High-Resolution Phenotypic Landscape of the RNA Polymerase II Trigger Loop

Lineage-specific variations in the trigger loop modulate RNA proofreading by bacterial RNA polymerases

(2016) Daria Esyunina et al.   NUCLEIC ACIDS RESEARCH

Structures ofE.coliσS-transcription initiation complexes provide new insights into polymerase mechanism

(2016) Bin Liu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Bridge helix bending promotes RNA polymerase II backtracking through a critical and conserved threonine residue

(2016) Lin-Tai Da et al.   Nature Communications

Crystal Structure of a Transcribing RNA Polymerase II Complex Reveals a Complete Transcription Bubble

(2015) Christopher O. Barnes et al.   MOLECULAR CELL

The Ratcheted and Ratchetable Structural States of RNA Polymerase Underlie Multiple Transcriptional Functions

(2015) Shun-ichi Sekine et al.   MOLECULAR CELL

Trigger loop folding determines transcription rate ofEscherichia coli’sRNA polymerase

(2015) Yara X. Mejia et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Pre-mRNA splicing is facilitated by an optimal RNA polymerase II elongation rate

(2014) Nova Fong et al.   GENES & DEVELOPMENT

Deep mutational scanning: a new style of protein science

(2014) Douglas M Fowler et al.   NATURE METHODS

RNA polymerase pausing and nascent-RNA structure formation are linked through clamp-domain movement

(2014) Pyae P Hein et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Trigger-helix folding pathway and SI3 mediate catalysis and hairpin-stabilized pausing by Escherichia coli RNA polymerase

(2014) Tricia A. Windgassen et al.   NUCLEIC ACIDS RESEARCH

Dissecting the chemical interactions and substrate structural signatures governing RNA polymerase II trigger loop closure by synthetic nucleic acid analogues

(2014) Liang Xu et al.   NUCLEIC ACIDS RESEARCH

Millisecond dynamics of RNA polymerase II translocation at atomic resolution

(2014) D.-A. Silva et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Relationships of RNA Polymerase II Genetic Interactors to Transcription Start Site Usage Defects and Growth in Saccharomyces cerevisiae

(2014) Huiyan Jin et al.   G3-Genes Genomes Genetics

A Genetic Assay for Transcription Errors Reveals Multilayer Control of RNA Polymerase II Fidelity

(2014) Jordan D. Irvin et al.   PLoS Genetics

Energetic and Structural Details of the Trigger-Loop Closing Transition in RNA Polymerase II

(2013) Beibei Wang et al.   BIOPHYSICAL JOURNAL

From Structure to Systems: High-Resolution, Quantitative Genetic Analysis of RNA Polymerase II

(2013) Hannes Braberg et al.   CELL

Structural Basis of Transcriptional Pausing in Bacteria

(2013) Albert Weixlbaumer et al.   CELL

Control of Transcriptional Fidelity by Active Center Tuning as Derived from RNA Polymerase Endonuclease Reaction

(2013) Ekaterina Sosunova et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

High-throughput Analysis ofin vivoProtein Stability

(2013) Ikjin Kim et al.   MOLECULAR & CELLULAR PROTEOMICS

Cys-Pair Reporters Detect a Constrained Trigger Loop in a Paused RNA Polymerase

(2013) Dhananjaya Nayak et al.   MOLECULAR CELL

RNA polymerase I structure and transcription regulation

(2013) Christoph Engel et al.   NATURE

Interplay between the trigger loop and the F loop during RNA polymerase catalysis

(2013) Nataliya Miropolskaya et al.   NUCLEIC ACIDS RESEARCH

The RNA polymerase trigger loop functions in all three phases of the transcription cycle

(2013) T. Fouqueau et al.   NUCLEIC ACIDS RESEARCH

Divergent Contributions of Conserved Active Site Residues to Transcription by Eukaryotic RNA Polymerases I and II

(2013) Olga V. Viktorovskaya et al.   Cell Reports

Complete dissection of transcription elongation reveals slow translocation of RNA polymerase II in a linear ratchet mechanism

(2013) Manchuta Dangkulwanich et al.   eLife

Basic mechanisms of RNA polymerase II activity and alteration of gene expression in Saccharomyces cerevisiae

(2012) Craig D. Kaplan   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

RNA polymerase II transcription: Structure and mechanism

(2012) Xin Liu et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Direct interactions between the coiled-coil tip of DksA and the trigger loop of RNA polymerase mediate transcriptional regulation

(2012) C. W. Lennon et al.   GENES & DEVELOPMENT

Mechanism of Translesion Transcription by RNA Polymerase II and Its Role in Cellular Resistance to DNA Damage

(2012) Celine Walmacq et al.   MOLECULAR CELL

The spatial architecture of protein function and adaptation

(2012) Richard N. McLaughlin Jr et al.   NATURE

Active site opening and closure control translocation of multisubunit RNA polymerase

(2012) Anssi M. Malinen et al.   NUCLEIC ACIDS RESEARCH

Trigger loop dynamics mediate the balance between the transcriptional fidelity and speed of RNA polymerase II

(2012) M. H. Larson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A fundamental protein property, thermodynamic stability, revealed solely from large-scale measurements of protein function

(2012) C. L. Araya et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Dissection of Pol II Trigger Loop Function and Pol II Activity–Dependent Control of Start Site Selection In Vivo

(2012) Craig D. Kaplan et al.   PLoS Genetics

Structural basis of initial RNA polymerase II transcription

(2011) Alan C M Cheung et al.   EMBO JOURNAL

Synthetic Antibodies Designed on Natural Sequence Landscapes

(2011) Wenwu Zhai et al.   JOURNAL OF MOLECULAR BIOLOGY

Dynamics of Pyrophosphate Ion Release and Its Coupled Trigger Loop Motion from Closed to Open State in RNA Polymerase II

(2011) Lin-Tai Da et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Structural basis of RNA polymerase II backtracking, arrest and reactivation

(2011) Alan C. M. Cheung et al.   NATURE

Conformational coupling, bridge helix dynamics and active site dehydration in catalysis by RNA polymerase

(2010) Steve A. Seibold et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

The nucleotide addition cycle of RNA polymerase is controlled by two molecular hinges in the Bridge Helix domain

(2010) Robert OJ Weinzierl   BMC BIOLOGY

Stepwise mechanism for transcription fidelity

(2010) Yulia Yuzenkova et al.   BMC BIOLOGY

Novel RNA polymerase II mutation suppresses transcriptional fidelity and oxidative stress sensitivity inrpb9Δyeast

(2010) Hiroshi Koyama et al.   GENES TO CELLS

RNA polymerase II trigger loop residues stabilize and position the incoming nucleotide triphosphate in transcription

(2010) X. Huang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Central role of the RNA polymerase trigger loop in intrinsic RNA hydrolysis

(2010) Y. Yuzenkova et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Jalview Version 2--a multiple sequence alignment editor and analysis workbench

(2009) A. M. Waterhouse et al.   BIOINFORMATICS

Microdroplet-based PCR enrichment for large-scale targeted sequencing

(2009) Ryan Tewhey et al.   NATURE BIOTECHNOLOGY

Role of the RNA polymerase trigger loop in catalysis and pausing

(2009) Jinwei Zhang et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Nucleic acid polymerases use a general acid for nucleotidyl transfer

(2009) Christian Castro et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Structural Basis of Transcription: Backtracked RNA Polymerase II at 3.4 Angstrom Resolution

(2009) D. Wang et al.   SCIENCE

A novel solid phase technology for high-throughput gene synthesis

(2008) Jan Van den Brulle et al.   BIOTECHNIQUES

Properties of an Intergenic Terminator and Start Site Switch That Regulate IMD2 Transcription in Yeast

(2008) M. H. Jenks et al.   MOLECULAR AND CELLULAR BIOLOGY

Transient Reversal of RNA Polymerase II Active Site Closing Controls Fidelity of Transcription Elongation

(2008) Maria L. Kireeva et al.   MOLECULAR CELL

Regulation of a Eukaryotic Gene by GTP-Dependent Start Site Selection and Transcription Attenuation

(2008) Jason N. Kuehner et al.   MOLECULAR CELL

The RNA Polymerase II Trigger Loop Functions in Substrate Selection and Is Directly Targeted by α-Amanitin

(2008) Craig D. Kaplan et al.   MOLECULAR CELL

The X-ray crystal structure of RNA polymerase from Archaea

(2008) Akira Hirata et al.   NATURE