Nascent RNA structure modulates the transcriptional dynamics of RNA polymerases (Q36061367)

11 August 2017

Nascent RNA structure modulates the transcriptional dynamics of RNA polymerases (English)

1 reference

11 August 2017

Toyotaka Ishibashi

3

0 references

Carlos Bustamante

object named as

Carlos Bustamante

series ordinal

4

0 references

author name string

Bradley Zamft

series ordinal

1

1 reference

PMCID

3384149

11 August 2017

Lacramioara Bintu

series ordinal

2

1 reference

PMCID

3384149

11 August 2017

language of work or name

English

0 references

publication date

21 May 2012

1 reference

Proceedings of the National Academy of Sciences of the United States of America

11 August 2017

1 reference

11 August 2017

109

1 reference

11 August 2017

8948-8953

1 reference

11 August 2017

23

1 reference

Termination and antitermination: RNA polymerase runs a stop sign

11 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3384149

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3384149

Structural basis of RNA polymerase II backtracking, arrest and reactivation

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3384149

Revisiting the central dogma one molecule at a time

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3384149

Evolution of multisubunit RNA polymerases in the three domains of life.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3384149

Nucleosomal fluctuations govern the transcription dynamics of RNA polymerase II.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3384149

Overlapping pathways dictate termination of RNA polymerase II transcription.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3384149

RNA helix stability in mixed Na+/Mg2+ solution

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3384149

The regulatory roles and mechanism of transcriptional pausing

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3384149

Differential detection of dual traps improves the spatial resolution of optical tweezers

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3384149

High guanine and cytosine content increases mRNA levels in mammalian cells

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3384149

Rho-dependent transcription termination: more questions than answers

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3384149

Thermodynamic and kinetic modeling of transcriptional pausing

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3384149

Bacteriophage origins of mitochondrial replication and transcription proteins

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3384149

Kinefold web server for RNA/DNA folding path and structure prediction including pseudoknots and knots

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3384149

Backtracking by single RNA polymerase molecules observed at near-base-pair resolution

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3384149

A slow RNA polymerase II affects alternative splicing in vivo

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3384149

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3384149

Pet111p, an inner membrane-bound translational activator that limits expression of the Saccharomyces cerevisiae mitochondrial gene COX2.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3384149

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3384149

Promoter-proximal pausing on the hsp70 promoter in Drosophila melanogaster depends on the upstream regulator

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3384149

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3384149

Increased accommodation of nascent RNA in a product site on RNA polymerase II during arrest

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3384149

Expression of a recoded nuclear gene inserted into yeast mitochondrial DNA is limited by mRNA-specific translational activation.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3384149

Dissection of the his leader pause site by base substitution reveals a multipartite signal that includes a pause RNA hairpin

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3384149

Entropic elasticity of lambda-phage DNA

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3384149

Comparison of Pause Predictions of Two Sequence-Dependent Transcription Models

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3384149

The origin of short transcriptional pauses

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3384149

T7 RNA polymerase studied by force measurements varying cofactor concentration.

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3384149

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

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3384149

Pausing and termination by bacteriophage T7 RNA polymerase.

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3384149

Transcriptional pausing at +62 of the HIV-1 nascent RNA modulates formation of the TAR RNA structure

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3384149

Yeast mitochondrial RNA polymerase is homologous to those encoded by bacteriophages T3 and T7.

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3384149

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

11 July 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1205063109

The transcriptional regulator RfaH stimulates RNA chain synthesis after recruitment to elongation complexes by the exposed nontemplate DNA strand.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1205063109

RfaH and the ops element, components of a novel system controlling bacterial transcription elongation

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1205063109

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1205063109

Fluctuations, pauses, and backtracking in DNA transcription

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1205063109

Promoter binding, initiation, and elongation by bacteriophage T7 RNA polymerase. A single-molecule view of the transcription cycle.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1205063109

Understanding and predicting viscous, elastic, plastic flows.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1205063109

Roles of RNA:DNA hybrid stability, RNA structure, and active site conformation in pausing by human RNA polymerase II.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1205063109

Base composition bias might result from competition for metabolic resources.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1205063109

Expression and purification of wild type and mutant forms of the yeast mitochondrial core RNA polymerase, Rpo41.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1205063109

The diffusion constant of a labeled protein sliding along DNA.

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3384149

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3384149

Transcription against an applied force

23 September 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22615360

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Nature of the nucleosomal barrier to RNA polymerase II

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22615360

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1073/PNAS.1205063109

1 reference

11 August 2017

0 references

1 reference

11 August 2017

1 reference

PMCID

3384149