Structural elements of bulk chromatin within metaphase chromosomes

Chromosome Research

Volumn 13, Issue 7, 2005, Pages 725-743

  Caravaca, Juan Manuel ^a   Caño, Silvia ^a   Gállego, Isaac ^a   Daban, Joan Ramon ^a  

^a UNIVERSITAT AUTÒNOMA DE BARCELONA   (Spain)

Author keywords

Chromatin; DNA; Electron microscopy; Metaphase chromosome

Indexed keywords

ANIMAL CELL; ARTICLE; CELL SIZE; CELL ULTRASTRUCTURE; CELLULAR DISTRIBUTION; CHROMATIN CONDENSATION; CHROMATIN STRUCTURE; CONTROLLED STUDY; DNA DENATURATION; ELECTRON MICROSCOPY; EUCHROMATIN; HELA CELL; HUMAN; HUMAN CELL; INCUBATION TIME; ION PERMEABILITY; METAPHASE CHROMOSOME; NONHUMAN; NUCLEOSOME; PRIORITY JOURNAL; STRUCTURE ANALYSIS;

ACETIC ACID; ANIMALS; BUFFERS; CELL NUCLEUS; CHICKENS; CHROMATIN; CHROMOSOMES, HUMAN; COLD; CROSS-LINKING REAGENTS; DNA, NEOPLASM; EGTAZIC ACID; ELECTROPHORESIS, AGAR GEL; ERYTHROCYTES; FIXATIVES; GLUTARAL; HELA CELLS; HUMANS; MAGNESIUM; METAPHASE; METHANOL; MODELS, BIOLOGICAL; MOLECULAR WEIGHT; NUCLEIC ACID CONFORMATION; NUCLEOSOMES; OSMOLAR CONCENTRATION; TIME FACTORS;

EID: 26944477745     PISSN: 09673849     EISSN: 15736849     Source Type: Journal    
DOI: 10.1007/s10577-005-1008-3     Document Type: Article

References (69)

1. Almagro S, Riveline D, Hirano T, Houchmandzadeh B, Dimitrov S (2004) The mitotic chromosome is an assembly of rigid elastic axes organized by structural maintenance of chromosomes (SMC) proteins and surrounded by a soft chromatin envelope. J Biol Chem 279: 5118-5126.
2. Aragay AM, Fernandez-Busquets X, Daban J-R (1991) Different mechanisms for in vitro formation of nucleosome core particles. Biochemistry 30: 5022-5032.
3. Arents G, Burlingame RW, Wang B-C, Love WE, Moudrianakis EN (1991) The nucleosomal core histone octamer at 3.1 Å resolution: A tripartite protein assembly and a left-handed superhelix. Proc Natl Acad Sci USA 88: 10148-10152.
4. Ausio J, Dong F, van Holde KE (1989) Use of selectively tripsinized nucleosome core particles to analyze the role of the histone "tails" in the stabilization of the nucleosome. J Mol Biol 206: 451-463.
5. Ausubel FM, Brent R, Kingston RE et al. (2001) Current Protocols in Molecular Biology. New York: John Wiley & Sons.
6. Bartolomé S, Bermúdez A, Daban J-R (1994) Internal structure of the 30 nm chromatin fiber. J Cell Sci 107: 2983-2992.
7. 2+. Self-assembly of small chromatin fragments and folding of the 30-nm fiber. J Biol Chem 22: 22514-22521.
8. Bednar J, Horowitz RA, Grigoryev SA et al. (1998) Nucleosomes, linker DNA, and linker histone form a unique structural motif that directs the higher-order folding and compaction of chromatin. Proc Natl Acad Sci USA 95: 14173-14178.
9. Bermúdez A, Bartolomé S, Daban J-R (1998) Partial denaturation of small chromatin fragments: Direct evidence for the radial distribution of nucleosomes in folded chromatin fibers. J Cell Sci 111: 1707-1715.
10. 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.
11. Craig J (1999) Isolation of vertebrate methapase chromosomes and their analysis by FISH. In: Bickmore WA, ed. Chromosome Structural Analysis. A Practical Approach. Oxford, UK: Oxford University Press, pp 59-80.
12. Daban J-R (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.
13. Daban J-R (2003) High concentration of DNA in condensed chromatin. Biochem Cell Biol 81: 91-99.
14. Daban J-R, Bermúdez A (1998) Interdigitated solenoid model for compact chromatin fibers. Biochemistry 37: 4299-4304.
15. de Frutos M, Raspaud E, Leforestier A, Livolant F (2001) Aggregation of nucleosomes by divalent cations. Biophys J 81: 1127-1132.
16. Dorigo B, Schalch T, Kulangara A, Duda S, Schroeder RR, Richmond TJ (2004) Nucleosome arrays reveal the two-start organization of the chromatin fiber. Science 306: 1571-1573.
17. DuPraw EJ (1966) Evidence for a 'folded-fibre' organization in human chromosomes. Nature 209: 577-581.
18. Earnshaw WC, Laemmli UK (1983) Architecture of metaphase chromosomes and chromosome scaffolds. J Cell Biol 96: 84-93.
19. Filipski J, Leblanc J, Youdale T, Sikorska M, Walker PR (1990) Periodicity of DNA folding in higher order chromatin structures. EMBO J 9: 1319-1327.
20. Gassmann R, Vagnarelli P, Hudson D, Earnshaw WC (2004) Mitotic chromosome formation and the condensin paradox. Exp Cell Res 296: 35-42.
21. Grigoryev SA (2004) Keeping fingers crossed: heterochromatin spreading through interdigitation of nucleosome arrays. FEBS Lett 564: 4-8.
22. Hansen JC (2002) Conformational dynamics of the chromatin fiber in solution: Determinants, mechanisms, and functions. Annu Rev Biophys Biomol Struct 31: 361-392.
23. Harp JM, Hanson BL, Timm DE, Bunick GJ (2000) Asymmetries in the nucleosome core particle at 2.5 Å resolution. Acta Crystallogr D 56: 1513-1534.
24. Harrison CJ, Allen TD, Britch M, Harris R (1982) High-resolution scanning electron microscopy of human metaphase chromosomes. J Cell Sci 56: 409-422.
25. Hayes JJ, Hansen JC (2001) Nucleosomes and the chromatin fiber. Curr Opin Genet Dev 11: 124-129.
26. Hirano T (2000) Chromosome cohesion, condensation, and separation. Annu Rev Biochem 69: 115-144.
27. Houchmandzadeh B, Dimitrov S (1999) Elasticity measurements show the existence of thin rigid cores inside mitotic chromosomes. J Cell Biol 145: 215-223.
28. Internacional Human Genome Sequencing Consortium (2001) Initial sequencing and analysis of the human genome. Nature 409: 860-921.
29. Kiryanov GI, Smirnova TA, Polyakov VY (1982) Nucleomeric organization of chromatin. Eur J Biochem 124: 331-338.
30. Koshland D, Strunnikov A (1996) Mitotic chromosome condensation. Annu Rev Cell Dev Biol 12: 305-333.
31. Leforestier A, Dubochet J, Livolant F (2001) Bilayers of nucleosome core particles. Biophys J 81: 2414-2421.
32. Leuba SH, Yang G, Robert C 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.
33. Luger K, Hansen JC (2005) Nucleosome and chromatin fiber dynamics. Curr Opin Struct Biol 15: 188-196.
34. Luger K, Mäder AW, Richmond RK, Sargent DF, Richmond TJ (1997) Crystal structure of the nucleosome core particle at 2.8 Å resolution. Nature 389: 251-260.
35. Maeshima K, Laemmli UK (2003) A two-step scaffolding model for mitotic chromosome assembly. Dev Cell 4: 467-480.
36. Mangenot S, Leforestier A, Durand D, Livolant F (2003) Phase diagram of nucleosome core particles. J Mol Biol 333: 907-916.
37. Manuelidis L, Chen TL (1990) A unified model of eukaryotic chromosomes. Cytometry 11: 8-25.
38. Marsden MPF, Laemmli UK (1979) Metaphase chromosome structure: Evidence for a radial loop model. Cell 17: 849-858.
39. Mozziconacci J, Victor J-M (2003) Nucleosome gaping supports a functional structure for the 30 nm chromatin fiber. J Struct Biol 143: 72-76.
40. Muyldermans S, Lasters I, Wyns L, Hamers R (1980) Upon the observation of superbeads in chromatin. Nucleic Acids Res 8: 2165-2172.
41. Nicholls DG, Ferguson SJ (2002) Bioenergetics 3. London: Academic Press.
42. Pienta KJ, Coffey DS (1984) A structural analysis of the role of the nuclear matrix and DNA loops in the organization of the nucleus and chromosome. J Cell Sci Suppl 1: 123-135.
43. Poirier MG, Marko JF (2002) Mitotic chromosomes are chromatin networks without a mechanically contiguous protein scaffold. Proc Natl Acad Sci USA 99: 15393-15397.
44. Poirier MG, Eroglu S, Marko JF (2002a) The bending rigidity of mitotic chromosomes. Mol Biol Cell 13: 2170-2179.
45. Poirier MG, Monhait T, Marko JF (2002b) Reversible hyper-condensation and decondensation of mitotic chromosomes studied using combined chemical-micromechanical techniques. J Cell Biochem 85: 422-434.
46. Renz M, Nehls P, Hozier J (1977) Involvement of histone H1 in the organization of the chromosome fiber. Proc Natl Acad Sci USA 74: 1879-1883.
47. Richmond TJ, Davey CA (2003) The structure of DNA in the nucleosome core. Nature 423: 145-150.
48. Richmond TJ, Widom J (2000) Nucleosome and chromatin structure. In: Elgin SCR, Workman JL, eds. Chromatin Structure and Gene Expression. Oxford, UK: Oxford University Press, pp 1-23.
49. Rill RL, Shaw BR, van Holde KE (1978) Isolation and characterization of chromatin subunits. Meth Cell Biol 18: 69-103.
50. Saitoh Y, Laemmli UK (1994) Metaphase chromosome structure: Bands arise from a differential folding path of the highly AT-rich scaffold. Cell 76: 609-622.
51. Schroth GP, Yau P, Imai BS, Gatewood JM, Bradbury EM (1990) A NMR study of mobility in the histone octamer. FEBS Lett 268: 117-120.
52. 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.
53. Strukov YG, Wang Y, Belmont AS (2003) Engineered chromosome regions with altered sequence composition demonstrate hierarchical large-scale folding within metaphase chromosomes. J Cell Biol 162: 23-35.
54. Subirana JA, Muñoz-Guerra S, Aymamí J, Radermacher M, Frank J (1985) The layered organization of nucleosomes in 30 nm chromatin fibers. Chromosoma 91: 377-390.
55. Sumner AT (2003) Chromosomes: Organization and Function. Oxford: Blackwell Publishing.
56. Taniguchi T, Takayama S (1986) High-order structure of metaphase chromosomes: Evidence for a multiple coiling model. Chromosoma 93: 511-514.
57. Wang X, He C, Moore SC, Ausió J (2001) Effects of histone acetylation on the solubility and folding of the chromatin fiber. J Biol Chem 276: 12764-12768.
58. Wagner RP, Maguire MP, Stallings RL (1993) Chromosomes: A Synthesis. New York: Wiley-Liss.
59. White CL, Suto RK, Luger K (2001) Structure of the yeast nucleosome core particle reveals fundamental changes in internucleosome interactions. EMBO J 20: 5207-5218.
60. Widom J (1989) Toward a unified model of chromatin folding. Annu Rev Biophys Chem 18: 365-395.
61. Widom J (1998) Structure, dynamics and function of chromatin in vitro. Annu Rev Biophys Biomol Struct 27: 285-327.
62. Widom J, Klug A (1985) Structure of the 300 Å chromatin filament: X-ray diffraction from oriented samples. Cell 43: 207-213.
63. Williams SP, Langmore JP (1991) Small angle X-ray scattering of chromatin. Radius and mass per unit length depend on linker length. Biophys J 59: 606-618.
64. Williams SP, Athey BD, Muglia LJ, Schappe RS, Gough AH, Langmore JP (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.
65. Wolffe AP (1998) Chromatin Structure and Function. London: Academic Press.
66. Woodcock CL, Dimitrov S (2001) Higher-order structure of chromatin and chromosomes. Curr Opin Genet Dev 11: 130-135.
67. Zentgraf H, Franke WW (1984) Differences of supranucleosomal organization in different kinds of chromatin: Cell type-specific globular subunit containing different numbers of nucleosomes. J Cell Biol 99: 272-286.
68. Zentgraf H, Müller U, Franke WW (1980) Reversible in vitro packing of nucleosomal filaments into globular supranucleosomal units in chromatin of whole chick erythrocyte nuclei. Eur J Cell Biol 23: 171-188.
69. Zlatanova J, Leuba SH, Yang G, Bustamante C, van Holde K (1994) Linker DNA accessibility in chromatin fibers of different conformations: A reevaluation. Proc Natl Acad Sci USA 91: 5277-5280.