(Q37186482)

18 August 2017

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

1 reference

18 August 2017

Toyotaka Ishibashi

2

0 references

Maria L Kireeva

object named as

Maria L Kireeva

4

0 references

Carlos Bustamante

object named as

Carlos J Bustamante

7

0 references

author name string

Manchuta Dangkulwanich

1

1 reference

18 August 2017

Shixin Liu

3

1 reference

18 August 2017

Lucyna Lubkowska

5

1 reference

18 August 2017

Mikhail Kashlev

6

1 reference

18 August 2017

language of work or name

English

0 references

publication date

24 September 2013

1 reference

18 August 2017

1 reference

18 August 2017

2

1 reference

18 August 2017

e00971

1 reference

Eukaryotic transcriptional dynamics: from single molecules to cell populations

18 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3778554

Structural basis of transcriptional pausing in bacteria

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3778554

RNA polymerase stalls in a post-translocated register and can hyper-translocate

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3778554

Nascent RNA structure modulates the transcriptional dynamics of RNA polymerases

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3778554

Active site opening and closure control translocation of multisubunit RNA polymerase

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3778554

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3778554

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3778554

Unwrapping of nucleosomal DNA ends: a multiscale molecular dynamics study

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3778554

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3778554

The elongation rate of RNA polymerase determines the fate of transcribed nucleosomes.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3778554

Structural basis of initial RNA polymerase II transcription

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3778554

A unified model of transcription elongation: what have we learned from single-molecule experiments?

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3778554

Structural basis of RNA polymerase II backtracking, arrest and reactivation

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3778554

Translocation by multi-subunit RNA polymerases.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3778554

Nucleosomal fluctuations govern the transcription dynamics of RNA polymerase II.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3778554

Structural basis of transcription: mismatch-specific fidelity mechanisms and paused RNA polymerase II with frayed RNA

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3778554

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3778554

Mechanism of sequence-specific pausing of bacterial RNA polymerase

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3778554

Bridge helix and trigger loop perturbations generate superactive RNA polymerases.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3778554

Thermal probing of E. coli RNA polymerase off-pathway mechanisms

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3778554

Structural basis of transcription inhibition by alpha-amanitin and implications for RNA polymerase II translocation

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3778554

The RNA polymerase II trigger loop functions in substrate selection and is directly targeted by alpha-amanitin

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3778554

Single-molecule studies of RNA polymerase: motoring along

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3778554

Structural basis for substrate loading in bacterial RNA polymerase

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3778554

DNA translocation and loop formation mechanism of chromatin remodeling by SWI/SNF and RSC.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3778554

Structural basis of transcription: role of the trigger loop in substrate specificity and catalysis

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3778554

The regulatory roles and mechanism of transcriptional pausing

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3778554

Thermodynamic and kinetic modeling of transcriptional pausing

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3778554

Mutations in the Saccharomyces cerevisiae RPB1 gene conferring hypersensitivity to 6-azauracil

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3778554

Direct observation of base-pair stepping by RNA polymerase

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3778554

Structural basis of transcription inhibition by antibiotic streptolydigin.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3778554

Thinking quantitatively about transcriptional regulation.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3778554

Rapid spontaneous accessibility of nucleosomal DNA.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3778554

Structural basis of transcription: nucleotide selection by rotation in the RNA polymerase II active center

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3778554

Measurement of histone-DNA interaction free energy in nucleosomes

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3778554

Architecture of the RNA polymerase II-TFIIS complex and implications for mRNA cleavage

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3778554

Using mechanical force to probe the mechanism of pausing and arrest during continuous elongation by Escherichia coli RNA polymerase

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3778554

Pausing by bacterial RNA polymerase is mediated by mechanistically distinct classes of signals

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3778554

Transcriptional arrest: Escherichia coli RNA polymerase translocates backward, leaving the 3' end of the RNA intact and extruded

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3778554

A model for the mechanism of polymerase translocation

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3778554

Entropic elasticity of lambda-phage DNA

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3778554

The single-nucleotide addition cycle in transcription: a biophysical and biochemical perspective

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3778554

Improved thermodynamic parameters and helix initiation factor to predict stability of DNA duplexes

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3778554

Conformational coupling in DNA polymerase fidelity

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3778554

Nucleosomal elements that control the topography of the barrier to transcription

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3778554

The origin of short transcriptional pauses

26 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3778554

Transient reversal of RNA polymerase II active site closing controls fidelity of transcription elongation

26 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3778554

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

26 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3778554

Downstream DNA sequence effects on transcription elongation. Allosteric binding of nucleoside triphosphates facilitates translocation via a ratchet motion

26 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3778554

Single-molecule study of transcriptional pausing and arrest by E. coli RNA polymerase

26 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3778554

Ribonucleic acid chain elongation by Escherichia coli ribonucleic acid polymerase. I. Isolation of ternary complexes and the kinetics of elongation.

26 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3778554

A thermodynamic analysis of RNA transcript elongation and termination in Escherichia coli

26 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3778554

Partition analysis and concept of net rate constants as tools in enzyme kinetics

26 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3778554

Intrinsic translocation barrier as an initial step in pausing by RNA polymerase II.

26 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3778554

RNA polymerase backtracking in gene regulation and genome instability

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3778554

Backtracking determines the force sensitivity of RNAP II in a factor-dependent manner

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3778554

Dynamic error correction and regulation of downstream bubble opening by human RNA polymerase II.

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3778554

The structural mechanism of translocation and helicase activity in T7 RNA polymerase

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3778554

DNA translocation and nucleosome remodeling assays by the RSC chromatin remodeling complex.

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3778554

NTP-driven translocation by human RNA polymerase II.

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3778554

Allosteric binding of nucleoside triphosphates to RNA polymerase regulates transcription elongation.

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3778554

RNA polymerase switches between inactivated and activated states By translocating back and forth along the DNA and the RNA.

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3778554

The RNA-DNA hybrid maintains the register of transcription by preventing backtracking of RNA polymerase.

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3778554

A Ratchet Mechanism of Transcription Elongation and Its Control

3 September 2018

1 reference

Crossref

https://api.crossref.org/works/10.7554%2FELIFE.00971

Temperature dependence of thermodynamic properties for DNA/DNA and RNA/DNA duplex formation

21 January 2018

1 reference

12 December 2020

Reaction pathways in transcript elongation

1 reference

12 December 2020

New DNA sequence rules for high affinity binding to histone octamer and sequence-directed nucleosome positioning

1 reference

12 December 2020

Sequence-dependent kinetic model for transcription elongation by RNA polymerase

1 reference

12 December 2020

Nature of the nucleosomal barrier to RNA polymerase II

1 reference

12 December 2020

Nucleosomes can form a polar barrier to transcript elongation by RNA polymerase II

1 reference

12 December 2020

Mechanochemical kinetics of transcription elongation

1 reference

12 December 2020

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

1 reference

12 December 2020

Nucleosome Immobilization Strategies for Single-Pair FRET Microscopy

1 reference

12 December 2020

Identifiers

DOI

10.7554/ELIFE.00971

1 reference

18 August 2017

1 reference

18 August 2017

1 reference