(Q34145524)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25108353%20AND%20SRC:MED&resulttype=core&format=json

12 March 2020

title

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

1 reference

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12 March 2020

3

1 reference

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12 March 2020

Michael J Bellecourt

4

1 reference

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12 March 2020

7

Robert Landick

1 reference

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12 March 2020

author name string

Pyae P Hein

1

1 reference

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12 March 2020

Kellie E Kolb

2

1 reference

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12 March 2020

Seth A Darst

5

1 reference

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12 March 2020

Rachel A Mooney

6

1 reference

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12 March 2020

publication date

10 August 2014

1 reference

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Nature Structural & Molecular Biology

12 March 2020

published in

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12 March 2020

volume

21

1 reference

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12 March 2020

issue

9

1 reference

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12 March 2020

page(s)

794-802

1 reference

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describes a project that uses

12 March 2020

ImageQuant

1 reference

11 June 2022

https://www.ebi.ac.uk/europepmc/webservices/rest/PMC4156911/fullTextXML

based on heuristic

inferred from PubMed Central ID database lookup

ImageJ

1 reference

11 June 2022

https://www.ebi.ac.uk/europepmc/webservices/rest/PMC4156911/fullTextXML

based on heuristic

inferred from PubMed Central ID database lookup

exact match

https://scigraph.springernature.com/pub.10.1038/nsmb.2867

0 references

cites work

A pause sequence enriched at translation start sites drives transcription dynamics in vivo

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4156911

CBR antimicrobials alter coupling between the bridge helix and the β subunit in RNA polymerase.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4156911

Antisense oligonucleotide-stimulated transcriptional pausing reveals RNA exit channel specificity of RNA polymerase and mechanistic contributions of NusA and RfaH.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4156911

On the importance of cotranscriptional RNA structure formation

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4156911

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4156911

Cys-pair reporters detect a constrained trigger loop in a paused RNA polymerase.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4156911

Structural basis of transcriptional pausing in bacteria

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4156911

Nascent RNA structure modulates the transcriptional dynamics of RNA polymerases

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4156911

A rule of seven in Watson-Crick base-pairing of mismatched sequences.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4156911

Active site opening and closure control translocation of multisubunit RNA polymerase

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4156911

Transcriptional pausing coordinates folding of the aptamer domain and the expression platform of a riboswitch

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4156911

Applied force provides insight into transcriptional pausing and its modulation by transcription factor NusA.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4156911

The β subunit gate loop is required for RNA polymerase modification by RfaH and NusG.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4156911

RNA transcript 3'-proximal sequence affects translocation bias of RNA polymerase

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4156911

RNA folding in transcription elongation complex: implication for transcription termination

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4156911

Complete Structural Model of Escherichia coli RNA Polymerase from a Hybrid Approach

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4156911

The NusA N-terminal domain is necessary and sufficient for enhancement of transcriptional pausing via interaction with the RNA exit channel of RNA polymerase

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4156911

Mechanism of NusG-stimulated pausing, hairpin-dependent pause site selection and intrinsic termination at overlapping pause and termination sites in the Bacillus subtilis trp leader

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4156911

E. coli NusG inhibits backtracking and accelerates pause-free transcription by promoting forward translocation of RNA polymerase

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4156911

Fluorescent pteridine probes for nucleic acid analysis

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4156911

Allosteric control of the RNA polymerase by the elongation factor RfaH

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4156911

Structural basis for substrate loading in bacterial RNA polymerase

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4156911

Structural basis for transcription elongation by bacterial RNA polymerase

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4156911

Direct versus limited-step reconstitution reveals key features of an RNA hairpin-stabilized paused transcription complex

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4156911

Structural Basis for Converting a General Transcription Factor into an Operon-Specific Virulence Regulator

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4156911

The regulatory roles and mechanism of transcriptional pausing

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4156911

Sequence-resolved detection of pausing by single RNA polymerase molecules.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4156911

RNA folding during transcription

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4156911

Investigating local conformations of double-stranded DNA by low-energy circular dichroism of pyrrolo-cytosine

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4156911

Using pyrrolo-deoxycytosine to probe RNA/DNA hybrids containing the human immunodeficiency virus type-1 3' polypurine tract.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4156911

Fluorescence characterization of the transcription bubble in elongation complexes of T7 RNA polymerase

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4156911

Allosteric control of RNA polymerase by a site that contacts nascent RNA hairpins

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4156911

Structural basis of transcription: RNA polymerase II at 2.8 angstrom resolution

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4156911

Folding of a large ribozyme during transcription and the effect of the elongation factor NusA.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4156911

Sequential Folding of the Genomic Ribozyme of the Hepatitis Delta Virus: Structural Analysis of RNA Transcription Intermediates

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4156911

Coupling of rRNA transcription and ribosomal assembly in vivo. Formation of active ribosomal subunits in Escherichia coli requires transcription of rRNA genes by host RNA polymerase which cannot be replaced by bacteriophage T7 RNA polymerase.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4156911

Ultrasensitive hybridization analysis using fluorescence correlation spectroscopy

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4156911

Fate of an intervening sequence ribonucleic acid: excision and cyclization of the Tetrahymena ribosomal ribonucleic acid intervening sequence in vivo

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4156911

Sequential folding of a messenger RNA molecule

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4156911

Amino acid changes in conserved regions of the beta-subunit of Escherichia coli RNA polymerase alter transcription pausing and termination.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4156911

1H NMR study of the base-pairing reactions of d(GGAATTCC): salt effects on the equilibria and kinetics of strand association.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4156911

DNA probes: applications of the principles of nucleic acid hybridization

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4156911

RNA folding during transcription: protocols and studies.

5 July 2018

1 reference

RNA polymerase backtracking in gene regulation and genome instability

21 January 2018

1 reference

Ubiquitous transcriptional pausing is independent of RNA polymerase backtracking.

21 January 2018

1 reference

Pyrrolo-dC and pyrrolo-C: fluorescent analogs of cytidine and 2′-deoxycytidine for the study of oligonucleotides

21 January 2018

1 reference

Pyrrolo-C as a fluorescent probe for monitoring RNA secondary structure formation

21 January 2018

1 reference

Promoter clearance by T7 RNA polymerase. Initial bubble collapse and transcript dissociation monitored by base analog fluorescence

21 January 2018

1 reference

A New Class of Bacterial RNA Polymerase Inhibitor Affects Nucleotide Addition

21 January 2018

1 reference

Role of the RNA polymerase trigger loop in catalysis and pausing.

21 January 2018

1 reference

The role of the bacterial RNA polymerase beta subunit flexible flap domain in transcription termination

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4156911

The Speed of RNA Transcription and Metabolite Binding Kinetics Operate an FMN Riboswitch

28 October 2018

1 reference

The flap domain is required for pause RNA hairpin inhibition of catalysis by RNA polymerase and can modulate intrinsic termination

21 January 2018

1 reference

A central role of the RNA polymerase trigger loop in active-site rearrangement during transcriptional pausing

31 March 2020

1 reference

Co-overexpression of Escherichia coli RNA polymerase subunits allows isolation and analysis of mutant enzymes lacking lineage-specific sequence insertions

31 March 2020

1 reference

31 March 2020

Identifiers

DOI

10.1038/NSMB.2867

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25108353%20AND%20SRC:MED&resulttype=core&format=json

12 March 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25108353%20AND%20SRC:MED&resulttype=core&format=json

12 March 2020

1 reference