell , vol.128 , pp. 651-654
    • Tremethick, D.J.1
  • 6
    • 35648930403 scopus 로고    scopus 로고
    • Chromatin fiber structure: Where is the problem now?
    • DOI 10.1016/j.semcdb.2007.08.005, PII S1084952107001206, Membrane Lipid Microdomains: Roles in Signalling and Disease and 3D Chromatin
    • van Holde K, Zlatanova J (2007) Chromatin fiber structure: Where is the problem now? Semin Cell Dev Biol 18:651-658. (Pubitemid 350026429)
    • (2007) Seminars in Cell and Developmental Biology , vol.18 , Issue.5 , pp. 651-658
    • Van Holde, K.1    Zlatanova, J.2
  • 7
    • 0021250785 scopus 로고
    • The higher-order structure of chromatin: Evidence for a helical ribbon arrangement
    • Woodcock CL, Frado LL, Rattner JB (1984) The higher-order structure of chromatin: Evidence for a helical ribbon arrangement. J Cell Biol 99:42-52.
    • (1984) J Cell Biol , vol.99 , pp. 42-52
    • Woodcock, C.L.1    Frado, L.L.2    Rattner, J.B.3
  • 8
    • 0027960444 scopus 로고
    • Three-dimensional structure of extended chromatin fibers as revealed by tapping-mode scanning force microscopy
    • Leuba SH, et al. (1994) Three-dimensional structure of extended chromatin fibers as revealed by tapping-mode scanning force microscopy. Proc Natl Acad Sci USA 91:11621-11625.
    • (1994) Proc Natl Acad Sci USA , vol.91 , pp. 11621-11625
    • Leuba, S.H.1
  • 10
    • 21844436803 scopus 로고    scopus 로고
    • X-ray structure of a tetranucleosome and its implications for the chromatin fibre
    • DOI 10.1038/nature03686
    • Schalch T, Duda S, Sargent DF, Richmond TJ (2005) X-ray structure of a tetranucleosome and its implications for the chromatin fibre. Nature 436:138-141. (Pubitemid 40966200)
    • (2005) Nature , vol.436 , Issue.7047 , pp. 138-141
    • Schalch, T.1    Duda, S.2    Sargent, D.F.3    Richmond, T.J.4
  • 11
    • 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 RA, Agard DA, Sedat JW, Woodcock CL (1994) The three-dimensional architecture of chromatin in situ: Electron tomography reveals fibers composed of a continuously variable zig-zag nucleosomal ribbon. J Cell Biol 125:1-10.
    • (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
  • 12
    • 0022650876 scopus 로고
    • Chromatin fibers are left-handed double helices with diameter and mass per unit length that depend on linker length
    • Williams SP, et al. (1986) Chromatin fibers are left-handed double helices with diameter and mass per unit length that depend on linker length. Biophys J 49:233-248.
    • (1986) Biophys J , vol.49 , pp. 233-248
    • Williams, S.P.1
  • 13
    • 36749082174 scopus 로고    scopus 로고
    • An all-atom model of the chromatin fiber containing linker histones reveals a versatile structure tuned by the nucleosomal repeat length
    • Wong H, Victor JM, Mozziconacci J (2007) An all-atom model of the chromatin fiber containing linker histones reveals a versatile structure tuned by the nucleosomal repeat length. PLoS ONE 2:e877.
    • (2007) PLoS ONE , vol.2
    • Wong, H.1    Victor, J.M.2    Mozziconacci, J.3
  • 14
    • 0018581187 scopus 로고
    • Involvement of histone H1 in the organization of the nucleosome and of the salt-dependent superstructures of chromatin
    • DOI 10.1083/jcb.83.2.403
    • Thoma F, Koller T, Klug A (1979) Involvement of histone H1 in the organization of the nucleosome and of the salt-dependent superstructures of chromatin. J Cell Biol 83:403-427. (Pubitemid 10205723)
    • (1979) Journal of Cell Biology , vol.83 , Issue.2 I , pp. 403-427
    • Thoma, F.1    Koller, Th.2    Klug, A.3
  • 15
    • 66149144002 scopus 로고    scopus 로고
    • Single-molecule force spectroscopy reveals a highly compliant helical folding for the 30-nm chromatin fiber
    • Kruithof M, et al. (2009) Single-molecule force spectroscopy reveals a highly compliant helical folding for the 30-nm chromatin fiber. Nat Struct Mol Biol 16:534-540.
    • (2009) Nat Struct Mol Biol , vol.16 , pp. 534-540
    • Kruithof, M.1
  • 16
    • 0039591501 scopus 로고    scopus 로고
    • Physical constraints in the condensation of eukaryotic chromosomes. Local concentration of DNA versus linear packing ratio in higher order chromatin structures
    • Daban JR (2000) Physical constraints in the condensation of eukaryotic chromosomes. Local concentration of DNA versus linear packing ratio in higher order chromatin structures. Biochemistry 39:3861-3866.
    • (2000) Biochemistry , vol.39 , pp. 3861-3866
    • Daban, J.R.1
  • 17
    • 33646242052 scopus 로고    scopus 로고
    • EM measurements define the dimensions of the "30-nm" chromatin fiber: Evidence for a compact, interdigitated structure
    • Robinson PJ, Fairall L, Huynh VA, Rhodes D (2006) EM measurements define the dimensions of the "30-nm" chromatin fiber: Evidence for a compact, interdigitated structure. Proc Natl Acad Sci USA 103:6506-6511.
    • (2006) Proc Natl Acad Sci USA , vol.103 , pp. 6506-6511
    • Robinson, P.J.1    Fairall, L.2    Huynh, V.A.3    Rhodes, D.4
  • 18
    • 48249103503 scopus 로고    scopus 로고
    • Nucleosome repeat length and linker histone stoichiometry determine chromatin fiber structure
    • Routh A, Sandin S, Rhodes D (2008) Nucleosome repeat length and linker histone stoichiometry determine chromatin fiber structure. Proc Natl Acad Sci USA 105:8872-8877.
    • (2008) Proc Natl Acad Sci USA , vol.105 , pp. 8872-8877
    • Routh, A.1    Sandin, S.2    Rhodes, D.3
  • 19
    • 48249116182 scopus 로고    scopus 로고
    • Nucleosome geometry and internucleosomal interactions control the chromatin fiber conformation
    • Kepper N, Foethke D, Stehr R, Wedemann G, Rippe K (2008) Nucleosome geometry and internucleosomal interactions control the chromatin fiber conformation. Biophys J 95:3692-3705.
    • (2008) Biophys J , vol.95 , pp. 3692-3705
    • Kepper, N.1    Foethke, D.2    Stehr, R.3    Wedemann, G.4    Rippe, K.5
  • 20
    • 56049111628 scopus 로고    scopus 로고
    • The effect of internucleosomal interaction on folding of the chromatin fiber
    • Stehr R, Kepper N, Rippe K, Wedemann G (2008) The effect of internucleosomal interaction on folding of the chromatin fiber. Biophys J 95:3677-3691.
    • (2008) Biophys J , vol.95 , pp. 3677-3691
    • Stehr, R.1    Kepper, N.2    Rippe, K.3    Wedemann, G.4
  • 21
    • 0035066656 scopus 로고    scopus 로고
    • DNA folding: Structural and mechanical properties of the two-angle model for chromatin
    • Schiessel H, Gelbart WM, Bruinsma R (2001) DNA folding: Structural and mechanical properties of the two-angle model for chromatin. Biophys J 80:1940-1956. (Pubitemid 32281009)
    • (2001) Biophysical Journal , vol.80 , Issue.4 , pp. 1940-1956
    • Schiessel, H.1    Gelbart, W.M.2    Bruinsma, R.3
  • 22
    • 0036099317 scopus 로고    scopus 로고
    • Computer simulation of the 30-nanometer chromatin fiber
    • Wedemann G, Langowski J (2002) Computer simulation of the 30-nanometer chromatin fiber. Biophys J 82:2847-2859. (Pubitemid 34547629)
    • (2002) Biophysical Journal , vol.82 , Issue.6 , pp. 2847-2859
    • Wedemann, G.1    Langowski, J.2
  • 25
    • 0034614436 scopus 로고    scopus 로고
    • Pulling chromatin fibers: Computer simulations of direct physical micromanipulations
    • DOI 10.1006/jmbi.1999.3021
    • Katritch V, Bustamante C, Olson WK (2000) Pulling chromatin fibers: Computer simulations of direct physical micromanipulations. J Mol Biol 295:29-40. (Pubitemid 30025899)
    • (2000) Journal of Molecular Biology , vol.295 , Issue.1 , pp. 29-40
    • Katritch, V.1    Bustamante, C.2    Olson, W.K.3
  • 26
    • 0035093560 scopus 로고    scopus 로고
    • Computational modeling predicts the structure and dynamics of chromatin fiber
    • Beard DA, Schlick T (2001) Computational modeling predicts the structure and dynamics of chromatin fiber. Structure 9:105-114.
    • (2001) Structure , vol.9 , pp. 105-114
    • Beard, D.A.1    Schlick, T.2
  • 28
    • 33745738426 scopus 로고    scopus 로고
    • Flexible histone tails in a new mesoscopic oligonucleosome model
    • DOI 10.1529/biophysj.106.083006
    • Arya G, Zhang Q, Schlick T (2006) Flexible histone tails in a new mesoscopic oligonucleosome model. Biophys J 91:133-150. (Pubitemid 44015314)
    • (2006) Biophysical Journal , vol.91 , Issue.1 , pp. 133-150
    • Arya, G.1    Zhang, Q.2    Schlick, T.3
  • 30
    • 33947201778 scopus 로고    scopus 로고
    • The H3 tail domain participates in multiple interactions during folding and self-association of nucleosome arrays
    • DOI 10.1128/MCB.02181-06
    • Kan PY, Lu X, Hansen JC, Hayes JJ (2007) The H3 tail domain participates in multiple interactions during folding and self-association of nucleosome arrays. Mol Cell Biol 27:2084-2091. (Pubitemid 46418466)
    • (2007) Molecular and Cellular Biology , vol.27 , Issue.6 , pp. 2084-2091
    • Kan, P.-Y.1    Lu, X.2    Hansen, J.C.3    Hayes, J.J.4
  • 31
    • 65649099698 scopus 로고    scopus 로고
    • A tale of tails: How histone tails mediate chromatin compaction in different salt and linker histone environments
    • Arya G, Schlick T (2009) A tale of tails: How histone tails mediate chromatin compaction in different salt and linker histone environments. J Phys Chem A 113:4045-4059.
    • (2009) J Phys Chem a , vol.113 , pp. 4045-4059
    • Arya, G.1    Schlick, T.2
  • 32
    • 0032848160 scopus 로고    scopus 로고
    • Formaldehyde cross-linking for studying nucleosomal dynamics
    • Jackson V (1999) Formaldehyde cross-linking for studying nucleosomal dynamics. Methods 17:125-139.
    • (1999) Methods , vol.17 , pp. 125-139
    • Jackson, V.1
  • 33
    • 0032553013 scopus 로고    scopus 로고
    • Linker histones stabilize the intrinsic salt-dependent folding of nucleosomal arrays: Mechanistic ramifications for higher-order chromatin folding
    • DOI 10.1021/bi981684e
    • Carruthers LM, Bednar J, Woodcock CL, Hansen JC (1998) Linker histones stabilize the intrinsic salt-dependent folding of nucleosomal arrays: Mechanistic ramifications for higher-order chromatin folding. Biochemistry 37:14776-14787. (Pubitemid 28487585)
    • (1998) Biochemistry , vol.37 , Issue.42 , pp. 14776-14787
    • Carruthers, L.M.1    Bednar, J.2    Woodcock, C.L.3    Hansen, J.C.4
  • 34
    • 26644471508 scopus 로고    scopus 로고
    • The core histone N-terminal tail domains function independently and additively during salt-dependent oligomerization of nucleosomal arrays
    • DOI 10.1074/jbc.M507048200
    • Gordon F, Luger K, Hansen JC (2005) The core histone N-terminal tail domains function independently and additively during salt-dependent oligomerization of nucleosomal arrays. J Biol Chem 280:33701-33706. (Pubitemid 41443087)
    • (2005) Journal of Biological Chemistry , vol.280 , Issue.40 , pp. 33701-33706
    • Gordon, F.1    Luger, K.2    Hansen, J.C.3
  • 35
    • 0032512794 scopus 로고    scopus 로고
    • New DNA sequence rules for high affinity binding to histone octamer and sequence-directed nucleosome positioning
    • Lowary PT, Widom J (1998) New DNA sequence rules for high affinity binding to histone octamer and sequence-directed nucleosome positioning. JMB 276:19-42.
    • (1998) JMB , vol.276 , pp. 19-42
    • Lowary, P.T.1    Widom, J.2
  • 36
    • 0026517738 scopus 로고
    • A relationship between the helical twist of DNA and the ordered positioning of nucleosomes in all eukaryotic cells
    • Widom J (1992) A relationship between the helical twist of DNA and the ordered positioning of nucleosomes in all eukaryotic cells. Proc Natl Acad Sci USA 89:1095-1099.
    • (1992) Proc Natl Acad Sci USA , vol.89 , pp. 1095-1099
    • Widom, J.1
  • 38
    • 11844299709 scopus 로고    scopus 로고
    • A method for the in vitro reconstitution of a defined "30 nm" chromatin fibre containing stoichiometric amounts of the linker histone
    • Huynh VA, Robinson PJ, Rhodes D (2005) A method for the in vitro reconstitution of a defined "30 nm" chromatin fibre containing stoichiometric amounts of the linker histone. J Mol Biol 345:957-968.
    • (2005) J Mol Biol , vol.345 , pp. 957-968
    • Huynh, V.A.1    Robinson, P.J.2    Rhodes, D.3
  • 39
    • 0014057375 scopus 로고
    • Frictional coefficients of multisubunit structures. I. Theory
    • Bloomfield V, Dalton WO, Van Holde KE (1967) Frictional coefficients of multisubunit structures. I. Theory. Biopolymers 5:135-148.
    • (1967) Biopolymers , vol.5 , pp. 135-148
    • Bloomfield, V.1    Dalton, W.O.2    Van Holde, K.E.3
  • 40
    • 1842411320 scopus 로고    scopus 로고
    • Crystal structure of the nucleosome core particle at 2.8 A resolution
    • DOI 10.1038/38444
    • Luger K, Mader AW, Richmond RK, Sargent DF, Richmond TJ (1997) Crystal structure of the nucleosome core particle at 2.8 A resolution. Nature 389:251-260. (Pubitemid 27406632)
    • (1997) Nature , vol.389 , Issue.6648 , pp. 251-260
    • Luger, K.1    Mader, A.W.2    Richmond, R.K.3    Sargent, D.F.4    Richmond, T.J.5
  • 42
    • 0029882454 scopus 로고    scopus 로고
    • Reversible oligonucleosome self-association: Dependence on divalent cations and core histone tail domains
    • DOI 10.1021/bi9525684
    • Schwarz PM, Felthauser A, Fletcher TM, Hansen JC (1996) Reversible oligonucleosome self-association: Dependence on divalent cations and core histone tail domains. Biochemistry 35:4009-4015. (Pubitemid 26113457)
    • (1996) Biochemistry , vol.35 , Issue.13 , pp. 4009-4015
    • Schwarz, P.M.1    Felthauser, A.2    Fletcher, T.M.3    Hansen, J.C.4
  • 43
    • 0021964610 scopus 로고
    • Structural studies of chromatin by using proteases
    • Crane-Robinson C, Bohm L (1985) Structural studies of chromatin by using proteases. Biochem Soc Trans 13:303-306. (Pubitemid 15096180)
    • (1985) Biochemical Society Transactions , vol.13 , Issue.2 , pp. 303-308
    • Crane-Robinson, C.1    Bohm, L.2
  • 44
    • 0345412722 scopus 로고    scopus 로고
    • Conformation of reconstituted mononucleosomes and effect of linker histone H1 binding studied by scanning force microscopy
    • Kepert JF, et al. (2003) Conformation of reconstituted mononucleosomes and effect of linker histone H1 binding studied by scanning force microscopy. Biophys J 85:4012-4022.
    • (2003) Biophys J , vol.85 , pp. 4012-4022
    • Kepert, J.F.1
  • 45
    • 32344434540 scopus 로고    scopus 로고
    • Chromatin compaction at the mononucleosome level
    • Toth K, Brun N, Langowski J (2006) Chromatin compaction at the mononucleosome level. Biochemistry 45:1591-1598.
    • (2006) Biochemistry , vol.45 , pp. 1591-1598
    • Toth, K.1    Brun, N.2    Langowski, J.3
  • 47
    • 39149106101 scopus 로고    scopus 로고
    • Hydrodynamic studies on defined heterochromatin fragments support a 30-nm fiber having six nucleosomes per turn
    • Ghirlando R, Felsenfeld G (2008) Hydrodynamic studies on defined heterochromatin fragments support a 30-nm fiber having six nucleosomes per turn. J Mol Biol 376:1417-1425.
    • (2008) J Mol Biol , vol.376 , pp. 1417-1425
    • Ghirlando, R.1    Felsenfeld, G.2
  • 48
    • 0026015325 scopus 로고
    • Linker DNA bending induced by the core histones of chromatin
    • Yao J, Lowary PT, Widom J (1991) Linker DNA bending induced by the core histones of chromatin. Biochemistry 30:8408-8414.
    • (1991) Biochemistry , vol.30 , pp. 8408-8414
    • Yao, J.1    Lowary, P.T.2    Widom, J.3
  • 49
    • 0032555763 scopus 로고    scopus 로고
    • Dinucleosomes show compaction by ionic strength, consistent with bending of linker DNA
    • DOI 10.1006/jmbi.1998.1954
    • Butler P, Thomas J (1998) Dinucleosomes show compaction by ionic strength consistent with binding tolinker DNA. JMB 281:401-407. (Pubitemid 28372118)
    • (1998) Journal of Molecular Biology , vol.281 , Issue.3 , pp. 401-407
    • Butler, P.J.G.1    Thomas, J.O.2
  • 50
    • 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 379:772-786.
    • (2008) J Mol Biol , vol.379 , pp. 772-786
    • Poirier, M.G.1    Bussiek, M.2    Langowski, J.3    Widom, J.4
  • 51
    • 33644800314 scopus 로고    scopus 로고
    • 0 with the nucleosome of native chromatin in vivo
    • DOI 10.1038/nsmb1050, PII N1050
    • Brown DT, Izard T, Misteli T (2006) Mapping the interaction surface of linker histone H1(0) with the nucleosome of native chromatin in vivo. Nat Struct Mol Biol 13:250-255. (Pubitemid 43348511)
    • (2006) Nature Structural and Molecular Biology , vol.13 , Issue.3 , pp. 250-255
    • Brown, D.T.1    Izard, T.2    Misteli, T.3
  • 52
    • 1842861622 scopus 로고    scopus 로고
    • Keeping fingers crossed: Heterochromatin spreading through interdigitation of nucleosome arrays
    • Grigoryev SA (2004) Keeping fingers crossed: Heterochromatin spreading through interdigitation of nucleosome arrays. FEBS Lett 564:4-8.
    • (2004) FEBS Lett , vol.564 , pp. 4-8
    • Grigoryev, S.A.1
  • 53
    • 0035842899 scopus 로고    scopus 로고
    • Cation-chromatin binding as shown by ion microscopy is essential for the structural integrity of chromosomes
    • DOI 10.1083/jcb.200105026
    • Strick R, Strissel PL, Gavrilov K, Levi-Setti R (2001) Cation-chromatin binding as shown by ion microscopy is essential for the structural integrity of chromosomes. J Cell Biol 155:899-910. (Pubitemid 34286242)
    • (2001) Journal of Cell Biology , vol.155 , Issue.6 , pp. 899-910
    • Strick, R.1    Strissel, P.L.2    Gavrilov, K.3    Levi-Setti, R.4
  • 54
    • 58149401194 scopus 로고    scopus 로고
    • Analysis of cryo-electron microscopy images does not support the existence of 30-nm chromatin fibers in mitotic chromosomes in situ
    • Eltsov M, Maclellan KM, Maeshima K, Frangakis AS, Dubochet J (2008) Analysis of cryo-electron microscopy images does not support the existence of 30-nm chromatin fibers in mitotic chromosomes in situ. Proc Natl Acad Sci USA 105:19732-19737.
    • (2008) Proc Natl Acad Sci USA , vol.105 , pp. 19732-19737
    • Eltsov, M.1    Maclellan, K.M.2    Maeshima, K.3    Frangakis, A.S.4    Dubochet, J.5


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