Codon optimality, bias and usage in translation and mRNA decay

Emerging Themes in Regulation of Global mRNA Turnover in cis

(2017) Chyi-Ying A. Chen et al.   TRENDS IN BIOCHEMICAL SCIENCES

Widespread position-specific conservation of synonymous rare codons within coding sequences

(2017) Julie L. Chaney et al.   PLoS Computational Biology

Analysis of the association between codon optimality and mRNA stability in Schizosaccharomyces pombe

(2016) Yuriko Harigaya et al.   BMC GENOMICS

Dynamics of Translation of Single mRNA Molecules In Vivo

(2016) Xiaowei Yan et al.   CELL

Adjacent Codons Act in Concert to Modulate Translation Efficiency in Yeast

(2016) Caitlin E. Gamble et al.   CELL

The DEAD-Box Protein Dhh1p Couples mRNA Decay and Translation by Monitoring Codon Optimality

(2016) Aditya Radhakrishnan et al.   CELL

Quality over quantity: optimizing co-translational protein folding with non-‘optimal’ synonymous codons

(2016) Giselle N Jacobson et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Codon identity regulates mRNA stability and translation efficiency during the maternal‐to‐zygotic transition

(2016) Ariel A Bazzini et al.   EMBO JOURNAL

Eyes on Translation

(2016) Marina Chekulaeva et al.   MOLECULAR CELL

Codon Usage and 3′ UTR Length Determine Maternal mRNA Stability in Zebrafish

(2016) Yuichiro Mishima et al.   MOLECULAR CELL

Synonymous Codons Direct Cotranslational Folding toward Different Protein Conformations

(2016) Florian Buhr et al.   MOLECULAR CELL

Codon influence on protein expression in E. coli correlates with mRNA levels

(2016) Grégory Boël et al.   NATURE

The ribosome in action: Tuning of translational efficiency and protein folding

(2016) Marina V. Rodnina   PROTEIN SCIENCE

Codon optimality controls differential mRNA translation during amino acid starvation

(2016) Mridusmita Saikia et al.   RNA

Seeing translation

(2016) S. Iwasaki et al.   SCIENCE

Translation dynamics of single mRNAs in live cells and neurons

(2016) B. Wu et al.   SCIENCE

Real-time quantification of single RNA translation dynamics in living cells

(2016) T. Morisaki et al.   SCIENCE

Improved Ribosome-Footprint and mRNA Measurements Provide Insights into Dynamics and Regulation of Yeast Translation

(2016) David E. Weinberg et al.   Cell Reports

Clarifying the Translational Pausing Landscape in Bacteria by Ribosome Profiling

(2016) Fuad Mohammad et al.   Cell Reports

On the Ribosomal Density that Maximizes Protein Translation Rate

(2016) Yoram Zarai et al.   PLoS One

Roles for Synonymous Codon Usage in Protein Biogenesis

(2015) Julie L. Chaney et al.   Annual Review of Biophysics

Why should cancer biologists care about tRNAs? tRNA synthesis, mRNA translation and the control of growth

(2015) Savraj S. Grewal   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

A comparative genomics study on the effect of individual amino acids on ribosome stalling

(2015) Renana Sabi et al.   BMC GENOMICS

Optimization of Codon Translation Rates via tRNA Modifications Maintains Proteome Integrity

(2015) Danny D. Nedialkova et al.   CELL

Codon Optimality Is a Major Determinant of mRNA Stability

(2015) Vladimir Presnyak et al.   CELL

Pausing on Polyribosomes: Make Way for Elongation in Translational Control

(2015) Joel D. Richter et al.   CELL

Codon Usage Influences the Local Rate of Translation Elongation to Regulate Co-translational Protein Folding

(2015) Chien-Hung Yu et al.   MOLECULAR CELL

Codon Bias as a Means to Fine-Tune Gene Expression

(2015) Tessa E.F. Quax et al.   MOLECULAR CELL

Nonoptimal codon usage influences protein structure in intrinsically disordered regions

(2015) Mian Zhou et al.   MOLECULAR MICROBIOLOGY

Codon-biased translation can be regulated by wobble-base tRNA modification systems during cellular stress responses

(2015) Lauren Endres et al.   RNA Biology

Synthesis at the Speed of Codons

(2015) Kristin S. Koutmou et al.   TRENDS IN BIOCHEMICAL SCIENCES

Understanding Biases in Ribosome Profiling Experiments Reveals Signatures of Translation Dynamics in Yeast

(2015) Jeffrey A. Hussmann et al.   PLoS Genetics

Trm9-Catalyzed tRNA Modifications Regulate Global Protein Expression by Codon-Biased Translation

(2015) Wenjun Deng et al.   PLoS Genetics

A Dual Program for Translation Regulation in Cellular Proliferation and Differentiation

(2014) Hila Gingold et al.   CELL

Global Analysis of mRNA Isoform Half-Lives Reveals Stabilizing and Destabilizing Elements in Yeast

(2014) Joseph V. Geisberg et al.   CELL

Quantifying Absolute Protein Synthesis Rates Reveals Principles Underlying Allocation of Cellular Resources

(2014) Gene-Wei Li et al.   CELL

Modelling the Efficiency of Codon–tRNA Interactions Based on Codon Usage Bias

(2014) Renana Sabi et al.   DNA RESEARCH

Ribosome profiling: new views of translation, from single codons to genome scale

(2014) Nicholas T. Ingolia   NATURE REVIEWS GENETICS

Translation inhibitors cause abnormalities in ribosome profiling experiments

(2014) Maxim V. Gerashchenko et al.   NUCLEIC ACIDS RESEARCH

Measurement of average decoding rates of the 61 sense codons in vivo

(2014) Justin Gardin et al.   eLife

Distinct stages of the translation elongation cycle revealed by sequencing ribosome-protected mRNA fragments

(2014) Liana F Lareau et al.   eLife

Rate-Limiting Steps in Yeast Protein Translation

(2013) Premal Shah et al.   CELL

Translation elongation can control translation initiation on eukaryotic mRNAs

(2013) Dominique Chu et al.   EMBO JOURNAL

Non-optimal codon usage affects expression, structure and function of clock protein FRQ

(2013) Mian Zhou et al.   NATURE

Non-optimal codon usage is a mechanism to achieve circadian clock conditionality

(2013) Yao Xu et al.   NATURE

Translational sensitivity of the Escherichia coli genome to fluctuating tRNA availability

(2013) Sibylle E. Wohlgemuth et al.   NUCLEIC ACIDS RESEARCH

Distinct XPPX sequence motifs induce ribosome stalling, which is rescued by the translation elongation factor EF-P

(2013) L. Peil et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2013) D. B. Goodman et al.   SCIENCE

Positively Charged Residues Are the Major Determinants of Ribosomal Velocity

(2013) Catherine A. Charneski et al.   PLOS BIOLOGY

Ribosome Traffic on mRNAs Maps to Gene Ontology: Genome-wide Quantification of Translation Initiation Rates and Polysome Size Regulation

(2013) Luca Ciandrini et al.   PLoS Computational Biology

Modification of tRNALysUUU by Elongator Is Essential for Efficient Translation of Stress mRNAs

(2013) Jorge Fernández-Vázquez et al.   PLoS Genetics

Loss of a Conserved tRNA Anticodon Modification Perturbs Cellular Signaling

(2013) Boris Zinshteyn et al.   PLoS Genetics

Decoding properties of tRNA leave a detectable signal in codon usage bias

(2012) Alexander C. Roth   BIOINFORMATICS

The Relation of Codon Bias to Tissue-Specific Gene Expression in Arabidopsis thaliana

(2012) S. Camiolo et al.   GENETICS

Silent Substitutions Predictably Alter Translation Elongation Rates and Protein Folding Efficiencies

(2012) Paige S. Spencer et al.   JOURNAL OF MOLECULAR BIOLOGY

Effects of codon sequence on the dynamics of genetic networks

(2012) Ilya Potapov et al.   JOURNAL OF THEORETICAL BIOLOGY

The anti-Shine–Dalgarno sequence drives translational pausing and codon choice in bacteria

(2012) Gene-Wei Li et al.   NATURE

The translational landscape of mTOR signalling steers cancer initiation and metastasis

(2012) Andrew C. Hsieh et al.   NATURE

Evolutionary conservation of codon optimality reveals hidden signatures of cotranslational folding

(2012) Sebastian Pechmann et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

miRNA-Mediated Gene Silencing by Translational Repression Followed by mRNA Deadenylation and Decay

(2012) S. Djuranovic et al.   SCIENCE

Ribosome Profiling Shows That miR-430 Reduces Translation Before Causing mRNA Decay in Zebrafish

(2012) A. A. Bazzini et al.   SCIENCE

Speeding with control: codon usage, tRNAs, and ribosomes

(2012) Eva Maria Novoa et al.   TRENDS IN GENETICS

Reprogramming of tRNA modifications controls the oxidative stress response by codon-biased translation of proteins

(2012) Clement T.Y. Chan et al.   Nature Communications

The DEAD-Box Protein Dhh1 Promotes Decapping by Slowing Ribosome Movement

(2012) Thomas Sweet et al.   PLOS BIOLOGY

Balanced Codon Usage Optimizes Eukaryotic Translational Efficiency

(2012) Wenfeng Qian et al.   PLoS Genetics

Codon usage: Nature's roadmap to expression and folding of proteins

(2011) Evelina Angov   Biotechnology Journal

Codon usage variability determines the correlation between proteome and transcriptome fold changes

(2011) Roberto Olivares-Hernández et al.   BMC Systems Biology

The ribosomal tunnel as a functional environment for nascent polypeptide folding and translational stalling

(2011) Daniel N Wilson et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Determinants of translation efficiency and accuracy

(2011) H. Gingold et al.   Molecular Systems Biology

Disruptive mRNA folding increases translational efficiency of catechol-O-methyltransferase variant

(2011) Douglas Tsao et al.   NUCLEIC ACIDS RESEARCH

The role of tRNA and ribosome competition in coupling the expression of different mRNAs in Saccharomyces cerevisiae

(2011) Dominique Chu et al.   NUCLEIC ACIDS RESEARCH

Regulation of mRNA Translation and Stability by microRNAs

(2010) Marc Robert Fabian et al.   Annual Review of Biochemistry

An Evolutionarily Conserved Mechanism for Controlling the Efficiency of Protein Translation

(2010) Tamir Tuller et al.   CELL

GroEL dependency affects codon usage—support for a critical role of misfolding in gene evolution

(2010) Tobias Warnecke et al.   Molecular Systems Biology

Sequence signatures and mRNA concentration can explain two-thirds of protein abundance variation in a human cell line

(2010) Christine Vogel et al.   Molecular Systems Biology

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

(2010) Joshua B. Plotkin et al.   NATURE REVIEWS GENETICS

Synonymous codon usage influences the local protein structure observed

(2010) Rhodri Saunders et al.   NUCLEIC ACIDS RESEARCH

A comprehensive analysis of translational missense errors in the yeast Saccharomyces cerevisiae

(2010) E. B. Kramer et al.   RNA

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

(2010) Wanjun Gu et al.   PLoS Computational Biology

A Quantitative Systems Approach Reveals Dynamic Control of tRNA Modifications during Cellular Stress

(2010) Clement T. Y. Chan et al.   PLoS Genetics

Effect of Correlated tRNA Abundances on Translation Errors and Evolution of Codon Usage Bias

(2010) Premal Shah et al.   PLoS Genetics

Translationally Optimal Codons Associate with Structurally Sensitive Sites in Proteins

(2009) T. Zhou et al.   MOLECULAR BIOLOGY AND EVOLUTION

Co-translational mRNA decay in Saccharomyces cerevisiae

(2009) Wenqian Hu et al.   NATURE

Transient ribosomal attenuation coordinates protein synthesis and co-translational folding

(2009) Gong Zhang et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

tRNA over-expression in breast cancer and functional consequences

(2009) Mariana Pavon-Eternod et al.   NUCLEIC ACIDS RESEARCH

Universal function-specificity of codon usage

(2009) Hamed Shateri Najafabadi et al.   NUCLEIC ACIDS RESEARCH

Selection for minimization of translational frameshifting errors as a factor in the evolution of codon usage

(2009) Yang Huang et al.   NUCLEIC ACIDS RESEARCH

Generic Algorithm to Predict the Speed of Translational Elongation: Implications for Protein Biogenesis

(2009) Gong Zhang et al.   PLoS One

Coding-Sequence Determinants of Gene Expression in Escherichia coli

(2009) G. Kudla et al.   SCIENCE

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

(2009) N. T. Ingolia et al.   SCIENCE

Mistranslation-Induced Protein Misfolding as a Dominant Constraint on Coding-Sequence Evolution

(2008) D. Allan Drummond et al.   CELL

Implication of leucyl-tRNA synthetase 1 (LARS1) over-expression in growth and migration of lung cancer cells detected by siRNA targeted knock-down analysis

(2008) Seung-Hun Shin et al.   EXPERIMENTAL AND MOLECULAR MEDICINE

Electrostatics in the Ribosomal Tunnel Modulate Chain Elongation Rates

(2008) Jianli Lu et al.   JOURNAL OF MOLECULAR BIOLOGY

Ribosome Collisions and Translation Efficiency: Optimization by Codon Usage and mRNA Destabilization

(2008) Namiko Mitarai et al.   JOURNAL OF MOLECULAR BIOLOGY

Mutation-Selection Models of Codon Substitution and Their Use to Estimate Selective Strengths on Codon Usage

(2008) Z. Yang et al.   MOLECULAR BIOLOGY AND EVOLUTION

Slow peptide bond formation by proline and other N-alkylamino acids in translation

(2008) M. Y. Pavlov et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Codon optimization can improve expression of human genes in Escherichia coli: A multi-gene study

(2008) Nicola A. Burgess-Brown et al.   PROTEIN EXPRESSION AND PURIFICATION

Virus Attenuation by Genome-Scale Changes in Codon Pair Bias

(2008) J. R. Coleman et al.   SCIENCE

A pause for thought along the co-translational folding pathway

(2008) Anton A. Komar   TRENDS IN BIOCHEMICAL SCIENCES