Relative affinities of DNA sequences for the histone octamer depend strongly upon both the temperature and octamer concentration

Biochemistry

Volumn 44, Issue 43, 2005, Pages 14329-14334

  Wu, Chenyi ^a   Travers, Andrew ^a  

^a MRC LABORATORY OF MOLECULAR BIOLOGY   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

CHEMICAL BONDS; CONCENTRATION (PROCESS); STRUCTURE (COMPOSITION); SYNTHESIS (CHEMICAL); YEAST;

DNA DEFORMABILITY; HISTONE OCTAMER; NUCLEOSOME FORMATION; YEAST PROMOTERS;

DNA;

CURVED DNA; DNA; HISTONE; POLYMER;

ANISOTROPY; ARTICLE; BINDING AFFINITY; BINDING ASSAY; BINDING SITE; CONCENTRATION RESPONSE; CONFORMATIONAL TRANSITION; CONSENSUS SEQUENCE; CONTROLLED STUDY; DNA CONFORMATION; DNA SEQUENCE; FLUORESCENCE; NONHUMAN; NUCLEOSOME; PARAMETER; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN DNA BINDING; PROTEIN MODIFICATION; TECHNIQUE; TEMPERATURE DEPENDENCE; YEAST;

ANISOTROPY; BASE SEQUENCE; BINDING SITES; DNA; HISTONES; LIGANDS; MOLECULAR SEQUENCE DATA; NUCLEOSOMES; OLIGONUCLEOTIDES; TEMPERATURE;

EID: 27444439375     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi050915w     Document Type: Article

References (24)

1. Simpson, R. T., and Stafford, D.W. (1983) Structural features of a phased nucleosome core particle, Proc. Natl. Acad. Sci. U.S.A. 80, 51-55.
2. Aimer, A., and Hörz, W. (1986) Nuclease hypersensitive regions with adjacent positioned nucleosomes mark the gene boundaries of the PHO5/PHO3 locus in yeast, EMBO J. 5, 2681-2687.
3. Richard-Foy, H., and Hager, G. L. (1987) Sequence-specific positioning of nucleosomes over the steroid-inducible MMTV promoter, EMBO J. 6, 2321-2328.
4. Pifia, B., Bruggemeier, U., and Beato, M. (1990) Nucleosome positioning modulates accessibility of regulatory proteins to the mouse mammary tumor virus promoter, Cell 60, 719-731.
5. Verdone, L., Camilloni, G., Di Mauro, E., and Caserta, M. (1996) Chromatin remodeling during Saccharomyces cerevisiae ADH2 gene activation, Mol. Cell Biol. 16, 1978-1988.
6. Shrader, T. E., and Crothers, D. M. (1989) Artificial nucleosome positioning sequences, Proc. Natl. Acad. Sci. U.S.A. 86, 7418-7422.
7. Anderson, J. D., and Widom, J. (2000) Sequence and position-dependence of the equilibrium accessibility of nucleosomal DNA target sites, J. Mol. Biol. 296, 979-987.
8. Thastrom, A., Bingham, L. M., and Widom, J. (2004) Nucleosomal locations of dominant DNA sequence motifs for histone-DNA interactions and nucleosome positioning, J. Mol. Biol. 338, 695-709.
9. Tanaka, S., Zatchej, M., and Thoma, F. (1992) Artificial nucleosome positioning sequences tested in yeast minichromosomes: A strong rotational setting is not sufficient to position nucleosomes in vivo, EMBO J. 11, 1187-1193.
10. Wallrath, L. L., Lu, Q., Granok, H., and Elgin, S. C. R. (1994) Architectural variations of inducible eukaryotic promoters: Preset and remodeling chromatin structures, BiloEssays 16, 165-170.
11. Stein, A. (1979) DNA folding by histones: The kinetics of chromatin core particle reassembly and the interaction of nucleosomes with histones, J. Mol. Biol. 130, 103-134.
12. Ausio, J., Seger, D., and Eisenberg, H. (1984) Nucleosome core particle stability and conformational change. Effect of temperature, particle, and NaCl concentrations, and crosslinking of histone H3 sulfhydryl groups, J. Mol. Biol. 176, 77-104.
13. Gottesfeld, J. M., and Luger, K. (2001) Energetics and affinity of the histone octamer for defined DNA sequences, Biochemistry 40, 10927-10933.
14. Thåström, A., Gottesfeld, J. M., Luger, K., and Widom, J. (2004) Histone-DNA binding free energy cannot be measured in dilution-driven dissociation experiments, Biochemistry 43, 736-741.
15. Huynh, V. A., Robinson, P. J., and 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.
16. Barbaric, S., Fascher, K. D., and Hörz, W. (1992) Activation of the weakly regulated PHO8 promoter in S. cerevisiae: Chromatin transition and binding sites for the positive regulatory protein PHO4, Nucleic Acids Res. 20, 1031-1038.
17. Moreira, J. M., and Holmberg, S. (1998) Nucleosome structure of the yeast CHA1 promoter: Analysis of activation-dependent chromatin remodeling of an RNA-polymerase-II-transcribed gene in TBP and RNA pol II mutants defective in vivo in response to acidic activators, EMBO J. 17, 6028-6038.
18. Thåström, A., Lowary, P. T., Widlund, H. R., Cao, H, Kubista, M., and Widom, J. (1999) Sequence motifs and free energies of selected natural and non-natural nucleosome positioning DNA sequences. J. Mol. Biol. 288, 213-229.
19. Protozanova, E., Yakovchuk, P., and Frank-Kamenetskii, M. D. (2004) Stacked-unstacked equilibrium at the nick site of DNA, J. Mol. Biol. 342, 775-785.
20. Yan, J., and Marko, J. F. (2004) Localized single-stranded bubble mechanism for cyclization of short double helix DNA, Phys. Rev. Lett. 93, 108108.
21. Travers, A. (2005) DNA dynamics: Bubble 'n flip for DNA cyclization? Curr. Biol. 15, R377-R379.
22. Widlund, H. R., Cao, H., Simonsson, S., Magnusson, E., Simonsson, T., Nielsen, P. E., Kahn, J. D., Crothers, D. M., and Kubista, M. (1997) Identification and characterization of genomic nucleosome-positioning sequences, J. Mol. Biol. 267, 807-817.
23. Lowary, P. T., and Widom, J. (1998) New DNA sequence rules for high affinity binding to histone octamer and sequence-directed nucleosome positioning, J. Mol. Biol. 276, 19-42.
24. Satchwell, S. C., Drew, H. R., and Travers, A. A. (1986) Sequence periodicities in chicken nucleosome core DNA, J. Mol. Biol. 191, 659-675.