(Q37236782)

19 August 2017

Direct assessment of transcription fidelity by high-resolution RNA sequencing (English)

1 reference

19 August 2017

0 references

Masahiko Imashimizu

1

1 reference

19 August 2017

Taku Oshima

series ordinal

2

1 reference

19 August 2017

Lucyna Lubkowska

series ordinal

3

1 reference

19 August 2017

Mikhail Kashlev

series ordinal

4

1 reference

19 August 2017

language of work or name

English

0 references

publication date

7 August 2013

1 reference

19 August 2017

Nucleic Acids Research

1 reference

19 August 2017

41

1 reference

19 August 2017

19

1 reference

19 August 2017

9090-9104

1 reference

Ultra-deep mutant spectrum profiling: improving sequencing accuracy using overlapping read pairs

19 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3799451

Identifying RNA editing sites using RNA sequencing data alone

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3799451

Control of transcriptional fidelity by active center tuning as derived from RNA polymerase endonuclease reaction

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3799451

The RNA polymerase bridge helix YFI motif in catalysis, fidelity and translocation

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3799451

HIV-1 reverse transcription

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3799451

Detection of ultra-rare mutations by next-generation sequencing

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3799451

Molecular dynamics and mutational analysis of the catalytic and translocation cycle of RNA polymerase

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3799451

Comparative Study of Cyanobacterial and E. coli RNA Polymerases: Misincorporation, Abortive Transcription, and Dependence on Divalent Cations

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3799451

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

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3799451

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

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3799451

Isolation and characterization of transcription fidelity mutants

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3799451

T7 RNA polymerases backed up by covalently trapped proteins catalyze highly error prone transcription

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3799451

Accurate sampling and deep sequencing of the HIV-1 protease gene using a Primer ID

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3799451

Linking RNA polymerase backtracking to genome instability in E. coli

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3799451

Addressing challenges in the production and analysis of illumina sequencing data

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3799451

Comparative analysis of RNA-Seq alignment algorithms and the RNA-Seq unified mapper (RUM).

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3799451

Barcoding bias in high-throughput multiplex sequencing of miRNA.

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3799451

Widespread RNA and DNA sequence differences in the human transcriptome.

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3799451

Detection and quantification of rare mutations with massively parallel sequencing

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3799451

Nascent transcript sequencing visualizes transcription at nucleotide resolution

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3799451

Nature, position, and frequency of mutations made in a single cycle of HIV-1 replication

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3799451

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

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3799451

The Sequence Alignment/Map format and SAMtools

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3799451

Rpb9 subunit controls transcription fidelity by delaying NTP sequestration in RNA polymerase II.

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3799451

Potential role of phenotypic mutations in the evolution of protein expression and stability

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3799451

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3799451

A gripping tale of ribosomal frameshifting: extragenic suppressors of frameshift mutations spotlight P-site realignment

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3799451

Transcriptional infidelity promotes heritable phenotypic change in a bistable gene network

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3799451

8-Oxoguanine-mediated transcriptional mutagenesis causes Ras activation in mammalian cells

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3799451

Knockdown of TFIIS by RNA silencing inhibits cancer cell proliferation and induces apoptosis

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3799451

RNA polymerase II subunit Rpb9 is important for transcriptional fidelity in vivo

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3799451

Transcriptional slippage in bacteria: distribution in sequenced genomes and utilization in IS element gene expression

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3799451

WebLogo: A Sequence Logo Generator

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3799451

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

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3799451

Use of an in vivo reporter assay to test for transcriptional and translational fidelity in yeast

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3799451

Frequency of replication/transcription errors in (A)/(T) runs of human genes

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3799451

Cluster analysis and display of genome-wide expression patterns

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3799451

Functional topography of nascent RNA in elongation intermediates of RNA polymerase

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3799451

Base-calling of automated sequencer traces using phred. II. Error probabilities

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3799451

Intrinsic transcript cleavage activity of RNA polymerase

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3799451

Effect of several metal ions on misincorporation during transcription

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3799451

Sequence logos: a new way to display consensus sequences

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3799451

A constant rate of spontaneous mutation in DNA-based microbes

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3799451

Comment on "Widespread RNA and DNA sequence differences in the human transcriptome".

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3799451

Transcriptional slippage occurs during elongation at runs of adenine or thymine in Escherichia coli

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3799451

Structural and mechanistic relationships between nucleic acid polymerases

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3799451

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

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3799451

Template misalignment in multisubunit RNA polymerases and transcription fidelity

26 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3799451

Histidine-tagged RNA polymerase of Escherichia coli and transcription in solid phase.

26 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3799451

Purification and assay of Escherichia coli transcript cleavage factors GreA and GreB.

26 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3799451

Deletion-insertion mapping of the region non-essential for functioning of the beta-subunit of Escherichia 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=3799451

Fidelity of HIV-1 reverse transcriptase copying RNA in vitro

26 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3799451

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=3799451

Comment on "Widespread RNA and DNA sequence differences in the human transcriptome".

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3799451

Controlled interplay between trigger loop and Gre factor in the RNA polymerase active centre

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3799451

Analysis of promoter targets for Escherichia coli transcription elongation factor GreA in vivo and in vitro

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3799451

Kinetic investigation of Escherichia coli RNA polymerase mutants that influence nucleotide discrimination and transcription fidelity.

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3799451

Engineering of elongation complexes of bacterial and yeast RNA polymerases.

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3799451

Assays and affinity purification of biotinylated and nonbiotinylated forms of double-tagged core RNA polymerase II from Saccharomyces cerevisiae.

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3799451

A New Class of Bacterial RNA Polymerase Inhibitor Affects Nucleotide Addition

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3799451

Cancerous hyper-mutagenesis in p53 genes is possibly associated with transcriptional bypass of DNA lesions

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3799451

Shortening of RNA:DNA hybrid in the elongation complex of RNA polymerase is a prerequisite for transcription termination

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3799451

Counteraction by MutT protein of transcriptional errors caused by oxidative damage.

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3799451

Transcript cleavage factors from E. coli.

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3799451

A Ratchet Mechanism of Transcription Elongation and Its Control

3 September 2018

1 reference

Crossref

https://api.crossref.org/works/10.1093%2FNAR%2FGKT698

An RNA polymerase mutant with reduced accuracy of chain elongation

21 January 2018

1 reference

12 December 2020

Invariance of the nucleoside triphosphate pools of Escherichia coli with growth rate

1 reference

12 December 2020

The frequency of transcriptional and translational errors at nonsense codons in the lacZ gene of Escherichia coli

1 reference

12 December 2020

Multiple RNA polymerase conformations and GreA: control of the fidelity of transcription

1 reference

12 December 2020

Comment on "Widespread RNA and DNA sequence differences in the human transcriptome"

1 reference

12 December 2020

Identifiers

DOI

10.1093/NAR/GKT698

1 reference

19 August 2017

1 reference

19 August 2017

PubMed publication ID

23925128

1 reference