An all-atom model of the chromatin fiber containing linker histones reveals a versatile structure tuned by the nucleosomal repeat length

PLoS ONE

Volumn 2, Issue 9, 2007, Pages

  Wong, Hua ^a   Victor, Jean Marc ^a   Mozziconacci, Julien ^a,b  

^a UNIVERSITÉ PIERRE ET MARIE CURIE   (France)

^b EUROPEAN MOLECULAR BIOLOGY LABORATORY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

CURVED DNA; DNA B; GLOBULAR PROTEIN; HISTONE H5; DNA;

ARTICLE; CHROMATIN STRUCTURE; DNA HISTONE INTERACTION; ELECTRON MICROSCOPY; GENETIC LINKAGE; MATHEMATICAL COMPUTING; MOLECULAR MODEL; NUCLEOTIDE REPEAT; STRUCTURAL GENOMICS; STRUCTURE ANALYSIS; CHEMISTRY; CHROMATIN; METABOLISM; NUCLEOSOME;

EUKARYOTA;

CHROMATIN; DNA; NUCLEOSOMES;

EID: 36749082174     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0000877     Document Type: Article

References (41)

1. Van Holde KE Chromatin. Springer series in molecular biology.
2. Woodcock CL, Dimitrov S (2001) Higher-order structure of chromatin and chromosomes. Curr Opin Genet Dev 11: 130-135.
3. Travers A (1999) The location of the linker historic on the nucleosome. Trends Biochem Sci 24: 4-7.
4. Bednar J, Horowitz RA, Dubochet J, Woodcock CL (1995) Chromatin conformation and salt-induced compaction: three-dimensional structural information from cryoelectron microscopy. J Cell Biol 131: 1365-1376.
5. Bednar J, Horowitz RA, Grigoryev SA, Carruthers LM, Hansen JC, et al. (1998) Nucleosomes, linker DNA, and linker historic form a unique structural motif that directs the higher-order folding and compaction of chromatin. Proc Natl Acad Sci U S A 95: 14173-14178.
6. Daban JR (2000) Physical constraints in the condensation of eukaryotic chromosomes. Local concentration of DNA versus linear packing ratio in higher order chromatin structures. Biochemistry 39: 3861-3866.
7. Robinson PJ, Fairall L, Huynh VA, Rhodes D (2006) EM measurements define the dimensions of the "30-nm" chromatin fiber: evidence for a compact, interdigitated structure. Proc Natl Acad Sci U S A 103: 6506-6511.
8. Dorigo B, Schalch T, Kulangara A, Duda S, Schroeder RR, et al. (2004) Nucleosome arrays reveal the two-start organization of the chromatin fiber. Science 306: 1571-1573.
9. Widom J, Klug A (1985) Structure of the 300A chromatin filament: X-ray diffraction from oriented samples. Cell 43: 207-213.
10. Worcel A, Strogatz S, Riley D (1981) Structure of chromatin and the linking number of DNA. Proc Natl Acad Sci U S A 78: 1461-1465.
11. Williams SP, Athey BD, Muglia LJ, Schappe RS, Gough AH, et al. (1986) Chromatin fibers are left-handed double helices with diameter and mass per unit length that depend on linker length. Biophys J 49: 233-248.
12. Daban JR, Bermudez A (1998) Interdigitated solenoid model for compact chromatin fibers. Biochemistry 37: 4299-4304.
13. Schalch T, Duda S, Sargent DF, Richmond TJ (2005) X-ray structure of a tetranucleosome and its implications for the chromatin fibre. Nature 436: 138-141.
14. Makarov V, Dimitrov S, Smirnov V, Pashev I (1985) A triple helix model for the structure of chromatin fiber. FEBS Lett 181: 357-361.
15. van Holde K, Zlatanova J (1995) Chromatin higher order structure: chasing a mirage? J Biol Chem 270: 8373-8376.
16. Ben-Haim E, Lesne A, Victor JM (2001) Chromatin: a tunable spring at work inside chromosomes. Phys Rev E Stat Nonlin Soft Matter Phys 64: 051921.
17. Barbi M, Mozziconacci J, Victor JM (2005) How the chromatin fiber deals with topological constraints. Phys Rev E Star Nonlin Soft Matter Phys 71: 031910.
18. Tatchell K, Van Holde KE (1978) Compact oligomers and nucleosome phasing. Proc Natl Acad Sci U S A 75: 3583-3587.
19. Dubochet J, Noll M (1978) Nucleosome arcs and helices. Science 202: 280-286.
20. Mangenot S, Leforestier A, Durand D, Livolant F (2003) Phase diagram of nucleosome core particles. J Mol Biol 333: 907-916.
21. Bartolome S, Bermudez A, Daban JR (1994) Internal structure of the 30 nm chromatin fiber. J Cell Sci 107 ( Pt 11): 2983-2992.
22. Davey CA, Sargent DF, Luger K, Maeder AW, Richmond TJ (2002) Solvent mediated interactions in the structure of the nucleosome core particle at 1.9 a resolution. J Mol Biol 319: 1097-1113.
23. Widom J (1992) A relationship between the helical twist of DNA and the ordered positioning of nucleosomes in all eukaryotic cells. Proc Natl Acad Sci U S A 89: 1095-1099.
24. Yao J, Lowary PT, Widom J (1993) Twist constraints on linker DNA in the 30-nm chromatin fiber: implications for nucleosome phasing. Proc Natl Acad Sci U S A 90: 9364-9368.
25. Duggan MM, Thomas JO (2000) Two DNA-binding sites on the globular domain of historic H5 are required for binding to both bulk and 5 S reconstituted nucleosomes. J Mol Biol 304: 21-33.
26. Mirzabekov AD, Pruss DV, Ebralidse KK (1990) Chromatin superstructure-dependent crosslinking with DNA of the histone H5 residues Thrl, His25 and His62. J Mol Biol 211: 479-491.
27. Brown DT, Izard T, Misteli T (2006) Mapping the interaction surface of linker histone H1(0) with the nucleosome of native chromatin in vivo. Nat Struct Mol Biol 13: 250-255.
28. Fan L, Roberts VA (2006) Complex of linker histone H5 with the nucleosome and its implications for chromatin packing. Proc Natl Acad Sci U S A 103: 8384-8389.
29. Ramakrishnan V, Finch JT, Graziano V, Lee PL Sweet RM (1993) Crystal structure of globular domain of historic H5 and its implications for nucleosome binding. Nature 362: 219-223.
30. Allan J, Hartman PG, Crane-Robinson C, Aviles FX (1980) The structure of histone H1 and its location in chromatin. Nature 288: 675-679.
31. Harrriche A, Schultz P, Ramakrishnari V, Outlet P, Prunell A (1996) Linker histone-dependent DNA structure in linear mononucleosomes. J Mol Biol 257: 30-42.
32. Sivolob A, Prunell A (2003) Linker histone-dependent organization and dynamics of nucleasome entry/exit DNAs. J Mol Biol 331: 1025-1040.
33. Leforestier A, Livolant F (1993) Supramolecular ordering of DNA in the cholesteric liquid crystalline phase: an ultrastructural study. Biophys J 65: 56-72.
34. Hud NV, Downing KH (2001) Cryoelectron microscopy of lambda phage DNA condensates in vitreous ice: the fine structure of DNA toroids. Proc Natl Acad Sci U S A 98: 14925-14930.
35. Lee KC, Borukhov I, Gelbart WM, Liu AJ, Stevens MJ (2004) Effect of mono-and multivalent salts on angle-dependent attractions between charged rods. Phys Rev Lett 93: 128101.
36. Mozziconacci J, Victor JM (2003) Nucleosome gaping supports a functional structure for the 30 nm chromatin fiber. J Struct Biol 143: 72-76.
37. Arya G, Schlick T (2006) Role of historic tails in chromatin folding revealed by a mesoscopic oligonucleosome model. Proc Natl Acad Sci U S A 103: 16236-16241.
38. Lavery R, Zakrzewska K, Sklenar H (1995) JUMNA (junction minimisation of nucleic acids). Computer Physics Communications 91: 135-158.
39. Boomsma W, Hamelryck T (2005) Full cyclic coordinate descent: solving the protein loop closure problem in Calpha space. BMC Bioinformatics 6: 159.
40. Buss SR, Kim J-S (2005) Selectively Damped Least Squares for Inverse Kinematics. J Graph Tools 10: 37-49.
41. Berendsen HJC, van der Spoel D, van Drunen R (1995) GROMACS: a message-passing parallel molecular dynamics implementation. Computer Physics Communications 91: 43-56.