Spontaneous access of proteins to buried nucleosomal DNA target sites occurs via a mechanism that is distinct from nucleosome translocation

Molecular and Cellular Biology

Volumn 22, Issue 20, 2002, Pages 7147-7157

  Anderson, J D ^a   Thastrom A ^a   Widom, J ^a  

^a NORTHWESTERN UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ADENOSINE TRIPHOSPHATE; DNA; HISTONE; PROTEIN; RESTRICTION ENDONUCLEASE; RIBOSOME RNA; RNA POLYMERASE; TRANSCRIPTION FACTOR;

ARTICLE; CONFORMATIONAL TRANSITION; ELECTROPHORETIC MOBILITY; GENE; GENE TARGETING; GENE TRANSLOCATION; NUCLEOSOME; PRIORITY JOURNAL;

ANIMALS; BIOLOGICAL TRANSPORT; CHICKENS; DNA; DNA, RIBOSOMAL; ELECTROPHORESIS, POLYACRYLAMIDE GEL; ELECTROPHORETIC MOBILITY SHIFT ASSAY; MICE; NUCLEOSOMES; PROTEINS; RNA, RIBOSOMAL, 5S; TEMPLATES, GENETIC;

EID: 0036786970     PISSN: 02707306     EISSN: None     Source Type: Journal    
DOI: 10.1128/MCB.22.20.7147-7157.2002     Document Type: Article

References (50)

1. Anderson, J. D., P. T. Lowary, and J. Widom. 2001. Effects of histone acetylation on the dynamic equilibrium accessibility of nucleosomal DNA target sites. J. Mol. Biol. 307:977-985.
2. Anderson, J. D., and J. Widom. 2001. Poly(dA-dT) promoter elements increase the equilibrium accessibility of nucleosomal DNA target sites. Mol. Cell. Biol. 21:3830-3839.
3. Anderson, J. D., and J. Widom. 2000. Sequence- and position-dependence of the equilibrium accessibility of nucleosomal DNA target sites. J. Mol. Biol. 296:979-987.
4. Astumian, R. D., and M. Bier. 1994. Fluctuation driven ratchets: molecular motors. Phys. Rev. Lett. 72:1766-1769.
5. Bednar, J., V. M. Studitsky, S. A. Grigoryev, G. Felsenfeld, and C. L. Woodcock. 1999. The nature of the nucleosomal barrier to transcription: direct observation of paused intermediates by electron cryomicroscopy. Mol. Cell 4:377-386.
6. Cosma, M. P., T. Tanaka, and K. Nasmyth. 1999. Ordered recruitment of transcription and chromatin remodeling factors to a cell cycle- and developmentally regulated promoter. Cell 97:299-311.
7. Dong, F., J. C. Hansen, and K. E. van Holde. 1990. DNA and protein determinants of nucleosome positioning on sea urchin 5S rRNA gene sequences in vitro. Proc. Natl. Acad. Sci. USA 87:5724-5728.
8. Felsenfeld, G. 1996. Chromatin unfolds. Cell 86:13-19.
9. Feynman, R. P., R. B. Leighton, and M. Sands. 1963. The Feynman lectures on Physics, vol. I. Addison-Wesley, Reading, Mass.
10. FitzGerald, P. C., and R. T. Simpson. 1985. Effects of sequence alterations in a DNA segment containing the 5S RNA gene from Lytechinus variegatus on positioning of a nucleosome core particle in vitro. J. Biol. Chem. 260: 15318-15324.
11. Fragoso, G., S. John, M. S. Roberts, and G. L. Hager. 1995. Nucleosome positioning on the MMTV LTR results from the frequency-biased occupancy of multiple frames. Genes Dev. 9:1933-1947.
12. Goldmark, J. P., T. G. Fazzio, P. W. Estep, G. M. Church, and T. Tsukiyima. 2000. The Isw2 chromatin remodeling complex represses early meiotic genes upon recruitment by Ume6p. Cell 103:423-433.
13. Iyer, V., and K. Struhl. 1995. Poly(dA:dT), a ubiquitous promoter element that stimulates transcription via its intrinsic DNA structure. EMBO J. 14: 2570-2579.
14. Kingston, R. E., and G. J. Narlikar. 1999. ATP-dependent remodeling and acetylation as regulators of chromatin fluidity. Genes Dev. 13:2339-2352.
15. Langst, G., E. J. Bonte, D. F. V. Corona, and P. B. Becker. 1999. Nucleosome movement by CHRAC and ISWI without disruption or trans-displacement of the histone octamer. Cell 97:843-852.
16. Lorch, Y., J. W. LaPointe, and R. D. Kornberg. 1987. Nucleosomes inhibit the initiation of transcription but allow chain elongation with the displacement of histones. Cell 49:203-210.
17. Lowary, P. T., and J. Widom. 1998. New DNA sequence rules for high affinity binding to histone octamer and sequence-directed nucleosome positioning. J. Mol. Biol. 276:19-42.
18. Lowary, P. T., and J. Widom. 1997. Nucleosome packaging and nucleosome positioning of genomic DNA. Proc. Natl. Acad. Sci. USA 94:1183-1188.
19. Luger, K., A. W. Mader, R. K. Richmond, D. F. Sargent, and T. J. Richmond. 1997. Structure of the nucleosome core particle at 2.8 Å resolution. Nature 389:251-260.
20. Luger, K., T. J. Rechsteiner, A. J. Flaus, M. M. Y. Waye, and T. J. Richmond. 1997. Characterization of nucleosome core particles containing histone proteins made in bacteria. J. Mol. Biol. 272:301-311.
21. Meersseman, G., S. Pennings, and E. M. Bradbury. 1992. Mobile nucleosomes-a general behavior. EMBO J. 11:2951-2959.
22. Owen-Hughes, T., R. T. Utley, J. Cote, C. L. Peterson, and J. L. Workman. 1996. Persistent site-specific remodeling of a nucleosome array by transient action of the SWI/SNF complex. Science 273:513-516.
23. Owen-Hughes, T., and J. L. Workman. 1996. Remodeling the chromatin structure of a nucleosome array by transcription factor-targeted trans-displacement of histones. EMBO J 15:4702-4712.
24. Pennings, S., G. Meersseman, and M. E. Bradbury. 1991. Mobility of positioned nucleosomes on 5S rDNA. J. Mol. Biol. 220:101-110.
25. Peterson, C. L., and C. Logie. 2000. Recruitment of chromatin remodeling machines. J. Cell. Biochem. 78:179-185.
26. Peterson, C. L., and J. L. Workman. 2000. Promoter targeting and chromatin remodeling by the SWI/SNF complex. Curr. Opin. Genet. Dev. 10:187-192.
27. Polach, K. J., P. T. Lowary, and J. Widom. 2000. Effects of core histone tail domains on the equilibrium constants for dynamic DNA site accessibility in nucleosomes. J. Mol. Biol. 298:211-223.
28. Polach, K. J., and J. Widom. 1995. Mechanism of protein access to specific DNA sequences in chromatin: a dynamic equilibrium model for gene regulation. J. Mol. Biol. 254:130-149.
29. Polach, K. J., and J. Widom. 1996. A model for the cooperative binding of eukaryotic regulatory proteins to nucleosomal target sites. J. Mol. Biol. 258:800-812.
30. Polach, K. J., and J. Widom. 1999. Restriction enzymes as probes of nucleosome stability. Methods Enzymol. 304:278-298.
31. Protacio, R. U., K. J. Polach, and J. Widom. 1997. Coupled enzymatic assays for the rate and mechanism of DNA site-exposure in a nucleosome. J. Mol. Biol. 274:708-721.
32. Richmond, T. J., and J. Widom. 2000. Nucleosome and chromatin structure. In S. Elgin and J. L. Workman (ed.), Chromatin structure and gene expression: frontiers in molecular biology 2/e. Oxford University Press, Oxford, United Kingdom.
33. Schiessel, H., J. Widom, R. F. Bruinsma, and W. M. Gelbart. 2001. Polymer reptation and nucleosome repositioning. Phys. Rev. Lett. 86:4414-4417.
34. Shrader, T. E., and D. M. Crothers. 1989. Artificial nucleosome positioning sequences. Proc. Natl. Acad. Sci. USA 86:7418-7422.
35. Shrader, T. E., and D. M. Crothers. 1990. Effects of DNA sequence and histone-histone interactions on nucleosome placement. J. Mol. Biol. 216:69-84.
36. Simpson, R. T., S. Y. Roth, R. H. Morse, H.-G. Patterton, J. P. Cooper, M. Murphy, M. P. Kladde, and M. Shimizu. 1993. Nucleosome positioning and transcription. Cold Spring Harbor Symp. Quant. Biol. 58:237-245.
37. Simpson, R. T., and D. W. Stafford. 1983. Structural features of a phased nucleosome core particle. Proc. Natl. Acad. Sci. USA 80:51-55.
38. Simpson, R. T., F. Thoma, and J. M. Brubaker. 1985. Chromatin reconstituted from tandemly repeated cloned DNA fragments and core histones: a model system for study of higher order structure. Cell 42:799-808.
39. Studitsky, V. M., G. A. Kassavetis, E. P. Geiduschek, and G. Felsenfeld. 1997. Mechanism of transcription through the nucleosome by eukaryotic RNA polymerase, Science 278:1960-1963.
40. Svaren, J., and W. Horz. 1997. Transcription factors vs nucleosomes: regulation of the PHO5 promoter in yeast. Trends Biochem. Sci. 22:93-97.
41. Thåström, A., P. T. Lowary, H. R. Widlund, H. Cao, M. Kubista, and J. Widom. 1999. Sequence motifs and free energies of selected natural and non-natural nucleosome positioning DNA sequences. J. Mol. Biol. 288:213-229.
42. Travers, A. 1999. An engine for nucleosome remodeling. Cell 96:311-314.
43. Ura, K., J. J. Hayes, and A. P. Wolffe. 1995. A positive role for nucleosome mobility in the transcriptional activity of chromatin templates: restriction by linker histones. EMBO J. 14:3752-3765.
44. van Holde, K. E. 1989. Chromatin. Springer-Verlag, New York, N.Y.
45. Varga-Weisz, P. D., and P. B. Becker. 1998. Chromatin-remodeling factors: machines that regulate? Curr. Biol. 10:346-353.
46. Widom, J. 1999. Equilibrium and dynamic nucleosome stability. Methods Mol. Biol. 119:61-77.
47. Widom, J. 1998. Structure, dynamics, and function of chromatin in vitro. Annu. Rev. Biophys. Biomol. Struct. 27:285-327.
48. Widom, J. 1997. Transcription through nucleosomes. Science 278:1899-1901.
49. Workman, J. L., and R. E. Kingston. 1998. Alteration of nucleosome structure as a mechanism of transcriptional regulation. Annu. Rev. Biochem. 67:545-579.
50. Zhu, Z., and D. J. Thiele. 1996. A specialized nucleosome modulates transcription factor access to a C. glabrata metal responsive promoter. Cell 87:459-470.