Structural organization of dynamic chromatin

Subcellular Biochemistry

Volumn 41, Issue , 2007, Pages 3-28

  Hizume, Kohji ^a   Yoshimura, Shige H ^a   Kumeta, Masahiro ^a   Takeyasu, Kunio ^a  

^a KYOTO UNIVERSITY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

EUKARYOTA;

DNA; HISTONE;

AMINO ACID SEQUENCE; ANIMAL; CELL CYCLE; CELL NUCLEUS; CHEMISTRY; CHROMATIN; CHROMATIN ASSEMBLY AND DISASSEMBLY; CHROMOSOME; CONFORMATION; CYTOSKELETON; HETEROCHROMATIN; HUMAN; METABOLISM; MOLECULAR GENETICS; NUCLEOLUS; NUCLEOSOME; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEIN PROCESSING; REVIEW;

AMINO ACID SEQUENCE; ANIMALS; CELL CYCLE; CELL NUCLEOLUS; CELL NUCLEUS; CHROMATIN; CHROMATIN ASSEMBLY AND DISASSEMBLY; CHROMOSOMES; CYTOSKELETON; DNA; HETEROCHROMATIN; HISTONES; HUMANS; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; NUCLEOSOMES; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEIN PROCESSING, POST-TRANSLATIONAL;

EID: 34249788441     PISSN: 03060225     EISSN: None     Source Type: Book Series    
DOI: 10.1007/1-4020-5466-1_1     Document Type: Article

References (147)

1. Aagaard L, Laible G, Selenko P, Schmid M, Dorn R, Schotta G, Kuhfittig S, Wolf A, Lebersorger A, Singh PB et al (1999) Functional mammalian homologues of the Drosophila PEV-modifier Su(var)3-9 encode centromere-associated proteins which complex with the heterochromatin component M31. Embo J 18: 1923-1938.
2. Adachi Y, Kas E, Laemmli UK (1989) Preferential, cooperative binding of DNA topoisomerase II to scaffold-associated regions. Embo J 8: 3997-4006.
3. Adachi Y, Luke M, Laemmli UK (1991) Chromosome assembly in vitro: topoisomerase II is required for condensation. Cell 64: 137-148.
4. Adolph KW, Kreisman LR, Kuehn RL (1986) Assembly of chromatin fibers into metaphase chromosomes analyzed by transmission electron microscopy and scanning electron microscopy. Biophys J 49: 221-231.
5. Agresti A, Bianchi ME (2003) HMGB proteins and gene expression. Curr Opin Genet Dev 13: 170-178.
6. Anderson DE, Losada A, Erickson HP, Hirano T (2002) Condensin and cohesin display different arm conformations with characteristic hinge angles. J Cell Biol 156: 419-424.
7. Arents G, Burlingame RW, Wang BC, Love WE, Moudrianakis EN (1991) The nucleosomal core histone octamer at 3. 1 A resolution: a tripartite protein assembly and a left-handed superhelix. Proc Natl Acad Sci U S A 88: 10148-10152.
8. Bannister AJ, Zegerman P, Partridge JF, Miska EA, Thomas JO, Allshire RC, Kouzarides T (2001) Selective recognition of methylated lysine 9 on histone H3 by the HP1 chromo domain. Nature 410: 120-124.
9. Bauer UM, Daujat S, Nielsen SJ, Nightingale K, Kouzarides T (2002) Methylation at arginine 17 of histone H3 is linked to gene activation. EMBO Rep 3: 39-44.
10. Becker PB, Wu C (1992) Cell-free system for assembly of transcriptionally repressed chromatin from Drosophila embryos. Mol Cell Biol 12: 2241-2249.
11. Bell AC, Felsenfeld G (1999) Stopped at the border: boundaries and insulators. Curr Opin Genet Dev 9: 191-198.
12. Belmont AS, Bruce K (1994) Visualization of G1 chromosomes: a folded, twisted, supercoiled chromonema model of interphase chromatid structure. J Cell Biol 127: 287-302.
13. Bennink ML, Leuba SH, Leno GH, Zlatanova J, de Grooth BG, Greve J (2001) Unfolding individual nucleosomes by stretching single chromatin fibers with optical tweezers. Nat Struct Biol 8: 606-610.
14. Berger JM, Gamblin SJ, Harrison SC, Wang JC (1996) Structure and mechanism of DNA topoisomerase II. Nature 379: 225-232.
15. Berrios M, Osheroff N, Fisher PA (1985) In situ localization of DNA topoisomerase II, a major polypeptide component of the Drosophila nuclear matrix fraction. Proc Natl Acad Sci U S A 82: 4142-4146.
16. Bianchi ME, Agresti A (2005) HMG proteins: dynamic players in gene regulation and differentiation. Curr Opin Genet Dev 15: 496-506.
17. Bonaldi T, Langst G, Strohner R, Becker PB, Bianchi ME (2002) The DNA chaperone HMGB1 facilitates ACF/CHRAC-dependent nucleosome sliding. Embo J 21: 6865-6873.
18. Buschhausen G, Wittig B, Graessmann M, Graessmann A (1987) Chromatin structure is required to block transcription of the methylated herpes simplex virus thymidine kinase gene. Proc Natl Acad Sci U S A 84: 1177-1181.
19. Bustin M (2001) Chromatin unfolding and activation by HMGN(*) chromosomal proteins. Trends Biochem Sci 26: 431-437.
20. Bystricky K, Heun P, Gehlen L, Langowski J, Gasser SM (2004) Long-range compaction and flexibility of interphase chromatin in budding yeast analyzed by high-resolution imaging techniques. Proc Natl Acad Sci U S A 101: 16495-16500.
21. Catez F, Brown DT, Misteli T, Bustin M (2002) Competition between histone H1 and HMGN proteins for chromatin binding sites. EMBO Rep 3: 760-766.
22. Chen D, Ma H, Hong H, Koh SS, Huang SM, Schurter BT, Aswad DW, Stallcup MR (1999) Regulation of transcription by a protein methyltransferase. Science 284: 2174-2177.
23. Chubb JR, Boyle S, Perry P, Bickmore WA (2002) Chromatin motion is constrained by association with nuclear compartments in human cells. Curr Biol 12: 439-445.
24. Croston GE, Kadonaga JT (1993) Role of chromatin structure in the regulation of transcription by RNA polymerase II. Curr Opin Cell Biol 5: 417-423.
25. de Frutos M, Raspaud E, Leforestier A, Livolant F (2001) Aggregation of nucleosomes by divalent cations. Biophys J 81: 1127-1132.
26. de la Barre AE, Gerson V, Gout S, Creaven M, Allis CD, Dimitrov S (2000) Core histone N-termini play an essential role in mitotic chromosome condensation. Embo J 19: 379-391.
27. de Lanerolle P, Johnson T, Hofmann WA (2005) Actin and myosin I in the nucleus: what next? Nat Struct Mol Biol 12: 742-746.
28. Ding HF, Bustin M, Hansen U (1997) Alleviation of histone H1-mediated transcriptional repression and chromatin compaction by the acidic activation region in chromosomal protein HMG-14. Mol Cell Biol 17: 5843-5855.
29. Ellwood KB, Yen YM, Johnson RC, Carey M (2000) Mechanism for specificity by HMG-1 in enhanceosome assembly. Mol Cell Biol 20: 4359-4370.
30. Felsenfeld G, McGhee JD (1986) Structure of the 30 nm chromatin fiber. Cell 44: 375-377.
31. Felts SJ, Weil PA, Chalkley R (1990) Transcription factor requirements for in vitro formation of transcriptionally competent 5S rRNA gene chromatin. Mol Cell Biol 10: 2390-2401.
32. Fey EG, Krochmalnic G, Penman S (1986) The nonchromatin substructures of the nucleus: the ribonucleoprotein (RNP)-containing and RNP-depleted matrices analyzed by sequential fractionation and resinless section electron microscopy. J Cell Biol 102: 1654-1665.
33. Fisher PA, Berrios M, Blobel G (1982) Isolation and characterization of a proteinaceous subnuclear fraction composed of nuclear matrix, peripheral lamina, and nuclear pore complexes from embryos of Drosophila melanogaster. J Cell Biol 92: 674-686.
34. Gasser SM, Laemmli UK (1986) The organisation of chromatin loops: characterization of a scaffold attachment site. Embo J 5: 511-518.
35. Germond JE, Hirt B, Oudet P, Gross-Bellark M, Chambon P (1975) Folding of the DNA double helix in chromatin-like structures from simian virus 40. Proc Natl Acad Sci U S A 72: 1843-1847.
36. Godde JS, Widom J (1992) Chromatin structure of Schizosaccharomyces pombe. A nucleosome repeat length that is shorter than the chromatosomal DNA length. J Mol Biol 226: 1009-1025.
37. Gonsior SM, Platz S, Buchmeier S, Scheer U, Jockusch BM, Hinssen H (1999) Conformational difference between nuclear and cytoplasmic actin as detected by a monoclonal antibody. J Cell Sci 112(Pt 6): 797-809.
38. Goodwin GH, Sanders C, Johns EW (1973) A new group of chromatin-associated proteins with a high content of acidic and basic amino acids. Eur J Biochem 38: 14-19.
39. Goto H, Tomono Y, Ajiro K, Kosako H, Fujita M, Sakurai M, Okawa K, Iwamatsu A, Okigaki T, Takahashi T, Inagaki M (1999) Identification of a novel phosphorylation site on histone H3 coupled with mitotic chromosome condensation. J Biol Chem 274: 25543-25549.
40. Gurley LR, D'Anna, JA, Barham SS, Deaven LL, Tobey RA (1978) Histone phosphorylation and chromatin structure during mitosis in Chinese hamster cells. Eur J Biochem 84: 1-15.
41. Harata M, Oma Y, Mizuno S, Jiang YW, Stillman DJ, Wintersberger U (1999) The nuclear actinrelated protein of Saccharomyces cerevisiae, Act3p/Arp4, interacts with core histones. Mol Biol Cell 10: 2595-2605.
42. Hayes JJ, Lee KM (1997) In vitro reconstitution and analysis of mononucleosomes containing defined DNAs and proteins. Methods 12: 2-9.
43. Hernandez-Verdun D, Gautier T (1994) The chromosome periphery during mitosis. Bioessays 16: 179-185.
44. Hirano T, Kobayashi R, Hirano M (1997) Condensins, chromosome condensation protein complexes containing XCAP-C, XCAP-E and a Xenopus homolog of the Drosophila Barren protein. Cell 89: 511-521.
45. Hizume K, Yoshimura SH, Maruyama H, Kim J, Wada H, Takeyasu K (2002) Chromatin reconstitution: development of a salt-dialysis method monitored by nano-technology. Arch Histol Cytol 65: 405-413.
46. Hizume K, Yoshimura SH, Takeyasu K (2004) Atomic force microscopy demonstrates a critical role of DNA superhelicity in nucleosome dynamics. Cell Biochem Biophys 40: 249-262.
47. Hizume K, Yoshimura SH, Takeyasu K (2005) Linker histone H1 per se can induce three-dimensional folding of chromatin fiber. Biochemistry 44: 12978-12989.
48. Hofmann WA, de Lanerolle P (2006) Nuclear actin: to polymerize or not to polymerize. J Cell Biol 172: 495-496.
49. Horn PJ, Peterson CL (2002) Molecular biology: Chromatin higher order folding-Wrapping up transcription. Science 297: 1824-1827.
50. Hoshi O, Ushiki T (2001) Three-dimensional structure of G-banded human metaphase chromosomes observed by atomic force microscopy. Arch Histol Cytol 64: 475-482.
51. 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.
52. Ito T, Bulger M, Pazin MJ, Kobayashi R, Kadonaga JT (1997) ACF, an ISWI-containing and ATPutilizing chromatin assembly and remodeling factor. Cell 90: 145-155.
53. Jackson DA, Cook PR (1995) The structural basis of nuclear function. Int Rev Cytol 162A: 125-149.
54. James TC, Elgin SC (1986) Identification of a nonhistone chromosomal protein associated with heterochromatin in Drosophila melanogaster and its gene. Mol Cell Biol 6: 3862-3872.
55. Jarman AP, Higgs DR (1988) Nuclear scaffold attachment sites in the human globin gene complexes. Embo J 7: 3337-3344.
56. Karymov MA, Tomschik M, Leuba SH, Caiafa P, Zlatanova J (2001) DNA methylation-dependent chromatin fiber compaction in vivo and in vitro: requirement for linker histone. Faseb J 15: 2631-2641.
57. Kaszas E, Cande WZ (2000) Phosphorylation of histone H3 is correlated with changes in the maintenance of sister chromatid cohesion during meiosis in maize, rather than the condensation of the chromatin. J Cell Sci 113(Pt 18): 3217-3226.
58. Keller W (1975) Determination of the number of superhelical turns in simian virus 40 DNA by gel electrophoresis. Proc Natl Acad Sci U S A 72: 4876-4880.
59. Kelly TJ, Qin S, Gottschling DE, Parthun MR (2000) Type B histone acetyltransferase Hat1p participates in telomeric silencing. Mol Cell Biol 20: 7051-7058.
60. Kimura A, Matsubara K, Horikoshi M (2005) A decade of histone acetylation: marking eukaryotic chromosomes with specific codes. J Biochem (Tokyo) 138: 647-662.
61. Kimura K, Hirano T (1997) ATP-dependent positive supercoiling of DNA by 13S condensin: a biochemical implication for chromosome condensation. Cell 90: 625-634.
62. Kobori T, Kodama M, Hizume K, Yoshimura SH, Ohtani T, Takeyasu K (2006) Comparative structural biology of the genome: nano-scale imaging of single nucleus from different kingdoms reveals the common physicochemical property of chromatin with a 40 nm structural unit. J Electron Microsc (Tokyo) 55: 31-40.
63. Kornberg RD (1974) Chromatin structure: a repeating unit of histones and DNA. Science 184: 868-871.
64. Lachner M, O'Carroll D, Rea S, Mechtler K, Jenuwein T (2001) Methylation of histone H3 lysine 9 creates a binding site for HP1 proteins. Nature 410: 116-120.
65. Lane NJ (1969) Intranuclear fibrillar bodies in actinomycin D-treated oocytes. J Cell Biol 40: 286-291.
66. Leuba SH, Yang G, Robert C, Samori B, van Holde K, Zlatanova J, Bustamante C (1994) Threedimensional structure of extended chromatin fibers as revealed by tapping-mode scanning force microscopy. Proc Natl Acad Sci U S A 91: 11621-11625.
67. Leuba SH, Bustamante C, van Holde K, Zlatanova J (1998) Linker histone tails and N-tails of histone H3 are redundant: scanning force microscopy studies of reconstituted fibers. Biophys J 74: 2830-2839.
68. Li G, Sudlow G, Belmont AS (1998) Interphase cell cycle dynamics of a late-replicating, heterochromatic homogeneously staining region: precise choreography of condensation/decondensation and nuclear positioning. J Cell Biol 140: 975-989.
69. Lu W, Peterson R, Dasgupta A, Scovell WM (2000) Influence of HMG-1 and adenovirus oncoprotein E1A on early stages of transcriptional preinitiation complex assembly. J Biol Chem 275: 35006-35012.
70. 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.
71. Lusser A, Kadonaga JT (2004) Strategies for the reconstitution of chromatin. Nat Methods 1: 19-26.
72. Maeshima K, Laemmli UK (2003) A two-step scaffolding model for mitotic chromosome assembly. Dev Cell 4: 467-480.
73. Mahy NL, Perry PE, Gilchrist S, Baldock RA, Bickmore WA (2002) Spatial organization of active and inactive genes and noncoding DNA within chromosome territories. J Cell Biol 157: 579-589.
74. Mangenot S, Leforestier A, Vachette P, Durand D, Livolant F (2002) Salt-induced conformation and interaction changes of nucleosome core particles. Biophys J 82: 345-356.
75. Marsden MP, Laemmli UK (1979) Metaphase chromosome structure: evidence for a radial loop model. Cell 17: 849-858.
76. Marshall WF, Straight A, Marko JF, Swedlow J, Dernburg A, Belmont A, Murray AW, Agard DA, Sedat JW (1997) Interphase chromosomes undergo constrained diffusional motion in living cells. Curr Biol 7: 930-939.
77. McGhee JD, Felsenfeld G (1980) Nucleosome structure. Annu Rev Biochem 49: 1115-1156.
78. Melby TE, Ciampaglio CN, Briscoe G, Erickson HP (1998) The symmetrical structure of structural maintenance of chromosomes (SMC) and MukB proteins: long, antiparallel coiled coils, folded at a flexible hinge. J Cell Biol 142: 1595-1604.
79. Moll R, Franke WW, Schiller DL, Geiger B, Krepler R (1982) The catalog of human cytokeratins: patterns of expression in normal epithelia, tumors and cultured cells. Cell 31: 11-24.
80. Nabirochkin S, Ossokina M, Heidmann T (1998) A nuclear matrix/scaffold attachment region colocalizes with the gypsy retrotransposon insulator sequence. J Biol Chem 273: 2473-2479.
81. Nakai T, Hizume K, Yoshimura SH, Takeyasu K, Yoshikawa K (2005) Phase transition in reconstituted chromatin. Europhysics Letters 69: 1024-1030.
82. Namciu SJ, Blochlinger KB, Fournier RE (1998) Human matrix attachment regions insulate transgene expression from chromosomal position effects in Drosophila melanogaster. Mol Cell Biol 18: 2382-2391.
83. Narlikar GJ, Fan HY, Kingston RE (2002) Cooperation between complexes that regulate chromatin structure and transcription. Cell 108: 475-487.
84. Nettikadan SR, Furbee CS, Muller MT, Takeyasu K (1998) Molecular structure of human topoisomerase II alpha revealed by atomic force microscopy. J Electron Microsc (Tokyo) 47: 671-674.
85. Nickerson J (2001) Experimental observations of a nuclear matrix. J Cell Sci 114: 463-474.
86. Nowak SJ, Corces VG (2004) Phosphorylation of histone H3: a balancing act between chromosome condensation and transcriptional activation. Trends Genet 20: 214-220.
87. O'Neill TE, Roberge M, Bradbury EM (1992) Nucleosome arrays inhibit both initiation and elongation of transcripts by bacteriophage T7 RNA polymerase. J Mol Biol 223: 67-78.
88. Ohfuchi E, Kato M, Sasaki M, Sugimoto K, Oma Y, Harata M (2006) Vertebrate Arp6, a novel nuclear actin-related protein, interacts with heterochromatin protein 1. Eur J Cell Biol 85: 411-421.
89. Ohniwa RL, Morikawa K, Kim J, Kobori T, Hizume K, Matsumi R, Atomi H, Imanaka T, Ohta T, Yoshimura SH, Takeyasu K (2006) Atomic Force Microscopy Dissects the Hierarchy of Genome Architectures in Eukaryote, Prokaryote and Chloroplast. Microscopy & Microanalysis 13: 1-10.
90. Ohsumi K, Katagiri C, Kishimoto T (1993) Chromosome condensation in Xenopus mitotic extracts without histone H1. Science 262: 2033-2035.
91. Olave IA, Reck-Peterson SL, Crabtree GR (2002) Nuclear actin and actin-related proteins in chromatin remodeling. Annu Rev Biochem 71: 755-781.
92. Olins DE, Olins AL (1972) Physical studies of isolated eucaryotic nuclei. J Cell Biol 53: 715-736.
93. Ono T, Losada A, Hirano M, Myers MP, Neuwald AF, Hirano T (2003) Differential contributions of condensin I and condensin II to mitotic chromosome architecture in vertebrate cells. Cell 115: 109-121.
94. Opel ML, Arfin SM, Hatfield GW (2001) The effects of DNA supercoiling on the expression of operons of the ilv regulon of Escherichia coli suggest a physiological rationale for divergently transcribed operons. Mol Microbiol 39: 1109-1115.
95. Owen-Hughes T, Workman JL (1994) Experimental analysis of chromatin function in transcription control. Crit Rev Eukaryot Gene Expr 4: 403-441.
96. Paulson JR, Laemmli UK (1977) The structure of histone-depleted metaphase chromosomes. Cell 12: 817-828.
97. Peterson CL, Laniel MA (2004) Histones and histone modifications. Curr Biol 14, R546-551.
98. Pfaffle P, Gerlach V, Bunzel L, Jackson V (1990) In vitro evidence that transcription-induced stress causes nucleosome dissolution and regeneration. J Biol Chem 265: 16830-16840.
99. Poch O, Winsor B (1997) Who's who among the Saccharomyces cerevisiae actin-related proteins? A classification and nomenclature proposal for a large family. Yeast 13: 1053-1058.
100. Preuss U, Landsberg G, Scheidtmann KH (2003) Novel mitosis-specific phosphorylation of histone H3 at Thr11 mediated by Dlk/ZIP kinase. Nucleic Acids Res 31: 878-885.
101. Prymakowska-Bosak M, Misteli T, Herrera JE, Shirakawa H, Birger Y, Garfield S, Bustin M (2001) Mitotic phosphorylation prevents the binding of HMGN proteins to chromatin. Mol Cell Biol 21: 5169-5178.
102. Rattner JB, Hamkalo BA (1979) Nucleosome packing in interphase chromatin. J Cell Biol 81: 453-457.
103. Rattner JB, Lin CC (1985) Radial loops and helical coils coexist in metaphase chromosomes. Cell 42: 291-296.
104. Rattner JB, Saunders C, Davie JR, Hamkalo BA (1982) Ultrastructural organization of yeast chromatin. J Cell Biol 93: 217-222.
105. Rea S, Eisenhaber F, O'Carroll D, Strahl BD, Sun ZW, Schmid M, Opravil S, Mechtler K, Ponting CP, Allis CD, Jenuwein T (2000) Regulation of chromatin structure by site-specific histone H3 methyltransferases. Nature 406: 593-599.
106. Rhodes D, Klug A (1981) Sequence-dependent helical periodicity of DNA. Nature 292: 378-380.
107. Roussel P, Andre C, Comai L, Hernandez-Verdun D (1996) The rDNA transcription machinery is assembled during mitosis in active NORs and absent in inactive NORs. J Cell Biol 133: 235-246.
108. Satchwell SC, Drew HR, Travers AA (1986) Sequence periodicities in chicken nucleosome core DNA. J Mol Biol 191: 659-675.
109. Sato MH, Ura K, Hohmura KI, Tokumasu F, Yoshimura SH, Hanaoka F, Takeyasu K (1999) Atomic force microscopy sees nucleosome positioning and histone H1-induced compaction in reconstituted chromatin. FEBS Lett 452: 267-271.
110. Schafer DA, Schroer TA (1999) Actin-related proteins. Annu Rev Cell Dev Biol 15: 341-363.
111. Schurter BT, Koh SS, Chen D, Bunick GJ, Harp JM, Hanson BL, Henschen-Edman A, Mackay DR, Stallcup MR, Aswad DW (2001) Methylation of histone H3 by coactivator-associated arginine methyltransferase 1. Biochemistry 40: 5747-5756.
112. Shen X, Yu L, Weir JW, Gorovsky MA (1995) Linker histones are not essential and affect chromatin condensation in vivo. Cell 82: 47-56.
113. Simon RH, Felsenfeld G (1979) A new procedure for purifying histone pairs H2A + H2B and H3 + H4 from chromatin using hydroxylapatite. Nucleic Acids Res 6: 689-696.
114. Simpson RT (1978) Structure of the chromatosome, a chromatin particle containing 160 base pairs of DNA and all the histones. Biochemistry 17: 5524-5531.
115. Simpson RT, Stafford DW (1983) Structural features of a phased nucleosome core particle. Proc Natl Acad Sci U S A 80: 51-55.
116. Simpson RT, Thoma F, Brubaker JM (1985) Chromatin reconstituted from tandemly repeated cloned DNA fragments and core histones: a model system for study of higher order structure. Cell 42: 799-808.
117. Sugiyama S, Yoshino T, Kanahara H, Kobori T, Ohtani T (2003) Atomic force microscopic imaging of 30 nm chromatin fiber from partially relaxed plant chromosomes. Scanning 25: 132-136.
118. Sugiyama S, Yoshino T, Kanahara H, Shichiri M, Fukushi D, Ohtani T (2004) Effects of acetic acid treatment on plant chromosome structures analyzed by atomic force microscopy. Anal Biochem 324: 39-44.
119. Sutrias-Grau M, Bianchi ME, Bernues J (1999) High mobility group protein 1 interacts specifically with the core domain of human TATA box-binding protein and interferes with transcription factor IIB within the pre-initiation complex. J Biol Chem 274: 1628-1634.
120. Tamayo J, Miles M (2000) Human chromosome structure studied by scanning force microscopy after an enzymatic digestion of the covering cell material. Ultramicroscopy 82: 245-251.
121. Taniguchi T, Takayama S (1986) High-order structure of metaphase chromosomes: evidence for a multiple coiling model. Chromosoma 93: 511-514.
122. Tatchell K, Van Holde KE (1977) Reconstitution of chromatin core particles. Biochemistry 16: 5295-5303.
123. Thoma F, Koller T (1977) Influence of histone H1 on chromatin structure. Cell 12: 101-107.
124. 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.
125. Turner BM, Birley AJ, Lavender J (1992) Histone H4 isoforms acetylated at specific lysine residues define individual chromosomes and chromatin domains in Drosophila polytene nuclei. Cell 69: 375-384.
126. Uchiyama S, Kobayashi S, Takata H, Ishihara T, Hori N, Higashi T, Hayashihara K, Sone T, Higo D, Nirasawa T, et al (2005) Proteome analysis of human metaphase chromosomes. J Biol Chem 280: 16994-17004.
127. Udvardy A, Maine E, Schedl P (1985) The 87A7 chromomere. Identification of novel chromatin structures flanking the heat shock locus that may define the boundaries of higher order domains. J Mol Biol 185: 341-358.
128. Uemura T, Ohkura H, Adachi Y, Morino K, Shiozaki K, Yanagida M (1987) DNA topoisomerase II is required for condensation and separation of mitotic chromosomes in S. pombe. Cell 50: 917-925.
129. Ushiki T, Hoshi O, Iwai K, Kimura E, Shigeno M (2002) The structure of human metaphase chromosomes: its histological perspective and new horizons by atomic force microscopy. Arch Histol Cytol 65: 377-390.
130. Van Hooser A, Goodrich DW, Allis CD, Brinkley BR, Mancini MA (1998) Histone H3 phosphorylation is required for the initiation, but not maintenance, of mammalian chromosome condensation. J Cell Sci 111(Pt 23): 3497-3506.
131. Vazquez J, Belmont AS, Sedat JW (2001) Multiple regimes of constrained chromosome motion are regulated in the interphase Drosophila nucleus. Curr Biol 11: 1227-1239.
132. Verschure PJ, van der Kraan I, de Leeuw W, van der Vlag J, Carpenter AE, Belmont AS, van Driel R (2005) In vivo HP1 targeting causes large-scale chromatin condensation and enhanced histone lysine methylation. Mol Cell Biol 25: 4552-4564.
133. Wang H, Huang ZQ, Xia L, Feng Q, Erdjument-Bromage H, Strahl BD, Briggs SD, Allis CD, Wong J, Tempst P, Zhang Y (2001) Methylation of histone H4 at arginine 3 facilitating transcriptional activation by nuclear hormone receptor. Science 293: 853-857.
134. Wang JC (2002) Cellular roles of DNA topoisomerases: a molecular perspective. Nat Rev Mol Cell Biol 3: 430-440.
135. Wei Y, Mizzen CA, Cook RG, Gorovsky MA, Allis CD (1998) Phosphorylation of histone H3 at serine 10 is correlated with chromosome condensation during mitosis and meiosis in Tetrahymena. Proc Natl Acad Sci U S A 95: 7480-7484.
136. Widom J, Klug A (1985) Structure of the 300A chromatin filament: X-ray diffraction from oriented samples. Cell 43: 207-213.
137. Williams RR (2003) Transcription and the territory: the ins and outs of gene positioning. Trends Genet 19: 298-302.
138. Wood V, Gwilliam R, Rajandream MA, Lyne M, Lyne R, Stewart A, Sgouros J, Peat N, Hayles J, Baker S et al (2002) The genome sequence of Schizosaccharomyces pombe. Nature 415: 871-880.
139. 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.
140. Worcel A, Burgi E (1972) On the structure of the folded chromosome of Escherichia coli. J Mol Biol 71: 127-147.
141. Yoshimura SH, Ohniwa RL, Sato MH, Matsunaga F, Kobayashi G, Uga H, Wada C, Takeyasu K (2000) DNA phase transition promoted by replication initiator. Biochemistry 39: 9139-9145.
142. Yoshimura SH, Hizume K, Murakami A, Sutani T, Takeyasu K, Yanagida M (2002) Condensin architecture and interaction with DNA. Regulatory non-SMC subunits bind to the head of SMC heterodimer. Curr Biol 12: 508-513.
143. Yoshimura SH, Kim J, Takeyasu K (2003) On-substrate lysis treatment combined with scanning probe microscopy revealed chromosome structures in eukaryotes and prokaryotes. J Electron Microsc (Tokyo) 52: 415-423.
144. Zamore PD, Haley B (2005) Ribo-gnome: the big world of small RNAs. Science 309: 1519-1524.
145. Zhao K, Wang W, Rando OJ, Xue Y, Swiderek K, Kuo A, Crabtree GR (1998) Rapid and phosphoinositol-dependent binding of the SWI/SNF-like BAF complex to chromatin after T lymphocyte receptor signaling. Cell 95: 625-636.
146. Zheng C, Hayes JJ (2003) Structures and interactions of the core histone tail domains. Biopolymers 68: 539-546.
147. Zlatanova J, Leuba SH, van Holde K (1999) Chromatin structure revisited. Crit Rev Eukaryot Gene Expr 9: 245-255.