4.8 Article

Multiple roles of the coding sequence 5 ' end in gene expression regulation

Related references

Note: Only part of the references are listed.
Article Biochemistry & Molecular Biology

Challenges and obstacles related to solving the codon bias riddles

Tamir Tuller

BIOCHEMICAL SOCIETY TRANSACTIONS (2014)

Article Biochemistry & Molecular Biology

Translation elongation can control translation initiation on eukaryotic mRNAs

Dominique Chu et al.

EMBO JOURNAL (2014)

Article Biochemistry & Molecular Biology

Positive Charge Loading at Protein Termini Is Due to Membrane Protein Topology, Not a Translational Ramp

Catherine A. Charneski et al.

MOLECULAR BIOLOGY AND EVOLUTION (2014)

Article Biochemistry & Molecular Biology

Translation inhibitors cause abnormalities in ribosome profiling experiments

Maxim V. Gerashchenko et al.

NUCLEIC ACIDS RESEARCH (2014)

Article Biochemistry & Molecular Biology

The effect of tRNA levels on decoding times of mRNA codons

Alexandra Dana et al.

NUCLEIC ACIDS RESEARCH (2014)

Article Biochemistry & Molecular Biology

Codon-by-Codon Modulation of Translational Speed and Accuracy Via mRNA Folding

Jian-Rong Yang et al.

PLOS BIOLOGY (2014)

Article Biochemical Research Methods

Speed Controls in Translating Secretory Proteins in Eukaryotes - an Evolutionary Perspective

Shelly Mahlab et al.

PLOS COMPUTATIONAL BIOLOGY (2014)

Article Biochemistry & Molecular Biology

Rate-Limiting Steps in Yeast Protein Translation

Premal Shah et al.

Article Biotechnology & Applied Microbiology

Mapping the translation initiation landscape of an S-cerevisiae gene using fluorescent proteins

Tuval Ben-Yehezkel et al.

GENOMICS (2013)

Article Biochemistry & Molecular Biology

Widespread Regulation of Translation by Elongation Pausing in Heat Shock

Reut Shalgi et al.

MOLECULAR CELL (2013)

Article Biochemistry & Molecular Biology

Efficient translation initiation dictates codon usage at gene start

Kajetan Bentele et al.

MOLECULAR SYSTEMS BIOLOGY (2013)

Article Biochemistry & Molecular Biology

Evolutionary conservation of codon optimality reveals hidden signatures of cotranslational folding

Sebastian Pechmann et al.

NATURE STRUCTURAL & MOLECULAR BIOLOGY (2013)

Article Multidisciplinary Sciences

Nascent peptides that block protein synthesis in bacteria

Christopher J. Woolstenhulme et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2013)

Article Multidisciplinary Sciences

Exonic Transcription Factor Binding Directs Codon Choice and Affects Protein Evolution

Andrew B. Stergachis et al.

SCIENCE (2013)

Article Multidisciplinary Sciences

Causes and Effects of N-Terminal Codon Bias in Bacterial Genes

Daniel B. Goodman et al.

SCIENCE (2013)

Article Biochemistry & Molecular Biology

Positively Charged Residues Are the Major Determinants of Ribosomal Velocity

Catherine A. Charneski et al.

PLOS BIOLOGY (2013)

Article Biochemical Research Methods

New Universal Rules of Eukaryotic Translation Initiation Fidelity

Hadas Zur et al.

PLOS COMPUTATIONAL BIOLOGY (2013)

Article Biochemistry & Molecular Biology

Strong association between mRNA folding strength and protein abundance in S. cerevisiae

Hadas Zur et al.

EMBO REPORTS (2012)

Review Biochemical Research Methods

Engineering genes for predictable protein expression

Claes Gustafsson et al.

PROTEIN EXPRESSION AND PURIFICATION (2012)

Review Genetics & Heredity

Speeding with control: codon usage, tRNAs, and ribosomes

Eva Maria Novoa et al.

TRENDS IN GENETICS (2012)

Article Biochemical Research Methods

Determinants of Translation Elongation Speed and Ribosomal Profiling Biases in Mouse Embryonic Stem Cells

Alexandra Dana et al.

PLOS COMPUTATIONAL BIOLOGY (2012)

Article Evolutionary Biology

Reduced stability of mRNA secondary structure near the translation-initiation site in dsDNA viruses

Tong Zhou et al.

BMC EVOLUTIONARY BIOLOGY (2011)

Article Evolutionary Biology

Selection for Translation Efficiency on Synonymous Polymorphisms in Recent Human Evolution

Yedael Y. Waldman et al.

GENOME BIOLOGY AND EVOLUTION (2011)

Review Biochemistry & Molecular Biology

Determinants of translation efficiency and accuracy

Hila Gingold et al.

MOLECULAR SYSTEMS BIOLOGY (2011)

Review Genetics & Heredity

Synonymous but not the same: the causes and consequences of codon bias

Joshua B. Plotkin et al.

NATURE REVIEWS GENETICS (2011)

Review Genetics & Heredity

Understanding the contribution of synonymous mutations to human disease

Zuben E. Sauna et al.

NATURE REVIEWS GENETICS (2011)

Article Multidisciplinary Sciences

Sequence Features of E. coli mRNAs Affect Their Degradation

Gal Lenz et al.

PLOS ONE (2011)

Article Biochemistry & Molecular Biology

Wobble base-pairing slows in vivo translation elongation in metazoans

Michael Stadler et al.

Article Biotechnology & Applied Microbiology

Composite effects of gene determinants on the translation speed and density of ribosomes

Tamir Tuller et al.

GENOME BIOLOGY (2011)

Article Biochemical Research Methods

The mRNA landscape at yeast translation initiation sites

A. Robbins-Pianka et al.

BIOINFORMATICS (2010)

Article Biotechnology & Applied Microbiology

Increased incidence of rare codon clusters at 5′ and 3′ gene termini: implications for function

Thomas F. Clarke et al.

BMC GENOMICS (2010)

Review Biochemistry & Molecular Biology

How the Sequence of a Gene Can Tune Its Translation

Kurt Fredrick et al.

Article Biochemistry & Molecular Biology

An Evolutionarily Conserved Mechanism for Controlling the Efficiency of Protein Translation

Tamir Tuller et al.

Article Biochemistry & Molecular Biology

A Role for Codon Order in Translation Dynamics

Gina Cannarrozzi et al.

Review Virology

Insights into dengue virus genome replication

Sofia Lizeth Alcaraz-Estrada et al.

FUTURE VIROLOGY (2010)

Article Biochemistry & Molecular Biology

Overlapping codes within protein-coding sequences

Shalev Itzkovitz et al.

GENOME RESEARCH (2010)

Article Biochemistry & Molecular Biology

Dual Sites of Protein Initiation Control the Localization and Myristoylation of Methionine Sulfoxide Reductase A

Geumsoo Kim et al.

JOURNAL OF BIOLOGICAL CHEMISTRY (2010)

Article Biochemistry & Molecular Biology

Multifactorial Determinants of Protein Expression in Prokaryotic Open Reading Frames

Malin Allert et al.

JOURNAL OF MOLECULAR BIOLOGY (2010)

Article Multidisciplinary Sciences

Genome-wide measurement of RNA secondary structure in yeast

Michael Kertesz et al.

NATURE (2010)

Article Multidisciplinary Sciences

Deciphering the splicing code

Yoseph Barash et al.

NATURE (2010)

Article Biochemistry & Molecular Biology

Translation efficiency in humans: tissue specificity, global optimization and differences between developmental stages

Yedael Y. Waldman et al.

NUCLEIC ACIDS RESEARCH (2010)

Article Multidisciplinary Sciences

Translation efficiency is determined by both codon bias and folding energy

Tamir Tuller et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2010)

Editorial Material Multidisciplinary Sciences

New Roles for Codon Usage

Ivana Weygand-Durasevic et al.

SCIENCE (2010)

Article Biochemical Research Methods

A Universal Trend of Reduced mRNA Stability near the Translation-Initiation Site in Prokaryotes and Eukaryotes

Wanjun Gu et al.

PLOS COMPUTATIONAL BIOLOGY (2010)

Article Biochemistry & Molecular Biology

Estimating Translational Selection in Eukaryotic Genomes

Mario dos Reis et al.

MOLECULAR BIOLOGY AND EVOLUTION (2009)

Review Genetics & Heredity

The evolutionary consequences of erroneous protein synthesis

D. Allan Drummond et al.

NATURE REVIEWS GENETICS (2009)

Article Biochemistry & Molecular Biology

Transient ribosomal attenuation coordinates protein synthesis and co-translational folding

Gong Zhang et al.

NATURE STRUCTURAL & MOLECULAR BIOLOGY (2009)

Article Multidisciplinary Sciences

Design Parameters to Control Synthetic Gene Expression in Escherichia coli

Mark Welch et al.

PLOS ONE (2009)

Article Multidisciplinary Sciences

Coding-Sequence Determinants of Gene Expression in Escherichia coli

Grzegorz Kudla et al.

SCIENCE (2009)

Article Multidisciplinary Sciences

Genome-Wide Analysis in Vivo of Translation with Nucleotide Resolution Using Ribosome Profiling

Nicholas T. Ingolia et al.

SCIENCE (2009)

Review Biochemistry & Molecular Biology

Biased codon usage in signal peptides: a role in protein export

Yaramah M. Zalucki et al.

TRENDS IN MICROBIOLOGY (2009)

Review Genetics & Heredity

Selection on Codon Bias

Ruth Hershberg et al.

ANNUAL REVIEW OF GENETICS (2008)

Article Biotechnology & Applied Microbiology

Analysis of the distribution of functionally relevant rare codons

Michael Widmann et al.

BMC GENOMICS (2008)

Article Biochemistry & Molecular Biology

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

D. Allan Drummond et al.

Article Biochemistry & Molecular Biology

Electrostatics in the Ribosomal Tunnel Modulate Chain Elongation Rates

Jianli Lu et al.

JOURNAL OF MOLECULAR BIOLOGY (2008)

Article Biochemistry & Molecular Biology

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

So Nakagawa et al.

NUCLEIC ACIDS RESEARCH (2008)

Article Biochemistry & Molecular Biology

Combining models of protein translation and population genetics to predict protein production rates from codon usage patterns

Michael A. Gilchrist

MOLECULAR BIOLOGY AND EVOLUTION (2007)

Review Microbiology

Maturation and degradation of RNA in bacteria

Ciaran Condon

CURRENT OPINION IN MICROBIOLOGY (2007)

Article Multidisciplinary Sciences

A silent polymorphism in the MDR1 gene changes substrate specificity

Chava Kimchi-Sarfaty et al.

SCIENCE (2007)

Review Genetics & Heredity

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

JV Chamary et al.

NATURE REVIEWS GENETICS (2006)

Review Cell Biology

Plant organellar protein targeting: a traffic plan still under construction

SA Mackenzie

TRENDS IN CELL BIOLOGY (2005)

Article Biochemistry & Molecular Biology

Variation in the strength of selected codon usage bias among bacteria

PM Sharp et al.

NUCLEIC ACIDS RESEARCH (2005)

Article Biochemistry & Molecular Biology

Solving the riddle of codon usage preferences: a test for translational selection

M dos Reis et al.

NUCLEIC ACIDS RESEARCH (2004)

Article Multidisciplinary Sciences

The origins of genome complexity

M Lynch et al.

SCIENCE (2003)

Article Biochemistry & Molecular Biology

Distribution of rare triplets along mRNA and their relation to protein folding

CH Makhoul et al.

JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS (2002)

Article Biochemistry & Molecular Biology

Conserved RNA secondary structures in Picornaviridae genomes

C Witwer et al.

NUCLEIC ACIDS RESEARCH (2001)

Review Genetics & Heredity

Isochores and the evolutionary genomics of vertebrates

G Bernardi