Nucleosome dynamics IV. Protein and DNA contributions in the chiral transition of the tetrasome, the histone (H3-H4)2 tetramer-DNA particle

Journal of Molecular Biology

Volumn 291, Issue 4, 1999, Pages 815-841

  Alilat, Mohamed ^a   Sivolob, Andrei ^a   Révet, Bernard ^b   Prunell, Ariel ^a  

^a INSTITUT JACQUES MONOD   (France)

^b INSTITUT GUSTAVE ROUSSY   (France)

Author keywords

DNA minicircles; DNA supercoiling; Electron microscopy; H3 thiol oxidation; Tetrasome positioning

Indexed keywords

5,5' DITHIOBIS(2 NITROBENZOIC ACID); DNA TOPOISOMERASE; THIOL DERIVATIVE; DNA; HISTONE; HYDROXYL RADICAL; THIOL REAGENT;

ARTICLE; CHIRALITY; CONTROLLED STUDY; COVALENT BOND; DNA CONFORMATION; DNA HISTONE INTERACTION; DNA SUPERCOILING; ELECTRON MICROSCOPY; GEL ELECTROPHORESIS; NUCLEOSOME; PRIORITY JOURNAL; PROTEIN DNA INTERACTION; ANIMAL; CHEMISTRY; CONFORMATION; DIMERIZATION; ELECTROPHORESIS; GENETICS; IN VITRO STUDY; MACROMOLECULE; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PROTEIN CONFORMATION; THERMODYNAMICS; ULTRASTRUCTURE;

ANIMALS; BASE SEQUENCE; DIMERIZATION; DITHIONITROBENZOIC ACID; DNA; ELECTROPHORESIS; HISTONES; HYDROXYL RADICAL; MACROMOLECULAR SUBSTANCES; MICROSCOPY, ELECTRON; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; NUCLEOSOMES; PROTEIN CONFORMATION; SULFHYDRYL REAGENTS; THERMODYNAMICS;

EID: 0033609566     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1999.2988     Document Type: Article

References (63)

1. Arents G., Burlingame R. W., Wang B. C., Love W. E., Moudrianakis E. N. The nucleosomal core histone octamer at 3. 1 A resolution: a tripartite protein assembly and a left-handed superhelix. Proc. Natl Acad. Sci. USA. 88:1991;10148-10152.
2. 2tetramer: dependence on ionic environment. Biochemistry. 30:1991;8817-8823.
3. Cairns B. R. Chromatin remodeling machines: similar motors, ulterior motives. Trends Biochem. Sci. 23:1998;20-25.
4. Côté J., Peterson C. L., Workman J. L. Perturbation of nucleosome core structure by the SWI/SNF complex persists after its detachment, enhancing subsequent transcription factor binding. Proc. Natl Acad. Sci. USA. 95:1998;4947-4952.
5. Daban J. R., Cantor C. R. Role of histone pairs H2A,H2B and H3,H4 in the self-assembly of nucleosome core particles. J. Mol. Biol. 156:1982;771-789.
6. De Lucia F., Alilat M., Sivolob A., 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.
7. Dixon W. J., Hayes J. J., Levin J. R., Weidner M. F., Dombroski B. A., Tullius T. D. Hydroxyl radical footprinting. Methods Enzymol. 208:1991;380-413.
8. 2tetramer. Proc. Natl Acad. Sci. USA. 88:1991;10596-10600.
9. Dong F., Hansen J. C., van Holde K. E. DNA and protein determinants of nucleosome positioning on sea urchin 5S rRNA gene sequences in vitro. Proc. Natl Acad. Sci. USA. 87:1990;5724-5728.
10. Eickbush T. H., Moudrianakis E. N. The histone core complex: an octamer assembled by two sets of protein-protein interactions. Biochemistry. 17:1978;4955-4964.
11. Feinstein D. L., Moudrianakis E. N. Thiol reactivity of histone H3 in soluble and DNA-associated histone complexes: evidence for allosteric and torsional regulation. Biochemistry. 25:1986;8409-8418.
12. Flaus A., Luger K., Tan S., 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.
13. Gorin A. A., Zhurkin V. B., Olson W. K. B -DNA twisting correlates with base-pair morphology. J. Mol. Biol. 247:1995;34-48.
14. Goulet I. Y., Zivanovic Y., Prunell A. Helical repeat of DNA in solution. The V curve method. Nucl. Acids Res. 15:1987;2803-2821.
15. Goulet I., Zivanovic Y., Prunell A., Révet B. Chromatin reconstitution on small DNA rings. I. J. Mol. Biol. 200:1988;253-266.
16. Habeeb A. F. S. A. Reaction of protein sulfhydryl groups with Ellman's reagent. Methods Enzymol. 25:1972;457-464.
17. 2tetramer within a nucleoprotein particle requires a reorientation of the H3-H3 interface. J. Biol. Chem. 273:1998;9261-9269.
18. 2tetramer 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.
19. Hassig C. A., Schreiber S. L. Nuclear histone acetylases and deacetylases and transcriptiuonal regulation: HATs off to HDACs. Curr. Opin. Chem. Biol. 1:1997;300-308.
20. Hayes J. J., Tullius T. D., Wolffe A. P. The structure of DNA in a nucleosome. Proc. Natl Acad. Sci. USA. 87:1990;7405-7409.
21. Hayes J. J., Clark D. J., Wolffe A. P. Histone contributions to the structure of DNA in the nucleosome. Proc. Natl Acad. Sci. USA. 88:1991;6829-6833.
22. Hirschhorn J. N., Brown S. A., Clark C. D., Winston F. Evidence that SNF2/SWI2 and SNF5 activate transcription in yeast by altering chromatin structure. Genes Dev. 6:1992;2288-2298.
23. Horowitz D. S., Wang J. C. Torsional rigidity of DNA and length dependence of the free energy of DNA supercoiling. J. Mol. Biol. 173:1984;75-91.
24. Jackson S., Brooks W., Jackson V. Dynamics of the interactions of histones H2A,H2B and H3,H4 with torsionally stressed DNA. Biochemistry. 33:1994;5392-5403.
25. 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.
26. Jackson V. Preferential binding of histones H3 and H4 to highly positively coiled DNA. Biochemistry. 34:1995;10607-10619.
27. Kosower E. M., Kosower N. S. Bromobimane probes for thiols. Methods Enzymol. 251:1995;133-148.
28. Kruger W., Peterson C. L., Sil A., Coburn C., Arents G., Moudrianakis E. N., Herskowitz I. Amino acid substitutions in the structured domains of histones H3 and H4 partially relieve the requirement of the yeast SWI/SNF complex for transcription. Genes Dev. 9:1995;2770-2779.
29. Kurumizaka H., Wolffe A. P. Sin mutations of histone H3: influence on nucleosome core structure and function. Mol. Cell. Biol. 17:1997;6953-6969.
30. Liu L. F., Wang J. C. Supercoiling of the DNA template during transcription. Proc. Natl Acad. Sci. USA. 84:1987;7024-7027.
31. Louters L., Chalkley R. Exchange of histones H1, H2A, and H2B in vivo. Biochemistry. 24:1985;3080-3085.
32. Luger K., Richmond T. J. The histone tails of the nucleosome. Curr. Opin. Genet. Dev. 8:1998;140-146.
33. Luger K., Mäder A. W., Richmond R. K., Sargent D. F., Richmond T. J. Crystal structure of the nucleosome core particle at 2.8 Å resolution. Nature. 389:1997;251-260.
34. Lutter L. C. Kinetic analysis of deoxyribonuclease I cleavages in the nucleosome core: evidence for a DNA superhelix. J. Mol. Biol. 124:1978;391-420.
35. Maxam A. M., Gilbert W. Sequencing end-labeled DNA with base-specific chemical cleavages. Methods Enzymol. 65:1980;499-560.
36. Meersseman G., Pennings S., Bradbury E. M. Mobile nucleosomes - a general behavior. EMBO J. 11:1992;2951-2959.
37. Norton V. G., Imai B. S., Yau P., Bradbury E. M. Histone acetylation reduces nucleosome core particle linking number change. Cell. 57:1989;449-457.
38. Olson W. K., Gorin A. A., Lu X. J., Hock L. M., Zhurkin V. B. DNA sequence-dependent deformability deduced from protein-DNA crystal complexes. Proc. Natl Acad. Sci. USA. 95:1998;11163-11168.
39. Pennings S., Meersseman G., Bradbury E. M. Mobility of positioned nucleosomes on 5 S rDNA. J. Mol. Biol. 220:1991;101-110.
40. Pollard K. J., Peterson C. L. Chromatin remodelling: a marriage between two families? BioEssays. 20:1998;771-780.
41. Prunell A. Nucleosome reconstitution on plasmid-inserted poly(dA).poly(dT). EMBO J. 1:1982;173-179.
42. Prunell A. A topological approach to nucleosome structure and dynamics. The linking number paradox and other issues. Biophys. J. 74:1998;2531-2544.
43. Prunell A., Alilat M., De Lucia F. Nucleosome structure and dynamics: the DNA minicircle approach. Becker P. Chromatin protocols. Methods in Molecular Biology. 1999;Humana Press.
44. Puhl H. L., Gudibande S. R., Behe M. J. Poly[d(A. T)] and other synthetic polydeoxynucleotides containing oligoadenosine tracts form nucleosomes easily. J. Mol. Biol. 222:1991;1149-1160.
45. Quinn J., Fyrberg A. M., Ganster R. W., Schmidt M. C., Peterson C. L. DNA-binding properties of the yeast SWI/SNF complex. Nature. 379:1996;844-847.
46. Read C. M., Crane-Robinson C. The structure of sub-nucleosomal particles. The octameric (H3/H4)4-125-base-pair-DNA complex. Eur. J. Biochem. 152:1985;143-150.
47. Riordan J. F., Vallee B. L. Reactions with N-ethylmaleimide and p-mercuribenzoate. Methods Enzymol. 25:1972;449-456.
48. Ruiz-Carrillo A., Jorcano J. L. Nucleohistone assembly: sequential binding of histone H3-H4 tetramer and histone H2A-H2B dimer to DNA. Cold Spring Harbor Symp. Quant. Biol. 42:1978;165-170.
49. Schwager S., Retief J. D., de Groot P., von Holt C. Rapid exchange of histones H2A and H2B in sea urchin embryo chromatin. FEBS Letters. 189:1985;305-309.
50. Simpson R. T., Stafford D. W. Structural features of a phased nucleosome core particle. Proc. Natl Acad. Sci. USA. 80:1983;51-55.
51. Simpson R. T., Thoma F., Brubaker J. M. 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.
52. Sivolob A., De Lucia F., Révet B., Prunell A. Nucleosome dynamics II. High flexibility of nucleosome entering and exiting DNAs to positive crossing. An ethidium bromide fluorescence study of mononucleosomes on DNA minicircles. J. Mol. Biol. 285:1999;1081-1099.
53. Spangenberg C., Eisfeld K., Stunkel W., Luger K., Flaus A., Richmond T. J., Truss M., Beato M. The mouse mammary tumor virus promoter positioned on a tetramer of histones H3 and H4 binds nuclear factor 1 and OTF1. J. Mol. Biol. 278:1998;725-739.
54. Varga-Weisz P. D., Becker P. B. Chromatin-remodeling factors: machines that regulate? Curr. Opin. Cell. Biol. 10:1998;346-353.
55. Wang J. C., Peck L. J., Becherer K. DNA supercoiling and its effects on DNA structure and function. Cold Spring Harbor Symp. Quant. Biol. 47:1982;85-91.
56. Wechser M. A., Kladde M. P., Alfieri J. A., Peterson C. L. Effects of Sin- versions of histone H4 on yeast chromatin structure and function. EMBO J. 16:1997;2086-2095.
57. Wilhelm F. X., Wilhelm M. L., Erard M., Daune M. P. Reconstitution of chromatin: assembly of the nucleosome. Nucl. Acids Res. 5:1978;505-521.
58. Workman J. L., Kingston R. E. Alteration of nucleosome structure as a mechanism of transcriptional regulation. Annu. Rev. Biochem. 67:1998;545-579.
59. Wu H. M., Crothers D. M. The locus of sequence-directed and protein-induced DNA bending. Nature. 308:1984;509-513.
60. Zhang P., Tobias I., Olson W. K. Computer simulation of protein-induced structural changes in closed circular DNA. J. Mol. Biol. 242:1994;271-290.
61. Zivanovic Y., Goulet I., Prunell A. Properties of supercoiled DNA in gel electrophoresis. The V-like dependence of mobility on topological constraint. DNA-matrix interactions. J. Mol. Biol. 192:1986;645-660.
62. Zivanovic Y., Goulet I., Révet B., Le Bret M., Prunell A. Chromatin reconstitution on small DNA rings. II. DNA supercoiling on the nucleosome. J. Mol. Biol. 200:1988;267-290.
63. Zivanovic Y., Duband-Goulet I., Schultz P., Stofer E., Oudet P., Prunell A. Chromatin reconstitution on small DNA rings. III. Histone H5 dependence of DNA supercoiling in the nucleosome. J. Mol. Biol. 214:1990;479-495.