Codon optimality, bias and usage in translation and mRNA decay

Hanson, Gavin, Coller, Jeff·2018·Nature Reviews Molecular Cell Biology

DOI 10.1038/nrm.2017.91

Cited by (836)

Items 401–500 of 836

Monosomes buffer translational stress to allow for active ribosome elongation
Rico Schieweck, Giuliana Ciccopiedi, Kenneth Klau, Bastian Popper · 2023 · Frontiers in Molecular Biosciences
Quantification of elongation stalls and impact on gene expression in yeast
Wan-Fu Hou, Vince Harjono, Alex T. Harvey, A. R. Subramaniam, Brian M. Zid · 2023 · RNA: A publication of the RNA Society
Systematic analysis of the codon usage patterns of African swine fever virus genome coding sequences reveals its host adaptation phenotype
Yuening Wang, Chenglin Chi, Jiajia Zhang, Kaili Zhang, Dafu Deng, Wanglong Zheng, Nanhua Chen, François Meurens, Jianzhong Zhu · 2024 · Microbial Genomics
Comparative Analysis of Codon Usage Bias in Six Eimeria Genomes
Yu Juan Zhao, Shicheng Zhang · 2024 · International Journal of Molecular Sciences
Analysis of Codon Usage Bias in the Plastid Genome of Diplandrorchis sinica (Orchidaceae)
Xuhui Chen, Yudi Zhao, Shenghua Xu, Yingze Zhou, Lijie Zhang, Bo Qu, Yufeng Xu · 2024 · Current Issues in Molecular Biology
Selection on synonymous codon usage in soybean (Glycine max) WRKY genes
Krishnendu Sinha, Sourav Jana, Payel Pramanik, Bithika Bera · 2024 · Scientific Reports
Using the Ribodeblur pipeline to recover A-sites from yeast ribosome profiling data
Hao Wang, Carl Kingsford, C. Joel McManus · 2018 · Methods
A pair of non-optimal codons are necessary for the correct biosynthesis of the Aspergillus nidulans urea transporter, UreA
Manuel Sanguinetti, Andrés Iriarte, Sotiris Amillis, Mónica Marı́n, Héctor Musto, Ana Ramón · 2019 · Royal Society Open Science
De novo transcriptome assembly, functional annotation and characterization of the Atlantic bluefin tuna (Thunnus thynnus) larval stage
Luca Marisaldi, Danilo Basili, Giorgia Gioacchini, Adriana Canapa, Oliana Carnevali · 2020 · Marine Genomics
Codon-Restrained Method for Both Eliminating and Creating Intragenic Bacterial Promoters
Dominic Y. Logel, Ellina Trofimova, Paul R. Jaschke · 2022 · ACS Synthetic Biology
Design of typical genes for heterologous gene expression
Dominic Simm, Bilyana Popova, Gerhard H. Braus, Stephan Waack, Martin Kollmar · 2022 · Scientific Reports
Evolutionary dynamics of codon usages for peste des petits ruminants virus
Xin Wang, Jing Sun, Lei Lü, Feiyang Pu, Derong Zhang, Fuqiang Xie · 2022 · Frontiers in Veterinary Science
Potassium viroporins as model systems for understanding eukaryotic ion channel behaviour
Purva Asrani, Guiscard Seebohm, Raphael Stoll · 2022 · Virus Research
microRNAs slow translating ribosomes to prevent protein misfolding in eukaryotes
Hiroaki Sako, Mohieldin Youssef, Olga A. Elisseeva, Takayuki Akimoto, Katsuhiko Suzuki, Takashi Ushida, Tadashi S. Yamamoto · 2023 · The EMBO Journal
Decrypting the functional design of unmodified translation elongation factor P
2024
The fitness consequences of synonymous mutations in Escherichia coli: Experimental evidence for a pleiotropic effect of translational selection
Anne Ballard, Sarah Bieniek, David B. Carlini · 2019 · Gene
Codon Resolution Analysis of Ribosome Profiling Data
Alexander Bartholomäus, Zoya Ignatova · 2021 · Methods in molecular biology
Characterization of tRNA expression profiles in large offspring syndrome
Anna K. Goldkamp, Yahan Li, Rocío Melissa Rivera, Darren E. Hagen · 2022 · BMC Genomics
Protein yield is tunable by synonymous codon changes of translation initiation sites
Bikash Kumar Bhandari, Chun Shen Lim, Daniela M. Remus, Augustine Chen, Craig J. van Dolleweerd, Paul P. Gardner · 2019 · bioRxiv (Cold Spring Harbor Laboratory)
Poisonous plant grassland expands through adaptive resource strategies of above‐ and below‐ground communities
Jian‐Guo Ma, Yunfeng Yang, Fujiang Hou, Xingguo Han, Xiao‐Bo Wang · 2025 · Journal of Ecology
YTHDF2 phase separation promotes arsenite-induced oxidative stress by facilitating YTHDF2-mediated PIK3R2 mRNA degradation
Jin Man, Qian Zhang, Tianhe Zhao, Donglei Sun, Keyan Long, Wenxiao Xiong, Jingsilin Cai, Zunzhen Zhang · 2025 · International Journal of Biological Macromolecules
Codon usage and antibiotic resistance: A hidden evolutionary mechanism
Ujwal Dahal, Anu Bansal · 2025 · Biochimie
Mapping evolutionary paradigm of bovine viral diarrhea virus Npro associated with different organizations of nucleotide
Xili Feng, Zeyu Liu, Xiaoting Ren, Lele An, Xiao‐xia Ma · 2025 · Virulence
A giant virus forms a specialized subcellular environment within its amoeba host for efficient translation
Ruixuan Zhang, Lotte Mayer, Hiroyuki Hikida, Yuichi Shichino, Mari Mito, Anouk Willemsen, Shintaro Iwasaki, Hiroyuki Ogata · 2026 · Nature Microbiology
Beyond the Sequence: Chemical and Topological Design and Innovations in mRNA Therapeutics
Dangliang Liu, Hongyu Chen, Alisia Pan, Xiao Wang · 2026 · Chemical Reviews
Dicodon-based measures for modeling gene expression
Andrés M. Alonso, Luis Anibal Diambra · 2023 · Bioinformatics
Cellular energy regulates mRNA degradation in a codon-specific manner
Pedro Tomaz da Silva, Yujie Zhang, Evangelos Theodorakis, Laura D. Martens, Vicente A. Yépez, Vicent Pelechano, Julien Gagneur · 2024 · Molecular Systems Biology
De Novo assembly and phylogenetic analysis of the complete mitochondrial genome of Eleutherococcus senticosus and related araliaceous species
Zhihua Wang, Huizhi Wang, Xun Gong, Xiaobin Ou, Yinglu Guo, Min Tang · 2025 · BMC Plant Biology
The distinct roles of genome, methylation, transcription, and translation on protein expression in Arabidopsis thaliana resolve the Central Dogma’s information flow
Ziming Zhong, Mark Bailey, Yong‐In Kim, Nazanin P. Afsharyan, Briony Parker, Louise Arathoon, Xiaowei Li, Chelsea A. Rundle, Andrew Behrens, Danny D. Nedialkova et al. · 2025 · Genome biology
The Making and Breaking of RNAs: Dynamics of Rhythmic RNA Expression in Mammals
Benjamin A. Unruh, Shihoko Kojima · 2020 · Journal of Biological Rhythms
Enabling high-throughput single-animal gene-expression studies with molecular and micro-scale technologies
Jason Wan, Hang Lu · 2020 · Lab on a Chip
Potential role of the X circular code in the regulation of gene expression
Julie Thompson, Raymond Ripp, Claudine Mayer, Olivier Poch, Christian J. Michel · 2020 · Biosystems
Analysis of synonymous codon usage bias in Ancylostoma ceylanicum
Ravail Singh · 2021 · Gene Reports
Removing the Bottleneck: Introducing cMatch - A Lightweight Tool for Construct-Matching in Synthetic Biology
Alexis Casas, Matthieu Bultelle, Charles Motraghi, Richard Ian Kitney · 2022 · Frontiers in Bioengineering and Biotechnology
Bias at the third nucleotide of codon pairs in virus and host genomes
Ewan P. Plant, Zhiping Ye · 2022 · Scientific Reports
Nucleic Acid Therapeutics
Jonathan K. Watts · 2022 · Royal Society of Chemistry eBooks
Environmental implications of codon usage bias in Crocus sativus and its impact on host pathogen interactions
Shamsun Nisa, Suruchi Gupta, Ahmed Waqas, Ravail Singh · 2023 · Rhizosphere
Massively parallel identification of sequence motifs triggering ribosome-associated mRNA quality control
Katharine Y. Chen, Heungwon Park, Arvind Rasi Subramaniam · 2024 · Nucleic Acids Research
Engineering biology and automation–Replicability as a design principle
Matthieu Bultelle, Alexis Casas, Richard Ian Kitney · 2024 · Engineering Biology
Mutability and hypermutation antagonize immunoglobulin codon optimality
Joshua J.C. McGrath, Juyeon Park, Chloe A. Troxell, Jordan C. Chervin, Lei Li, Johnathan R. Kent, Siriruk Changrob, Yanbin Fu, Min Huang, Nai‐Ying Zheng et al. · 2024 · Molecular Cell
Codon usage bias affects α-amylase mRNA level by altering RNA stability and cytosine methylation patterns in Escherichia coli
Yanzi Xing, Ruiqing Gong, Yichun Xu, Kunshan Liu, Mian Zhou · 2020 · Canadian Journal of Microbiology
Modification of Transfer RNA Levels Affects Cyclin Aggregation and the Correct Duplication of Yeast Cells
Loreto Arias, Fabián Martínez, Daniela González, Rodrigo Flores-Ríos, Assaf Katz, Mario Tello, Sandra Moreira, Omar Orellana · 2021 · Frontiers in Microbiology
Senecavirus A Enhances Its Adaptive Evolution via Synonymous Codon Bias Evolution
Simiao Zhao, Huiqi Cui, Zhenru Hu, Du Li, Xuhua Ran, Xiaobo Wen · 2022 · Viruses
CPEB1 regulates the inflammatory immune response, phagocytosis, and alternative polyadenylation in microglia
Maria P. Ivshina, Heleen M. van ‘t Spijker, Suna Jung, Sithara Raju Ponny, Dorothy P. Schafer, Joel D. Richter · 2022 · Glia
Synthetic refactor of essential genes decodes functionally constrained sequences in yeast genome
Zhenzhen Liang, Zhouqing Luo, Weimin Zhang, Yu Kang, Hui Wang, Binan Geng, Qing Yang, Zuoyu Ni, Cheng Zeng, Yihui Zheng et al. · 2022 · iScience
Gaussian-Distributed Codon Frequencies of Genomes
Bohdan B. Khomtchouk, Wolfgang Nonner · 2019 · G3 Genes Genomes Genetics
Human DDX6 regulates translation and decay of inefficiently translated mRNAs
Weber, Ramona, Chang, Chung-Te · 2024 · eLife
The rise of mRNA therapeutic vaccines
Jinlu Du, Ziling Fan, Jiangming Huang, Zhengyuan Li, Haitao Hu, Yanxia Li · 2025 · RSC Pharmaceutics
Translation elongation: measurements and applications
Leslie Watkins, Mulin Li, Bin Wu · 2025 · RNA Biology
Chemokine CCL12 in trigeminal ganglion contributes to CFA-induced mechanical allodynia in mice
Xiaoxia Ma, Lijia Mai, Yifan He, Shilin Jia, Ruihan Yang, Wenguo Fan, Fang Ping Huang · 2025 · Neuroscience
Chemically modified tRNA enhances the translation capacity of mRNA rich in cognate codons
Liangzhen Dong, Jiayu Wang, Qing Xia · 2025 · Nature Communications
Lipid nanoparticle-assisted mRNA therapy for cancer treatment
Hyun-Jin Kim, Ngoc Duy Le, Hyun-Ji Oh, Beomsu Kim, Eunjae Yoo, Jeonghwan Kim, Hyungshin Yim · 2025 · Applied Physics Reviews
GCN2 monitors mRNA translation termination.
Kailey Worner, Katharine R Maschhoff, Gabrielle M Schuh, Wen-Qian Hu · 2025 · Molecules and Cells
Non-Coding RNAs: Regulators of Stress, Ageing, and Developmental Decisions in Yeast?
Michal Čáp, Zdena Palková · 2024 · Cells
Dynamic mRNA Stability Buffer Transcriptional Activation During Neuronal Differentiation and Is Regulated by SAMD4A
Yuan Zhou, Sherif Rashad, Daisuke Ando, Y. Kobayashi, Teiji Tominaga, Kuniyasu Niizuma · 2024 · Journal of Cellular Physiology
The Relationship Between Ribosome-Associated Quality Control and Neurological Disorders
Juan Wang, Jianhua Wang, Hanshuai Cao, Yingming Xing, Zhuoran Wang, Jing Ma, Rongjuan Zhao, Wei Zhang, Junhong Guo, Xueli Chang · 2024 · The Journals of Gerontology Series A
Inferring translational heterogeneity from Saccharomyces cerevisiae ribosome profiling
Pedro Couto Bordignon, Sebastian Pechmann · 2021 · The FEBS Journal
Enhancing immunogenicity of HPV16 E7 DNA vaccine by conjugating codon-optimized GM-CSF to HPV16 E7 DNA
Yi-Pin Chen, Chu-Chi Lin, Yu-Xin Xie, Chia‐Yuan Chen, Jian-Tai Timothy Qiu · 2021 · Taiwanese Journal of Obstetrics and Gynecology
SNPs Ability to Influence Disease Risk: Breaking the Silence on Synonymous Mutations in Cancer
Eduardo Herreros, Xander Janssens, Daniele Pepe, Kim De Keersmaecker · 2022 · Springer eBooks
Rare Amyloid Precursor Protein Point Mutations Recapitulate Worldwide Migration and Admixture in Healthy Individuals: Implications for the Study of Neurodegeneration
Paolo Abondio, Francesco Bruno, Amalia Cecilia Bruni, Donata Luiselli · 2022 · International Journal of Molecular Sciences
Transcriptomic, proteomic, and functional consequences of codon usage bias in human cells during heterologous gene expression
2023
A study on the design of an in silico self-amplifying mRNA vaccine against Nipah virus using immunoinformatics
Om Rangacharya, Avanti Parab, Shrikant Adkine, Rahul Nagargoje · 2023 · Journal of Biomolecular Structure and Dynamics
Translational landscape in human early neural fate determination
Chenchao Yan, Yajing Meng, Jie Yang, Jian Chen, Wei Jiang · 2023 · Development
Inferring protein from transcript abundances using convolutional neural networks
Patrick Schwehn, Pascal Falter-Braun · 2025 · BioData Mining
A comprehensive analysis of the phylogenetic signal in ramp sequences in 211 vertebrates
Lauren M. Harmon, Justin B. Miller, Michael F. Whiting, John S. K. Kauwe, Perry G. Ridge · 2021 · Scientific Reports
Association between a genetic variant in scavenger receptor class B type 1 and its role on codon usage bias with increased risk of developing coronary artery disease
Reza Sahebi, Hamideh Ghazizadeh, Amir Avan, Maryam Tayefi, Sara Saffar Soflaei, Mohsen Mouhebati, Habibollah Esmaily, Gordon A. Ferns, Morteza Hashemzadeh Chaleshtori, Majid Ghayour‐Mobarhan et al. · 2021 · Clinical Biochemistry
tRNA modifications inform tissue specific mRNA translation and codon optimization
Daisuke Ando, Sherif Rashad, Thomas J. Begley, Hidenori Endo, Masashi Aoki, Peter C. Dedon, Kuniyasu Niizuma · 2023 · bioRxiv (Cold Spring Harbor Laboratory)
The YTHDF1-3 proteins are bidirectionally influenced by the codon content of their mRNA targets
Clara Moch, Limei Zou, Nicolas Pythoud, Emilie Fillon, Gabrielle Bourgeois, Marc Graille, Christine Carapito, Clément Chapat · 2023 · bioRxiv (Cold Spring Harbor Laboratory)
Dissecting translation elongation dynamics through ultra-long tracking of single ribosomes
Maximilian F. Madern, Sora Yang, Olivier Witteveen, Marianne Bauer, Marvin E. Tanenbaum · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
Unconventional codon usage bias mediates mRNA translational dynamics in macrophages
Shiqi Luo, Qiuyi Wang, Ao Chen, Liang Huang, Yaoqi Liu, Xin Zong, Yuanhui Mao · 2025 · PLoS Biology
RNA vaccines for cancer: revolutionizing immunization strategies
Di Huang, Jiahui Zhang, Xin Zeng, Yin Zhang, Erwei Song · 2025 · Trends in cancer
Mitochondrial genome of Isatis indigotica reveals repeat-mediated recombination and phylogenetic insights in Cruciferae
Shao-Shuai Yu, Meiling Qin, Emmanuel Fleming, Xun Gong, Min Tang · 2025 · Frontiers in Plant Science
The intrinsic properties of mRNAs define their translation efficiency at ribosome shortage
Elena S. Babaylova, Alexander V. Gopanenko, Alexey E. Tupikin, Marsel Rasimovich Kabilov, Alexey A. Malygin · 2025 · Nucleic Acids Research
Engineering Anti-Tumor Immunity: An Immunological Framework for mRNA Cancer Vaccines
Olivia Roy, Karen S. Anderson · 2025 · Vaccines
Emerging roles of tRNA modification-mediated codon-specific translational reprogramming in cancer biology
Hanwei Wang, Junsi Zhang, Cen Jiang, Sunwang Xu · 2026 · Cell Death and Disease
Synonymous codon usage defines functional gene families
Farzan Ghanegolmohammadi, Shinsuke Ohnuki, Shane R. Byrne, Rahul Raman, Thomas J. Begley, Peter C. Dedon · 2026 · BMC Biology
Advancing Gene Therapy for Pancreatitis: From Genetic Insights to Clinical Translation
Yi-Zhou Zheng, Yuan‐Chen Wang, Hang-Ming Qi, Jie Gao, Zhao‐Shen Li, Zhuan Liao, Wen‐Bin Zou · 2026 · Research
Evolutionary paradigm of distinct viral coding regions of BVDV associated with different nucleotide usage patterns
Le-le An, Zeyu Liu, Xiaoting Ren, Y. J. Mo, Jianhua Zhou · 2025 · BMC Veterinary Research
Nuclear effects play an important role in determining codon usage-dependent human gene expression
Renu Garg, Pancheng Xie, Jiabin Duan, Huan Liu, Yi Liu · 2025 · Nature Communications
Strategies and Patterns of Codon Bias in Molluscum Contagiosum Virus
Rahul Raveendran Nair, Manikandan Mohan, Gudepalya Renukaiah Rudramurthy, Reethu Vivekanandam, Panayampalli Subbian Satheshkumar · 2021 · Pathogens
Changes in the genomes and methylomes of three Salmonella enterica serovars after long-term storage in ground black pepper
Cary Pirone Davies, Thomas Jurkiw, Julie Haendiges, Elizabeth A. Reed, Nathan M. Anderson, Elizabeth M. Grasso‐Kelley, Maria Hoffmann, Jie Zheng · 2022 · Frontiers in Microbiology
Bioinformatic Assessment of Factors Affecting the Correlation between Protein Abundance and Elongation Efficiency in Prokaryotes
Aleksandra E. Korenskaia, Yu. G. Matushkin, Sergey Alexandrovich Lashin, Alexandra Igorevna Klimenko · 2022 · International Journal of Molecular Sciences
RNA-seq reveals multifaceted gene expression response to Fab production in Escherichia coli fed-batch processes with particular focus on ribosome stalling
Sophie Vazulka, Matteo Schiavinato, Christopher Tauer, Martin Wagenknecht, Monika Cserjan‐Puschmann, Gerald Striedner · 2024 · Microbial Cell Factories
CbCyp51-Mediated Demethylation Inhibitor Resistance Is Modulated by Codon Bias
Lorena I. Rangel, Nathan A. Wyatt, Isaac Courneya, Mari B. Natwick, Gary A. Secor, Viviana V. Rivera-Varas, Melvin D. Bolton · 2024 · Phytopathology
Influence of Nucleophosmin ( NPM1 ) Genotypes on Outcome of Patients With AML: An AIEOP-BFM and COG-SWOG Intergroup Collaboration
Claudia Tregnago, Maddalena Benetton, Rhonda E. Ries, Jack H. Peplinski, Todd A. Alonzo, Derek L. Stirewalt, Megan K. D. Othus, Nicolas Duployez, Edwin Sonneveld, Jonas Abrahamsson et al. · 2024 · Journal of Clinical Oncology
The non-canonical nucleotides and prebiotic evolution
Alexey S. Ruzov, Alexander S. Ermakov · 2025 · Biosystems
Role of nucleotide pair frequency and synonymous codon usage in the evolution of bovine viral diarrhea virus
Xili Feng, Zeyu Liu, Y. J. Mo, Shubin Zhang, Xiao‐xia Ma · 2025 · Archives of Virology
Loss of Nup160 dysregulates Cdc42 in the podocytes of podocyte-specific Nup160 knockout mice
Deying Liu, Jiaxin Li, Chan Xu, Yuanyuan Li, Xiaohan Chen, Feng Zhao, Huajuan Tong, Yonghui Yang, Xiaojian Qiu, Zihua Yu · 2025 · Human Molecular Genetics
Molecular autopsy provides evidence for widespread ribosome-phased mRNA fragmentation
Tatsuaki Kurosaki, Lynne E. Maquat · 2018 · Nature Structural & Molecular Biology
A novel conditional NPM-ALK-driven model of CD30+ T-cell lymphoma mediated by a translational stop cassette
Khalid Shoumariyeh, Nicolas Schneider, Teresa Poggio, Pia Veratti, Sophia Ehrenfeld, Desiree Melanie Redhaber, Robin Khan, Dietmar Pfeifer, Cathrin Klingeberg, Stefanie Kreutmair et al. · 2019 · Oncogene
Regulatory role of cysteines in (2R, 3R)-butanediol dehydrogenase BdhA of Bacillus velezensis strain GH1-13
Yunhee Choi, Yong‐Hak Kim · 2022 · The Journal of Microbiology
Calculating and comparing codon usage values in rare disease genes highlights codon clustering with disease-and tissue- specific hierarchy
Rachele Rossi, Mingyan Fang, Lin Zhu, Chongyi Jiang, Cong Yu, Cristina Flesia, Chao Nie, Wenyan Li, Alessandra Ferlini · 2022 · PLoS ONE
Current Trends and Prospects in Antimicrobial Peptide Bioprocessing
Kamila Botelho Sampaio de Oliveira, Michel Lopes Leite, Gisele Regina Rodrigues, Nicolau Brito da Cunha, Simoni Campos Dias, Octávio Luiz Franco · 2022 · Microbiology monographs
Translation Enhancement by a Short Nucleotide Insertion at 5′UTR: Application to an In Vitro Cell-Free System and a Photosynthetic Bacterium
Tomo Kondo, Takayuki Shimizu · 2023 · Applied Microbiology
Triple Reporter Assay: A Non-Overlapping Luciferase Assay for the Measurement of Complex Macromolecular Regulation in Cancer Cells Using a New Mushroom Luciferase–Luciferin Pair
Aaiyas Mujawar, Pratham Phadte, Kseniia A. Palkina, Nadezhda M. Markina, Ameena Mohammad, Bhushan L. Thakur, Karen S. Sarkisyan, Anastasia V. Balakireva, Pritha Ray, Ilia V. Yampolsky et al. · 2023 · Sensors
Engineering of the cellular translational machinery and non-coding RNAs to enhance CHO cell growth, recombinant product yields and quality
Davide Vito, Christopher Mark Smales · 2018 · Current Opinion in Chemical Engineering
A role for circular code properties in translation
Simone Giannerini, Diego Luis Gonzalez, Greta Goracci, Alberto Danielli · 2021 · Scientific Reports
Mutations in the regulatory regions result in increased streptomycin resistance and keratinase synthesis in Bacillus thuringiensis
Lei Nie, Ruijiao Zhang, Linfang Zhang, Mengyuan Ma, Congcong Li, Yi Zhang, Yafei An, Hongju Xu, Sa Xiao, Tianwen Wang · 2021 · Archives of Microbiology
A laboratory module that explores RNA interference and codon optimization through fluorescence microscopy using Caenorhabditis elegans
Nicholas J. Palmisano, Maryam A. Azmi, Taylor N. Medwig-Kinney, Frances E. Q. Moore, Rumana Rahman, Wan Zhang, Rebecca C. Adikes, David Q. Matus · 2022 · CourseSource
An Examination of Mechanisms by which Synonymous Mutations may Alter Protein Levels, Structure and Functions
Yiming J. Zhang, Zsuzsa Bebők · 2022 · Springer eBooks