A universal trend of reduced mRNA stability near the translation-initiation site in prokaryotes and eukaryotes (Q33530134)

27 July 2017

title

A universal trend of reduced mRNA stability near the translation-initiation site in prokaryotes and eukaryotes (English)

1 reference

27 July 2017

0 references

3

1 reference

27 July 2017

2

1 reference

30 October 2018

Wanjun Gu

1

1 reference

27 July 2017

publication date

5 February 2010

1 reference

PLOS Computational Biology

27 July 2017

language of work or name

English

0 references

published in

1 reference

27 July 2017

volume

6

1 reference

27 July 2017

issue

2

1 reference

27 July 2017

page(s)

e1000664

1 reference

Creative Commons Attribution 4.0 International

27 July 2017

copyright license

start time

5 February 2010

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

Coding-sequence determinants of gene expression in Escherichia coli

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2816680

Translationally optimal codons associate with structurally sensitive sites in proteins

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2816680

Conflicting selection pressures on synonymous codon use in yeast suggest selection on mRNA secondary structures

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2816680

Mistranslation-induced protein misfolding as a dominant constraint on coding-sequence evolution.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2816680

Diversity of preferred nucleotide sequences around the translation initiation codon in eukaryote genomes

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2816680

Structural mapping of protein interactions reveals differences in evolutionary pressures correlated to mRNA level and protein abundance

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2816680

Translation initiation region sequence preferences in Escherichia coli

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2816680

Evidence for a trade-off between translational efficiency and splicing regulation in determining synonymous codon usage in Drosophila melanogaster

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2816680

Selection for efficient translation initiation biases codon usage at second amino acid position in secretory proteins

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2816680

Protein and DNA sequence determinants of thermophilic adaptation

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2816680

A "silent" polymorphism in the MDR1 gene changes substrate specificity

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2816680

Synonymous codon usage in Escherichia coli: selection for translational accuracy.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2816680

Naturally occurring adenines within mRNA coding sequences affect ribosome binding and expression in Escherichia coli

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2816680

Selection acts on DNA secondary structures to decrease transcriptional mutagenesis

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2816680

High guanine and cytosine content increases mRNA levels in mammalian cells

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2816680

On the correlation between genomic G+C content and optimal growth temperature in prokaryotes: data quality and confounding factors

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2816680

Highly expressed proteins have an increased frequency of alanine in the second amino acid position.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2816680

Memory efficient folding algorithms for circular RNA secondary structures

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2816680

Hearing silence: non-neutral evolution at synonymous sites in mammals

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2816680

Regulation of translation via mRNA structure in prokaryotes and eukaryotes

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2816680

Evidence for selection on synonymous mutations affecting stability of mRNA secondary structure in mammals

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2816680

AU-rich sequences within 5' untranslated leaders enhance translation and stabilize mRNA in Escherichia coli.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2816680

A codon window in mRNA downstream of the initiation codon where NGG codons give strongly reduced gene expression in Escherichia coli

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2816680

Integrating high-throughput and computational data elucidates bacterial networks

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2816680

A gene atlas of the mouse and human protein-encoding transcriptomes

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2816680

Comparative analysis of orthologous eukaryotic mRNAs: potential hidden functional signals

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2816680

Widespread selection for local RNA secondary structure in coding regions of bacterial genes

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2816680

DNA helix: the importance of being GC-rich

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2816680

Evolution of synonymous codon usage in metazoans

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2816680

Silent mutations affect in vivo protein folding in Escherichia coli

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2816680

The evolution of isochores

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2816680

Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2816680

Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2816680

mRNAs have greater negative folding free energies than shuffled or codon choice randomized sequences

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2816680

Dissecting the regulatory circuitry of a eukaryotic genome

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2816680

Relationships between genomic G+C content, RNA secondary structures, and optimal growth temperature in prokaryotes

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2816680

Ribosome-mediated translational pause and protein domain organization

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2816680

Codon usage in Caenorhabditis elegans: delineation of translational selection and mutational biases

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2816680

The influence of adenine-rich motifs in the 3' portion of the ribosome binding site on human IFN-gamma gene expression in Escherichia coli

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2816680

Synonymous codon usage in Drosophila melanogaster: natural selection and translational accuracy.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2816680

Codon usage and tRNA content in unicellular and multicellular organisms

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2816680

Codon usage in yeast: cluster analysis clearly differentiates highly and lowly expressed genes

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2816680

An analysis of 5'-noncoding sequences from 699 vertebrate messenger RNAs

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2816680

The 'effective number of codons' used in a gene

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2816680

Determinant of cistron specificity in bacterial ribosomes

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2816680

Translational selection and molecular evolution

21 June 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000664

A single determinant dominates the rate of yeast protein evolution

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000664

Coevolution of codon usage and tRNA genes leads to alternative stable states of biased codon usage

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000664

Synonymous mutations break their silence

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000664

Transient ribosomal attenuation coordinates protein synthesis and co-translational folding

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000664

Enhancement of translation initiation by A/T-rich sequences downstream of the initiation codon in Escherichia coli

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000664

Effects of codon usage versus putative 5'-mRNA structure on the expression of Fusarium solani cutinase in the Escherichia coli cytoplasm

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000664

Influences on translation initiation and early elongation by the messenger RNA region flanking the initiation codon at the 3' side

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000664

Alanine is the main second amino acid in vertebrate proteins and its coding entails increased use of the rare codon GCG.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000664

Evolution of proteins and gene expression levels are coupled in Drosophila and are independently associated with mRNA abundance, protein length, and number of protein-protein interactions

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000664

A gene expression map for the euchromatic genome of Drosophila melanogaster

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000664

Fast folding and comparison of RNA secondary structures

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000664

Highly expressed genes in yeast evolve slowly.

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2816680

Conservation of Translation Initiation Sites Based on Dinucleotide Frequency and Codon Usage in Escherichia coli K-12 (W3110): Non-random Distribution of A/T-rich Sequences Immediately Upstream of the Translation Initiation Codon

31 October 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000664

Evidence for Purifying Selection Against Synonymous Mutations in Mammalian Exonic Splicing Enhancers

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000664

Exonic Splicing Regulatory Elements Skew Synonymous Codon Usage near Intron-exon Boundaries in Mammals

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000664

Correlations between genomic GC levels and optimal growth temperatures in prokaryotes

21 January 2018

1 reference

12 December 2020

Translational enhancement by an element downstream of the initiation codon in Escherichia coli

1 reference

12 December 2020

Unifying measures of gene function and evolution

1 reference

12 December 2020

Synonymous codon substitutions affect ribosome traffic and protein folding during in vitro translation

1 reference

12 December 2020

Determinants of substitution rates in mammalian genes: expression pattern affects selection intensity but not mutation rate

1 reference

12 December 2020

10.1371/JOURNAL.PCBI.1000664

Identifiers

DOI

1 reference

27 July 2017

DBLP publication ID

journals/ploscb/GuZW10

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference

27 July 2017

1 reference