Nucleosomal locations of dominant DNA sequence motifs for histone-DNA interactions and nucleosome positioning

Journal of Molecular Biology

Volumn 338, Issue 4, 2004, Pages 695-709

  Thastrom A ^a   Bingham, L M ^a   Widom, J ^a  

^a NORTHWESTERN UNIVERSITY   (United States)

Author keywords

BZA, benzamidine hydrochloride; Chromatin; DNA; Free energy; Histone; PMSF, phenylmethyl sulfonyl fluoride

Indexed keywords

DNA; HISTONE; PALINDROMIC DNA;

ALGORITHM; ARTICLE; CALCULATION; DIALYSIS; DNA SEQUENCE; GENETIC DATABASE; NUCLEOSOME; PREDICTION; PRESSURE; PRIORITY JOURNAL; PROTEIN ASSEMBLY; PROTEIN DNA INTERACTION; PROTEIN MOTIF;

EID: 1942489758     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2004.03.032     Document Type: Article

References (34)

1. Lowary P.T., Widom J. Nucleosome packaging and nucleosome positioning of genomic DNA. Proc. Natl Acad. Sci. USA. 94:1997;1183-1188.
2. Simpson R.T. Nucleosome positioning: occurrence, mechanisms, and functional consequences. Prog. Nucl. Acid Res. Mol. Biol. 40:1991;143-183.
3. Lu Q., Wallrath L.L., Elgin S.C. Nucleosome positioning and gene regulation. J. Cell. Biochem. 55:1994;83-92.
4. Wolffe A.P. Nucleosome positioning and modification: chromatin structures that potentiate transcription. Trends Biochem. Sci. 19:1994;240-244.
5. Satchwell S.C., Drew H.R., Travers A.A. Sequence periodicities in chicken nucleosome core DNA. J. Mol. Biol. 191:1986;659-675.
6. Shrader T.E., Crothers D.M. Artificial nucleosome positioning sequences. Proc. Natl Acad. Sci. USA. 86:1989;7418-7422.
7. Widom J. Role of DNA sequence in nucleosome stability and dynamics. Quart. Rev. Biophys. 34:2001;269-324.
8. Richmond T.J., Davey C.A. The structure of DNA in the nucleosome core. Nature. 423:2003;145-150.
9. Shrader T.E., Crothers D.M. Effects of DNA sequence and histone-histone interactions on nucleosome placement. J. Mol. Biol. 216:1990;69-84.
10. Lowary P.T., Widom J. New DNA sequence rules for high affinity binding to histone octamer and sequence-directed nucleosome positioning. J. Mol. Biol. 276:1998;19-42.
11. Olson W.K., Gorin A.A., Lu X., 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.
12. FitzGerald P.C., Simpson R.T. Effects of sequence alterations in a DNA segment containing the 5 S RNA gene from Lytechinus variegatus on positioning of a nucleosome core particle in vitro. J. Biol. Chem. 260:1985;15318-15324.
13. 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.
14. Dong F., Hansen J.C., van Holde K.E. DNA and protein determinants of nucleosome positioning on sea urchin 5 S rRNA gene sequences in vitro. Proc. Natl Acad. Sci. USA. 87:1990;5724-5728.
15. Crothers D.M. DNA curvature and deformation in protein-DNA complexes: a step in the right direction. Proc. Natl Acad. Sci. USA. 95:1998;15163-15165.
16. Roychoudhury M., Sitlani A., Lapham J., Crothers D.M. Global structure and mechanical properties of a 10-bp nucleosome positioning motif. Proc. Natl Acad. Sci. USA. 97:2000;13608-13613.
17. Zhang Y., Crothers D.M. High-throughput approach for detection of DNA bending and flexibility based on cyclization. Proc. Natl Acad. Sci. USA. 100:2003;3161-3166.
18. Irvine D., Tuerk C., Gold L. SELEXION: systematic evolution of ligands by exponential enrichment with integrated optimization by non-linear analysis. J. Mol. Biol. 222:1991;739-761.
19. Dorigo B., Schalch T., Bystricky K., Richmond T.J. Chromatin fiber folding: requirement for the histone H4 N-terminal tail. J. Mol. Biol. 327:2003;85-96.
20. Anderson J.D., Widom J. Sequence- and position-dependence of the equilibrium accessibility of nucleosomal DNA target sites. J. Mol. Biol. 296:2000;979-987.
21. Anderson J.D., Thåström A., Widom J. Spontaneous access of proteins to buried nucleosomal DNA target sites occurs via a mechanism that is distinct from nucleosome translocation. Mol. Cell. Biol. 22:2002;7147-7157.
22. Thåström A., Lowary P.T., Widom J. Measurement of histone-DNA interaction free energy in nucleosomes. Methods. 33:2003;33-44.
23. Thåström A., Lowary P.T., Widlund H.R., Cao H., Kubista M., Widom J. Sequence motifs and free energies of selected natural and non-natural nucleosome positioning DNA sequences. J. Mol. Biol. 288:1999;213-229.
24. Luger K., Mader A.W., Richmond R.K., Sargent D.F., Richmond T.J. Structure of the nucleosome core particle at 2.8 Å resolution. Nature. 389:1997;251-260.
25. Thompson J.D., Higgins D.G., Gibson T.J. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucl. Acids Res. 22:1994;4673-4680.
26. Fitzgerald D.J., Anderson J.N. DNA distortion as a factor in nucleosome positioning. J. Mol. Biol. 293:1999;477-491.
27. Ioshikhes I., Bolshoy A., Derenshteyn K., Borodovsky M., Trifonov E.N. Nucleosome DNA sequence pattern revealed by multiple alignment of experimentally mapped sequences. J. Mol. Biol. 262:1996;129-139.
28. van Holde K.E. Chromatin. 1989;Springer-Verlag, New York.
29. Polach K.J., Widom J. Mechanism of protein access to specific DNA sequences in chromatin: a dynamic equilibrium model for gene regulation. J. Mol. Biol. 254:1995;130-149.
30. Polach K.J., Widom J. A model for the cooperative binding of eukaryotic regulatory proteins to nucleosomal target sites. J. Mol. Biol. 258:1996;800-812.
31. Widom J. Structure, dynamics, and function of chromatin in vitro. Annu. Rev. Biophys. Biomol. Struct. Dynam. 27:1998;285-327.
32. Luger K., Rechsteiner T.J., Flaus A.J., Waye M.M.Y., Richmond T.J. Characterization of nucleosome core particles containing histone proteins made in bacteria. J. Mol. Biol. 272:1997;301-311.
33. Feng H.-P., Scherl D.S., Widom J. Lifetime of the histone octamer studied by continuous-flow quasielastic light scattering: test of a model for nucleosome transcription. Biochemistry. 32:1993;7824-7831.
34. Widom J. Physicochemical studies of the folding of the 100 Å nucleosome filament into the 300 Å filament. J. Mol. Biol. 190:1986;411-424.