Structure of a RSC–nucleosome complex and insights into chromatin remodeling (original) (raw)

• Boeger, H., Griesenbeck, J., Strattan, J.S. & Kornberg, R.D. Nucleosomes unfold completely at a transcriptionally active promoter. Mol. Cell 11, 1587–1598 (2003).
  Article CAS PubMed Google Scholar
• Boeger, H., Griesenbeck, J., Strattan, J.S. & Kornberg, R.D. Removal of promoter nucleosomes by disassembly rather than sliding in vivo. Mol. Cell 14, 667–673 (2004).
  Article CAS PubMed Google Scholar
• Karagiannis, T.C. & El-Osta, A. Chromatin modifications and DNA double-strand breaks: the current state of play. Leukemia 21, 195–200 (2007).
  Article CAS PubMed Google Scholar
• Cairns, B.R. et al. RSC, an abundant and essential chromatin remodeling complex. Cell 87, 1249–1260 (1996).
  Article CAS PubMed Google Scholar
• 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).
  Article CAS PubMed Google Scholar
• 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).
  Article CAS PubMed PubMed Central Google Scholar
• Lorch, Y., Zhang, M. & Kornberg, R.D. RSC unravels the nucleosome. Mol. Cell 7, 89–95 (2001).
  Article CAS PubMed Google Scholar
• Lorch, Y., Maier-Davis, B. & Kornberg, R.D. Chromatin remodeling by nucleosome disassembly in vitro. Proc. Natl. Acad. Sci. USA 103, 3090–3093 (2006).
  Article CAS PubMed PubMed Central Google Scholar
• Lorch, Y., Zhang, M. & Kornberg, R.D. Histone octamer transfer by a chromatin-remodeling complex. Cell 96, 389–392 (1999).
  Article CAS PubMed Google Scholar
• Saha, A., Wittmeyer, J. & Cairns, B.R. Chromatin remodeling through directional DNA translocation from an internal nucleosomal site. Nat. Struct. Mol. Biol. 12, 747–755 (2005).
  Article CAS PubMed Google Scholar
• Lorch, Y., Davis, B. & Kornberg, R.D. Chromatin remodeling by DNA bending, not twisting. Proc. Natl. Acad. Sci. USA 102, 1329–1332 (2005).
  Article CAS PubMed PubMed Central Google Scholar
• Zofall, M., Persinger, J., Kassabov, S.R. & Bartholomew, B. Chromatin remodeling by ISW2 and SWI/SNF requires DNA translocation inside the nucleosome. Nat. Struct. Mol. Biol. 13, 339–346 (2006).
  Article CAS PubMed Google Scholar
• Lia, G. et al. Direct observation of DNA distortion by the RSC complex. Mol. Cell 21, 417–425 (2006).
  Article CAS PubMed PubMed Central Google Scholar
• Zhang, Y. et al. DNA translocation and loop formation mechanism of chromatin remodeling by SWI/SNF and RSC. Mol. Cell 24, 559–568 (2006).
  Article CAS PubMed PubMed Central Google Scholar
• Penczek, P.A., Grassucci, R.A. & Frank, J. The ribosome at improved resolution: new techniques for merging and orientation refinement in 3D cryo-electron microscopy of biological particles. Ultramicroscopy 53, 251–270 (1994).
  Article CAS PubMed Google Scholar
• Saxton, W.O. & Baumeister, W. The correlation averaging of a regularly arranged bacterial cell envelope protein. J. Microsc. 127, 127–138 (1982).
  Article CAS PubMed Google Scholar
• Skiniotis, G., Moazed, D. & Walz, T. Acetylated histone tail peptides induce structural rearrangements in the RSC chromatin remodeling complex. J. Biol. Chem. 282, 20804–20808 (2007).
  Article CAS PubMed Google Scholar
• Leschziner, A.E. et al. Conformational flexibility in the chromatin remodeler RSC observed by electron microscopy and the orthogonal tilt reconstruction method. Proc. Natl. Acad. Sci. USA 104, 4913–4918 (2007).
  Article CAS PubMed PubMed Central Google Scholar
• Frank, J. Three-Dimensional Electron Microscopy of Macromolecular Assemblies 342 (Academic Press, San Diego, 1996).
• Craighead, J.L., Chang, W.H. & Asturias, F.J. Structure of yeast RNA polymerase II in solution. Implications for enzyme regulation and interaction with promoter DNA. Structure 10, 1117–1125 (2002).
  Article CAS PubMed Google Scholar
• Gao, H., Valle, M., Ehrenberg, M. & Frank, J. Dynamics of EF-G interaction with the ribosome explored by classification of a heterogeneous cryo-EM dataset. J. Struct. Biol. 147, 283–290 (2004).
  Article CAS PubMed Google Scholar
• Leforestier, A., Dubochet, J. & Livolant, F. Bilayers of nucleosome core particles. Biophys. J. 81, 2414–2421 (2001).
  Article CAS PubMed PubMed Central Google Scholar
• Sengupta, S.M. et al. The interactions of yeast SWI/SNF and RSC with the nucleosome before and after chromatin remodeling. J. Biol. Chem. 276, 12636–12644 (2001).
  Article CAS PubMed Google Scholar
• 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).
  Article PubMed Google Scholar
• Dechassa, M.L. et al. Architecture of the SWI/SNF-nucleosome complex. Mol. Cell Biol. 28, 6010–6021 (2008).
  Article CAS PubMed PubMed Central Google Scholar
• Strohner, R. et al. A 'loop recapture' mechanism for ACF-dependent nucleosome remodeling. Nat. Struct. Mol. Biol. 12, 683–690 (2005).
  Article CAS PubMed Google Scholar
• Saeki, H. et al. Linker histone variants control chromatin dynamics during early embryogenesis. Proc. Natl. Acad. Sci. USA 102, 5697–5702 (2005).
  Article CAS PubMed PubMed Central Google Scholar
• Horn, P.J. et al. Phosphorylation of linker histones regulates ATP-dependent chromatin remodeling enzymes. Nat. Struct. Biol. 9, 263–267 (2002).
  Article CAS PubMed Google Scholar
• Boeger, H., Griesenbeck, J. & Kornberg, R.D. Nucleosome retention and the stochastic nature of promoter chromatin remodeling for transcription. Cell 133, 716–726 (2008).
  Article CAS PubMed PubMed Central Google Scholar
• Cairns, B.R. Chromatin remodeling: insights and intrigue from single-molecule studies. Nat. Struct. Mol. Biol. 14, 989–996 (2007).
  Article CAS PubMed PubMed Central Google Scholar
• Dubochet, J. et al. Cryo-electron microscopy of vitrified specimens. Q. Rev. Biophys. 21, 129–228 (1988).
  Article CAS PubMed Google Scholar
• Frank, J. et al. SPIDER and WEB: processing and visualization of images in 3D electron microscopy and related fields. J. Struct. Biol. 116, 190–199 (1996).
  Article CAS PubMed Google Scholar
• Radermacher, M. Three-dimensional reconstruction of single particles from random and nonrandom tilt series. J. Electron Microsc. Tech. 9, 359–394 (1988).
  Article CAS PubMed Google Scholar
• Penczek, P., Radermacher, M. & Frank, J. Three-dimensional reconstruction of single particles embedded in ice. Ultramicroscopy 40, 33–53 (1992).
  Article CAS PubMed Google Scholar
• Borland, L. & Vanheel, M. Classification of image data in conjugate representation spaces. J. Opt. Soc. Am. A Opt. Image Sci. Vis. 7, 601–610 (1990).
  Article Google Scholar
• Ward, J.H. Hierarchical grouping to optimize an objective function. Am. Stat. Assoc. J. 58, 236–244 (1963).
  Article Google Scholar
• Pettersen, E.F. et al. UCSF Chimera–a visualization system for exploratory research and analysis. J. Comput. Chem. 25, 1605–1612 (2004).
  Article CAS PubMed Google Scholar
• Wriggers, W. & Birmanns, S. Using situs for flexible and rigid-body fitting of multiresolution single-molecule data. J. Struct. Biol. 133, 193–202 (2001).
  Article CAS PubMed Google Scholar
• Luger, K., Mader, A.W., Richmond, R.K., Sargent, D.F. & Richmond, T.J. Crystal structure of the nucleosome core particle at 2.8Å resolution. Nature 389, 251–260 (1997).
  Article CAS PubMed Google Scholar
• Volkmann, N. & Hanein, D. Docking of atomic models into reconstructions from electron microscopy. Methods Enzymol. 374, 204–225 (2003).
  Article CAS PubMed Google Scholar