标题
Codon optimality, bias and usage in translation and mRNA decay
作者
关键词
-
出版物
NATURE REVIEWS MOLECULAR CELL BIOLOGY
Volume 19, Issue 1, Pages 20-30
出版商
Springer Nature
发表日期
2017-10-11
DOI
10.1038/nrm.2017.91
参考文献
相关参考文献
注意:仅列出部分参考文献,下载原文获取全部文献信息。- 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
Find Funding. Review Successful Grants.
Explore over 25,000 new funding opportunities and over 6,000,000 successful grants.
ExploreBecome a Peeref-certified reviewer
The Peeref Institute provides free reviewer training that teaches the core competencies of the academic peer review process.
Get Started