Chromatin remodeling through directional DNA translocation from an internal nucleosomal site

Nature Structural and Molecular Biology

Volumn 12, Issue 9, 2005, Pages 747-755

  Saha, Anjanabha ^a   Wittmeyer, Jacqueline ^a   Cairns, Bradley R ^a  

^a UNIVERSITY OF UTAH SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ADENOSINE TRIPHOSPHATE; CARRIER PROTEIN; DEOXYRIBONUCLEASE I; DNA; DOUBLE STRANDED DNA; HISTONE; PROTEIN RSC; UNCLASSIFIED DRUG; TRANSCRIPTION FACTOR;

ARTICLE; CHROMATIN ASSEMBLY AND DISASSEMBLY; CONTROLLED STUDY; DNA METABOLISM; NONHUMAN; NUCLEOSOME; POLARIZATION; PRIORITY JOURNAL; PROTEIN DNA BINDING; PROTEIN FUNCTION; PROTEIN PROTEIN INTERACTION; PROTEIN TRANSPORT; XENOPUS LAEVIS; ANIMAL; CHEMISTRY; GENETICS; METABOLISM; TRANSPORT AT THE CELLULAR LEVEL;

XENOPUS LAEVIS;

ANIMALS; BIOLOGICAL TRANSPORT; CHROMATIN ASSEMBLY AND DISASSEMBLY; DEOXYRIBONUCLEASE I; DNA; NUCLEOSOMES; TRANSCRIPTION FACTORS; XENOPUS LAEVIS;

EID: 26944461283     PISSN: 15459993     EISSN: 15459985     Source Type: Journal    
DOI: 10.1038/nsmb973     Document Type: Article

References (41)

1. Almer, A., Rudolph, H., Hinnen, A. & Horz, W. Removal of positioned nucleosomes from the yeast PHO5 promoter upon PHO5 induction releases additional upstream activating DNA elements. EMBO J. 5, 2689-2696 (1986).
2. Boeger, H., Griesenbeck, J., Strattan, J.S. & Kornberg, R.D. Nucleosomes unfold completely at a transcriptionally active promoter. Mol. Cell 11, 1587-1598 (2003).
3. Phelan, M.L., Sif, S., Narlikar, G.J. & Kingston, R.E. Reconstitution of a core chromatin remodeling complex from SWI/SNF subunits. Mol. Cell 3, 247-253 (1999).
4. Corona, D.F. et al. ISWI is an ATP-dependent nucleosome remodeling factor. Mol. Cell 3, 239-245 (1999).
5. Tran, H.G., Steger, D.J., Iyer, V.R. & Johnson, A.D. The chromo domain protein chdlp from budding yeast is an ATP-dependent chromatin-modifying factor. EMBO J. 19, 2323-2331 (2000).
6. Boyer, L.A. et al. Functional delineation of three groups of the ATP-dependent family of chromatin remodeling enzymes. J. Biol. Chem. 275, 18864-18870 (2000).
7. Cairns, B.R. et al. RSC, an essential, abundant chromatin-remodeling complex. Cell 87, 1249-1260 (1996).
8. Laurent, B.C., Yang, X. & Carlson, M. An essential Saccharomyces cerevisiae gene homologous to SNF2 encodes a helicase-related protein in a new family. Mol. Cell. Biol. 12, 1893-1902 (1992).
9. Peterson, C.L., Zhao, Y. & Chait, B.T. Subunits of the yeast SWI/SNF complex are members of the actin-related protein (ARP) family. J. Biol. Chem. 273, 23641-23644 (1998).
10. Wang, W. et al. Diversity and specialization of mammalian SWI/SNF complexes. Genes Dev. 10, 2117-2130 (1996).
11. Imbalzano, A.N., Kwon, H., Green, M.R. & Kingston, R.E. Facilitated binding of TATA-binding protein to nucleosomal DNA. Nature 370, 481-485 (1994).
12. Saha, A., Wittmeyer, J. & Cairns, B.R. Chromatin remodeling by RSC involves ATP-dependent DNA translocation. Genes Dev. 16, 2120-2134 (2002).
13. Flaus, A. & Owen-Hughes, T. Mechanisms for nucleosome mobilization. Biopolymers 68, 563-578 (2003).
14. Whitehouse, I., Stockdale, C., Flaus, A., Szczelkun, M.D. & Owen-Hughes, T. Evidence for DNA translocation by the ISWI chromatin-remodeling enzyme. Mol. Cell. Biol. 23, 1935-1945 (2003).
15. Whitehouse, I. et al. Nucleosome mobilization catalysed by the yeast SWI/SNF complex. Nature 400, 784-787 (1999).
16. Langst, G., Bonte, E.J., Corona, D.F. & Becker, P.B. Nucleosome movement by CHRAC and ISWI without disruption or trans-displacement of the histone octamer. Cell 97, 843-852 (1999).
17. Hamiche, A., Sandaltzopoulos, R., Gdula, D.A. & Wu, C. ATP-dependent histone octamer sliding mediated by the chromatin remodeling complex NURF. Cell 97, 833-842 (1999).
18. Fyodorov, D.V. & Kadonaga, J.T. Dynamics of ATP-dependent chromatin assembly by ACF. Nature 418, 897-900 (2002).
19. Havas, K. et al. Generation of superhelical torsion by ATP-dependent chromatin remodel ing activities. Cell 103, 1133-1142 (2000).
20. Langst, G. & Becker, P.B. ISWI induces nucleosome sliding on nicked DNA. Mol. Cell 8, 1085-1092 (2001).
21. Lorch, Y., Zhang, M. & Kornberg, R.D. RSC unravels the nucleosome. Mol. Cell 7, 89-95 (2001).
22. Kassabov, S.R., Zhang, B., Persinger, J. & Bartholomew, B. SWI/SNF unwraps, slides, and rewraps the nucleosome. Mol. Cell 11, 391-403 (2003).
23. Narlikar, G.J., Phelan, M.L. & Kingston, R.E. Generation and interconversion of multiple distinct nucleosomal states as a mechanism for catalyzing chromatin fluidity. Mol. Cell 8, 1219-1230 (2001).
24. Asturias, F.J., Chung, W.H., Kornberg, R.D. & Lorch, Y. Structural analysis of the RSC chromatin-remodeling complex. Proc. Natl. Acad. Sci. USA 99, 13477-13480 (2002).
25. Leschziner, A.E., Lemon, B., Tjian, R. & Nogales, E. Structural studies of the human PBAF chromatin-remodeling complex. Structure (Camb.) 13, 267-275 (2005).
26. 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, 19-42 (1998).
27. 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, 130-149 (1995).
28. Anderson, J.D., Thastrom, 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, 7147-7157 (2002).
29. Lorch, Y., Cairns, B.R., Zhang, M. & Kornberg, R.D. Activated RSC-nucleosome complex and persistently altered form of the nucleosome. Cell 94, 29-34 (1998).
30. Fan, H.Y., He, X., Kingston, R.E. & Narlikar, G.J. Distinct strategies to make nucleosomal DNA accessible. Mol. Cell 11, 1311-1322 (2003).
31. Li, G. & Widom, J. Nucleosomes facilitate their own invasion. Nat. Struct. Mol. Biol. 11, 763-769 (2004).
32. Jaskelioff, M., Van Komen, S., Krebs, J.E., Sung, P. & Peterson, C.L. Rad54p is a chromatin remodeling enzyme required for heteroduplex DNA joint formation with chromatin. J. Biol. Chem. 278, 9212-9218 (2003).
33. Schwanbeck, R., Xiao, H. & Wu, C. Spatial contacts and nucleosome step movements induced by the NURF chromatin remodeling complex. J. Biol. Chem. 279, 39933-39941 (2004).
34. Kagalwala, M.N., Glaus, B.J., Dang, W., Zofall, M. & Bartholomew, B. Topography of the ISW2-nucleosome complex: insights into nucleosome spacing and chromatin remodeling. EMBO J. 23, 2092-2104 (2004).
35. Flaus, A. & Owen-Hughes, T. Dynamic properties of nucleosomes during thermal and ATP-driven mobilization. Mol. Cell. Biol. 23, 7767-7779 (2003).
36. Lorch, Y., Davis, B. & Kornberg, R.D. Chromatin remodeling by DNA bending, not twisting. Proc. Natl. Acad. Sci. USA 102, 1329-1332 (2005).
37. Velankar, S.S., Soultanas, P., Dillingham, M.S., Subramanya, H.S. & Wigley, D.B. Crystal structures of complexes of PcrA DNA helicase with a DNA substrate indicate an inchworm mechanism. Cell 97, 75-84 (1999).
38. Soultanas, P., Dillingham, M.S., Wiley, P., Webb, M.R. & Wigley, D.B. Uncoupling DNA translocation and helicase activity in PcrA: direct evidence for an active mechanism. EMBO J. 19, 3799-3810 (2000).
39. Durr, H., Korner, C., Muller, M., Hickmann, V. & Hopfner, K.P. X-ray structures of the Sulfolobus solfataricus SWI2/SNF2 ATPase core and its complex with DNA. Cell 121, 363-373 (2005).
40. Thoma, N.H. et al. Structure of the SWI2/SNF2 chromatin-remodeling domain of eukaryotic Rad54. Nat. Struct. Mol. Biol. 12, 350-356 (2005).
41. Wittmeyer, J., Saha, A. & Cairns, B. DNA translocation and nucleosome remodeling assays by the RSC chromatin remodeling complex. Methods Enzymol. 377, 322-343 (2004).