Research Topics
Genomes and Genes | Roger KornbergSummaryAffiliation: Stanford University Country: USA Publications
Research Grants
| Collaborators
|
Detail Information
Publications
Structural basis of transcription: nucleotide selection by rotation in the RNA polymerase II active centerKenneth D Westover
Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
Cell 119:481-9. 2004..3 a...- A bridge to transcription by RNA polymeraseCraig D Kaplan
Department of Structural Biology, Stanford University, 299 Campus Dr, West, Stanford, CA 94305, USA
J Biol 7:39. 2008.... - The molecular basis of eukaryotic transcription (Nobel Lecture)Roger Kornberg
Department of Structural Biology, Stanford University Medical School, 299 Campus Dr. West, Stanford CA, 94305-5126, USA
Angew Chem Int Ed Engl 46:6956-65. 2007 - Mediator and the mechanism of transcriptional activationRoger D Kornberg
Department of Structural Biology, Stanford School of Medicine, Stanford, CA 94305, USA
Trends Biochem Sci 30:235-9. 2005..The transduction of regulatory signals through this pathway is crucial for transcription of almost all pol II promoters in all eukaryote organisms... - The molecular basis of eukaryotic transcriptionRoger D Kornberg
Stanford University School of Medicine, Stanford, CA 94305-5400, USA
Proc Natl Acad Sci U S A 104:12955-61. 2007 - Head module control of mediator interactionsYuichiro Takagi
Department of Structural Biology, Stanford University School of Medicine, Stanford, California 94305, USA
Mol Cell 23:355-64. 2006..The head module evidently controls Mediator-RNA polymerase II and Mediator-promoter interactions... - Structural basis of transcription: an RNA polymerase II-TFIIB cocrystal at 4.5 AngstromsDavid A Bushnell
Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305 5126, USA
Science 303:983-8. 2004..The trajectory of promoter DNA determined by the C-terminal domain of TFIIB traverses sites of interaction with TFIIE, TFIIF, and TFIIH, serving to define their roles in the transcription initiation process... - Structural basis of transcription: role of the trigger loop in substrate specificity and catalysisDong Wang
Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
Cell 127:941-54. 2006..A histidine side chain in the trigger loop, precisely positioned by these interactions, may literally "trigger" phosphodiester bond formation. Recognition and catalysis are thus coupled, ensuring the fidelity of transcription... - Isolation and assay of the RSC chromatin-remodeling complex from Saccharomyces cerevisiaeYahli Lorch
Department of Structural Biology, Stanford University School of Medicine, Stanford, California 94305, USA
Methods Enzymol 377:316-22. 2004 - A complex of the Srb8, -9, -10, and -11 transcriptional regulatory proteins from yeastTilman Borggrefe
Department of Structural Biology, Stanford University School of Medicine, California 94305 5400, USA
J Biol Chem 277:44202-7. 2002.... - Mediator as a general transcription factorYuichiro Takagi
Department of Structural Biology, Stanford University School of Medicine, Stanford, California 94305-5400, USA
J Biol Chem 281:80-9. 2006..The possibility that Mediator serves as an anti-inhibitor, opposing the effects of global negative regulators, is largely excluded... - A trithorax-group complex purified from Saccharomyces cerevisiae is required for methylation of histone H3Peter L Nagy
Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
Proc Natl Acad Sci U S A 99:90-4. 2002..These studies suggest that epigenetic regulation of developmental and sex-specific gene expression are species-specific readouts for a common chromatin remodeling machinery associated mechanistically with histone methylation... - Removal of promoter nucleosomes by disassembly rather than sliding in vivoHinrich Boeger
Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
Mol Cell 14:667-73. 2004..Whereas sliding would conserve the number of nucleosomes on the circle, we found that the number was diminished, demonstrating chromatin remodeling by nucleosome disassembly... - Affinity purification of specific chromatin segments from chromosomal loci in yeastJoachim Griesenbeck
Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
Mol Cell Biol 23:9275-82. 2003..Activator proteins interact in the manner anticipated from previous studies in vivo. This work opens the way to the direct study of specific gene regions of eukaryotic chromosomes in diverse functional and structural states... - The RNA polymerase II trigger loop functions in substrate selection and is directly targeted by alpha-amanitinCraig D Kaplan
Department of Structural Biology, Stanford University, Stanford, CA 94305, USA
Mol Cell 30:547-56. 2008..We propose that alpha-amanitin-inhibited Pol II elongation, which is slow and exhibits reduced substrate selectivity, results from direct alpha-amanitin interference with the TL... - Mechanism of chromatin remodelingYahli Lorch
Department of Structural Biology, Stanford School of Medicine, Stanford, CA 94305, USA
Proc Natl Acad Sci U S A 107:3458-62. 2010..Bulging of the DNA from the octamer surface is possible, and twisting is unavoidable, but neither is the basis of remodeling... - Nucleosomes unfold completely at a transcriptionally active promoterHinrich Boeger
Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
Mol Cell 11:1587-98. 2003..Although nucleosome loss occurs at all promoter sites, it is not complete at any of them, suggesting the existence of an equilibrium between the removal of nucleosomes and their reformation... - Complete, 12-subunit RNA polymerase II at 4.1-A resolution: implications for the initiation of transcriptionDavid A Bushnell
Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
Proc Natl Acad Sci U S A 100:6969-73. 2003.... - Structure of an RNA polymerase II-TFIIB complex and the transcription initiation mechanismXin Liu
Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
Science 327:206-9. 2010..The two structures, taken together with others previously obtained, dispel long-standing mysteries of the transcription initiation process... - Ubiquitin ligase activity of TFIIH and the transcriptional response to DNA damageYuichiro Takagi
Department of Structural Biology, School of Medicine, Stanford University, Stanford, California 94305, USA
Mol Cell 18:237-43. 2005..Rather, it correlates with reduced transcriptional induction of genes involved in DNA repair, suggesting that the E3 Ub ligase activity of TFIIH mediates the transcriptional response to DNA damage... - Structural basis of transcription: backtracked RNA polymerase II at 3.4 angstrom resolutionDong Wang
Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
Science 324:1203-6. 2009..Structure determination of a cocrystal with TFIIS reveals a rearrangement whereby cleavage of the RNA may take place... - Schizosacharomyces pombe RNA polymerase II at 3.6-A resolutionHenrik Spahr
Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
Proc Natl Acad Sci U S A 106:9185-90. 2009..pombe and humans. Amino acid changes apparently responsible for the structural differences are also conserved between S. pombe and humans, suggesting that the S. pombe structure may be a good surrogate for that of the human enzyme... - Structural basis of eukaryotic gene transcriptionHinrich Boeger
Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
FEBS Lett 579:899-903. 2005..X-ray and electron crystallography have led to a picture of the entire transcription initiation complex, elucidating the mechanisms of promoter recognition, DNA unwinding, abortive initiation, and promoter escape... - Chromatin remodeling by nucleosome disassembly in vitroYahli Lorch
Department of Structural Biology, Stanford University School of Medicine, CA 94305 5126, USA
Proc Natl Acad Sci U S A 103:3090-3. 2006..RSC and related chromatin-remodeling complexes may be responsible for the removal of promoter nucleosomes during transcriptional activation in vivo... - Chromatin and transcription: where do we go from hereRoger D Kornberg
Department of Structural Biology, Stanford School of Medicine, Stanford, California 94305, USA
Curr Opin Genet Dev 12:249-51. 2002 - Revised subunit structure of yeast transcription factor IIH (TFIIH) and reconciliation with human TFIIHYuichiro Takagi
Department of Structural Biology, Stanford University School of Medicine, California 94305 5400, USA
J Biol Chem 278:43897-900. 2003..This reassignment of subunits resolves a longstanding discrepancy between yeast and human TFIIH complexes... - Structural basis of transcription: alpha-amanitin-RNA polymerase II cocrystal at 2.8 A resolutionDavid A Bushnell
Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305-5126, USA
Proc Natl Acad Sci U S A 99:1218-22. 2002..The structure of the complex indicates the likely basis of inhibition and gives unexpected insight into the transcription mechanism... - Structural basis of transcription: separation of RNA from DNA by RNA polymerase IIKenneth D Westover
Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305-5126, USA
Science 303:1014-6. 2004..This separation of nucleic acid strands is brought about by interaction with a set of proteins loops in a strand/loop network. Formation of the network must occur in the transition from abortive initiation to promoter escape... - Chromatin remodeling by DNA bending, not twistingYahli Lorch
Department of Structural Biology, School of Medicine, Stanford University, Stanford, CA 94305, USA
Proc Natl Acad Sci U S A 102:1329-32. 2005..These findings suggest a remodeling process involving bending, but not twisting, of the DNA and further point to the propagation of a bent region (loop or bulge) from one end of the nucleosome to the other... - Synthesis and bioconjugation of 2 and 3 nm-diameter gold nanoparticlesChristopher J Ackerson
Department of Structural Biology, Stanford School of Medicine, 299 Campus Drive West, Stanford, California 94305, USA
Bioconjug Chem 21:214-8. 2010..Conjugates with antibody Fc fragment could be used to identify TAP-tagged proteins of interest in electron micrographs, through the binding of a pair of particles to the pair of protein A domains in the TAP tag... - Diffusion of nucleoside triphosphates and role of the entry site to the RNA polymerase II active centerNizar N Batada
Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305-5126, USA
Proc Natl Acad Sci U S A 101:17361-4. 2004..Binding to the entry site greatly enhances the lifetime of an NTP in the active center region, and it prevents "backtracking" and the consequent occlusion of the active site... - Purification of defined chromosomal domainsJoachim Griesenbeck
Department of Structural Biology, Stanford University School of Medicine, Stanford, California 94305, USA
Methods Enzymol 375:170-8. 2004 - Electron microscopic analysis of the RSC chromatin remodeling complexFrancisco J Asturias
Department of Cell Biology, The Scripps Research Institute, La Jolla, California 92037, USA
Methods Enzymol 376:48-62. 2004 - Structure of the yeast RNA polymerase II holoenzyme: Mediator conformation and polymerase interactionJoshua A Davis
Department of Cell Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
Mol Cell 10:409-15. 2002..Implications for the possible mechanism of transcription regulation by Mediator are discussed... - Structural analysis of the RSC chromatin-remodeling complexFrancisco J Asturias
Department of Cell Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
Proc Natl Acad Sci U S A 99:13477-80. 2002..Results of nuclease protection analysis are consistent with nucleosome binding in the cavity. Such binding could explain the ability of RSC to expose nucleosomal DNA in the presence of ATP without loss of associated histones... - RNA polymerase II/TFIIF structure and conserved organization of the initiation complexWen Hsiang Chung
Department of Cell Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
Mol Cell 12:1003-13. 2003..The structure of the RNAPII/TFIIF complex suggests a model for the organization of a minimal transcription initiation complex... - Nucleosome retention and the stochastic nature of promoter chromatin remodeling for transcriptionHinrich Boeger
Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
Cell 133:716-26. 2008.... - An autobiographic conversation with Roger D. Kornberg on his work on transcription regulationRoger D Kornberg
Cell Death Differ 14:1977-80. 2007 - A unified nomenclature for protein subunits of mediator complexes linking transcriptional regulators to RNA polymerase IIHenri-Marc Bourbon
Mol Cell 14:553-7. 2004 - [The Nobel Prize in Chemistry for 2006 for molecular unravelment of DNA transcription]J Brouwer
Universiteit Leiden, Leids Instituut voor Chemisch Onderzoek, afd Moleculaire Genetica, Leiden
Ned Tijdschr Geneeskd 150:2854-6. 2006..Kornberg's work has provided more insight into the various stages of the transcription process and possible disruptions that lead to illness... - [Roger Kornberg]Toshio Fukasawa
Tanpakushitsu Kakusan Koso 51:2356-9. 2006 - Association of the Mediator complex with enhancers of active genesLaurent Kuras
Centre de Genetique Moleculaire, Centre National de la Recherche Scientifique, 91198 Gif sur Yvette, France
Proc Natl Acad Sci U S A 100:13887-91. 2003..These findings support the idea of Mediator as a primary conduit of regulatory information from enhancers to promoters in eukaryotic cells... - Structure of a thiol monolayer-protected gold nanoparticle at 1.1 A resolutionPablo D Jadzinsky
Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
Science 318:430-3. 2007..The particles are chiral, with the two enantiomers alternating in the crystal lattice. The discrete nature of the particle may be explained by the closing of a 58-electron shell...
Research Grants
- Structure of the Eukaryote Transcription ApparatusRoger Kornberg; Fiscal Year: 2009....
- Gene Activation In VitroRoger D Kornberg; Fiscal Year: 2011....
- Heavy Atom Electron MicroscopyRoger Kornberg; Fiscal Year: 2004..3) Construction of a modified scFv library, as well as computational tools, for use of the method by the biomedical research community. ..
- STRUCTURE OF RNA POLYMERASE IIRoger Kornberg; Fiscal Year: 2003..They are likely to be more closely related to one another than to the enzyme from Saccharomyces cerevisiae, the object of our current investigations. ..
- Structure of the Eukaryote Transcription ApparatusRoger Kornberg; Fiscal Year: 2006..For example, mutations in subunits of factor H are responsible for a number of inherited human disease syndromes. Mutations in RSC or RSC-related proteins are implicated in oncogenesis. ..
- RNA POLYMERASE II TRANSCRIPTION SYSTEM FROM YEASTRoger Kornberg; Fiscal Year: 2007..2. Reconstitution and functional analysis of mediator. 3. Characterization of mammalian mediator. 4. Reconstitution of yeast TAF-dependent transcription in vitro. 5. Studies of RSC-nucleosome interaction. ..
- Gene Activation In VitroRoger D Kornberg; Fiscal Year: 2010....
- STRUCTURE OF RNA POLYMERASE IIRoger D Kornberg; Fiscal Year: 2010....
- Structure of the Eukaryote Transcription ApparatusRoger D Kornberg; Fiscal Year: 2010....
- Gene Activation In VitroRoger Kornberg; Fiscal Year: 2009....
- STRUCTURE OF RNA POLYMERASE IIRoger Kornberg; Fiscal Year: 2009....
- Structure of the Eukaryote Transcription ApparatusRoger Kornberg; Fiscal Year: 2007..For type specifications, see instructions on page 6.) RESEARCH GRANT TABLE OF CONTENTS Page Numbers Face Page Description, ..
- STRUCTURE OF RNA POLYMERASE IIRoger Kornberg; Fiscal Year: 2007....
- CRYSTALLOGRAPHY OF THE EUKARYOTE TRANSCRIPTION APPARATUSRoger Kornberg; Fiscal Year: 2001....
- STRUCTURE OF RNA POLYMERASE IIRoger Kornberg; Fiscal Year: 1999....
- CRYSTALLOGRAPHY OF THE EUKARYOTE TRANSCRIPTION APPARATUSRoger Kornberg; Fiscal Year: 1993....
- LIPID LAYER CRYSTALLIZATION TECHNIQUERoger Kornberg; Fiscal Year: 1991..The monolayer X-ray diffraction technique will be developed and applied to obtain information missing from the electron microscope image analysis...