Structure and mechanism of the chromatin remodelling factor ISW1a (original) (raw)

• Lee, W. et al. A high-resolution atlas of nucleosome occupancy in yeast. Nature Genet. 39, 1235–1244 (2007)
  Article CAS Google Scholar
• Valouev, A. et al. A high-resolution, nucleosome position map of C. elegans reveals a lack of universal sequence-dictated positioning. Genome Res. 18, 1051–1063 (2008)
  Article CAS Google Scholar
• Kaplan, N. et al. The DNA-encoded nucleosome organization of a eukaryotic genome. Nature 458, 362–366 (2009)
  Article ADS CAS Google Scholar
• Sasaki, S. et al. Chromatin-associated periodicity in genetic variation downstream of transcriptional start sites. Science 323, 401–404 (2009)
  Article ADS CAS Google Scholar
• Mavrich, T. N. et al. Nucleosome organization in the Drosophila genome. Nature 453, 358–362 (2008)
  Article ADS CAS Google Scholar
• Schones, D. E. et al. Dynamic regulation of nucleosome positioning in the human genome. Cell 132, 887–898 (2008)
  Article CAS Google Scholar
• Clapier, C. R. & Cairns, B. R. The biology of chromatin remodeling complexes. Annu. Rev. Biochem. 78, 273–304 (2009)
  Article CAS Google Scholar
• Tsukiyama, T., Palmer, J., Landel, C. C., Shiloach, J. & Wu, C. Characterization of the imitation switch subfamily of ATP-dependent chromatin-remodeling factors in Saccharomyces cerevisiae . Genes Dev. 13, 686–697 (1999)
  Article CAS Google Scholar
• Vary, J. C., Jr et al. Yeast Isw1p forms two separable complexes in vivo . Mol. Cell. Biol. 23, 80–91 (2003)
  Article CAS Google Scholar
• Fyodorov, D. V. & Kadonaga, J. T. Dynamics of ATP-dependent chromatin assembly by ACF. Nature 418, 896–900 (2002)
  Article ADS Google Scholar
• Eberharter, A. et al. Acf1, the largest subunit of CHRAC, regulates ISWI-induced nucleosome remodelling. EMBO J. 20, 3781–3788 (2001)
  Article CAS Google Scholar
• Mizuguchi, G., Tsukiyama, T., Wisniewski, J. & Wu, C. Role of nucleosome remodeling factor NURF in transcriptional activation of chromatin. Mol. Cell 1, 141–150 (1997)
  Article CAS Google Scholar
• Becker, P. B. & Horz, W. ATP-dependent nucleosome remodeling. Annu. Rev. Biochem. 71, 247–273 (2002)
  Article CAS Google Scholar
• Lusser, A. & Kadonaga, J. T. Chromatin remodeling by ATP-dependent molecular machines. Bioessays 25, 1192–1200 (2003)
  Article CAS Google Scholar
• Corona, D. F. & Tamkun, J. W. Multiple roles for ISWI in transcription, chromosome organization and DNA replication. Biochim. Biophys. Acta 1677, 113–119 (2004)
  Article CAS Google Scholar
• Mellor, J. & Morillon, A. ISWI complexes in Saccharomyces cerevisiae . Biochim. Biophys. Acta 1677, 100–112 (2004)
  Article CAS Google Scholar
• Dürr, 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 Google Scholar
• Thomä, N. H. et al. Structure of the SWI2/SNF2 chromatin-remodeling domain of eukaryotic Rad54. Nature Struct. Mol. Biol. 12, 350 (2005)
  Article Google Scholar
• Grüne, T. et al. Crystal structure and functional analysis of a nucleosome recognition module of the remodeling factor ISWI. Mol. Cell 12, 449–460 (2003)
  Article Google Scholar
• Holm, L., Kaariainen, S., Rosenstrom, P. & Schenkel, A. Searching protein structure databases with DaliLite v.3. Bioinformatics 24, 2780–2781 (2008)
  Article CAS Google Scholar
• Horton, J. R. et al. Structure of the SANT domain from the Xenopus chromatin remodeling factor ISWI. Proteins 67, 1198–1202 (2007)
  Article CAS Google Scholar
• Cuperus, G. & Shore, D. Restoration of silencing in Saccharomyces cerevisiae by tethering of a novel Sir2-interacting protein, Esc8. Genetics 162, 633–645 (2002)
  CAS PubMed PubMed Central Google Scholar
• Gavin, A. C. et al. Proteome survey reveals modularity of the yeast cell machinery. Nature 440, 631–636 (2006)
  Article ADS CAS Google Scholar
• Ogata, K. et al. Solution structure of a specific DNA complex of the Myb DNA-binding domain with cooperative recognition helices. Cell 79, 639–648 (1994)
  Article CAS Google Scholar
• Tahirov, T. H. et al. Mechanism of c-Myb-C/EBPβ cooperation from separated sites on a promoter. Cell 108, 57–70 (2002)
  Article CAS Google Scholar
• 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)
  Article CAS Google Scholar
• Davey, C. A., Sargent, D. F., Luger, K., Mäder, A. W. & Richmond, T. J. Solvent mediated interactions in the structure of the nucleosome core particle at 1.9 Å resolution. J. Mol. Biol. 319, 1097–1113 (2002)
  Article CAS Google Scholar
• Wang, J. P. et al. Preferentially quantized linker DNA lengths in Saccharomyces cerevisiae . PLOS Comput. Biol. 4, e1000175 (2008)
  Article MathSciNet Google Scholar
• Gangaraju, V. K. & Bartholomew, B. Dependency of ISW1a chromatin remodeling on extranucleosomal DNA. Mol. Cell. Biol. 27, 3217–3225 (2007)
  Article CAS Google Scholar
• Flaus, A., Luger, K., Tan, S. & Richmond, T. J. Mapping nucleosome position at single base-pair resolution by using site-directed hydroxyl radicals. Proc. Natl Acad. Sci. USA 93, 1370–1375 (1996)
  Article ADS CAS Google Scholar
• Luger, K., Maeder, A. W., Richmond, R. K., Sargent, D. F. & Richmond, T. J. Crystal structure of the nucleosome core particle at 2.8 Å resolution. Nature 389, 251–260 (1997)
  Article ADS CAS Google Scholar
• Makde, R. D., England, J. R., Yennawar, H. P. & Tan, S. Structure of RCC1 chromatin factor bound to the nucleosome core particle. Nature 467, 562–566 (2010)
  Article ADS CAS Google Scholar
• Ong, M. S., Richmond, T. J. & Davey, C. A. DNA stretching and extreme kinking in the nucleosome core. J. Mol. Biol. 368, 1067–1074 (2007)
  Article CAS Google Scholar
• Vasudevan, D., Chua, E. Y. D. & Davey, C. A. Crystal structures of nucleosome core particles containing the ‘601’ strong positioning sequence. J. Mol. Biol. 403, 1–10 (2010)
  Article CAS Google Scholar
• Morillon, A. et al. Isw1 chromatin remodeling ATPase coordinates transcription elongation and termination by RNA polymerase II. Cell 115, 425–435 (2003)
  Article CAS Google Scholar
• Pinskaya, M., Nair, A., Clynes, D., Morillon, A. & Mellor, J. Nucleosome remodeling and transcriptional repression are distinct functions of Isw1 in Saccharomyces cerevisiae . Mol. Cell. Biol. 29, 2419–2430 (2009)
  Article CAS Google Scholar
• Stockdale, C., Flaus, A., Ferreira, H. & Owen-Hughes, T. Analysis of nucleosome repositioning by yeast ISWI and Chd1 chromatin remodeling complexes. J. Biol. Chem. 281, 16279–16288 (2006)
  Article CAS Google Scholar
• Jones, D. T. Protein secondary structure prediction based on position-specific scoring matrices. J. Mol. Biol. 292, 195–202 (1999)
  Article CAS Google Scholar
• Berger, I., Fitzgerald, D. J. & Richmond, T. J. Baculovirus expression system for heterologous multiprotein complexes. Nature Biotechnol. 22, 1583–1587 (2004)
  Article CAS Google Scholar
• Kabsch, W. Automatic processing of rotation diffraction data from crystals of initially unknown symmetry and cell constants. J. Appl. Cryst. 26, 795–800 (1993)
  Article CAS Google Scholar
• Evans, P. Scaling and assessment of data quality. Acta Crystallogr. D 62, 72–82 (2006)
  Article Google Scholar
• Pape, T. & Schneider, T. R. HKL2MAP: a graphical user interface for macromolecular phasing with SHELX programs. J. Appl. Cryst. 37, 843–844 (2004)
  Article CAS Google Scholar
• Bricogne, G., Vonrhein, C., Flensburg, C., Schiltz, M. & Paciorek, W. Generation, representation and flow of phase information in structure determination: recent developments in and around SHARP 2.0. Acta Crystallogr. D 59, 2023–2030 (2003)
  Article CAS Google Scholar
• Abrahams, J. P. & Leslie, A. G. Methods used in the structure determination of bovine mitochondrial F1 ATPase. Acta Crystallogr. D 52, 30–42 (1996)
  Article CAS Google Scholar
• Emsley, P. & Cowtan, K. Coot: model-building tools for molecular graphics. Acta Crystallogr. D 60, 2126–2132 (2004)
  Article Google Scholar
• Adams, P. D. et al. PHENIX: building new software for automated crystallographic structure determination. Acta Crystallogr. D 58, 1948–1954 (2002)
  Article Google Scholar
• Ludtke, S. J., Baldwin, P. R. & Chiu, W. EMAN: Semiautomated software for high-resolution single-particle reconstructions. J. Struct. Biol. 128, 82–97 (1999)
  Article CAS 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 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 Google Scholar
• Bieniossek, C., Richmond, T. J. & Berger, I. in Curr. Prot. Protein Sci. 5.20.21–5.20.26 (John Wiley & Sons, 2008)
  Google Scholar
• Luger, K., Rechsteiner, T. J. & Richmond, T. J. Expression and purification of recombinant histones and nucleosome reconstitution. Methods Mol. Biol. 119, 1–16 (1999)
  CAS PubMed Google Scholar
• Bellizzi, J. J., Widom, J., Kemp, C. W. & Clardy, J. Producing selenomethionine-labeled proteins with a baculovirus expression vector system. Structure 7, R263–R267 (1999)
  Article CAS Google Scholar
• Van Heel, M. Angular reconstitution: A posteriori assignment of projection directions for 3D reconstruction. Ultramicroscopy 21, 111–123 (1987)
  Article CAS Google Scholar
• Unser, M. et al. Spectral signal-to-noise ratio and resolution assessment of 3D reconstructions. J. Struct. Biol. 149, 243–255 (2005)
  Article CAS Google Scholar
• Hu, D., Crist, M., Duan, X., Quiocho, F. A. & Gimble, F. S. Probing the structure of the PI-SceI-DNA complex by affinity cleavage and affinity photocross-linking. J. Biol. Chem. 275, 2705–2712 (2000)
  Article CAS Google Scholar