The Nucleosome Family: Dynamic and Growing

Structure

Volumn 17, Issue 2, 2009, Pages 160-171

  Zlatanova, Jordanka ^a   Bishop, Thomas C ^b   Victor, Jean Marc ^c   Jackson, Vaughn ^d   van Holde, Ken ^e  

^a UNIVERSITY OF WYOMING   (United States)

^b TULANE UNIVERSITY   (United States)

^c UNIVERSITÉ PIERRE ET MARIE CURIE   (France)

^d MEDICAL COLLEGE OF WISCONSIN   (United States)

^e OREGON STATE UNIVERSITY   (United States)

Author keywords

DNA; PROTEINS

Indexed keywords

DNA; HEAT SHOCK PROTEIN 70; HISTONE; HISTONE H2A; HISTONE H2B; HISTONE H3; HISTONE H4; NUCLEASE; RNA POLYMERASE;

CHROMATIN IMMUNOPRECIPITATION; CHROMATIN STRUCTURE; CONFORMATIONAL TRANSITION; DNA PACKAGING; DROSOPHILA; ELECTRON MICROSCOPY; FLUORESCENCE CORRELATION SPECTROSCOPY; FLUORESCENCE RESONANCE ENERGY TRANSFER; IONIC STRENGTH; NONHUMAN; NUCLEOSOME; PRIORITY JOURNAL; REVIEW; SCHIZOSACCHAROMYCES POMBE; STEADY STATE; X RAY CRYSTALLOGRAPHY;

ANIMALS; DNA; HISTONES; HUMANS; MODELS, BIOLOGICAL; MODELS, MOLECULAR; MULTIGENE FAMILY; NUCLEIC ACID CONFORMATION; NUCLEOSOMES; PROTEIN BINDING; PROTEIN MULTIMERIZATION;

EUKARYOTA;

EID: 59649087452     PISSN: 09692126     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.str.2008.12.016     Document Type: Review

References (100)

1. Alilat M., Sivolob A., Revet B., and Prunell A. Nucleosome dynamics: protein and DNA contributions in the chiral transition of the tetrasome, the histone (H3-H4)2 tetramer-DNA particle. J. Mol. Biol. 291 (1999) 815-841
2. Altenburger W., Horz W., and Zachau H.G. Nuclease cleavage of chromatin at 100-nucleotide pair intervals. Nature 264 (1976) 517-522
3. Annunziato A.T. Split decision: what happens to nucleosomes during DNA replication?. J. Biol. Chem. 280 (2005) 12065-12068
4. Asahara H., Tartare-Deckert S., Nakagawa T., Ikehara T., Hirose F., Hunter T., Ito T., and Montminy M. Dual roles of p300 in chromatin assembly and transcriptional activation in cooperation with nucleosome assembly protein 1 in vitro. Mol. Cell. Biol. 22 (2002) 2974-2983
5. Baer B.W., and Rhodes D. Eukaryotic RNA polymerase II binds to nucleosome cores from transcribed genes. Nature 301 (1983) 482-488
6. Bancaud A., Conde e Silva N., Barbi M., Wagner G., Allemand J.F., Mozziconacci J., Lavelle C., Croquette V., Victor J.M., Prunell A., and Viovy J.L. Structural plasticity of single chromatin fibers revealed by torsional manipulation. Nat. Struct. Mol. Biol. 13 (2006) 444-450
7. Bancaud A., Wagner G., Conde E.S.N., Lavelle C., Wong H., Mozziconacci J., Barbi M., Sivolob A., Le Cam E., Mouawad L., et al. Nucleosome chiral transition under positive torsional stress in single chromatin fibers. Mol. Cell 27 (2007) 135-147
8. Banks D.D., and Gloss L.M. Folding mechanism of the (H3-H4)2 histone tetramer of the core nucleosome. Protein Sci. 13 (2004) 1304-1316
9. Bao Y., Konesky K., Park Y.J., Rosu S., Dyer P.N., Rangasamy D., Tremethick D.J., Laybourn P.J., and Luger K. Nucleosomes containing the histone variant H2A.Bbd organize only 118 base pairs of DNA. EMBO J. 23 (2004) 3314-3324
10. Bazett-Jones D.P., Mendez E., Czarnota G.J., Ottensmeyer F.P., and Allfrey V.G. Visualization and analysis of unfolded nucleosomes associated with transcribing chromatin. Nucleic Acids Res. 24 (1996) 321-329
11. Belotserkovskaya R., Oh S., Bondarenko V.A., Orphanides G., Studitsky V.M., and Reinberg D. FACT facilitates transcription-dependent nucleosome alteration. Science 301 (2003) 1090-1093
12. Bina-Stein M., and Simpson R.T. Specific folding and contraction of DNA by histones H3 and H4. Cell 11 (1977) 609-618
13. Bruno M., Flaus A., Stockdale C., Rencurel C., Ferreira H., and Owen-Hughes T. Histone H2A/H2B dimer exchange by ATP-dependent chromatin remodeling activities. Mol. Cell 12 (2003) 1599-1606
14. Camahort R., Li B., Florens L., Swanson S.K., Washburn M.P., and Gerton J.L. Scm3 is essential to recruit the histone h3 variant cse4 to centromeres and to maintain a functional kinetochore. Mol. Cell 26 (2007) 853-865
15. Camerini-Otero R.D., Sollner-Webb B., and Felsenfeld G. The organization of histones and DNA in chromatin: evidence for an arginine-rich histone kernel. Cell 8 (1976) 333-347
16. Cartwright I.L., and Elgin S.C. Nucleosomal instability and induction of new upstream protein-DNA associations accompany activation of four small heat shock protein genes in Drosophila melanogaster. Mol. Cell. Biol. 6 (1986) 779-791
17. Chen T.A., and Allfrey V.G. Rapid and reversible changes in nucleosome structure accompany the activation, repression, and superinduction of murine fibroblast protooncogenes c-fos and c-myc. Proc. Natl. Acad. Sci. USA 84 (1987) 5252-5256
18. Chen T.A., Sterner R., Cozzolino A., and Allfrey V.G. Reversible and irreversible changes in nucleosome structure along the c-fos and c-myc oncogenes following inhibition of transcription. J. Mol. Biol. 212 (1990) 481-493
19. Conde e Silva N., Black B.E., Sivolob A., Filipski J., Cleveland D.W., and Prunell A. CENP-A-containing nucleosomes: easier disassembly versus exclusive centromeric localization. J. Mol. Biol. 370 (2007) 555-573
20. Dalal Y., Wang H., Lindsay S., and Henikoff S. Tetrameric structure of centromeric nucleosomes in interphase Drosophila cells. PLoS Biol. 5 (2007) e218
21. Dalal Y., Furuyama T., Vermaak D., and Henikoff S. Structure, dynamics, and evolution of centromeric nucleosomes. Proc. Natl. Acad. Sci. USA 104 (2007) 15974-15981
22. Davey C.A., Sargent D.F., Luger K., Maeder A.W., and Richmond T.J. Solvent mediated interactions in the structure of the nucleosome core particle at 1.9 a resolution. J. Mol. Biol. 319 (2002) 1097-1113
23. De Lucia F., Alilat M., Sivolob A., and Prunell A. Nucleosome dynamics. III. Histone tail-dependent fluctuation of nucleosomes between open and closed DNA conformations. Implications for chromatin dynamics and the linking number paradox. A relaxation study of mononucleosomes on DNA minicircles. J. Mol. Biol. 285 (1999) 1101-1119
24. Dong F., and van Holde K.E. Nucleosome positioning is determined by the (H3-H4)2 tetramer. Proc. Natl. Acad. Sci. USA 88 (1991) 10596-10600
25. Doyen C.M., Montel F., Gautier T., Menoni H., Claudet C., Delacour-Larose M., Angelov D., Hamiche A., Bednar J., Faivre-Moskalenko C., et al. Dissection of the unusual structural and functional properties of the variant H2A.Bbd nucleosome. EMBO J. 25 (2006) 4234-4244
26. Eirín-López J.M., Ishibashi T., and Ausio J. H2A.Bbd: a quickly evolving hypervariable mammalian histone that destabilizes nucleosomes in an acetylation-independent way. FASEB J. 22 (2008) 316-326
27. English C.M., Maluf N.K., Tripet B., Churchill M.E., and Tyler J.K. 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 (2005) 13673-13682
28. Flaus A., Luger K., Tan S., and Richmond T.J. Mapping nucleosome position at single base-pair resolution by using site-directed hydroxyl radicals. Proc. Natl. Acad. Sci. USA 93 (1996) 1370-1375
29. Flaus A., and Owen-Hughes T. Mechanisms for ATP-dependent chromatin remodelling: farewell to the tuna-can octamer?. Curr. Opin. Genet. Dev. 14 (2004) 165-173
30. Furuyama T., Dalal Y., and Henikoff S. Chaperone-mediated assembly of centromeric chromatin in vitro. Proc. Natl. Acad. Sci. USA 103 (2006) 6172-6177
31. Godde J.S., and Widom J. Chromatin structure of Schizosaccharomyces pombe: a nucleosome repeat length that is shorter than the chromatosomal DNA length. J. Mol. Biol. 226 (1992) 1009-1025
32. Hamiche A., Carot V., Alilat M., De Lucia F., O'Donohue M.F., Revet B., and Prunell A. Interaction of the histone (H3-H4)2 tetramer of the nucleosome with positively supercoiled DNA minicircles: potential flipping of the protein from a left- to a right-handed superhelical form. Proc. Natl. Acad. Sci. USA 93 (1996) 7588-7593
33. Hamiche A., and Richard-Foy H. The switch in the helical handedness of the histone (H3-H4)2 tetramer within a nucleoprotein particle requires a reorientation of the H3-H3 interface. J. Biol. Chem. 273 (1998) 9261-9269
34. Harp J.M., Hanson B.L., Timm D.E., and Bunick G.J. Asymmetries in the nucleosome core particle at 2.5 A resolution. Acta Crystallogr. D Biol. Crystallogr. 56 (2000) 1513-1534
35. Hayes J.J., Clark D.J., and Wolffe A.P. Histone contributions to the structure of DNA in the nucleosome. Proc. Natl. Acad. Sci. USA 88 (1991) 6829-6833
36. Hutcheon T., Dixon G.H., and Levy-Wilson B. Transcriptionally active mononucleosomes from trout testis are heterogeneous in composition. J. Biol. Chem. 255 (1980) 681-685
37. Ito T., Ikehara T., Nakagawa T., Kraus W.L., and Muramatsu M. p300-mediated acetylation facilitates the transfer of histone H2A-H2B dimers from nucleosomes to a histone chaperone. Genes Dev. 14 (2000) 1899-1907
38. Jackson V. In vivo studies on the dynamics of histone-DNA interaction: evidence for nucleosome dissolution during replication and transcription and a low level of dissolution independent of both. Biochemistry 29 (1990) 719-731
39. Jackson V. Preferential binding of histones H3 and H4 to highly positively coiled DNA. Biochemistry 34 (1995) 10607-10619
40. Jackson V., and Chalkley R. Histone synthesis and deposition in the G1 and S phases of hepatoma tissue culture cells. Biochemistry 24 (1985) 6921-6930
41. Jorcano J.L., and Ruiz-Carrillo A. H3.H4 tetramer directs DNA and core histone octamer assembly in the nucleosome core particle. Biochemistry 18 (1979) 768-774
42. Karantza V., Freire E., and Moudrianakis E.N. Thermodynamic studies of the core histones: pH and ionic strength effects on the stability of the (H3-H4)/(H3-H4)2 system. Biochemistry 35 (1996) 2037-2046
43. Kimura H. Histone dynamics in living cells revealed by photobleaching. DNA Repair (Amst.) 4 (2005) 939-950
44. Kimura H., and Cook P.R. Kinetics of core histones in living human cells: little exchange of H3 and H4 and some rapid exchange of H2B. J. Cell Biol. 153 (2001) 1341-1353
45. Kireeva M.L., Walter W., Tchernajenko V., Bondarenko V., Kashlev M., and Studitsky V.M. Nucleosome remodeling induced by RNA polymerase II: loss of the H2A/H2B dimer during transcription. Mol. Cell 9 (2002) 541-552
46. Koopmans W.J., Brehm A., Logie C., Schmidt T., and van Noort J. Single-pair FRET microscopy reveals mononucleosome dynamics. J. Fluoresc. 17 (2007) 785-795
47. Korolev N., Vorontsova O.V., and Nordenskiold L. Physicochemical analysis of electrostatic foundation for DNA-protein interactions in chromatin transformations. Prog. Biophys. Mol. Biol. 95 (2007) 23-49
48. Lavelle C., and Prunell A. Chromatin polymorphism and the nucleosome superfamily: a genealogy. Cell Cycle 6 (2007) 2113-2119
49. Lee C.K., Shibata Y., Rao B., Strahl B.D., and Lieb J.D. Evidence for nucleosome depletion at active regulatory regions genome-wide. Nat. Genet. 36 (2004) 900-905
50. Lee M.S., and Garrard W.T. Transcription-induced nucleosome 'splitting': an underlying structure for DNase I sensitive chromatin. EMBO J. 10 (1991) 607-615
51. Lee M.S., and Garrard W.T. Positive DNA supercoiling generates a chromatin conformation characteristic of highly active genes. Proc. Natl. Acad. Sci. USA 88 (1991) 9675-9679
52. Lesne A., and Victor J.M. Chromatin fiber functional organization: some plausible models. Eur. Phys. J. E Soft Matter 19 (2006) 279-290
53. Levchenko V., Jackson B., and Jackson V. Histone release during transcription: displacement of the two H2A-H2B dimers in the nucleosome is dependent on different levels of transcription-induced positive stress. Biochemistry 44 (2005) 5357-5372
54. Li G., and Widom J. Nucleosomes facilitate their own invasion. Nat. Struct. Mol. Biol. 11 (2004) 763-769
55. Li G., Levitus M., Bustamante C., and Widom J. Rapid spontaneous accessibility of nucleosomal DNA. Nat. Struct. Mol. Biol. 12 (2005) 46-53
56. Locklear Jr. L., Ridsdale J.A., Bazett-Jones D.P., and Davie J.R. Ultrastructure of transcriptionally competent chromatin. Nucleic Acids Res. 18 (1990) 7015-7024
57. Lohr D., and van Holde K.E. Organization of spacer DNA in chromatin. Proc. Natl. Acad. Sci. USA 76 (1979) 6326-6330
58. Luger K., Mader A.W., Richmond R.K., Sargent D.F., and Richmond T.J. Crystal structure of the nucleosome core particle at 2.8 A resolution. Nature 389 (1997) 251-260
59. Marc F., Sandman K., Lurz R., and Reeve J.N. Archaeal histone tetramerization determines DNA affinity and the direction of DNA supercoiling. J. Biol. Chem. 277 (2002) 30879-30886
60. Marky N.L., and Manning G.S. The elastic resilience of DNA can induce all-or-none structural transitions in the nucleosome core particle. Biopolymers 31 (1991) 1543-1557
61. Marky N.L., and Manning G.S. A theory of DNA dissociation from the nucleosome. J. Mol. Biol. 254 (1995) 50-61
62. Mason P.B., and Struhl K. Distinction and relationship between elongation rate and processivity of RNA polymerase II in vivo. Mol. Cell 17 (2005) 831-840
63. McBryant S.J., Park Y.J., Abernathy S.M., Laybourn P.J., Nyborg J.K., and Luger K. Preferential binding of the histone (H3-H4)2 tetramer by NAP1 is mediated by the amino-terminal histone tails. J. Biol. Chem. 278 (2003) 44574-44583
64. Mello J.A., Sillje H.H., Roche D.M., Kirschner D.B., Nigg E.A., and Almouzni G. Human Asf1 and CAF-1 interact and synergize in a repair-coupled nucleosome assembly pathway. EMBO Rep. 3 (2002) 329-334
65. Mizuguchi G., Xiao H., Wisniewski J., Smith M.M., and Wu C. Nonhistone Scm3 and histones CenH3-H4 assemble the core of centromere-specific nucleosomes. Cell 129 (2007) 1153-1164
66. Mosammaparast N., Ewart C.S., and Pemberton L.F. A role for nucleosome assembly protein 1 in the nuclear transport of histones H2A and H2B. EMBO J. 21 (2002) 6527-6538
67. Mozziconacci J., and Victor J.M. Nucleosome gaping supports a functional structure for the 30nm chromatin fiber. J. Struct. Biol. 143 (2003) 72-76
68. Mozziconacci J., Lavelle C., Barbi M., Lesne A., and Victor J.M. A physical model for the condensation and decondensation of eukaryotic chromosomes. FEBS Lett. 580 (2006) 368-372
69. Orphanides G., LeRoy G., Chang C.H., Luse D.S., and Reinberg D. FACT, a factor that facilitates transcript elongation through nucleosomes. Cell 92 (1998) 105-116
70. Oudet P., Spadafora C., and Chambon P. Nucleosome structure II: structure of the SV40 minichromosome and electron microscopic evidence for reversible transitions of the nucleosome structure. Cold Spring Harb. Symp. Quant. Biol. 42 (1978) 301-312
71. Peterson S., Danowit R., Wunsch A., and Jackson V. NAP1 catalyzes the formation of either positive or negative supercoils on DNA on basis of the dimer-tetramer equilibrium of histones H3/H4. Biochemistry 46 (2007) 8634-8646
72. Petesch S.J., and Lis J.T. Rapid, transcription-independent loss of nucleosomes over a large chromatin domain at Hsp70 Loci. Cell 134 (2008) 74-84
73. Polach K.J., and Widom J. Mechanism of protein access to specific DNA sequences in chromatin: a dynamic equilibrium model for gene regulation. J. Mol. Biol. 254 (1995) 130-149
74. Prior C.P., Cantor C.R., Johnson E.M., and Allfrey V.G. Incorporation of exogenous pyrene-labeled histone into Physarum chromatin: a system for studying changes in nucleosomes assembled in vivo. Cell 20 (1980) 597-608
75. Prior C.P., Cantor C.R., Johnson E.M., Littau V.C., and Allfrey V.G. Reversible changes in nucleosome structure and histone H3 accessibility in transcriptionally active and inactive states of rDNA chromatin. Cell 34 (1983) 1033-1042
76. Protacio R.U., and Widom J. Nucleosome transcription studied in a real-time synchronous system: test of the lexosome model and direct measurement of effects due to histone octamer. J. Mol. Biol. 256 (1996) 458-472
77. Rasnik I., McKinney S.A., and Ha T. Nonblinking and long-lasting single-molecule fluorescence imaging. Nat. Methods 3 (2006) 891-893
78. Reeve J.N., Bailey K.A., Li W.T., Marc F., Sandman K., and Soares D.J. Archaeal histones: structures, stability and DNA binding. Biochem. Soc. Trans. 32 (2004) 227-230
79. Sandman K., and Reeve J.N. Archaeal histones and the origin of the histone fold. Curr. Opin. Microbiol. 9 (2006) 520-525
80. Sathyanarayana U.G., Freeman L.A., Lee M.S., and Garrard W.T. RNA polymerase-specific nucleosome disruption by transcription in vivo. J. Biol. Chem. 274 (1999) 16431-16436
81. Schwabish M.A., and Struhl K. Evidence for eviction and rapid deposition of histones upon transcriptional elongation by RNA polymerase II. Mol. Cell. Biol. 24 (2004) 10111-10117
82. Schwabish M.A., and Struhl K. Asf1 mediates histone eviction and deposition during elongation by RNA polymerase II. Mol. Cell 22 (2006) 415-422
83. Sollner-Webb B., Camerini-Otero R.D., and Felsenfeld G. Chromatin structure as probed by nucleases and proteases: evidence for the central role of histones H3 and H4. Cell 9 (1976) 179-193
84. Stoler S., Rogers K., Weitze S., Morey L., Fitzgerald-Hayes M., and Baker R.E. Scm3, an essential Saccharomyces cerevisiae centromere protein required for G2/M progression and Cse4 localization. Proc. Natl. Acad. Sci. USA 104 (2007) 10571-10576
85. Szent-Gyorgyi C., Finkelstein D.B., and Garrard W.T. Sharp boundaries demarcate the chromatin structure of a yeast heat-shock gene. J. Mol. Biol. 193 (1987) 71-80
86. Tagami H., Ray-Gallet D., Almouzni G., and Nakatani Y. Histone H3.1 and H3.3 complexes mediate nucleosome assembly pathways dependent or independent of DNA synthesis. Cell 116 (2004) 51-61
87. Thiriet C., and Hayes J.J. Replication-independent core histone dynamics at transcriptionally active loci in vivo. Genes Dev. 19 (2005) 677-682
88. Tomschik M., Zheng H., van Holde K., Zlatanova J., and Leuba S.H. Fast, long-range, reversible conformational fluctuations in nucleosomes revealed by single-pair fluorescence resonance energy transfer. Proc. Natl. Acad. Sci. USA 102 (2005) 3278-3283
89. Tomschik M., van Holde K., and Zlatanova J. Nucleosome dynamics as studied by single-pair fluorescence resonance energy transfer: a reevaluation. J. Fluoresc. (2008) 10.1007/s10895-008-0379-1 Published online May 15, 2008
90. Tsanev R., and Petrov P. The substructure of chromatin and its variations as revealed by electron microscopy. J. Microsc. Biol. Cell. 27 (1976) 11-19
91. Tsanev R., Russev G., Pashev I., and Zlatanova J. Replication and Transcription of Chromatin (1992), CRC Press, Boca Raton
92. van Holde K., and Zlatanova J. The nucleosome core particle: does it have structural and physiologic relevance?. Bioessays 21 (1999) 776-780
93. van Holde K., and Zlatanova J. Scanning chromatin: a new paradigm?. J. Biol. Chem. 281 (2006) 12197-12200
94. van Holde K.E. Chromatin (1988), Springer Verlag, New York
95. Walker J., Chen T.A., Sterner R., Berger M., Winston F., and Allfrey V.G. Affinity chromatography of mammalian and yeast nucleosomes. J. Biol. Chem. 265 (1990) 5736-5746
96. Weintraub H., Worcel A., and Alberts B. A model for chromatin based upon two symmetrically paired half-nucleosomes. Cell 9 (1976) 409-417
97. Yamasu K., and Senshu T. Conservative segregation of tetrameric units of H3 and H4 histones during nucleosome replication. J Biochem. 107 (1990) 15-20
98. Zhang W., Mellone B.G., and Karpen G.H. A specialized nucleosome has a "point" to make. Cell 129 (2007) 1047-1049
99. Zlatanova J. Archaeal chromatin: virtual or real?. Proc. Natl. Acad. Sci. USA 94 (1997) 12251-12254
100. Zlatanova J., Seebart C., and Tomschik M. Nap1: taking a closer look at a juggler protein of extraordinary skills. FASEB J. 21 (2007) 1294-1310