Structure of SWI/SNF chromatin remodeler RSC bound to a nucleosome

[1]  Hao Wu,et al.  Structure of the RSC complex bound to the nucleosome , 2019, Science.

[2]  E. Nogales,et al.  Architecture of the chromatin remodeler RSC and insights into its nucleosome engagement , 2019, bioRxiv.

[3]  Yan Han,et al.  Cryo-electron microscopy structure of a nucleosome-bound SWI/SNF chromatin remodeling complex , 2019, bioRxiv.

[4]  Poul Nissen,et al.  Namdinator – automatic molecular dynamics flexible fitting of structural models into cryo-EM and crystallography experimental maps , 2019, IUCrJ.

[5]  N. Luscombe,et al.  Genome-wide reconstitution of chromatin transactions reveals that RSC preferentially disrupts H2AZ-containing nucleosomes , 2019, Genome research.

[6]  Daniel W. A. Buchan,et al.  The PSIPRED Protein Analysis Workbench: 20 years on , 2019, Nucleic Acids Res..

[7]  Ming Li,et al.  Mechanism of DNA translocation underlying chromatin remodelling by Snf2 , 2019, Nature.

[8]  C. Wolberger,et al.  Mechanism of Cross-talk between H2B Ubiquitination and H3 Methylation by Dot1L , 2019, Cell.

[9]  N. Friedman,et al.  Dynamics of Chromatin and Transcription during Transient Depletion of the RSC Chromatin Remodeling Complex , 2019, Cell reports.

[10]  S. Henikoff,et al.  RSC-Associated Subnucleosomes Define MNase-Sensitive Promoters in Yeast. , 2019, Molecular cell.

[11]  Poul Nissen,et al.  Namdinator – automatic molecular dynamics flexible fitting of structural models into cryo-EM and crystallography experimental maps , 2018, bioRxiv.

[12]  B. Maier-Davis,et al.  Histone Acetylation Inhibits RSC and Stabilizes the +1 Nucleosome. , 2018, Molecular cell.

[13]  Erik Lindahl,et al.  New tools for automated high-resolution cryo-EM structure determination in RELION-3 , 2018, eLife.

[14]  Rafael Ayala,et al.  Structure and dynamics of the yeast SWR1-nucleosome complex , 2018, Science.

[15]  Mahavir Singh,et al.  Domain architecture of BAF250a reveals the ARID and ARM-repeat domains with implication in function and assembly of the BAF remodeling complex , 2018, PloS one.

[16]  Kevin Schall,et al.  The nuclear actin-containing Arp8 module is a linker DNA sensor driving INO80 chromatin remodeling , 2018, Nature Structural & Molecular Biology.

[17]  E. O'Duibhir,et al.  Sequence-Directed Action of RSC Remodeler and General Regulatory Factors Modulates +1 Nucleosome Position to Facilitate Transcription. , 2018, Molecular cell.

[18]  Dimitry Tegunov,et al.  Real-time cryo–EM data pre-processing with Warp , 2018, Nature Methods.

[19]  Torsten Schwede,et al.  SWISS-MODEL: homology modelling of protein structures and complexes , 2018, Nucleic Acids Res..

[20]  Rafael Ayala,et al.  Structure and regulation of the human INO80–nucleosome complex , 2018, Nature.

[21]  Karl-Peter Hopfner,et al.  Structural basis for nucleosome remodeling by the INO80 complex , 2018, Nature.

[22]  T. Owen-Hughes,et al.  Structure of the chromatin remodelling enzyme Chd1 bound to a ubiquitinylated nucleosome , 2018, bioRxiv.

[23]  Christopher J. Williams,et al.  MolProbity: More and better reference data for improved all‐atom structure validation , 2018, Protein science : a publication of the Protein Society.

[24]  Conrad C. Huang,et al.  UCSF ChimeraX: Meeting modern challenges in visualization and analysis , 2018, Protein science : a publication of the Protein Society.

[25]  Lukas Zimmermann,et al.  A Completely Reimplemented MPI Bioinformatics Toolkit with a New HHpred Server at its Core. , 2017, Journal of molecular biology.

[26]  Patrick Cramer,et al.  Nucleosome-Chd1 structure and implications for chromatin remodelling , 2017, Nature.

[27]  Janet Iwasa,et al.  Mechanisms of action and regulation of ATP-dependent chromatin-remodelling complexes , 2017, Nature Reviews Molecular Cell Biology.

[28]  R. Kornberg,et al.  Chromatin-remodeling for transcription , 2017, Quarterly Reviews of Biophysics.

[29]  Torsten Schwede,et al.  The SWISS-MODEL Repository—new features and functionality , 2016, Nucleic Acids Res..

[30]  Bongsoo Park,et al.  Genomic Nucleosome Organization Reconstituted with Pure Proteins , 2016, Cell.

[31]  S. Henikoff.  Mechanisms of Nucleosome Dynamics In Vivo. , 2016, Cold Spring Harbor perspectives in medicine.

[32]  F. Antequera,et al.  Histone H2B ubiquitylation represses gametogenesis by opposing RSC-dependent chromatin remodeling at the ste11 master regulator locus , 2016, eLife.

[33]  H. Szerlong,et al.  Regulation of DNA Translocation Efficiency within the Chromatin Remodeler RSC/Sth1 Potentiates Nucleosome Sliding and Ejection. , 2016, Molecular cell.

[34]  A. Plückthun,et al.  Structures of designed armadillo-repeat proteins show propagation of inter-repeat interface effects , 2016, Acta crystallographica. Section D, Structural biology.

[35]  D. Shore,et al.  Nucleosome Stability Distinguishes Two Different Promoter Types at All Protein-Coding Genes in Yeast. , 2015, Molecular cell.

[36]  Maximilian Grimm,et al.  xVis: a web server for the schematic visualization and interpretation of crosslink-derived spatial restraints , 2015, Nucleic Acids Res..

[37]  Rishi Matadeen,et al.  Structural basis for retroviral integration into nucleosomes , 2015, Nature.

[38]  Srinivas Ramachandran,et al.  Asymmetric nucleosomes flank promoters in the budding yeast genome , 2015, Genome research.

[39]  Colin W. Combe,et al.  xiNET: Cross-link Network Maps With Residue Resolution , 2015, Molecular & Cellular Proteomics.

[40]  Roger D Kornberg,et al.  Role of DNA sequence in chromatin remodeling and the formation of nucleosome-free regions , 2014, Genes & development.

[41]  Xavier Robert,et al.  Deciphering key features in protein structures with the new ENDscript server , 2014, Nucleic Acids Res..

[42]  David Baker,et al.  High-resolution comparative modeling with RosettaCM. , 2013, Structure.

[43]  L. Pearl,et al.  The BAH domain of Rsc2 is a histone H3 binding domain , 2013, Nucleic acids research.

[44]  Benjamin E. Gross,et al.  Integrative Analysis of Complex Cancer Genomics and Clinical Profiles Using the cBioPortal , 2013, Science Signaling.

[45]  B. Cairns,et al.  Structure of an actin-related subcomplex of the SWI/SNF chromatin remodeler , 2013, Proceedings of the National Academy of Sciences.

[46]  M. Poirier,et al.  The SnAC Domain of SWI/SNF Is a Histone Anchor Required for Remodeling , 2012, Molecular and Cellular Biology.

[47]  M. Dong,et al.  Identification of cross-linked peptides from complex samples , 2012, Nature Methods.

[48]  Kristin R Brogaard,et al.  A base pair resolution map of nucleosome positions in yeast , 2012, Nature.

[49]  Benjamin E. Gross,et al.  The cBio cancer genomics portal: an open platform for exploring multidimensional cancer genomics data. , 2012, Cancer discovery.

[50]  B. Pugh,et al.  A new, highly conserved domain in Swi2/Snf2 is required for SWI/SNF remodeling , 2011, Nucleic acids research.

[51]  Yongchao Liu,et al.  MSAProbs: multiple sequence alignment based on pair hidden Markov models and partition function posterior probabilities , 2010, Bioinform..

[52]  M. L. Dechassa,et al.  SWI/SNF has intrinsic nucleosome disassembly activity that is dependent on adjacent nucleosomes. , 2010, Molecular cell.

[53]  P. Emsley,et al.  Features and development of Coot , 2010, Acta crystallographica. Section D, Biological crystallography.

[54]  Randy J. Read,et al.  Acta Crystallographica Section D Biological , 2003 .

[55]  Alexandre M. J. J. Bonvin,et al.  3D-DART: a DNA structure modelling server , 2009, Nucleic Acids Res..

[56]  Charles Simon Bond,et al.  ALINE: a WYSIWYG protein-sequence alignment editor for publication-quality alignments. , 2009, Acta crystallographica. Section D, Biological crystallography.

[57]  Christopher L. Warren,et al.  A library of yeast transcription factor motifs reveals a widespread function for Rsc3 in targeting nucleosome exclusion at promoters. , 2008, Molecular cell.

[58]  Fan Zhang,et al.  Structure of a RSC–nucleosome complex and insights into chromatin remodeling , 2008, Nature Structural &Molecular Biology.

[59]  H. Szerlong,et al.  The HSA domain binds nuclear actin-related proteins to regulate chromatin-remodeling ATPases , 2008, Nature Structural &Molecular Biology.

[60]  B. Cairns,et al.  RSC regulates nucleosome positioning at Pol II genes and density at Pol III genes , 2008, The EMBO journal.

[61]  B. Cairns,et al.  Autoregulation of the rsc4 tandem bromodomain by gcn5 acetylation. , 2007, Molecular cell.

[62]  Andres E Leschziner,et al.  Conformational flexibility in the chromatin remodeler RSC observed by electron microscopy and the orthogonal tilt reconstruction method , 2007, Proceedings of the National Academy of Sciences.

[63]  B. Cairns,et al.  Structure and function of the SWIRM domain, a conserved protein module found in chromatin regulatory complexes , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[64]  Torsten Schwede,et al.  The SWISS-MODEL Repository: new features and functionalities , 2005, Nucleic Acids Res..

[65]  Anjanabha Saha,et al.  Chromatin remodeling through directional DNA translocation from an internal nucleosomal site , 2005, Nature Structural &Molecular Biology.

[66]  Kairong Cui,et al.  PBAF chromatin-remodeling complex requires a novel specificity subunit, BAF200, to regulate expression of selective interferon-responsive genes. , 2005, Genes & development.

[67]  H. Dyson,et al.  ZZ domain of CBP: an unusual zinc finger fold in a protein interaction module. , 2004, Journal of molecular biology.

[68]  Conrad C. Huang,et al.  UCSF Chimera—A visualization system for exploratory research and analysis , 2004, J. Comput. Chem..

[69]  H. Szerlong,et al.  Tandem bromodomains in the chromatin remodeler RSC recognize acetylated histone H3 Lys14 , 2004, The EMBO journal.

[70]  A. Kikuchi,et al.  Genetic analysis of RSC58, which encodes a component of a yeast chromatin remodeling complex, and interacts with the transcription factor Swi6 , 2004, Molecular Genetics and Genomics.

[71]  R. Kornberg,et al.  Isolation and assay of the RSC chromatin-remodeling complex from Saccharomyces cerevisiae. , 2003, Methods in enzymology.

[72]  Francisco J. Asturias,et al.  Structural analysis of the RSC chromatin-remodeling complex , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[73]  Anjanabha Saha,et al.  Chromatin remodeling by RSC involves ATP-dependent DNA translocation. , 2002, Genes & development.

[74]  Kevin Struhl,et al.  Genome-wide location and regulated recruitment of the RSC nucleosome-remodeling complex. , 2002, Genes & development.

[75]  D G Oscier,et al.  The BCL11 gene family: involvement of BCL11A in lymphoid malignancies. , 2001, Blood.

[76]  B. Cairns,et al.  A Rsc3/Rsc30 zinc cluster dimer reveals novel roles for the chromatin remodeler RSC in gene expression and cell cycle control. , 2001, Molecular cell.

[77]  K. Luger,et al.  Crystal structure of a nucleosome core particle containing the variant histone H2A.Z , 2000, Nature Structural Biology.

[78]  E. Salmon,et al.  The human SWI/SNF-B chromatin-remodeling complex is related to yeast rsc and localizes at kinetochores of mitotic chromosomes. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[79]  B. Cairns,et al.  Two functionally distinct forms of the RSC nucleosome-remodeling complex, containing essential AT hook, BAH, and bromodomains. , 1999, Molecular cell.

[80]  B. Séraphin,et al.  A generic protein purification method for protein complex characterization and proteome exploration , 1999, Nature Biotechnology.

[81]  D T Jones,et al.  Protein secondary structure prediction based on position-specific scoring matrices. , 1999, Journal of molecular biology.

[82]  B. Cairns,et al.  Two actin-related proteins are shared functional components of the chromatin-remodeling complexes RSC and SWI/SNF. , 1998, Molecular cell.

[83]  M. Carlson,et al.  Direct interaction between Rsc6 and Rsc8/Swh3,two proteins that are conserved in SWI/SNF-related complexes. , 1998, Nucleic acids research.

[84]  J. Widom,et al.  New DNA sequence rules for high affinity binding to histone octamer and sequence-directed nucleosome positioning. , 1998, Journal of molecular biology.

[85]  G. Crabtree,et al.  Architectural DNA binding by a high-mobility-group/kinesin-like subunit in mammalian SWI/SNF-related complexes. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[86]  B. Cairns,et al.  Sfh1p, a component of a novel chromatin-remodeling complex, is required for cell cycle progression , 1997, Molecular and cellular biology.

[87]  Paul Tempst,et al.  RSC, an Essential, Abundant Chromatin-Remodeling Complex , 1996, Cell.

[88]  G. Goodwin,et al.  Molecular cloning of polybromo, a nuclear protein containing multiple domains including five bromodomains, a truncated HMG-box, and two repeats of a novel domain. , 1996, Gene.

[89]  Steven A. Brown,et al.  Evidence that SNF2/SWI2 and SNF5 activate transcription in yeast by altering chromatin structure. , 1992, Genes & development.

[90]  I. Herskowitz,et al.  Characterization of the yeast SWI1, SWI2, and SWI3 genes, which encode a global activator of transcription , 1992, Cell.

[91]  Hao Wu,et al.  Structures of the ISWI–nucleosome complex reveal a conserved mechanism of chromatin remodeling , 2019, Nature Structural & Molecular Biology.

[92]  Cigall Kadoch,et al.  Composition and Function of Mammalian SWI/SNF Chromatin Remodeling Complexes in Human Disease. , 2016, Cold Spring Harbor symposia on quantitative biology.

[93]  S. Chellappan,et al.  Chromatin Protocols , 2015, Methods in Molecular Biology.

[94]  Holger Stark,et al.  GraFix: stabilization of fragile macromolecular complexes for single particle cryo-EM. , 2010, Methods in enzymology.

[95]  Ming-Ming Zhou,et al.  Structural insights into selective histone H3 recognition by the human Polybromo bromodomain 2 , 2010, Cell Research.

[96]  Oliver F. Lange,et al.  Structure prediction for CASP8 with all‐atom refinement using Rosetta , 2009, Proteins.

[97]  Henning Urlaub,et al.  GraFix: sample preparation for single-particle electron cryomicroscopy , 2008, Nature Methods.

[98]  Uma M. Muthurajan,et al.  Reconstitution of nucleosome core particles from recombinant histones and DNA. , 2004, Methods in enzymology.

[99]  W. Delano.  The PyMOL Molecular Graphics System , 2002 .

[100]  T. Richmond,et al.  Expression and purification of recombinant histones and nucleosome reconstitution. , 1999, Methods in molecular biology.