The Yin and Yang of codon usage

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

Codon Pair Bias Is a Direct Consequence of Dinucleotide Bias

(2016) Dusan Kunec et al.   Cell Reports

Roles for Synonymous Codon Usage in Protein Biogenesis

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

Codon Optimality Is a Major Determinant of mRNA Stability

(2015) Vladimir Presnyak et al.   CELL

Initiation of mRNA translation in bacteria: structural and dynamic aspects

(2015) Claudio O. Gualerzi et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

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

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

Translational tuning optimizes nascent protein folding in cells

(2015) S. J. Kim et al.   SCIENCE

Understanding the Influence of Codon Translation Rates on Cotranslational Protein Folding

(2014) Edward P. O’Brien et al.   ACCOUNTS OF CHEMICAL RESEARCH

A Dual Program for Translation Regulation in Cellular Proliferation and Differentiation

(2014) Hila Gingold et al.   CELL

Distinctive tRNA Repertoires in Proliferating versus Differentiating Cells

(2014) Ivan Topisirovic et al.   CELL

Expanding Anfinsen’s Principle: Contributions of Synonymous Codon Selection to Rational Protein Design

(2014) Ian M. Sander et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Local slowdown of translation by nonoptimal codons promotes nascent-chain recognition by SRP in vivo

(2014) Sebastian Pechmann et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Protein mistranslation: friend or foe?

(2014) Liuís Ribas de Pouplana et al.   TRENDS IN BIOCHEMICAL SCIENCES

Exposing synonymous mutations

(2014) Ryan C. Hunt et al.   TRENDS IN GENETICS

mRNA-programmed translation pauses in the targeting of E. coli membrane proteins

(2014) Nir Fluman et al.   eLife

Co-translational mechanisms of protein maturation

(2013) Felix Gloge et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Genetic Code-guided Protein Synthesis and Folding inEscherichia coli

(2013) Shaoliang Hu et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Efficient translation initiation dictates codon usage at gene start

(2013) K. Bentele et al.   Molecular Systems Biology

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

(2013) Mian Zhou et al.   NATURE

Exonic Transcription Factor Binding Directs Codon Choice and Affects Protein Evolution

(2013) A. B. Stergachis et al.   SCIENCE

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

(2013) D. B. Goodman et al.   SCIENCE

Large-scale analysis of conserved rare codon clusters suggests an involvement in co-translational molecular recognition events

(2012) Matthieu Chartier et al.   BIOINFORMATICS

Codon usage bias: causative factors, quantification methods and genome-wide patterns: with emphasis on insect genomes

(2012) Susanta K. Behura et al.   BIOLOGICAL REVIEWS

Coding exons function as tissue-specific enhancers of nearby genes

(2012) Ramon Y. Birnbaum et al.   GENOME RESEARCH

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

(2012) Gene-Wei Li et al.   NATURE

Transcriptional Enhancers in Protein-Coding Exons of Vertebrate Developmental Genes

(2012) Deborah I. Ritter et al.   PLoS One

Discovery and Characterization of Human Exonic Transcriptional Regulatory Elements

(2012) Arshad H. Khan et al.   PLoS One

Coupling between codon usage, translation and protein export in Escherichia coli

(2011) Yaramah M. Zalucki et al.   Biotechnology Journal

Efficiency of translation termination in humans is highly dependent upon nucleotides in the neighbourhood of a (premature) termination codon

(2011) F. Pacho et al.   JOURNAL OF MEDICAL GENETICS

Understanding the contribution of synonymous mutations to human disease

(2011) Zuben E. Sauna et al.   NATURE REVIEWS GENETICS

Species-Specific Codon Context Rules Unveil Non-Neutrality Effects of Synonymous Mutations

(2011) Gabriela R. Moura et al.   PLoS One

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

(2010) Thomas F Clarke et al.   BMC GENOMICS

Folding at the birth of the nascent chain: coordinating translation with co-translational folding

(2010) Gong Zhang et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

The mechanism of eukaryotic translation initiation and principles of its regulation

(2010) Richard J. Jackson et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Forces that influence the evolution of codon bias

(2010) P. M. Sharp et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

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

Fidelity at the Molecular Level: Lessons from Protein Synthesis

(2009) Hani S. Zaher et al.   CELL

Transient ribosomal attenuation coordinates protein synthesis and co-translational folding

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

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

(2009) Yang Huang et al.   NUCLEIC ACIDS RESEARCH

Coding-Sequence Determinants of Gene Expression in Escherichia coli

(2009) G. Kudla et al.   SCIENCE

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

(2009) Yaramah M. Zalucki et al.   TRENDS IN MICROBIOLOGY

Selection on Codon Bias

(2008) Ruth Hershberg et al.   Annual Review of Genetics

Preferred and avoided codon pairs in three domains of life

(2008) Age Tats et al.   BMC GENOMICS

Analysis of the distribution of functionally relevant rare codons

(2008) Michael Widmann et al.   BMC GENOMICS

Synonymous Mutations and Ribosome Stalling Can Lead to Altered Folding Pathways and Distinct Minima

(2008) Chung-Jung Tsai et al.   JOURNAL OF MOLECULAR BIOLOGY

Rare Codons Cluster

(2008) Thomas F. Clarke et al.   PLoS One

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