Nucleosomes as Control Elements for Accessing the Genome

Genome Organization and Function in the Cell Nucleus

Volumn , Issue , 2011, Pages 55-87

  Dechassa, Mekonnen Lemma ^a   Luger, Karolin ^a  

^a Department of Environmental and Radiological Health Sciences   (United States)

Author keywords

Chromatin; DNA sequence; Dynamics; Genome; Nucleosome; Structure

Indexed keywords

EID: 84862997440     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1002/9783527639991.ch3     Document Type: Chapter

References (218)

1. Van Holde, K.E. (1988) Chromatin, Springer-Verlag, New York.
2. Marino-Ramirez, L., Hsu, B., Baxevanis, A.D., and Landsman, D. (2006) The Histone Database: a comprehensive resource for histones and histone fold-containing proteins. Proteins, 62, 838-842.
3. Luger, K. (2000) Nucleosomes: Structure and Function. Encyclopedia of Life Sciences, www.els.net.
4. Luger, K., Maeder, A.W., Richmond, R. K., Sargent, D.F., and Richmond, T.J. (1997) Crystal structure of the nucleosome core particle at 2.8 Å resolution. Nature, 389, 251-259.
5. Jiang, C. and Pugh, B.F. (2009) Nucleosome positioning and gene regulation: advances through genomics. Nat Rev Genet, 10, 161-172.
6. Hansen, J.C. (2002) Conformational dynamics of the chromatin fiber in solution: determinants, mechanisms, and functions. Annu Rev Biophys Biomol Struct, 31, 361-392.
7. Robinson, P.J. and Rhodes, D. (2006) Structure of the '30 nm' chromatin fibre: a key role for the linker histone. Curr Opin Struct Biol, 16, 336-343.
8. McBryant, S.J., Lu, X., and Hansen, J. C. (2010) Multifunctionality of the linker histones: an emerging role for protein-protein interactions. Cell Res, 20, 519-528.
9. Luger, K. and Hansen, J.C. (2005) Nucleosome and chromatin fiber dynamics. Curr Opin Struct Biol, 15, 188-196.
10. Dorigo, B., Schalch, T., Bystricky, K., and Richmond, T.J. (2003) Chromatin fiber folding: requirement for the histone H4 N-terminal tail. J Mol Biol, 327, 85-96.
11. Fletcher, T.M. and Hansen, J.C. (1995) Core histone tail domains mediate oligonucleosome folding and nucleosomal DNA organization through distinct molecular mechanisms. J Biol Chem, 270, 25359-25362.
12. Sinha, D. and Shogren-Knaak, M.A. (2010) The role of direct interactions between the histone H4 tail and the H2A core in long-range nucleosome contacts. J Biol Chem, 285, 16572-16581.
13. Luger, K. and Richmond, T.J. (1998) DNA binding within the nucleosome core. Curr Opin Struct Biol, 8, 33-40.
14. Arents, G., Burlingame, R.W., Wang, B.C., Love, W.E. and Moudrianakis, E. N. (1991) The nucleosomal core histone octamer at 3.1 Å resolution: a tripartite protein assembly and a lefthanded superhelix. Proc Natl Acad Sci USA, 88, 10148-10152.
15. Akey, C.W. and Luger, K. (2003) Histone chaperones and nucleosome assembly. Curr Opin Struct Biol, 13, 6-14.
16. Arents, G. and Moudrianakis, E.N. (1993) Topography of the histone octamer surface: repeating structural motifs utilized in the docking of nucleosomal DNA. PNAS, 90, 10489-10493.
17. Davey, C.A., Sargent, D.F., Luger, K., Maeder, A.W., and Richmond, T.J. (2002) Solvent mediated interactions in the structure of the nucleosome core particle at 1.9 Å resolution. J Mol Biol, 319, 1097-1113.
18. Luger, K., Rechsteiner, T.J., Flaus, A.J., Waye, M.M., and Richmond, T.J. (1997) Characterization of nucleosome core particles containing histone proteins made in bacteria. J Mol Biol, 272, 301-311.
19. Rohs, R., West, S.M., Sosinsky, A., Liu, P., Mann, R.S., and Honig, B. (2009) The role of DNA shape in protein-DNA recognition. Nature, 461, 1248-1253.
20. West, S.M., Rohs, R., Mann, R.S., and Honig, B. (2010) Electrostatic interactions between arginines and the minor groove in the nucleosome. J Biomol Struct Dyn, 27, 861-866.
21. Kruger, W., Peterson, C.L., Sil, A., Coburn, C., Arents, G., Moudrianakis, E.N., and Herskowitz, I. (1995) Amino acid substitutions in the structured domains of histones H3 and H4 partially relieve the requirement of the yeast SWI/SNF complex for transcription. Genes Dev, 9, 2770-2779.
22. Park, J.H., Cosgrove, M.S., Youngman, E., Wolberger, C., and Boeke, J.D. (2002) A core nucleosome surface crucial for transcriptional silencing. Nat Genet, 16, 273-279.
23. Flaus, A., Rencurel, C., Ferreira, H., Wiechens, N., and Owen-Hughes, T. (2004) Sin mutations alter inherent nucleosome mobility. EMBO J, 23, 343-353.
24. Luger, K. (2003) Structure and dynamic behavior of nucleosomes. Curr Opin Genet Dev, 13, 127-135.
25. Muthurajan, U.M., Bao, Y., Forsberg, L.J., Edayathumangalam, R.S., Dyer, P. N., White, C.L., and Luger, K. (2004) Crystal structures of histone Sin mutant nucleosomes reveal altered protein-DNA interactions. EMBO J, 23, 260-271.
26. Luger, K., Rechsteiner, T.J., and Richmond, T.J. (1999) Preparation of nucleosome core particle from recombinant histones. Meth Enzymol, 304, 3-19.
27. Luger, K. and Richmond, T.J. (1998) The histone tails of the nucleosome. Curr Opin Genet Dev, 8, 140-146.
28. Polach, K.J., Lowary, P.T. and Widom, J. (2000) Effects of core histone tail domains on the equilibrium constants for dynamic DNA site accessibility in nucleosomes. J Mol Biol, 298, 211-223.
29. Protacio, R.U., Li, G., Lowary, P.T., and Widom, J. (2000) Effects of histone tail domains on the rate of transcriptional elongation through a nucleosome [In Process Citation]. Mol Cell Biol, 20, 8866-8878.
30. Vitolo, J.M., Thiriet, C., and Hayes, J.J. (2000) The H3-H4 N-terminal tail domains are the primary mediators of transcription factor IIIA access to 5S DNA within a nucleosome. Mol Cell Biol, 20, 2167-2175.
31. Hall, M.A., Shundrovsky, A., Bai, L., Fulbright, R.M., Lis, J.T., and Wang, M.D. (2009) High-resolution dynamic mapping of histone-DNA interactions in a nucleosome. Nat Struct Mol Biol, 16, 124-129.
32. Richmond, T.J. and Davey, C.A. (2003) The structure of DNA in the nucleosome core. Nature, 423, 145-150.
33. Richmond, T.J., Finch, J.T., Rushton, B., Rhodes, D. and Klug, A. (1984) Structure of the nucleosome core particle at 7 Å resolution. Nature, 311, 532-537.
34. Muthurajan, U.M., Park, Y.J., Edayathumangalam, R.S., Suto, R.K., Chakravarthy, S., Dyer, P.N., and Luger, K. (2003) Structure and dynamics of nucleosomal DNA. Biopolymers, 68, 547-556.
35. Suto, R.K., Clarkson, M.J., Tremethick, D.J., and Luger, K. (2000) Crystal structure of a nucleosome core particle containing the variant histone H2A.Z. Nat Struct Biol, 7, 1121-1124.
36. Ong, M.S., Richmond, T.J., and Davey, C.A. (2007) DNA stretching and extreme kinking in the nucleosome core. J Mol Biol, 368, 1067-1074.
37. Lowary, P.T. and Widom, J. (1998) New DNA sequence rules for high affinity binding to histone octamer and sequence-directed nucleosome positioning. J Mol Biol, 276, 19-42.
38. Satchwell, S.C., Drew, H.R., and Travers, A.A. (1986) Sequence periodicities in chicken nucleosome core DNA. J Mol Biol, 191, 659-675.
39. Shrader, T.E. and Crothers, D.M. (1990) Effects of DNA sequence and histone-histone interactions on nucleosome placement. J Mol Biol, 216, 69-84.
40. Edayathumangalam, R.S., Weyermann, P., Gottesfeld, J.M., Dervan, P.B., and Luger, K. (2004) Molecular recognition of the nucleosomal "supergroove". PNAS, 101, 6864-6869.
41. Jamai, A., Imoberdorf, R.M., and Strubin, M. (2007) Continuous Histone H2B and transcription-dependent histone H3 exchange in yeast cells outside of replication. Mol Cell, 25, 345-355.
42. Kimura, H. (2005) Histone dynamics in living cells revealed by photobleaching. DNA Repair, (Amst).
43. Thiriet, C. and Hayes, J.J. (2005) Replication-independent core histone dynamics at transcriptionally active loci in vivo. Genes Dev, 19, 677-682.
44. Xu, M., Long, C., Chen, X., Huang, C., Chen, S., and Zhu, B. (2010) Partitioning of histone H3-H4 tetramers during DNA replicationdependent chromatin assembly. Science, 328, 94-98.
45. Verzijlbergen, K.F., Menendez-Benito, V., van Welsem, T., van Deventer, S.J., Lindstrom, D.L., Ovaa, H., Neefjes, J., Gottschling, D.E., and van Leeuwen, F. (2010) Recombination-induced tag exchange to track old and new proteins. Proc Natl Acad Sci USA, 107, 64-68.
46. Li, G. and Widom, J. (2004) Nucleosomes facilitate their own invasion. Nat Struct Mol Biol., 11, 763-769.
47. Kaplan, N., Moore, I.K., Fondufe-Mittendorf, Y., Gossett, A.J., Tillo, D., Field, Y., Leproust, E.M., Hughes, T.R., Lieb, J.D., Widom, J., and Segal, E. (2008) The DNA-encoded nucleosome organization of a eukaryotic genome. Nature, 458, 362-366.
48. Neumann, H., Hancock, S.M., Buning, R., Routh, A., Chapman, L., Somers, J., Owen-Hughes, T., van Noort, J., Rhodes, D., and Chin, J.W. (2009) A method for genetically installing sitespecific acetylation in recombinant histones defines the effects of h3 k56 acetylation. Mol Cell, 36, 153-163.
49. Cairns, B.R. (2009) The logic of chromatin architecture and remodelling at promoters. Nature, 461, 193-198.
50. Clapier, C.R. and Cairns, B.R. (2009) The biology of chromatin remodeling complexes. Annu Rev Biochem, 78, 273-304.
51. Becker, P.B. and Horz, W. (2002) ATPdependent nucleosome remodeling. Annu Rev Biochem, 71, 247-273.
52. Gangaraju, V.K. and Bartholomew, B. (2007) Mechanisms of ATP dependent chromatin remodeling. Mutat Res, 618, 3-17.
53. Lusser, A. and Kadonaga, J.T. (2003) Chromatin remodeling by ATPdependent molecular machines. Bioessays, 25, 1192-1200.
54. Belotserkovskaya, R., Saunders, A., Lis, J.T., and Reinberg, D. (2004) Transcription through chromatin: understanding a complex FACT. Biochim Biophys Acta, 1677, 87-99.
55. Groth, A., Rocha, W., Verreault, A., and Almouzni, G. (2007) Chromatin challenges during DNA replication and repair. Cell, 128, 721-733.
56. Park, Y.J. and Luger, K. (2008) Histone chaperones in nucleosome eviction and histone exchange. Curr Opin Struct Biol, 18, 282-289.
57. Ransom, M., Dennehey, B.K., and Tyler, J.K. (2010) Chaperoning histones during DNA replication and repair. Cell, 140, 183-195.
58. De Koning, L., Corpet, A., Haber, J.E., and Almouzni, G. (2007) Histone chaperones: an escort network regulating histone traffic. Nat Struct Mol Biol, 14, 997-1007.
59. Polach, K.J. and Widom, J. (1999) Restriction enzymes as probes of nucleosome stability and dynamics. Meth Enzymol, 304, 278-298.
60. Li, G., Levitus, M., Bustamante, C., and Widom, J. (2005) Rapid spontaneous accessibility of nucleosomal DNA. Nat Struct Mol Biol, 12, 46-53.
61. Poirier, M.G., Bussiek, M., Langowski, J., and Widom, J. (2008) Spontaneous access to DNA target sites in folded chromatin fibers. J Mol Biol, 379, 772-786.
62. Xin, H., Takahata, S., Blanksma, M., McCullough, L., Stillman, D.J., and Formosa, T. (2009) FACT induces global accessibility of nucleosomal DNA without H2A-H2B displacement. Mol Cell, 35, 365-376.
63. Thastrom, A., Bingham, L.M., and Widom, J. (2004) Nucleosomal locations of dominant DNA sequence motifs for histone-DNA interactions and nucleosome positioning. J Mol Biol, 338, 695-709.
64. Wilhelm, F.X., Wilhelm, M.L., Erard, M., and Duane, M.P. (1978) Reconstitution of chromatin: assembly of the nucleosome. Nucl Acids Res, 5, 505-521.
65. Yager, T.D., McMurray, C.T., and van Holde, K.E. (1989) Salt-induced release of DNA from nucleosome core particles. Biochemistry, 28, 2271-2281.
66. Oohara, I. and Wada, A. (1987) Spectroscopic studies on histone-DNA interactions. II. Three transitions in nucleosomes resolved by salt-titration. J Mol Biol, 196, 399-411.
67. Oohara, I. and Wada, A. (1987) Spectroscopic studies on histone-DNA interactions. I. The interaction of histone (H2A, H2B) dimer with DNA: DNA sequence dependence. J Mol Biol, 196, 389-397.
68. Jin, C. and Felsenfeld, G. (2007) Nucleosome stability mediated by histone variants H3.3 and H2A.Z. Genes Dev, 21, 1519-1529.
69. Park, Y.J., Dyer, P.N., Tremethick, D.J., and Luger, K. (2004) A new fluorescence resonance energy transfer approach demonstrates that the histone variant h2az stabilizes the histone octamer within the nucleosome. J Biol Chem, 279, 24274-24282.
70. Lowary, P.T. and Widom, J. (1997) Nucleosome packaging and nucleosome positioning of genomic DNA. Proc Natl Acad Sci USA, 94, 1183-1188.
71. Shrader, T.E. and Crothers, D.M. (1989) Artificial nucleosome positioning sequences. Proc Natl Acad Sci USA, 86, 7418-7422.
72. Andrews, A.J., Chen, X., Zevin, A., Stargell, L.A., and Luger, K. (2010) The histone chaperone nap1 promotes nucleosome assembly by eliminating nonnucleosomal histone-DNA interactions. Mol Cell, 37, 834-842.
73. Thastrom, A., Gottesfeld, J.M., Luger, K., and Widom, J. (2004) Histone-DNA binding free energy cannot be measured in dilution-driven dissociation experiments. Biochemistry, 43, 736-741.
74. Clarkson, M.J., Wells, J.R., Gibson, F., Saint, R., and Tremethick, D.J. (1999) Regions of variant histone His2AvD required for Drosophila development. Nature, 399, 694-697.
75. Faast, R., Thonglairoam, V., Schulz, T. C., Beall, J., Wells, J.R., Taylor, H., Matthaei, K., Rathjen, P.D., Tremethick, D.J., and Lyons, I. (2001) Histone variant H2A.Z is required for early mammalian development. Curr Biol, 11, 1183-1187.
76. van Daal, A. and Elgin, S.C. (1992) A histone variant, H2AvD, is essential in Drosophila melanogaster. Mol Biol Cell, 3, 593-602.
77. Ausio, J. (2006) Histone variants -the structure behind the function. Brief Funct Genomic Proteomic, 5, 228-243.
78. Henikoff, S., Furuyama, T., and Ahmad, K. (2004) Histone variants, nucleosome assembly and epigenetic inheritance. Trends Genet, 20, 320-326.
79. Loyola, A. and Almouzni, G. (2007) Marking histone H3 variants: how, when and why? Trends Biochem Sci, 32, 425-433.
80. Sarma, K. and Reinberg, D. (2005) Histone variants meet their match. Nat Rev Mol Cell Biol, 6, 139-149.
81. Wieland, G., Orthaus, S., Ohndorf, S., Diekmann, S., and Hemmerich, P. (2004) Functional complementation of human centromere protein a (CENP-A) by Cse4p from Saccharomyces cerevisiae. Mol Cell Biol, 24, 6620-6630.
82. Kusch, T. and Workman, J.L. (2007) Histone variants and complexes involved in their exchange. Subcell Biochem, 41, 91-109.
83. Talbert, P.B. and Henikoff, S. (2010) Histone variants -ancient wrap artists of the epigenome. Nat Rev Mol Cell Biol, 11, 264-275.
84. Henikoff, S. and Ahmad, K. (2005) Assembly of variant histones into chromatin. Annu Rev Cell Dev Biol, 21, 133-153.
85. Ingouff, M. and Berger, F. (2010) Histone3 variants in plants. Chromosoma, 119, 27-33.
86. Bell, O. and Schubeler, D. (2009) Chromatin: sub out the replacement. Curr Biol, 19, R545-R547.
87. Boulard, M., Bouvet, P., Kundu, T.K., and Dimitrov, S. (2007) Histone variant nucleosomes: structure, function and implication in disease. Subcell Biochem, 41, 71-89.
88. Buschbeck, M. and Di Croce, L. (2010) Approaching the molecular and physiological function of macroH2A variants. Epigenetics, 5, 118-123.
89. Marques, M., Laflamme, L., Gervais, A. L., and Gaudreau, L. (2010) Reconciliating the positive and negative roles of histone H2A.Z in gene transcription. Epigenetics, 5, 267-272.
90. Pehrson, J.R. and Fried, V.A. (1992) MacroH2A, a core histone containing a large nonhistone region. Science, 257, 1398-1400.
91. Till, S. and Ladurner, A.G. (2009) Sensing NAD metabolites through macro domains. Front Biosci, 14, 3246-3258.
92. Timinszky, G., Till, S., Hassa, P.O., Hothorn, M., Kustatscher, G., Nijmeijer, B., Colombelli, J., Altmeyer, M., Stelzer, E.H., Scheffzek, K., and Hottiger, M.O. et al. (2009) A macrodomain-containing histone rearranges chromatin upon sensing PARP1 activation. Nat Struct Mol Biol, 16, 923-929.
93. Chakravarthy, S., Gundimella, S.K., Caron, C., Perche, P.Y., Pehrson, J.R., Khochbin, S., and Luger, K. (2005) Structural characterization of the histone variant macroH2A. Mol Cell Biol, 25, 7616-7624.
94. Chakravarthy, S. and Luger, K. (2006) The histone variant macro-H2A preferentially forms "hybrid nucleosomes". J Biol Chem, 281, 25522-25531.
95. Chodaparambil, J.V., Barbera, A.J., Lu, X., Kaye, K.M., Hansen, J.C., and Luger, K. (2007) A charged and contoured surface on the nucleosome regulates chromatin compaction.[see comment]. Nat Struct Mol Biol, 14, 1105-1107.
96. Chakravarthy, S., Bao, Y., Roberts, V. A., Tremethick, D., and Luger, K. (2004) Structural characterization of histone H2A variants. Cold Spring Harb Symp Quant Biol, 69, 227-234.
97. Fan, J.Y., Gordon, F., Luger, K., Hansen, J.C., and Tremethick, D.J. (2002) The essential histone variant H2A.Z regulates the equilibrium between different chromatin conformational states. Nat Struct Biol, 19, 172-176.
98. Zhou, J., Fan, J.Y., Rangasamy, D., and Tremethick, D.J. (2007) The nucleosome surface regulates chromatin compaction and couples it with transcriptional repression.[see comment]. Nat Struct Mol Biol, 14, 1070-1076.
99. Bao, Y., Konesky, K., Park, Y.J., Rosu, S., Dyer, P.N., Rangasamy, D., Tremethick, D.J., Laybourn, P.J., and Luger, K. (2004) Nucleosomes containing the histone variant H2A. Bbd organize only 118 base pairs of DNA. EMBO J, 23, 3314-3324.
100. Doyen, C.M., Montel, F., Gautier, T., Menoni, H., Claudet, C., Delacour-Larose, M., Angelov, D., Hamiche, A., Bednar, J., Faivre-Moskalenko, C., and Bouvet, P. et al. (2006) Dissection of the unusual structural and functional properties of the variant H2A.Bbd nucleosome. EMBO J, 25, 4234-4244.
101. Elsaesser, S.J., Goldberg, A.D., and Allis, C.D. (2010) New functions for an old variant: no substitute for histone H3.3. Curr Opin Genet Dev, 20, 110-117.
102. Jin, C., Zang, C., Wei, G., Cui, K., Peng, W., Zhao, K., and Felsenfeld, G. (2009) H3.3/H2A.Z double variantcontaining nucleosomes mark 'nucleosome-free regions' of active promoters and other regulatory regions. Nat Genet, 41, 941-945.
103. Black, B.E. and Bassett, E.A. (2008) The histone variant CENP-A and centromere specification. Curr Opin Cell Biol, 20, 91-100.
104. Black, B.E., Foltz, D.R., Chakravarthy, S., Luger, K., Woods, V.L. Jr, and Cleveland, D.W. (2004) Structural determinants for generating centromeric chromatin. Nature, 430, 578-582.
105. Henikoff, S., Ahmad, K., and Malik, H. S. (2001) The centromere paradox: stable inheritance with rapidly evolving DNA. Science, 293, 1098-1102.
106. Dechassa, M.L., D'Arcy, S., and Luger, K. (2009) A positive spin on the centromere. Cell, 138, 22-24.
107. Foltz, D.R., Jansen, L.E., Black, B.E., Bailey, A.O., Yates, J.R. 3rd, and Cleveland, D.W. (2006) The human CENP-A centromeric nucleosomeassociated complex. Nat Cell Biol, 8, 458-469.
108. Yoda, K., Ando, S., Morishita, S., Houmura, K., Hashimoto, K., Takeyasu, K., and Okazaki, T. (2000) Human centromere protein A (CENPA) can replace histone H3 in nucleosome reconstitution in vitro. Proc Natl Acad Sci USA, 97, 7266-7271.
109. Dalal, Y., Wang, H., Lindsay, S., and Henikoff, S. (2007) Tetrameric structure of centromeric nucleosomes in interphase Drosophila cells. PLoS Biol, 5, e218.
110. Furuyama, S. and Biggins, S. (2007) Centromere identity is specified by a single centromeric nucleosome in budding yeast. PNAS, 104, 14706-14711.
111. Camahort, R., Li, B., Florens, L., Swanson, S.K., Washburn, M.P., and Gerton, J.L. (2007) Scm3 is essential to recruit the histone h3 variant cse4 to centromeres and to maintain a functional kinetochore. Mol Cell, 26, 853-865.
112. Mizuguchi, G., Xiao, H., Wisniewski, J., Smith, M.M., and Wu, C. (2007) Nonhistone Scm3 and histones CenH3-H4 assemble the core of centromere-specific nucleosomes. Cell, 129, 1153-1164.
113. Camahort, R., Shivaraju, M., Mattingly, M., Li, B., Nakanishi, S., Zhu, D., Shilatifard, A., Workman, J.L., and Gerton, J.L. (2009) Cse4 is part of an octameric nucleosome in budding yeast. Mol Cell, 35, 794-805.
114. Furuyama, T. and Henikoff, S. (2009) Centromeric nucleosomes induce positive DNA supercoils. Cell, 138, 104-113.
115. Panchenko, T. and Black, B.E. (2009) The epigenetic basis for centromere identity. Prog Mol Subcell Biol, 48, 1-32.
116. Andrews, A.J. and Luger, K. (2009) Histone modifications: chemistry and structural consequences. Wiley Encycl Chem Biol, 1, 275-284.
117. Campos, E.I. and Reinberg, D. (2009) Histones: annotating chromatin. Annu Rev Genet, 43, 559-599.
118. Xu, D., Bai, J., Duan, Q., Costa, M., and Dai, W. (2009) Covalent modifications of histones during mitosis and meiosis. Cell Cycle, 8, 3688-3694.
119. Shogren-Knaak, M.A. and Peterson, C. L. (2004) Creating designer histones by native chemical ligation. Meth Enzymol, 375, 62-76.
120. Chatterjee, C., McGinty, R.K., Fierz, B., and Muir, T.W. (2010) Disulfidedirected histone ubiquitylation reveals plasticity in hDot1L activation. Nat Chem Biol, 6, 267-269.
121. Simon, M.D., Chu, F., Racki, L.R., de la Cruz, C.C., Burlingame, A.L., Panning, B., Narlikar, G.J., and Shokat, K.M. (2007) The site-specific installation of methyl-lysine analogs into recombinant histones. Cell, 128, 1003-1012.
122. Neumann, H., Peak-Chew, S.Y., and Chin, J.W. (2008) Genetically encoding N(epsilon)-acetyllysine in recombinant proteins. Nat Chem Biol, 4, 232-234.
123. Nguyen, D.P., Garcia Alai, M.M., Kapadnis, P.B., Neumann, H., and Chin, J.W. (2009) Genetically encoding n()-methyl-l-lysine in recombinant histones. J Am Chem Soc, 131, 14194-14195.
124. Dyer, P.N., Edayathumangalam, R.S., White, C.L., Bao, Y., Chakravarthy, S., Muthurajan, U.M., and Luger, K. (2004) Reconstitution of nucleosome core particles from recombinant histones and DNA. Meth Enzymol, 375, 23-44.
125. Gordon, F., Luger, K., and Hansen, J. C. (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.
126. Watanabe, S., Resch, M., Lilyestrom, W., Clark, N., Hansen, J.C., Peterson, C., and Luger, K. (2010) Structural characterization of H3K56Q nucleosomes and nucleosomal arrays. Biochim Biophys Acta, 1799, 480-486.
127. Lu, X., Simon, M.D., Chodaparambil, J. V., Hansen, J.C., Shokat, K.M., and Luger, K. (2008) The effect of H3K79 dimethylation and H4K20 trimethylation on nucleosome and chromatin structure. Nat Struct Mol Biol, 15, 1122-1124.
128. Kato, H., Gruschus, J., Ghirlando, R., Tjandra, N., and Bai, Y. (2009) Characterization of the N-terminal tail domain of histone H3 in condensed nucleosome arrays by hydrogen exchange and NMR. J Am Chem Soc, 131, 15104-15105.
129. Shogren-Knaak, M., Ishii, H., Sun, J. M., Pazin, M.J., Davie, J.R., and Peterson, C.L. (2006) Histone H4-K16 acetylation controls chromatin structure and protein interactions. Science, 311, 844-847.
130. Wang, X. and Hayes, J.J. (2008) Acetylation mimics within individual core histone tail domains indicate distinct roles in regulating the stability of higher-order chromatin structure. Mol Cell Biol, 28, 227-236.
131. Segal, E. and Widom, J. (2009) What controls nucleosome positions? Trends Genet, 25, 335-343.
132. Johnson, S.M., Tan, F.J., McCullough, H.L., Riordan, D.P. and Fire, A.Z. (2006) Flexibility and constraint in the nucleosome core landscape of Caenorhabditis elegans chromatin. Genome Res, 16, 1505-1516.
133. Kaplan, N., Moore, I.K., Fondufe-Mittendorf, Y., Gossett, A.J., Tillo, D., Field, Y., LeProust, E.M., Hughes, T.R., Lieb, J.D., Widom, J., and Segal, E. (2009) The DNA-encoded nucleosome organization of a eukaryotic genome. Nature, 458, 362-366.
134. Lantermann, A.B., Straub, T., Stralfors, A., Yuan, G.C., Ekwall, K., and Korber, P. (2010) Schizosaccharomyces pombe genome-wide nucleosome mapping reveals positioning mechanisms distinct from those of Saccharomyces cerevisiae. Nat Struct Mol Biol, 17, 251-257.
135. Mavrich, T.N., Jiang, C., Ioshikhes, I. P., Li, X., Venters, B.J., Zanton, S.J., Tomsho, L.P., Qi, J., Glaser, R.L., Schuster, S.C., and Gilmour, D.S. et al. (2008) Nucleosome organization in the drosophila genome. Nature, 453, 358-362.
136. Schones, D.E., Cui, K., Cuddapah, S., Roh, T.Y., Barski, A., Wang, Z., Wei, G., and Zhao, K. (2008) Dynamic regulation of nucleosome positioning in the human genome. Cell, 132, 887-898.
137. Yuan, G.C., Liu, Y.J., Dion, M.F., Slack, M.D., Wu, L.F., Altschuler, S.J., and Rando, O.J. (2005) Genome-scale identification of nucleosome positions in S. cerevisiae. Science, 309, 626-630.
138. Widom, J. (2001) Role of DNA sequence in nucleosome stability and dynamics. Q Rev Biophys, 34, 269-324.
139. Segal, E. and Widom, J. (2009) Poly (dA:dT) tracts: major determinants of nucleosome organization. Curr Opin Struct Biol, 19, 65-71.
140. Suter, B., Schnappauf, G., and Thoma, F. (2000) Poly(dA.dT) sequences exist as rigid DNA structures in nucleosome-free yeast promoters in vivo. Nucleic Acids Res, 28, 4083-4089.
141. Drew, H.R. and Travers, A.A. (1985) DNA bending and its relation to nucleosome positioning. J Mol Biol, 186, 773-790.
142. Anselmi, C., Bocchinfuso, G., De Santis, P., Savino, M., and Scipioni, A. (1999) Dual role of DNA intrinsic curvature and flexibility in determining nucleosome stability. J Mol Biol, 286, 1293-1301.
143. Anderson, J.D. and Widom, J. (2001) Poly(dA-dT) promoter elements increase the equilibrium accessibility of nucleosomal DNA target sites. Mol Cell Biol, 21, 3830-3839.
144. Kunkel, G.R. and Martinson, H.G. (1981) Nucleosomes will not form on double-stranded RNa or over poly(dA). poly(dT) tracts in recombinant DNA. Nucleic Acids Res, 9, 6869-6888.
145. Struhl, K. (1985) Naturally occurring poly(dA-dT) sequences are upstream promoter elements for constitutive transcription in yeast. Proc Natl Acad Sci USA, 82, 8419-8423.
146. Radman-Livaja, M. and Rando, O.J. (2010) Nucleosome positioning: how is it established, and why does it matter? Dev Biol, 339, 258-266.
147. Shimizu, M., Mori, T., Sakurai, T., and Shindo, H. (2000) Destabilization of nucleosomes by an unusual DNA conformation adopted by poly(dA) small middle dotpoly(dT) tracts in vivo. EMBO J, 19, 3358-3365.
148. Nelson, H.C., Finch, J.T., Luisi, B.F., and Klug, A. (1987) The structure of an oligo(dA).oligo(dT) tract and its biological implications. Nature, 330, 221-226.
149. Woods, K.K., Maehigashi, T., Howerton, S.B., Sines, C.C., Tannenbaum, S., and Williams, L.D. (2004) High-resolution structure of an extended A-tract: [d(CGCAAATTT GCG)]2. J Am Chem Soc, 126, 15330-15331.
150. Bao, Y., White, C.L., and Luger, K. (2006) Nucleosome core particles containing a poly(dA.dT) sequence element exhibit a locally distorted DNA structure. J Mol Biol, 361, 617-624.
151. Fox, K.R. (1992) Wrapping of genomic polydA.polydT tracts around nucleosome core particles. Nucl Acids Res, 20, 1235-1242.
152. Losa, R., Omari, S., and Thoma, F. (1990) Poly(dA).poly(dT) rich sequences are not sufficient to exclude nucleosome formation in a constitutive yeast promoter. Nucl Acids Res, 18, 3495-3502.
153. Bao, Y., White, C.L., and Luger, K. (2006) Nucleosome core particles containing a poly(dA.dT) sequence element exhibit a Locally Distorted DNA Structure. J Mol Biol, 361, 617-624.
154. Whitehouse, I., Rando, O.J., Delrow, J., and Tsukiyama, T. (2007) Chromatin remodelling at promoters suppresses antisense transcription. Nature, 450, 1031-1035.
155. Whitehouse, I. and Tsukiyama, T. (2006) Antagonistic forces that position nucleosomes in vivo. Nat Struct Mol Biol, 13, 633-640.
156. Hartley, P.D. and Madhani, H.D. (2009) Mechanisms that specify promoter nucleosome location and identity. Cell, 137, 445-458.
157. Zhang, Y., Moqtaderi, Z., Rattner, B. P., Euskirchen, G., Snyder, M., Kadonaga, J.T., Liu, X.S., and Struhl, K. (2009) Intrinsic histone-DNA interactions are not the major determinant of nucleosome positions in vivo. Nat Struct Mol Biol, 16, 847-852.
158. Sharma, N. and Nyborg, J.K. (2008) The coactivators CBP/p300 and the histone chaperone NAP1 promote transcription-independent nucleosome eviction at the HTLV-1 promoter. Proc Natl Acad Sci USA, 105, 7959-7963.
159. Segal, E., Fondufe-Mittendorf, Y., Chen, L., Thastrom, A., Field, Y., Moore, I.K., Wang, J.P., and Widom, J. (2006) A genomic code for nucleosome positioning. Nature, 442, 772-778.
160. Ioshikhes, I., Bolshoy, A., Derenshteyn, K., Borodovsky, M., and Trifonov, E.N. (1996) Nucleosome DNA sequence pattern revealed by multiple alignment of experimentally mapped sequences. J Mol Biol, 262, 129-139.
161. Lowary, P.T. and Widom, J. (1998) New DNA sequence rules for high affinity binding to histone octamer and sequence-directed nucleosome positioning. J Mol Biol, 276, 19-42.
162. Field, Y., Kaplan, N., Fondufe-Mittendorf, Y., Moore, I.K., Sharon, E., Lubling, Y., Widom, J., and Segal, E. (2008) Distinct modes of regulation by chromatin encoded through nucleosome positioning signals. PLoS Comput Biol, 4, e1000216.
163. Lee, W., Tillo, D., Bray, N., Morse, R. H., Davis, R.W., Hughes, T.R., and Nislow, C. (2007) A high-resolution atlas of nucleosome occupancy in yeast. Nat Genet, 39, 1235-1244.
164. Ozsolak, F., Song, J.S., Liu, X.S., and Fisher, D.E. (2007) High-throughput mapping of the chromatin structure of human promoters. Nat Biotechnol, 25, 244-248.
165. McManus, J., Perry, P., Sumner, A.T., Wright, D.M., Thomson, E.J., Allshire, R.C., Hastie, N.D., and Bickmore, W.A. (1994) Unusual chromosome structure of fission yeast DNA in mouse cells. J Cell Sci, 107 (3), 469-486.
166. Bernardi, F., Zatchej, M., and Thoma, F. (1992) Species specific protein -DNA interactions may determine the chromatin units of genes in S. cerevisiae and in S.pombe. EMBO J, 11, 1177-1185.
167. Williams, S.K. and Tyler, J.K. (2007) Transcriptional regulation by chromatin disassembly and reassembly. Curr Opin Genet Dev, 17, 88-93.
168. Adkins, M.W., Howar, S.R., and Tyler, J.K. (2004) Chromatin disassembly mediated by the histone chaperone Asf1 is essential for transcriptional activation of the yeast PHO5 and PHO8 genes. Mol Cell, 14, 657-666.
169. Adkins, M.W., Williams, S.K., Linger, J., and Tyler, J.K. (2007) Chromatin disassembly from the PHO5 promoter is essential for the recruitment of the general transcription machinery and coactivators. Mol Cell Biol, 27, 6372-6382.
170. Gkikopoulos, T., Havas, K.M., Dewar, H., and Owen-Hughes, T. (2009) SWI/ SNF and Asf1p cooperate to displace histones during induction of the Saccharomyces cerevisiae HO promoter. Mol Cell Biol, 29, 4057-4066.
171. Korber, P., Barbaric, S., Luckenbach, T., Schmid, A., Schermer, U.J., Blaschke, D., and Horz, W. (2006) The histone chaperone Asf1 increases the rate of histone eviction at the yeast PHO5 and PHO8 promoters. J Biol Chem, 281, 5539-5545.
172. Korber, P., Luckenbach, T., Blaschke, D. and Horz, W. (2004) Evidence for histone eviction in trans upon induction of the yeast PHO5 promoter. Mol Cell Biol, 24, 10965-10974.
173. Ransom, M., Williams, S.K., Dechassa, M.L., Das, C., Linger, J., Adkins, M., Liu, C., Bartholomew, B., and Tyler, J. K. (2009) FACT and the proteasome promote promoter chromatin disassembly and transcriptional initiation. J Biol Chem, 284, 23461-23471.
174. Takahata, S., Yu, Y., and Stillman, D.J. (2009) FACT and Asf1 regulate nucleosome dynamics and coactivator binding at the HO promoter. Mol Cell, 34, 405-415.
175. Walfridsson, J., Khorosjutina, O., Matikainen, P., Gustafsson, C.M., and Ekwall, K. (2007) A genome-wide role for CHD remodelling factors and Nap1 in nucleosome disassembly. EMBO J, 26, 2868-2879.
176. Schermer, U.J., Korber, P., and Horz, W. (2005) Histones are incorporated in trans during reassembly of the yeast PHO5 promoter. Mol Cell, 19, 279-285.
177. Adkins, M.W. and Tyler, J.K. (2006) Transcriptional activators are dispensable for transcription in the absence of Spt6-mediated chromatin reassembly of promoter regions. Mol Cell, 21, 405-416.
178. Fleming, A.B. and Pennings, S. (2001) Antagonistic remodelling by Swi-Snf and Tup1-Ssn6 of an extensive chromatin region forms the background for FLO1 gene regulation. EMBO J, 20, 5219-5231.
179. Kaplan, C.D., Laprade, L., and Winston, F. (2003) Transcription elongation factors repress transcription initiation from cryptic sites. Science, 301, 1096-1099.
180. Kulaeva, O.I., Gaykalova, D.A., Pestov, N.A., Golovastov, V.V., Vassylyev, D.G., Artsimovitch, I., and Studitsky, V.M. (2009) Mechanism of chromatin remodeling and recovery during passage of RNA polymerase II. Nat Struct Mol Biol, 16, 1272-1278.
181. Mason, P.B. and Struhl, K. (2003) The FACT complex travels with elongating RNA polymerase II and is important for the fidelity of transcriptional initiation in vivo. Mol Cell Biol, 23, 8323-8333.
182. Saha, A., Wittmeyer, J., and Cairns, B. R. (2002) Chromatin remodeling by RSC involves ATP-dependent DNA translocation. Genes Dev, 16, 2120-2134.
183. Schwabish, M.A. and Struhl, K. (2004) Evidence for eviction and rapid deposition of histones upon transcriptional elongation by RNA polymerase II. Mol Cell Biol, 24, 10111-10117.
184. Belotserkovskaya, R., Oh, S., Bondarenko, V.A., Orphanides, G., Studitsky, V.M., and Reinberg, D. (2003) FACT facilitates transcriptiondependent nucleosome alteration. Science, 301, 1090-1093.
185. Pavri, R., Zhu, B., Li, G., Trojer, P., Mandal, S., Shilatifard, A., and Reinberg, D. (2006) Histone H2B monoubiquitination functions cooperatively with FACT to regulate elongation by RNA polymerase II. Cell, 125, 703-717.
186. Saunders, A., Werner, J., Andrulis, E. D., Nakayama, T., Hirose, S., Reinberg, D., and Lis, J.T. (2003) Tracking FACT and the RNA polymerase II elongation complex through chromatin in vivo. Science, 301, 1094-1096.
187. Formosa, T. (2003) Changing the DNA landscape: putting a SPN on chromatin. Curr Top Microbiol Immunol, 274, 171-201.
188. Groth, A., Corpet, A., Cook, A.J., Roche, D., Bartek, J., Lukas, J., and Almouzni, G. (2007) Regulation of replication fork progression through histone supply and demand. Science, 318, 1928-1931.
189. Okuhara, K., Ohta, K., Seo, H., Shioda, M., Yamada, T., Tanaka, Y., Dohmae, N., Seyama, Y., Shibata, T., and Murofushi, H. (1999) A DNA unwinding factor involved in DNA replication in cell-free extracts of Xenopus eggs. Curr Biol, 9, 341-350.
190. Tan, B.C., Chien, C.T., Hirose, S., and Lee, S.C. (2006) Functional cooperation between FACT and MCM helicase facilitates initiation of chromatin DNA replication. EMBO J, 25, 3975-3985.
191. Schulz, L.L. and Tyler, J.K. (2006) The histone chaperone ASF1 localizes to active DNA replication forks to mediate efficient DNA replication. FASEB J, 20, 488-490.
192. Linger, J.G. and Tyler, J.K. (2007) Chromatin disassembly and reassembly during DNA repair. Mutat Res, 618, 52-64.
193. Chen, C.C., Carson, J.J., Feser, J., Tamburini, B., Zabaronick, S., Linger, J., and Tyler, J.K. (2008) Acetylated lysine 56 on histone H3 drives chromatin assembly after repair and signals for the completion of repair. Cell, 134, 231-243.
194. Heo, K., Kim, H., Choi, S.H., Choi, J., Kim, K., Gu, J., Lieber, M.R., Yang, A. S., and An, W. (2008) FACT-mediated exchange of histone variant H2AX regulated by phosphorylation of H2AX and ADP-ribosylation of Spt16. Mol Cell, 30, 86-97.
195. Guillemette, B. and Gaudreau, L. (2006) Reuniting the contrasting functions of H2A.Z. Biochem Cell Biol, 84, 528-535.
196. Kalocsay, M., Hiller, N.J., and Jentsch, S. (2009) Chromosome-wide Rad51 spreading and SUMO-H2A.Zdependent chromosome fixation in response to a persistent DNA doublestrand break. Mol Cell, 33, 335-343.
197. van Attikum, H., Fritsch, O., Hohn, B., and Gasser, S.M. (2004) Recruitment of the INO80 complex by H2A phosphorylation links ATP-dependent chromatin remodeling with DNA double-strand break repair. Cell, 119, 777-788.
198. van Attikum, H. and Gasser, S.M. (2009) Crosstalk between histone modifications during the DNA damage response. Trends Cell Biol, 19, 207-217.
199. Park, Y.J. and Luger, K. (2008) Histone chaperones in nucleosome eviction and histone exchange. Curr Opin Struct Biol, 18, 282-289.
200. Hansen, J.C., Nyborg, J.K., Luger, K., and Stargell, L.A. (2010) Histone chaperones, histone acetylation, and the fluidity of the chromogenome. J Cell Physiol. 224, 2890299.
201. English, C.M., Adkins, M.W., Carson, J.J., Churchill, M.E., and Tyler, J.K. (2006) Structural basis for the histone chaperone activity of Asf1. Cell, 127, 495-508.
202. English, C.M., Maluf, N.K., Tripet, B., Churchill, M.E., and Tyler, J.K. (2005) ASF1 binds to a heterodimer of histones H3 and H4: a two-step mechanism for the assembly of the H3-H4 heterotetramer on DNA. Biochemistry, 44, 13673-13682.
203. Natsume, R., Eitoku, M., Akai, Y., Sano, N., Horikoshi, M., and Senda, T. (2007) Structure and function of the histone chaperone CIA/ASF1 complexed with histones H3 and H4. Nature, 446, 338-341.
204. Han, J., Zhou, H., Horazdovsky, B., Zhang, K., Xu, R.M., and Zhang, Z. (2007) Rtt109 acetylates histone H3 lysine 56 and functions in DNA replication. Science, 315, 653-655.
205. Han, J., Zhou, H., Li, Z., Xu, R.M., and Zhang, Z. (2007) Acetylation of lysine 56 of histone H3 catalyzed by RTT109 and regulated by ASF1 is required for replisome integrity. J Biol Chem, 282, 28587-28596.
206. Das, C., Lucia, M.S., Hansen, K.C., and Tyler, J.K. (2009) CBP/p300-mediated acetylation of histone H3 on lysine 56. Nature, 459, 113-117.
207. Makde, R.D., England, J.R., Yennawar, H.P., and Tan, S. (2010) Structure of RCC1 chromatin factor bound to the nucleosome core particle. Nature, epub ahead of print.
208. Gill, J., Kumar, A., Yogavel, M., Belrhali, H., Jain, S.K., Rug, M., Brown, M., Maier, A.G., and Sharma, A. (2010) Structure, localization and histone binding properties of nuclearassociated nucleosome assembly protein from Plasmodium falciparum. Malar J, 9, 90.
209. Vasudevan, D., Chua, E.Y., and Davey, C.A. (2010) Crystal structures of nucleosome core particles containing the "601" strong positioning sequence. J Mol Biol, epub ahead of print.
210. Davey, G.E., Wu, B., Dong, Y., Surana, U., and Davey, C.A. (2010) DNA stretching in the nucleosome facilitates alkylation by an intercalating antitumour agent. Nucl Acids Res, 38, 2081-2088.
211. Wu, B., Droge, P., and Davey, C.A. (2008) Site selectivity of platinum anticancer therapeutics. Nat Chem Biol, 4, 110-112.
212. Clapier, C.R., Chakravarthy, S., Petosa, C., Fernandez-Tornero, C., Luger, K., and Muller, C.W. (2007) Structure of the Drosophila nucleosome core particle highlights evolutionary constraints on the H2A-H2B histone dimer. Proteins, 71, 1-7.
213. Barbera, A.J., Chodaparambil, J.V., Kelley-Clarke, B., Joukov, V., Walter, J. C., Luger, K., and Kaye, K.M. (2006) The nucleosomal surface as a docking station for Kaposi's sarcoma herpesvirus LANA. Science, 5762, 856-861.
214. Schalch, T., Duda, S., Sargent, D.F., and Richmond, T.J. (2005) X-ray structure of a tetranucleosome and its implications for the chromatin fibre. Nature, 436, 138-141.
215. Tsunaka, Y., Kajimura, N., Tate, S., and Morikawa, K. (2005) Alteration of the nucleosomal DNA path in the crystal structure of a human nucleosome core particle. Nucl Acids Res, 33, 3424-3434.
216. Suto, R.K., Edayathumangalam, R.S., White, C.L., Melander, C., Gottesfeld, J. M., Dervan, P.B., and Luger, K. (2003) Crystal structures of nucleosome core particles in complex with minor groove DNA-binding ligands. J Mol Biol, 326, 371-380.
217. White, C.L., Suto, R.K., and Luger, K. (2001) Structure of the yeast nucleosome core particle reveals fundamental changes in internucleosome interactions. EMBO J, 20, 5207-5218.
218. Harp, J.M., Hanson, B.L., Timm, D.E., and Bunick, G.J. (2000) Asymmetries in the nucleosome core particle at 2.5 Aresolution. Acta Crystallogr D Biol Crystallogr, 56 (Pt 12), 1513-1534.