DNA-loop formation on nucleosomes shown by in situ scanning force microscopy of supercoiled DNA

Journal of Molecular Biology

Volumn 345, Issue 4, 2005, Pages 695-706

  Bussiek, Malte ^a   Tóth, Katalin ^a   Brun, Nathalie ^a   Langowski, Jörg ^a  

^a GERMAN CANCER RESEARCH CENTER DKFZ   (Germany)

Author keywords

chromatin; intranucleosomal DNA loops; nucleosomes; scanning force microscopy; supercoiled DNA

Indexed keywords

DNA; HISTONE; MICA; PLASMID DNA; POLYLYSINE; SODIUM CHLORIDE;

ANIMAL CELL; AQUEOUS SOLUTION; ARTICLE; CHEMICAL STRUCTURE; CONCENTRATION (PARAMETERS); CONFORMATION; CONTROLLED STUDY; DNA SUPERCOILING; MATERIAL COATING; MORPHOLOGY; NONHUMAN; NUCLEOSOME; PRIORITY JOURNAL; SCANNING FORCE MICROSCOPY;

MICA;

EID: 10044241878     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2004.11.016     Document Type: Article

References (49)

1. R. Negri, G. Costanzo, M. Buttinelli, S. Venditti, and E. Dimauro Effects of DNA topology in the interaction with histone octamers and DNA topoisomerase I Biophys. Chem. 50 1994 169 181
2. V.G. Norton, K.W. Marvin, P. Yau, and E.M. Bradbury Nucleosome linking number change controlled by acetylation of histones H3 and H4 J. Biol. Chem. 265 1990 19848 19852
3. V.G. Norton, B.S. Imai, P. Yau, and E.M. Bradbury Histone acetylation reduces nucleosome core particle linking number change Cell 57 1989 449 457
4. R.T. Simpson, F. Thoma, and J.M. Brubaker Chromatin reconstituted from tandemly repeated cloned DNA fragments and core histones: a model system for study of higher order structure Cell 42 1985 799 808
5. J.E. Germond, B. Hirt, P. Oudet, M. Gross-Bellark, and P. Chambon Folding of the DNA double helix in chromatin-like structures from simian virus 40 Proc. Natl Acad. Sci. USA 72 1975 1843 1847
6. A. Hamiche, P. Schultz, V. Ramakrishnan, P. Oudet, and A. Prunell Linker histone-dependent DNA structure in linear mononucleosomes J. Mol. Biol. 257 1996 30 42
7. P. Furrer, J. Bednar, J. Dubochet, A. Hamiche, and A. Prunell DNA at the entry-exit of the nucleosome observed by cryoelectron microscopy J. Struct. Biol. 114 1995 177 183
8. I. Goulet, Y. Zivanovic, A. Prunell, and B. Révet Chromatin reconstitution on small DNA rings. I J. Mol. Biol. 200 1988 253 266
9. Y. Zivanovic, I. Goulet, B. Révet, M. le Bret, and A. Prunell Chromatin reconstitution on small DNA ringsII. DNA supercoiling on the nucleosome J. Mol. Biol. 200 1988 267 290
10. B. Thomsen, C. Bendixen, and O. Westergaard Histone hyperacetylation is accompanied by changes in DNA topology in vivo Eur. J. Biochem. 201 1991 107 111
11. V. Morales, and H. Richard-Foy Role of histone N-terminal tails and their acetylation in nucleosome dynamics Mol. Cell Biol. 20 2000 7230 7237
12. L.C. Lutter, L. Judis, and R.F. Paretti Effects of histone acetylation on chromatin topology in vivo Mol. Cell Biol. 12 1992 5004 5014
13. W.A. Krajewski Chromatin structural transitions in Drosophila embryo cell-free extract result in a high conformational flexibility of nucleosomal DNA FEBS 452 1999 215 218
14. P. Forte, L. Leoni, B. Sampaolese, and M. Savino Cooperativity in nucleosomes assembly on supercoiled pBR322 DNA Nucl. Acids Res. 17 1989 8683 8694
15. M. Buttinelli, L. Leoni, B. Sampaolese, and M. Savino Influence of DNA topology and histone tails in nucleosome organization on pBR322 DNA Nucl. Acids Res. 19 1991 4543 4549
16. Y.P. Tsao, H.Y. Wu, and L.F. Liu Transcription-driven supercoiling of DNA: direct biochemical evidence from in vitro studies Cell 56 1989 111 118
17. G. Langst, and P.B. Becker ISWI induces nucleosome sliding on nicked DNA Mol. Cell 8 2001 1085 1092
18. G. Langst, E.J. Bonte, D.F. Corona, and P.B. Becker Nucleosome movement by CHRAC and ISWI without disruption or trans- displacement of the histone octamer Cell 97 1999 843 852
19. I. Whitehouse, A. Flaus, B.R. Cairns, M.F. White, J.L. Workman, and T. Owen-Hughes Nucleosome mobilization catalysed by the yeast SWI/SNF complex Nature 400 1999 784 787
20. D.P. Bazett-Jones, J. Cote, C.C. Landel, C.L. Peterson, and J.L. Workman The SWI/SNF complex creates loop domains in DNA and polynucleosome arrays and can disrupt DNA-histone contacts within these domains Mol. Cell Biol. 19 1999 1470 1478
21. K. Havas, A. Flaus, M. Phelan, R. Kingston, P.A. Wade, D.M. Lilley, and T. Owen-Hughes Generation of superhelical torsion by ATP-dependent chromatin remodeling activities Cell 103 2000 1133 1142
22. S. Pennings, G. Meersseman, and E.M. Bradbury Mobility of positioned nucleosomes on 5 S rDNA J. Mol. Biol. 220 1991 101 110
23. G. Meersseman, S. Pennings, and E.M. Bradbury Mobile nucleosomes - a general behavior EMBO 11 1992 2951 2959
24. C.A. Davey, D.F. Sargent, K. Luger, A.W. Maeder, and T.J. Richmond Solvent mediated interactions in the structure of the nucleosome core particle at 1.9 a resolution J. Mol. Biol. 319 2002 1097 1113
25. I.M. Kulic, and H. Schiessel Nucleosome repositioning via loop formation Biophys. J. 84 2003 3197 3211
26. J. Bednar, P. Furrer, A. Stasiak, J. Dubochet, E.H. Egelman, and A.D. Bates The twist, writhe and overall shape of superhelical DNA change during counterion-induced transition from a loosely to a tightly interwound superhelix. Possible implications for DNA structure in vivo J. Mol. Biol. 235 1994 825 847
27. T.C. Boles, J.H. White, and N.R. Cozzarelli Structure of plectonemically supercoiled DNA J. Mol. Biol. 213 1990 931 951
28. M. Adrian, B. ten Heggeler-Bordier, W. Wahli, A.Z. Stasiak, A. Stasiak, and J. Dubochet Direct visualization of supercoiled DNA molecules in solution EMBO J. 9 1990 4551 4554
29. J. Langowski, and U. Giesen Configurational and dynamic properties of different length superhelical DNAs measured by dynamic light scattering Biophys. Chem. 34 1989 9 18
30. K. Rippe, P.H. von Hippel, and J. Langowski Action at a distance: DNA-looping and initiation of transcription Trends Biochem. Sci. 20 1995 500 506
31. A.V. Vologodskii, S.D. Levene, K.V. Klenin, M. Frank-Kamenetskii, and N.R. Cozzarelli Conformational and thermodynamic properties of supercoiled DNA J. Mol. Biol. 227 1992 1224 1243
32. M. Bussiek, K. Klenin, and J. Langowski Kinetics of site-site interactions in supercoiled DNA with bent sequences J. Mol. Biol. 322 2002 707 718
33. M. Hammermann, N. Brun, K.V. Klenin, R. May, K. Toth, and J. Langowski Salt-dependent DNA superhelix diameter studied by small angle neutron scattering measurements and Monte Carlo simulations Biophys. J. 75 1998 3057 3063
34. V.V. Rybenkov, A.V. Vologodskii, and N.R. Cozzarelli The effect of ionic conditions on the conformations of supercoiled DNA. 1. Sedimentation analysis J. Mol. Biol. 267 1997 299 311
35. J.F. Kepert, K.F. Toth, M. Caudron, N. Mucke, J. Langowski, and K. Rippe Conformation of reconstituted mononucleosomes and effect of linker histone H1 binding studied by scanning force microscopy Biophys. J. 85 2003 4012 4022
36. H. Wang, R. Bash, J.G. Yodh, G.L. Hager, D. Lohr, and S.M. Lindsay Glutaraldehyde modified mica: a new surface for atomic force microscopy of chromatin Biophys. J. 83 2002 3619 3625
37. H.G. Hansma Surface biology of DNA by atomic force microscopy Annu. Rev. Phys. Chem. 52 2001 71 92
38. M. Bussiek, N. Mucke, and J. Langowski Polylysine-coated mica can be used to observe systematic changes in the supercoiled DNA conformation by scanning force microscopy in solution Nucl. Acids Res. 31 2003 e137
39. C. Rivetti, M. Guthold, and C. Bustamante Scanning force microscopy of DNA deposited onto mica: equilibration versus kinetic trapping studied by statistical polymer chain analysis J. Mol. Biol. 264 1996 919 932
40. C. Pfannschmidt, and J. Langowski Superhelix organization by DNA curvature as measured through site-specific labeling J. Mol. Biol. 275 1998 601 611
41. K.V. Klenin, M.D. Frank-Kamenetskii, and J. Langowski Modulation of intramolecular interactions in superhelical DNA by curved sequences: a Monte Carlo simulation study Biophys. J. 68 1995 81 88
42. C.H. Laundon, and J.D. Griffith Curved helix segments can uniquely orient the topology of supertwisted DNA Cell 52 1988 545 549
43. J.G. Yodh, Y.L. Lyubchenko, L.S. Shlyakhtenko, N. Woodbury, and D. Lohr Evidence for nonrandom behavior in 208-12 subsaturated nucleosomal array populations analyzed by AFM Biochemistry 38 1999 15756 15763
44. Y.L. Lyubchenko, and L.S. Shlyakhtenko Visualization of supercoiled DNA with atomic force microscopy in situ Proc. Natl Acad. Sci. USA 94 1997 496 501
45. L.S. Shlyakhtenko, L. Miloseska, V.N. Potaman, R.R. Sinden, and Y.L. Lyubchenko Intersegmental interactions in supercoiled DNA: atomic force microscope study Ultramicroscopy 97 2003 263 270
46. K. Rippe, N. Mücke, and J. Langowski Superhelix dimensions of a 1868 base pair plasmid determined by scanning force microscopy in air and in aqueous solution Nucl. Acids Res. 25 1997 1736 1744
47. U. Kapp, and J. Langowski Preparation of DNA topoisomers by RP-18 high-performance liquid chromatography Anal. Biochem. 206 1992 293 299
48. K. Luger, T.J. Rechsteiner, and T.J. Richmond Expression and purification of recombinant histones and nucleosome reconstitution Methods Mol. Biol. 119 1999 1 16
49. D.V. Fyodorov, and J.T. Kadonaga Chromatin assembly in vitro with purified recombinant ACF and NAP-1 Methods Enzymol. 371 2003 499 515