Published in Nat Struct Mol Biol on June 13, 2008
Structural basis of transcription: backtracked RNA polymerase II at 3.4 angstrom resolution. Science (2009) 2.68
Remodeling of the enhancer landscape during macrophage activation is coupled to enhancer transcription. Mol Cell (2013) 2.55
Crystal structure of bacterial RNA polymerase bound with a transcription inhibitor protein. Nature (2010) 2.01
Inhibiting eukaryotic transcription: Which compound to choose? How to evaluate its activity? Transcription (2011) 1.94
RNA polymerase active center: the molecular engine of transcription. Annu Rev Biochem (2009) 1.94
Waves of early transcriptional activation and pluripotency program initiation during human preimplantation development. Development (2011) 1.88
Role of the RNA polymerase trigger loop in catalysis and pausing. Nat Struct Mol Biol (2009) 1.86
Interfacial inhibitors: targeting macromolecular complexes. Nat Rev Drug Discov (2011) 1.80
Structural basis of transcriptional pausing in bacteria. Cell (2013) 1.71
Transcription inactivation through local refolding of the RNA polymerase structure. Nature (2008) 1.63
Bridge helix and trigger loop perturbations generate superactive RNA polymerases. J Biol (2008) 1.60
RNA polymerase backtracking in gene regulation and genome instability. Cell (2012) 1.48
Molecular evolution of multisubunit RNA polymerases: structural analysis. J Mol Biol (2009) 1.45
Nano positioning system reveals the course of upstream and nontemplate DNA within the RNA polymerase II elongation complex. Nucleic Acids Res (2009) 1.32
Active site opening and closure control translocation of multisubunit RNA polymerase. Nucleic Acids Res (2012) 1.27
Rpb9 subunit controls transcription fidelity by delaying NTP sequestration in RNA polymerase II. J Biol Chem (2009) 1.25
Controlled interplay between trigger loop and Gre factor in the RNA polymerase active centre. Nucleic Acids Res (2011) 1.21
Dynamics of pyrophosphate ion release and its coupled trigger loop motion from closed to open state in RNA polymerase II. J Am Chem Soc (2012) 1.20
Allosteric control of catalysis by the F loop of RNA polymerase. Proc Natl Acad Sci U S A (2009) 1.20
Molecular basis for 5-carboxycytosine recognition by RNA polymerase II elongation complex. Nature (2015) 1.20
Dissection of Pol II trigger loop function and Pol II activity-dependent control of start site selection in vivo. PLoS Genet (2012) 1.19
RNA polymerase II trigger loop residues stabilize and position the incoming nucleotide triphosphate in transcription. Proc Natl Acad Sci U S A (2010) 1.17
Complete dissection of transcription elongation reveals slow translocation of RNA polymerase II in a linear ratchet mechanism. Elife (2013) 1.14
Tagetitoxin inhibits RNA polymerase through trapping of the trigger loop. J Biol Chem (2011) 1.14
The nucleotide addition cycle of RNA polymerase is controlled by two molecular hinges in the Bridge Helix domain. BMC Biol (2010) 1.11
Millisecond dynamics of RNA polymerase II translocation at atomic resolution. Proc Natl Acad Sci U S A (2014) 1.11
Macromolecular micromovements: how RNA polymerase translocates. Curr Opin Struct Biol (2009) 1.07
Conformational coupling, bridge helix dynamics and active site dehydration in catalysis by RNA polymerase. Biochim Biophys Acta (2010) 1.06
Molecular basis of transcriptional mutagenesis at 8-oxoguanine. J Biol Chem (2009) 1.04
Transcription termination by the eukaryotic RNA polymerase III. Biochim Biophys Acta (2012) 1.04
Millisecond phase kinetic analysis of elongation catalyzed by human, yeast, and Escherichia coli RNA polymerase. Methods (2009) 1.03
Crystal Structure of a Transcribing RNA Polymerase II Complex Reveals a Complete Transcription Bubble. Mol Cell (2015) 1.01
Schizosacharomyces pombe RNA polymerase II at 3.6-A resolution. Proc Natl Acad Sci U S A (2009) 1.01
Basic mechanism of transcription by RNA polymerase II. Biochim Biophys Acta (2012) 0.98
Basic mechanisms of RNA polymerase II activity and alteration of gene expression in Saccharomyces cerevisiae. Biochim Biophys Acta (2012) 0.98
Interaction of RNA polymerase II fork loop 2 with downstream non-template DNA regulates transcription elongation. J Biol Chem (2011) 0.96
Energetic and structural details of the trigger-loop closing transition in RNA polymerase II. Biophys J (2013) 0.95
Elongation by RNA polymerase: a race through roadblocks. Curr Opin Struct Biol (2009) 0.95
Activity map of the Escherichia coli RNA polymerase bridge helix. J Biol Chem (2011) 0.94
Structure-function studies of the RNA polymerase II elongation complex. Acta Crystallogr D Biol Crystallogr (2009) 0.93
The bridge helix coordinates movements of modules in RNA polymerase. BMC Biol (2010) 0.92
Structure of the 12-subunit RNA polymerase II refined with the aid of anomalous diffraction data. J Biol Chem (2009) 0.92
Effect of a monofunctional phenanthriplatin-DNA adduct on RNA polymerase II transcriptional fidelity and translesion synthesis. J Am Chem Soc (2013) 0.92
Multiple roles of the RNA polymerase {beta}' SW2 region in transcription initiation, promoter escape, and RNA elongation. Nucleic Acids Res (2010) 0.92
RNA polymerase stalls in a post-translocated register and can hyper-translocate. Transcription (2012) 0.90
The RNA polymerase trigger loop functions in all three phases of the transcription cycle. Nucleic Acids Res (2013) 0.90
The RNA polymerase bridge helix YFI motif in catalysis, fidelity and translocation. Biochim Biophys Acta (2012) 0.89
Forks, pincers, and triggers: the tools for nucleotide incorporation and translocation in multi-subunit RNA polymerases. Curr Opin Struct Biol (2009) 0.89
Coliphage HK022 Nun protein inhibits RNA polymerase translocation. Proc Natl Acad Sci U S A (2014) 0.88
CBR antimicrobials alter coupling between the bridge helix and the β subunit in RNA polymerase. Nat Commun (2014) 0.88
Phylogeny of parasitic parabasalia and free-living relatives inferred from conventional markers vs. Rpb1, a single-copy gene. PLoS One (2011) 0.87
Jamming the ratchet of transcription. Nat Struct Mol Biol (2008) 0.86
Human ISWI complexes are targeted by SMARCA5 ATPase and SLIDE domains to help resolve lesion-stalled transcription. Nucleic Acids Res (2014) 0.85
Structures of E. coli σS-transcription initiation complexes provide new insights into polymerase mechanism. Proc Natl Acad Sci U S A (2016) 0.85
Interplay between the trigger loop and the F loop during RNA polymerase catalysis. Nucleic Acids Res (2013) 0.85
A novel conformation of RNA polymerase sheds light on the mechanism of transcription. Transcription (2011) 0.85
Modulation of RNA polymerase activity through the trigger loop folding. Transcription (2012) 0.84
Activation and reactivation of the RNA polymerase II trigger loop for intrinsic RNA cleavage and catalysis. Transcription (2014) 0.84
Mechano-chemical kinetics of DNA replication: identification of the translocation step of a replicative DNA polymerase. Nucleic Acids Res (2015) 0.84
Trigger loop folding determines transcription rate of Escherichia coli's RNA polymerase. Proc Natl Acad Sci U S A (2014) 0.83
Computational simulation strategies for analysis of multisubunit RNA polymerases. Chem Rev (2013) 0.82
A genetic assay for transcription errors reveals multilayer control of RNA polymerase II fidelity. PLoS Genet (2014) 0.82
Dissecting the chemical interactions and substrate structural signatures governing RNA polymerase II trigger loop closure by synthetic nucleic acid analogues. Nucleic Acids Res (2014) 0.82
A small post-translocation energy bias aids nucleotide selection in T7 RNA polymerase transcription. Biophys J (2012) 0.82
Molecular Structures of Transcribing RNA Polymerase I. Mol Cell (2016) 0.81
A dual switch controls bacterial enhancer-dependent transcription. Nucleic Acids Res (2012) 0.80
Transcription elongation. Heterogeneous tracking of RNA polymerase and its biological implications. Transcription (2014) 0.80
Strand-specific (asymmetric) contribution of phosphodiester linkages on RNA polymerase II transcriptional efficiency and fidelity. Proc Natl Acad Sci U S A (2014) 0.79
Structural basis of viral RNA-dependent RNA polymerase catalysis and translocation. Proc Natl Acad Sci U S A (2016) 0.78
Understanding the Molecular Basis of RNA Polymerase II Transcription. Isr J Chem (2013) 0.78
Lineage-specific variations in the trigger loop modulate RNA proofreading by bacterial RNA polymerases. Nucleic Acids Res (2016) 0.78
Functional interplay between NTP leaving group and base pair recognition during RNA polymerase II nucleotide incorporation revealed by methylene substitution. Nucleic Acids Res (2016) 0.78
NusG inhibits RNA polymerase backtracking by stabilizing the minimal transcription bubble. Elife (2016) 0.77
Tie me up, tie me down: inhibiting RNA polymerase. Cell (2008) 0.77
Bacterial Transcription as a Target for Antibacterial Drug Development. Microbiol Mol Biol Rev (2016) 0.77
Genome-wide profiling of RNA polymerase transcription at nucleotide resolution in human cells with native elongating transcript sequencing. Nat Protoc (2016) 0.76
Amino Acid Substitutions in the Caenorhabditis elegans RNA Polymerase II Large Subunit AMA-1/RPB-1 that Result in α-Amanitin Resistance and/or Reduced Function. G3 (Bethesda) (2011) 0.76
RNA Polymerase II Trigger Loop Mobility: INDIRECT EFFECTS OF Rpb9. J Biol Chem (2016) 0.76
RNA polymerase II acts as a selective sensor for DNA lesions and endogenous DNA modifications. Transcription (2016) 0.75
Transcribing RNA polymerase III observed by electron cryomicroscopy. FEBS J (2016) 0.75
Elucidation of the Dynamics of Transcription Elongation by RNA Polymerase II using Kinetic Network Models. Acc Chem Res (2016) 0.75
Translocation and fidelity of Escherichia coli RNA polymerase. Transcription (2013) 0.75
Insights into centromeric transcription in mitosis. Transcription (2016) 0.75
A structure-based kinetic model of transcription. Transcription (2016) 0.75
Complete RNA polymerase II elongation complex structure and its interactions with NTP and TFIIS. Mol Cell (2004) 4.20
Architecture of the RNA polymerase II-TFIIF complex revealed by cross-linking and mass spectrometry. EMBO J (2010) 3.40
Architecture of the RNA polymerase II-TFIIS complex and implications for mRNA cleavage. Cell (2003) 3.30
Uniform transitions of the general RNA polymerase II transcription complex. Nat Struct Mol Biol (2010) 3.25
RNA polymerase II-TFIIB structure and mechanism of transcription initiation. Nature (2009) 2.98
Recognition of RNA polymerase II carboxy-terminal domain by 3'-RNA-processing factors. Nature (2004) 2.86
Functional architecture of RNA polymerase I. Cell (2007) 2.86
A structural perspective of CTD function. Genes Dev (2005) 2.85
Structures of complete RNA polymerase II and its subcomplex, Rpb4/7. J Biol Chem (2004) 2.52
Architecture of initiation-competent 12-subunit RNA polymerase II. Proc Natl Acad Sci U S A (2003) 2.39
Dynamic transcriptome analysis measures rates of mRNA synthesis and decay in yeast. Mol Syst Biol (2011) 2.37
Structural basis of transcription: alpha-amanitin-RNA polymerase II cocrystal at 2.8 A resolution. Proc Natl Acad Sci U S A (2002) 2.37
Architecture of the RNA polymerase-Spt4/5 complex and basis of universal transcription processivity. EMBO J (2011) 2.22
Structural basis of RNA polymerase II backtracking, arrest and reactivation. Nature (2011) 2.19
CTD tyrosine phosphorylation impairs termination factor recruitment to RNA polymerase II. Science (2012) 2.05
Structural basis of transcription: mismatch-specific fidelity mechanisms and paused RNA polymerase II with frayed RNA. Mol Cell (2009) 2.00
Mechanism of translesion transcription by RNA polymerase II and its role in cellular resistance to DNA damage. Mol Cell (2012) 1.96
Iwr1 directs RNA polymerase II nuclear import. Mol Cell (2011) 1.88
Conservation between the RNA polymerase I, II, and III transcription initiation machineries. Mol Cell (2012) 1.86
A nano-positioning system for macromolecular structural analysis. Nat Methods (2008) 1.84
Structure of human mitochondrial RNA polymerase. Nature (2011) 1.82
CPD damage recognition by transcribing RNA polymerase II. Science (2007) 1.80
A cytoplasmic complex mediates specific mRNA recognition and localization in yeast. PLoS Biol (2011) 1.78
Comparative dynamic transcriptome analysis (cDTA) reveals mutual feedback between mRNA synthesis and degradation. Genome Res (2012) 1.77
RNA polymerase fidelity and transcriptional proofreading. Curr Opin Struct Biol (2009) 1.77
Molecular basis of RNA-dependent RNA polymerase II activity. Nature (2007) 1.71
Structure of an archaeal RNA polymerase. J Mol Biol (2007) 1.65
Single-molecule tracking of mRNA exiting from RNA polymerase II. Proc Natl Acad Sci U S A (2007) 1.59
Molecular basis of RNA polymerase III transcription repression by Maf1. Cell (2010) 1.57
Structure of a bifunctional DNA primase-polymerase. Nat Struct Mol Biol (2004) 1.52
Structure and function of the initially transcribing RNA polymerase II-TFIIB complex. Nature (2012) 1.48
Structure and mechanism of RNA polymerase II CTD phosphatases. Mol Cell (2004) 1.46
Transcriptome surveillance by selective termination of noncoding RNA synthesis. Cell (2013) 1.43
Structure and TBP binding of the Mediator head subcomplex Med8-Med18-Med20. Nat Struct Mol Biol (2006) 1.43
RNA polymerase I structure and transcription regulation. Nature (2013) 1.42
RNA polymerase I contains a TFIIF-related DNA-binding subcomplex. Mol Cell (2010) 1.40
Structural biology of RNA polymerase III: subcomplex C17/25 X-ray structure and 11 subunit enzyme model. Mol Cell (2006) 1.39
Spt4/5 stimulates transcription elongation through the RNA polymerase clamp coiled-coil motif. Nucleic Acids Res (2010) 1.38
Global analysis of eukaryotic mRNA degradation reveals Xrn1-dependent buffering of transcript levels. Mol Cell (2013) 1.35
Mechanism of transcriptional stalling at cisplatin-damaged DNA. Nat Struct Mol Biol (2007) 1.32
Nano positioning system reveals the course of upstream and nontemplate DNA within the RNA polymerase II elongation complex. Nucleic Acids Res (2009) 1.32
Structural basis of initial RNA polymerase II transcription. EMBO J (2011) 1.29
Structural biology of RNA polymerase III: mass spectrometry elucidates subcomplex architecture. Structure (2007) 1.19
A conserved mediator hinge revealed in the structure of the MED7.MED21 (Med7.Srb7) heterodimer. J Biol Chem (2005) 1.17
Structure of the Mediator head module. Nature (2012) 1.17
A movie of RNA polymerase II transcription. Cell (2012) 1.17
Crosslinking-MS analysis reveals RNA polymerase I domain architecture and basis of rRNA cleavage. Nucleic Acids Res (2012) 1.17
Structure-function analysis of the RNA polymerase cleft loops elucidates initial transcription, DNA unwinding and RNA displacement. Nucleic Acids Res (2007) 1.17
A movie of the RNA polymerase nucleotide addition cycle. Curr Opin Struct Biol (2009) 1.17
Structure and in vivo requirement of the yeast Spt6 SH2 domain. J Mol Biol (2009) 1.16
Identification, structure, and functional requirement of the Mediator submodule Med7N/31. EMBO J (2008) 1.14
Structure of an RNA polymerase II-RNA inhibitor complex elucidates transcription regulation by noncoding RNAs. Nat Struct Mol Biol (2005) 1.14
Structure and carboxyl-terminal domain (CTD) binding of the Set2 SRI domain that couples histone H3 Lys36 methylation to transcription. J Biol Chem (2005) 1.14
Template misalignment in multisubunit RNA polymerases and transcription fidelity. Mol Cell (2006) 1.13
An extended winged helix domain in general transcription factor E/IIE alpha. J Biol Chem (2003) 1.13
A structural perspective on Mediator function. Curr Opin Cell Biol (2012) 1.13
The phosphatidylserine receptor from Hydra is a nuclear protein with potential Fe(II) dependent oxygenase activity. BMC Cell Biol (2004) 1.10
Periodic mRNA synthesis and degradation co-operate during cell cycle gene expression. Mol Syst Biol (2014) 1.10
Molecular basis of Rrn3-regulated RNA polymerase I initiation and cell growth. Genes Dev (2011) 1.09
Structural basis of transcription elongation. Biochim Biophys Acta (2012) 1.09
Genome-associated RNA polymerase II includes the dissociable Rpb4/7 subcomplex. J Biol Chem (2008) 1.08
Structure and VP16 binding of the Mediator Med25 activator interaction domain. Nat Struct Mol Biol (2011) 1.08
Fluorescence detection of nucleic acids and proteins in multi-component crystals. Acta Crystallogr D Biol Crystallogr (2006) 1.07
Structure of human mitochondrial RNA polymerase elongation complex. Nat Struct Mol Biol (2013) 1.06
Torpedo nuclease Rat1 is insufficient to terminate RNA polymerase II in vitro. J Biol Chem (2009) 1.05
Molecular basis of transcriptional mutagenesis at 8-oxoguanine. J Biol Chem (2009) 1.04
The mRNA transcription/processing factor Ssu72 is a potential tyrosine phosphatase. J Biol Chem (2003) 1.03
Structure-system correlation identifies a gene regulatory Mediator submodule. Genes Dev (2008) 1.03
Dynamic architecture of a minimal RNA polymerase II open promoter complex. Mol Cell (2012) 1.01
A tandem SH2 domain in transcription elongation factor Spt6 binds the phosphorylated RNA polymerase II C-terminal repeat domain (CTD). J Biol Chem (2010) 1.00
The spt5 C-terminal region recruits yeast 3' RNA cleavage factor I. Mol Cell Biol (2012) 0.99
Multisubunit RNA polymerases melt only a single DNA base pair downstream of the active site. J Biol Chem (2007) 0.99
Model of the Mediator middle module based on protein cross-linking. Nucleic Acids Res (2013) 0.98
A novel intermediate in transcription initiation by human mitochondrial RNA polymerase. Nucleic Acids Res (2014) 0.98
Archaeal transcription: function of an alternative transcription factor B from Pyrococcus furiosus. J Bacteriol (2007) 0.97
Structure of the mediator subunit cyclin C and its implications for CDK8 function. J Mol Biol (2005) 0.97
Evolution of two modes of intrinsic RNA polymerase transcript cleavage. J Biol Chem (2011) 0.97
Mediator head subcomplex Med11/22 contains a common helix bundle building block with a specific function in transcription initiation complex stabilization. Nucleic Acids Res (2011) 0.96
A conformational switch underlies ClpP protease function. Angew Chem Int Ed Engl (2011) 0.96
RNA polymerase III subunit architecture and implications for open promoter complex formation. Proc Natl Acad Sci U S A (2012) 0.96
Preparation and topology of the Mediator middle module. Nucleic Acids Res (2010) 0.95
Biogenesis of multisubunit RNA polymerases. Trends Biochem Sci (2012) 0.94
Site specific phosphorylation of yeast RNA polymerase I. Nucleic Acids Res (2007) 0.94
The transcription elongation factor Bur1-Bur2 interacts with replication protein A and maintains genome stability during replication stress. J Biol Chem (2010) 0.94
Multiplexed proteomics mapping of yeast RNA polymerase II and III allows near-complete sequence coverage and reveals several novel phosphorylation sites. Anal Chem (2008) 0.93
Structure-function studies of the RNA polymerase II elongation complex. Acta Crystallogr D Biol Crystallogr (2009) 0.93
Measurement of genome-wide RNA synthesis and decay rates with Dynamic Transcriptome Analysis (DTA). Bioinformatics (2012) 0.92
Cap completion and C-terminal repeat domain kinase recruitment underlie the initiation-elongation transition of RNA polymerase II. Mol Cell Biol (2013) 0.91
The RNA polymerase trigger loop functions in all three phases of the transcription cycle. Nucleic Acids Res (2013) 0.90
Drosophila miR-277 controls branched-chain amino acid catabolism and affects lifespan. RNA Biol (2013) 0.89
The dynamic machinery of mRNA elongation. Curr Opin Struct Biol (2005) 0.89
Recruitment of TREX to the transcription machinery by its direct binding to the phospho-CTD of RNA polymerase II. PLoS Genet (2013) 0.87
MC EMiNEM maps the interaction landscape of the Mediator. PLoS Comput Biol (2012) 0.87
Proteins: how RNA polymerases work. Curr Opin Struct Biol (2009) 0.86
DNA photodamage recognition by RNA polymerase II. FEBS Lett (2007) 0.85
The archaeal RNA polymerase subunit P and the eukaryotic polymerase subunit Rpb12 are interchangeable in vivo and in vitro. Mol Microbiol (2008) 0.85
BRF1 mutations alter RNA polymerase III-dependent transcription and cause neurodevelopmental anomalies. Genome Res (2015) 0.85
Mediator phosphorylation prevents stress response transcription during non-stress conditions. J Biol Chem (2012) 0.85
The RNA polymerase II C-terminal domain-interacting domain of yeast Nrd1 contributes to the choice of termination pathway and couples to RNA processing by the nuclear exosome. J Biol Chem (2013) 0.85