High-Resolution Phenotypic Landscape of the RNA Polymerase II Trigger Loop
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Craig D. Kaplan | S. Sze | C. Kaplan | Huiyan Jin | P. Cui | Nandhini Muthukrishnan | C. Qiu | L. Tang | J. van den Brulle | J. Dave | Paul J. Vandeventer | Ralf Strohner | Olivia C. Erinne | S. G. Babu | Kenny C. Lam
[1] Craig D. Kaplan,et al. Effects of Pol II catalytic mutants on in vivo elongation rate, processivity, gene expression, mRNA decay and response to nucleotide depletion , 2016 .
[2] Craig D. Kaplan,et al. Relationships Between RNA Polymerase II Activity and Spt Elongation Factors to Spt- Phenotype and Growth in Saccharomyces cerevisiae , 2016, G3: Genes, Genomes, Genetics.
[3] Craig D. Kaplan,et al. RNA Polymerase II Trigger Loop Mobility , 2016, The Journal of Biological Chemistry.
[4] Daniel‐Adriano Silva,et al. Bridge helix bending promotes RNA polymerase II backtracking through a critical and conserved threonine residue , 2016, Nature Communications.
[5] T. Steitz,et al. Structures of E. coli σS-transcription initiation complexes provide new insights into polymerase mechanism , 2016, Proceedings of the National Academy of Sciences.
[6] S. Klimašauskas,et al. Lineage-specific variations in the trigger loop modulate RNA proofreading by bacterial RNA polymerases , 2016, Nucleic acids research.
[7] Craig D. Kaplan,et al. Crystal Structure of a Transcribing RNA Polymerase II Complex Reveals a Complete Transcription Bubble. , 2015, Molecular cell.
[8] S. Yokoyama,et al. The ratcheted and ratchetable structural states of RNA polymerase underlie multiple transcriptional functions. , 2015, Molecular cell.
[9] C. Bustamante,et al. Trigger loop folding determines transcription rate of Escherichia coli’s RNA polymerase , 2014, Proceedings of the National Academy of Sciences.
[10] Hyunmin Kim,et al. Pre-mRNA splicing is facilitated by an optimal RNA polymerase II elongation rate , 2014, Genes & development.
[11] Craig D. Kaplan,et al. Relationships of RNA Polymerase II Genetic Interactors to Transcription Start Site Usage Defects and Growth in Saccharomyces cerevisiae , 2014, G3: Genes, Genomes, Genetics.
[12] Jinwei Zhang,et al. Trigger-helix folding pathway and SI3 mediate catalysis and hairpin-stabilized pausing by Escherichia coli RNA polymerase , 2014, Nucleic acids research.
[13] D. Gotte,et al. A Genetic Assay for Transcription Errors Reveals Multilayer Control of RNA Polymerase II Fidelity , 2014, PLoS genetics.
[14] S. Fields,et al. Deep mutational scanning: a new style of protein science , 2014, Nature Methods.
[15] Kellie E Kolb,et al. RNA polymerase pausing and nascent RNA structure formation are linked through clamp domain movement , 2014, Nature Structural &Molecular Biology.
[16] Craig D. Kaplan,et al. Activation and reactivation of the RNA polymerase II trigger loop for intrinsic RNA cleavage and catalysis , 2014, Transcription.
[17] Dahlia R. Weiss,et al. Millisecond dynamics of RNA polymerase II translocation at atomic resolution , 2014, Proceedings of the National Academy of Sciences.
[18] Kyle V. Butler,et al. Dissecting the chemical interactions and substrate structural signatures governing RNA polymerase II trigger loop closure by synthetic nucleic acid analogues , 2014, Nucleic acids research.
[19] Patrick Cramer,et al. RNA polymerase I structure and transcription regulation , 2013, Nature.
[20] S. Klimašauskas,et al. Interplay between the trigger loop and the F loop during RNA polymerase catalysis , 2013, Nucleic acids research.
[21] C. Bustamante,et al. Complete dissection of transcription elongation reveals slow translocation of RNA polymerase II in a linear ratchet mechanism , 2013, eLife.
[22] Craig D. Kaplan,et al. Divergent contributions of conserved active site residues to transcription by eukaryotic RNA polymerases I and II. , 2013, Cell reports.
[23] Craig D. Kaplan,et al. From Structure to Systems: High-Resolution, Quantitative Genetic Analysis of RNA Polymerase II , 2013, Cell.
[24] M. Feig,et al. Energetic and structural details of the trigger-loop closing transition in RNA polymerase II. , 2013, Biophysical journal.
[25] David L. Young,et al. High-throughput Analysis of in vivo Protein Stability* , 2013, Molecular & Cellular Proteomics.
[26] Robert Landick,et al. Cys-pair reporters detect a constrained trigger loop in a paused RNA polymerase. , 2013, Molecular cell.
[27] Patrick Cramer,et al. The RNA polymerase trigger loop functions in all three phases of the transcription cycle , 2013, Nucleic acids research.
[28] A. Weixlbaumer,et al. Structural Basis of Transcriptional Pausing in Bacteria , 2013, Cell.
[29] V. Epshtein,et al. Control of Transcriptional Fidelity by Active Center Tuning as Derived from RNA Polymerase Endonuclease Reaction* , 2013, The Journal of Biological Chemistry.
[30] S. Butcher,et al. Direct interactions between the coiled-coil tip of DksA and the trigger loop of RNA polymerase mediate transcriptional regulation. , 2012, Genes & development.
[31] F. J. Poelwijk,et al. The spatial architecture of protein function and adaptation , 2012, Nature.
[32] S. Fields,et al. A fundamental protein property, thermodynamic stability, revealed solely from large-scale measurements of protein function , 2012, Proceedings of the National Academy of Sciences.
[33] Mark S. Johnson,et al. Active site opening and closure control translocation of multisubunit RNA polymerase , 2012, Nucleic acids research.
[34] D. Gotte,et al. Mechanism of translesion transcription by RNA polymerase II and its role in cellular resistance to DNA damage. , 2012, Molecular cell.
[35] Craig D. Kaplan,et al. Trigger loop dynamics mediate the balance between the transcriptional fidelity and speed of RNA polymerase II , 2012, Proceedings of the National Academy of Sciences.
[36] Craig D. Kaplan,et al. Dissection of Pol II Trigger Loop Function and Pol II Activity–Dependent Control of Start Site Selection In Vivo , 2012, PLoS genetics.
[37] Xuhui Huang,et al. Dynamics of pyrophosphate ion release and its coupled trigger loop motion from closed to open state in RNA polymerase II. , 2012, Journal of the American Chemical Society.
[38] S. Sainsbury,et al. Structural basis of initial RNA polymerase II transcription , 2011, The EMBO journal.
[39] D. Cox,et al. Synthetic antibodies designed on natural sequence landscapes. , 2011, Journal of molecular biology.
[40] P. Cramer,et al. Structural basis of RNA polymerase II backtracking, arrest and reactivation , 2011, Nature.
[41] R. Weinzierl. The nucleotide addition cycle of RNA polymerase is controlled by two molecular hinges in the Bridge Helix domain , 2010, BMC Biology.
[42] Dahlia R. Weiss,et al. RNA polymerase II trigger loop residues stabilize and position the incoming nucleotide triphosphate in transcription , 2010, Proceedings of the National Academy of Sciences.
[43] Michael Feig,et al. Conformational coupling, bridge helix dynamics and active site dehydration in catalysis by RNA polymerase. , 2010, Biochimica et biophysica acta.
[44] Yulia Yuzenkova,et al. Central role of the RNA polymerase trigger loop in intrinsic RNA hydrolysis , 2010, Proceedings of the National Academy of Sciences.
[45] Yulia Yuzenkova,et al. Stepwise mechanism for transcription fidelity , 2010, BMC Biology.
[46] Takahiro Ito,et al. Novel RNA polymerase II mutation suppresses transcriptional fidelity and oxidative stress sensitivity in rpb9Δ yeast , 2010, Genes to cells : devoted to molecular & cellular mechanisms.
[47] K. Frazer,et al. Microdroplet-based PCR amplification for large scale targeted sequencing , 2009, Nature Biotechnology.
[48] M. Levitt,et al. Structural Basis of Transcription: Backtracked RNA Polymerase II at 3.4 Angstrom Resolution , 2009, Science.
[49] Simone C. Wiesler,et al. Bridge helix and trigger loop perturbations generate superactive RNA polymerases , 2008, Journal of biology.
[50] Thomas Waldmann,et al. A novel solid phase technology for high-throughput gene synthesis. , 2008, BioTechniques.
[51] D. Brow,et al. Regulation of a eukaryotic gene by GTP-dependent start site selection and transcription attenuation. , 2008, Molecular cell.
[52] J. Strathern,et al. Transient reversal of RNA polymerase II active site closing controls fidelity of transcription elongation. , 2008, Molecular cell.
[53] Craig D. Kaplan,et al. The RNA polymerase II trigger loop functions in substrate selection and is directly targeted by alpha-amanitin. , 2008, Molecular cell.
[54] U. Stenzel,et al. PatMaN: rapid alignment of short sequences to large databases , 2008, Bioinform..
[55] D. Reines,et al. Properties of an Intergenic Terminator and Start Site Switch That Regulate IMD2 Transcription in Yeast , 2008, Molecular and Cellular Biology.
[56] Akira Hirata,et al. The X-ray crystal structure of RNA polymerase from Archaea , 2008, Nature.
[57] Robert Landick,et al. A central role of the RNA polymerase trigger loop in active-site rearrangement during transcriptional pausing. , 2007, Molecular cell.
[58] Jonathan Tennyson,et al. Water vapour in the atmosphere of a transiting extrasolar planet , 2007, Nature.
[59] Craig D. Kaplan,et al. Structural Basis of Transcription: Role of the Trigger Loop in Substrate Specificity and Catalysis , 2006, Cell.
[60] H. Scheraga,et al. The role of hydrophobic interactions in initiation and propagation of protein folding , 2006, Proceedings of the National Academy of Sciences.
[61] Andrew D Griffiths,et al. Amplification of complex gene libraries by emulsion PCR , 2006, Nature Methods.
[62] B. Shafer,et al. Mutations in the Saccharomyces cerevisiae RPB1 Gene Conferring Hypersensitivity to 6-Azauracil , 2006, Genetics.
[63] 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.
[64] P. Cramer,et al. Complete RNA polymerase II elongation complex structure and its interactions with NTP and TFIIS. , 2004, Molecular cell.
[65] D. Bushnell,et al. Structural Basis of Transcription Nucleotide Selection by Rotation in the RNA Polymerase II Active Center , 2004, Cell.
[66] J. Nolan,et al. Open source clustering software. , 2004, Bioinformatics.
[67] Robert C. Edgar,et al. MUSCLE: multiple sequence alignment with high accuracy and high throughput. , 2004, Nucleic acids research.
[68] William J. Rice,et al. Structure and Function of the Transcription Elongation Factor GreB Bound to Bacterial RNA Polymerase , 2003, Cell.
[69] Judith W. Hyle,et al. Functional Distinctions between IMP Dehydrogenase Genes in Providing Mycophenolate Resistance and Guanine Prototrophy to Yeast* , 2003, Journal of Biological Chemistry.
[70] A. Kornblihtt,et al. A slow RNA polymerase II affects alternative splicing in vivo. , 2003, Molecular cell.
[71] S. Yokoyama,et al. Crystal structure of a bacterial RNA polymerase holoenzyme at 2.6 Å resolution , 2002 .
[72] S. Yokoyama,et al. Crystal structure of a bacterial RNA polymerase holoenzyme at 2.6 Å resolution , 2002, Nature.
[73] B. Séraphin,et al. The tandem affinity purification (TAP) method: a general procedure of protein complex purification. , 2001, Methods.
[74] P. Cramer,et al. Structural Basis of Transcription: An RNA Polymerase II Elongation Complex at 3.3 Å Resolution , 2001, Science.
[75] P. Cramer,et al. Structural Basis of Transcription: RNA Polymerase II at 2.8 Ångstrom Resolution , 2001, Science.
[76] T. Woolf,et al. Manganese Selectivity of Pmr1, the Yeast Secretory Pathway Ion Pump, Is Defined by Residue Gln783 in Transmembrane Segment 6 , 2000, The Journal of Biological Chemistry.
[77] N. Proudfoot,et al. Poly(A) signals control both transcriptional termination and initiation between the tandem GAL10 and GAL7 genes of Saccharomyces cerevisiae , 1998, The EMBO journal.
[78] J. Greenblatt,et al. Stimulation of Transcription by Mutations Affecting Conserved Regions of RNA Polymerase II , 1998, Journal of bacteriology.
[79] Fred Winston,et al. Construction of a set of convenient saccharomyces cerevisiae strains that are isogenic to S288C , 1995, Yeast.
[80] J. Ranish,et al. The yeast general transcription factor TFIIA is composed of two polypeptide subunits. , 1991, The Journal of biological chemistry.
[81] T. A. Brown,et al. A rapid and simple method for preparation of RNA from Saccharomyces cerevisiae. , 1990, Nucleic acids research.
[82] G. Fink,et al. The yeast secretory pathway is perturbed by mutations in PMR1, a member of a Ca2+ ATPase family , 1989, Cell.
[83] G. Fink,et al. A suppressor of a HIS4 transcriptional defect encodes a protein with homology to the catalytic subunit of protein phosphatases , 1989, Cell.
[84] A. Greenleaf,et al. A mutation in the largest subunit of RNA polymerase II alters RNA chain elongation in vitro. , 1985, The Journal of biological chemistry.
[85] G. Fink,et al. Ty-mediated gene expression of the LYS2 and HIS4 genes of Saccharomyces cerevisiae is controlled by the same SPT genes. , 1984, Proceedings of the National Academy of Sciences of the United States of America.
[86] S. Niyogi,et al. Effect of several metal ions on misincorporation during transcription. , 1981, Nucleic acids research.
[87] Craig D. Kaplan,et al. Basic mechanisms of RNA polymerase II activity and alteration of gene expression in Saccharomyces cerevisiae. , 2013, Biochimica et biophysica acta.
[88] Roger D Kornberg,et al. RNA polymerase II transcription: structure and mechanism. , 2013, Biochimica et biophysica acta.
[89] Robert Landick,et al. Role of the RNA polymerase trigger loop in catalysis and pausing , 2010, Nature Structural &Molecular Biology.
[90] Irina Artsimovitch,et al. Structural basis for substrate loading in bacterial RNA polymerase , 2007, Nature.
[91] Adam Godzik,et al. Tolerating some redundancy significantly speeds up clustering of large protein databases , 2002, Bioinform..
[92] D. Hoffman,et al. Selective effects of metal ions on RNA synthesis rates. , 1981, Toxicology.