Structure of activated transcription complex Pol II–DSIF–PAF–SPT6

[1]  P. Cramer,et al.  Structure of paused transcription complex Pol II-DSIF-NELF , 2018, Nature.

[2]  M. Kashlev,et al.  RNA–DNA and DNA–DNA base-pairing at the upstream edge of the transcription bubble regulate translocation of RNA polymerase and transcription rate , 2018, Nucleic acids research.

[3]  Adam D. Wier,et al.  Structural Basis for Eukaryotic Transcription-Coupled DNA Repair Initiation , 2017, Nature.

[4]  K. Arndt,et al.  Emerging Insights into the Roles of the Paf1 Complex in Gene Regulation. , 2017, Trends in biochemical sciences.

[5]  D. Tegunov,et al.  Structures of transcription pre-initiation complex with TFIIH and Mediator , 2017, Nature.

[6]  P. Cramer,et al.  Structure of a transcribing RNA polymerase II–DSIF complex reveals a multidentate DNA–RNA clamp , 2017, Nature Structural &Molecular Biology.

[7]  S. Yokoyama,et al.  Structure of the complete elongation complex of RNA polymerase II with basal factors , 2017, Science.

[8]  T. Formosa,et al.  A novel SH2 recognition mechanism recruits Spt6 to the doubly phosphorylated RNA polymerase II linker at sites of transcription , 2017, eLife.

[9]  D. Tegunov,et al.  Architecture of the RNA polymerase II-Paf1C-TFIIS transcription elongation complex , 2017, Nature Communications.

[10]  P. Cramer,et al.  RNA-dependent chromatin association of transcription elongation factors and Pol II CTD kinases , 2017, eLife.

[11]  D. Agard,et al.  MotionCor2: anisotropic correction of beam-induced motion for improved cryo-electron microscopy , 2017, Nature Methods.

[12]  G. Belogurov,et al.  NusG inhibits RNA polymerase backtracking by stabilizing the minimal transcription bubble , 2016, eLife.

[13]  Lin-Feng Chen,et al.  Multiple P-TEFbs cooperatively regulate the release of promoter-proximally paused RNA polymerase II , 2016, Nucleic acids research.

[14]  E. Lindahl,et al.  Accelerated cryo-EM structure determination with parallelisation using GPUs in RELION-2 , 2016, bioRxiv.

[15]  P. Cramer,et al.  Architecture and RNA binding of the human negative elongation factor , 2016, eLife.

[16]  R. Tjian,et al.  Near-atomic resolution visualization of human transcription promoter opening , 2016, Nature.

[17]  A. Heck,et al.  Six alternative proteases for mass spectrometry–based proteomics beyond trypsin , 2016, Nature Protocols.

[18]  Jesse J. Lipp,et al.  P-TEFb regulation of transcription termination factor Xrn2 revealed by a chemical genetic screen for Cdk9 substrates , 2016, Genes & development.

[19]  R. Roeder,et al.  RNA polymerase II–associated factor 1 regulates the release and phosphorylation of paused RNA polymerase II , 2015, Science.

[20]  Ashley R. Woodfin,et al.  PAF1, a Molecular Regulator of Promoter-Proximal Pausing by RNA Polymerase II , 2015, Cell.

[21]  H. Handa,et al.  Characterization of the Human Transcription Elongation Factor Rtf1: Evidence for Nonoverlapping Functions of Rtf1 and the Paf1 Complex , 2015, Molecular and Cellular Biology.

[22]  Kai Zhang,et al.  Gctf: Real-time CTF determination and correction , 2015, bioRxiv.

[23]  Michael J E Sternberg,et al.  The Phyre2 web portal for protein modeling, prediction and analysis , 2015, Nature Protocols.

[24]  Martin Beck,et al.  Xlink Analyzer: Software for analysis and visualization of cross-linking data in the context of three-dimensional structures , 2015, Journal of structural biology.

[25]  W. Baumeister,et al.  Architecture of the RNA polymerase II–Mediator core initiation complex , 2015, Nature.

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

[27]  Bin Zhang,et al.  PhosphoSitePlus, 2014: mutations, PTMs and recalibrations , 2014, Nucleic Acids Res..

[28]  Steven M. Block,et al.  A pause sequence enriched at translation start sites drives transcription dynamics in vivo , 2014, Science.

[29]  P. Cramer,et al.  Rpb4 Subunit Functions Mainly in mRNA Synthesis by RNA Polymerase II♦ , 2014, The Journal of Biological Chemistry.

[30]  T. Tomizaki,et al.  D3, the new diffractometer for the macromolecular crystallography beamlines of the Swiss Light Source , 2014, Journal of synchrotron radiation.

[31]  B. Strahl,et al.  A feed forward circuit comprising Spt6, Ctk1 and PAF regulates Pol II CTD phosphorylation and transcription elongation , 2013, Nucleic acids research.

[32]  M. Rode,et al.  The Yeast Ski Complex: Crystal Structure and RNA Channeling to the Exosome Complex , 2013, Cell.

[33]  Daniel W. A. Buchan,et al.  Scalable web services for the PSIPRED Protein Analysis Workbench , 2013, Nucleic Acids Res..

[34]  K. Katoh,et al.  MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability , 2013, Molecular biology and evolution.

[35]  S. Scheres RELION: Implementation of a Bayesian approach to cryo-EM structure determination , 2012, Journal of structural biology.

[36]  John T. Lis,et al.  Promoter-proximal pausing of RNA polymerase II: emerging roles in metazoans , 2012, Nature Reviews Genetics.

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

[38]  Kevin W Eliceiri,et al.  NIH Image to ImageJ: 25 years of image analysis , 2012, Nature Methods.

[39]  Christopher P. Davis,et al.  Cdc73 Subunit of Paf1 Complex Contains C-terminal Ras-like Domain That Promotes Association of Paf1 Complex with Chromatin* , 2012, The Journal of Biological Chemistry.

[40]  Sean J. Johnson,et al.  Crystal structures of the S. cerevisiae Spt6 core and C-terminal tandem SH2 domain. , 2011, Journal of molecular biology.

[41]  Jinrong Min,et al.  Structure and function of WD40 domain proteins , 2011, Protein & Cell.

[42]  M. Mann,et al.  Andromeda: a peptide search engine integrated into the MaxQuant environment. , 2011, Journal of proteome research.

[43]  P. Cramer,et al.  A Tandem SH2 Domain in Transcription Elongation Factor Spt6 Binds the Phosphorylated RNA Polymerase II C-terminal Repeat Domain (CTD)* , 2010, The Journal of Biological Chemistry.

[44]  F. Winston,et al.  Noncanonical Tandem SH2 Enables Interaction of Elongation Factor Spt6 with RNA Polymerase II* , 2010, The Journal of Biological Chemistry.

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

[46]  R. Roeder,et al.  The Human PAF1 Complex Acts in Chromatin Transcription Elongation Both Independently and Cooperatively with SII/TFIIS , 2010, Cell.

[47]  Vincent B. Chen,et al.  MolProbity: all-atom structure validation for macromolecular crystallography , 2009, Acta crystallographica. Section D, Biological crystallography.

[48]  H. Handa,et al.  DSIF, the Paf1 complex, and Tat-SF1 have nonredundant, cooperative roles in RNA polymerase II elongation. , 2009, Genes & development.

[49]  Steven Hahn,et al.  Phosphorylation of the Transcription Elongation Factor Spt5 by Yeast Bur1 Kinase Stimulates Recruitment of the PAF Complex , 2009, Molecular and Cellular Biology.

[50]  P. Cramer,et al.  Structural basis of transcription: mismatch-specific fidelity mechanisms and paused RNA polymerase II with frayed RNA. , 2009, Molecular cell.

[51]  Karen Zhou,et al.  Control of transcriptional elongation and cotranscriptional histone modification by the yeast BUR kinase substrate Spt5 , 2009, Proceedings of the National Academy of Sciences.

[52]  W. Webb,et al.  Spt6 enhances the elongation rate of RNA polymerase II in vivo , 2009, The EMBO journal.

[53]  H. Urlaub,et al.  SLP-65 Phosphorylation Dynamics Reveals a Functional Basis for Signal Integration by Receptor-proximal Adaptor Proteins* , 2009, Molecular & Cellular Proteomics.

[54]  Geoffrey J. Barton,et al.  Jalview Version 2—a multiple sequence alignment editor and analysis workbench , 2009, Bioinform..

[55]  K. Jones,et al.  The Iws1:Spt6:CTD complex controls cotranscriptional mRNA biosynthesis and HYPB/Setd2-mediated histone H3K36 methylation. , 2008, Genes & development.

[56]  M. Mann,et al.  MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification , 2008, Nature Biotechnology.

[57]  Johannes Söding,et al.  Genome-associated RNA Polymerase II Includes the Dissociable Rpb4/7 Subcomplex* , 2008, Journal of Biological Chemistry.

[58]  Leonardo G. Trabuco,et al.  Flexible fitting of atomic structures into electron microscopy maps using molecular dynamics. , 2008, Structure.

[59]  M. Mann,et al.  PHOSIDA (phosphorylation site database): management, structural and evolutionary investigation, and prediction of phosphosites , 2007, Genome Biology.

[60]  Randy J. Read,et al.  Phaser crystallographic software , 2007, Journal of applied crystallography.

[61]  Gerhard Klebe,et al.  PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations , 2007, Nucleic Acids Res..

[62]  R. Evans,et al.  The Spt6 SH2 domain binds Ser2-P RNAPII to direct Iws1-dependent mRNA splicing and export. , 2007, Genes & development.

[63]  Johannes Söding,et al.  TPRpred: a tool for prediction of TPR-, PPR- and SEL1-like repeats from protein sequences , 2007, BMC Bioinformatics.

[64]  A. Hinnebusch,et al.  The Spt4p Subunit of Yeast DSIF Stimulates Association of the Paf1 Complex with Elongating RNA Polymerase II , 2006, Molecular and Cellular Biology.

[65]  Hiroshi Handa,et al.  P-TEFb-mediated phosphorylation of hSpt5 C-terminal repeats is critical for processive transcription elongation. , 2006, Molecular cell.

[66]  D. Reinberg,et al.  Drosophila Paf1 Modulates Chromatin Structure at Actively Transcribed Genes , 2006, Molecular and Cellular Biology.

[67]  Finn Werner,et al.  Crystal structure and RNA binding of the Rpb4/Rpb7 subunits of human RNA polymerase II , 2005, Nucleic acids research.

[68]  Paul Tempst,et al.  The human PAF complex coordinates transcription with events downstream of RNA synthesis. , 2005, Genes & development.

[69]  M. Gstaiger,et al.  The HRPT2 Tumor Suppressor Gene Product Parafibromin Associates with Human PAF1 and RNA Polymerase II , 2005, Molecular and Cellular Biology.

[70]  Aleksey A. Porollo,et al.  Combining prediction of secondary structure and solvent accessibility in proteins , 2005, Proteins.

[71]  Craig D. Kaplan,et al.  Interaction between Transcription Elongation Factors and mRNA 3′-End Formation at the Saccharomyces cerevisiae GAL10-GAL7 Locus* , 2005, Journal of Biological Chemistry.

[72]  O. Rozenblatt-Rosen,et al.  The Parafibromin Tumor Suppressor Protein Is Part of a Human Paf1 Complex , 2005, Molecular and Cellular Biology.

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

[74]  David Baker,et al.  Protein structure prediction and analysis using the Robetta server , 2004, Nucleic Acids Res..

[75]  D. Reinberg,et al.  Human Spt6 Stimulates Transcription Elongation by RNA Polymerase II In Vitro , 2004, Molecular and Cellular Biology.

[76]  B. Peterlin,et al.  Dynamics of Human Immunodeficiency Virus Transcription: P-TEFb Phosphorylates RD and Dissociates Negative Effectors from the Transactivation Response Element , 2004, Molecular and Cellular Biology.

[77]  R. Henderson,et al.  Optimal determination of particle orientation, absolute hand, and contrast loss in single-particle electron cryomicroscopy. , 2003, Journal of molecular biology.

[78]  W. Heyer,et al.  NADH-coupled microplate photometric assay for kinetic studies of ATP-hydrolyzing enzymes with low and high specific activities. , 2003, Analytical biochemistry.

[79]  Craig D. Kaplan,et al.  Transcription Elongation Factors Repress Transcription Initiation from Cryptic Sites , 2003, Science.

[80]  K. Yano,et al.  Human Transcription Elongation Factor NELF: Identification of Novel Subunits and Reconstitution of the Functionally Active Complex , 2003, Molecular and Cellular Biology.

[81]  Kevin Struhl,et al.  Targeted recruitment of Set1 histone methylase by elongating Pol II provides a localized mark and memory of recent transcriptional activity. , 2003, Molecular cell.

[82]  G. Cagney,et al.  RNA Polymerase II Elongation Factors of Saccharomyces cerevisiae: a Targeted Proteomics Approach , 2002, Molecular and Cellular Biology.

[83]  J. Jaehning,et al.  Ctr9, Rtf1, and Leo1 Are Components of the Paf1/RNA Polymerase II Complex , 2002, Molecular and Cellular Biology.

[84]  S. Squazzo,et al.  The Paf1 complex physically and functionally associates with transcription elongation factors in vivo , 2002, The EMBO journal.

[85]  Nathan A. Baker,et al.  Electrostatics of nanosystems: Application to microtubules and the ribosome , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[86]  P. Sharp,et al.  Positive Transcription Elongation Factor b Phosphorylates hSPT5 and RNA Polymerase II Carboxyl-terminal Domain Independently of Cyclin-dependent Kinase-activating Kinase* , 2001, The Journal of Biological Chemistry.

[87]  M. Kashlev,et al.  Overextended RNA:DNA hybrid as a negative regulator of RNA polymerase II processivity. , 2000, Journal of molecular biology.

[88]  G. Orphanides,et al.  FACT relieves DSIF/NELF-mediated inhibition of transcriptional elongation and reveals functional differences between P-TEFb and TFIIH. , 2000, Molecular cell.

[89]  M. Kashlev,et al.  The 8-Nucleotide-long RNA:DNA Hybrid Is a Primary Stability Determinant of the RNA Polymerase II Elongation Complex* , 2000, The Journal of Biological Chemistry.

[90]  Hiroshi Handa,et al.  NELF, a Multisubunit Complex Containing RD, Cooperates with DSIF to Repress RNA Polymerase II Elongation , 1999, Cell.

[91]  M. Kashlev,et al.  Crucial role of the RNA:DNA hybrid in the processivity of transcription. , 1998, Molecules and Cells.

[92]  Ping Wei,et al.  A Novel CDK9-Associated C-Type Cyclin Interacts Directly with HIV-1 Tat and Mediates Its High-Affinity, Loop-Specific Binding to TAR RNA , 1998, Cell.

[93]  F. Winston,et al.  Evidence that Spt4, Spt5, and Spt6 control transcription elongation by RNA polymerase II in Saccharomyces cerevisiae. , 1998, Genes & development.

[94]  K. Yano,et al.  DSIF, a novel transcription elongation factor that regulates RNA polymerase II processivity, is composed of human Spt4 and Spt5 homologs. , 1998, Genes & development.

[95]  D. Price,et al.  Control of RNA Polymerase II Elongation Potential by a Novel Carboxyl-terminal Domain Kinase* , 1996, The Journal of Biological Chemistry.

[96]  F. Winston,et al.  Evidence That Spt6p Controls Chromatin Structure by a Direct Interaction with Histones , 1996, Science.

[97]  D. Price,et al.  Purification of P-TEFb, a Transcription Factor Required for the Transition into Productive Elongation (*) , 1995, The Journal of Biological Chemistry.

[98]  F. Winston,et al.  SPT4, SPT5 and SPT6 interactions: effects on transcription and viability in Saccharomyces cerevisiae. , 1992, Genetics.

[99]  R. Young,et al.  Two dissociable subunits of yeast RNA polymerase II stimulate the initiation of transcription at a promoter in vitro. , 1991, The Journal of biological chemistry.

[100]  D. Wessel,et al.  A method for the quantitative recovery of protein in dilute solution in the presence of detergents and lipids. , 1984, Analytical biochemistry.

[101]  J. Tainer,et al.  MacroBac: New Technologies for Robust and Efficient Large-Scale Production of Recombinant Multiprotein Complexes. , 2017, Methods in enzymology.

[102]  M. Mann,et al.  Protocol for micro-purification, enrichment, pre-fractionation and storage of peptides for proteomics using StageTips , 2007, Nature Protocols.

[103]  M. Kashlev,et al.  Engineering of elongation complexes of bacterial and yeast RNA polymerases. , 2003, Methods in enzymology.

[104]  D. Waugh,et al.  Escherichia coli maltose‐binding protein is uncommonly effective at promoting the solubility of polypeptides to which it is fused , 1999, Protein science : a publication of the Protein Society.

[105]  Vincent B. Chen,et al.  PHENIX: a comprehensive Python-based system for macromolecular structure solution , 2010, Acta crystallographica. Section D, Biological crystallography.