4.6 Review

What determines eukaryotic translation elongation: recent molecular and quantitative analyses of protein synthesis

Related references

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

Ribosome pausing, a dangerous necessity for co-translational events

Martine A. Collart et al.

NUCLEIC ACIDS RESEARCH (2020)

Article Biochemistry & Molecular Biology

Molecular mechanism of translational stalling by inhibitory codon combinations and poly(A) tracts

Petr Tesina et al.

EMBO JOURNAL (2020)

Article Multidisciplinary Sciences

Codon and amino acid content are associated with mRNA stability in mammalian cells

Megan E. Forrest et al.

PLOS ONE (2020)

Article Biochemistry & Molecular Biology

The Key Parameters that Govern Translation Efficiency

Dan D. Erdmann-Pham et al.

CELL SYSTEMS (2020)

Article Multidisciplinary Sciences

Robust landscapes of ribosome dwell times and aminoacyl-tRNAs in response to nutrient stress in liver

Cedric Gobet et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2020)

Review Cell Biology

Heterogeneity in mRNA Translation

Stijn Sonneveld et al.

TRENDS IN CELL BIOLOGY (2020)

Article Cell Biology

Genome-wide Survey of Ribosome Collision

Peixun Han et al.

CELL REPORTS (2020)

Article Biochemistry & Molecular Biology

Translational efficiency across healthy and tumor tissues is proliferation-related

Xavier Hernandez-Alias et al.

MOLECULAR SYSTEMS BIOLOGY (2020)

Article Biochemistry & Molecular Biology

Transcriptome-wide sites of collided ribosomes reveal principles of translational pausing

Alaaddin Bulak Arpat et al.

GENOME RESEARCH (2020)

Article Biology

EDF1 coordinates cellular responses to ribosome collisions

Niladri K. Sinha et al.

ELIFE (2020)

Article Biochemistry & Molecular Biology

Disome and Trisome Profiling Reveal Genome-wide Targets of Ribosome Quality Control

Sezen Meydan et al.

MOLECULAR CELL (2020)

Article Biochemical Research Methods

Whole cell biophysical modeling of codont-RNA competition reveals novel insights related to translation dynamics

Doron Levin et al.

PLOS COMPUTATIONAL BIOLOGY (2020)

Article Biotechnology & Applied Microbiology

A rare codon-based translational program of cell proliferation

Joao C. Guimaraes et al.

GENOME BIOLOGY (2020)

Article Biochemistry & Molecular Biology

Co-translational assembly of proteasome subunits in NOT1-containing assemblysomes

Olesya O. Panasenko et al.

NATURE STRUCTURAL & MOLECULAR BIOLOGY (2019)

Review Cell Biology

Mechanisms and functions of ribosome-associated protein quality control

Claudio A. P. Joazeiro

NATURE REVIEWS MOLECULAR CELL BIOLOGY (2019)

Article Biochemical Research Methods

A chemical kinetic basis for measuring translation initiation and elongation rates from ribosome profiling data

Ajeet K. Sharma et al.

PLOS COMPUTATIONAL BIOLOGY (2019)

Article Biochemistry & Molecular Biology

Multi-Color Single-Molecule Imaging Uncovers Extensive Heterogeneity in mRNA Decoding

Sanne Boersma et al.

Article Cell Biology

Fluorescence Imaging Methods to Investigate Translation in Single Cells

Jeetayu Biswas et al.

COLD SPRING HARBOR PERSPECTIVES IN BIOLOGY (2019)

Article Biochemistry & Molecular Biology

Live-Cell Single RNA Imaging Reveals Bursts of Translational Frameshifting

Kenneth Lyon et al.

MOLECULAR CELL (2019)

Article Multidisciplinary Sciences

Protein synthesis rates and ribosome occupancies reveal determinants of translation elongation rates

Andrea Riba et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2019)

Article Biochemistry & Molecular Biology

Coding regions affect mRNA stability in human cells

Ashrut Narula et al.

Article Biochemistry & Molecular Biology

Mechanism of ribosome stalling during translation of a poly(A) tail

Viswanathan Chandrasekaran et al.

NATURE STRUCTURAL & MOLECULAR BIOLOGY (2019)

Article Multidisciplinary Sciences

mRNA structure regulates protein expression through changes in functional half-life

David M. Mauger et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2019)

Article Biochemical Research Methods

Computational design and interpretation of single-RNA translation experiments

Luis U. Aguilera et al.

PLOS COMPUTATIONAL BIOLOGY (2019)

Article Biochemistry & Molecular Biology

Single-Molecule Imaging of mRNA Localization and Regulation during the Integrated Stress Response

Johannes H. Wilbertz et al.

MOLECULAR CELL (2019)

Review Cell Biology

Codon optimality, bias and usage in translation and mRNA decay

Gavin Hanson et al.

NATURE REVIEWS MOLECULAR CELL BIOLOGY (2018)

Article Biochemistry & Molecular Biology

Pseudouridylation of tRNA-Derived Fragments Steers Translational Control in Stem Cells

Nicola Guzzi et al.

Article Biochemistry & Molecular Biology

Translational Control through Differential Ribosome Pausing during Amino Acid Limitation in Mammalian Cells

Alicia M. Darnell et al.

MOLECULAR CELL (2018)

Review Cell Biology

Roadblocks and resolutions in eukaryotic translation

Anthony P. Schuller et al.

NATURE REVIEWS MOLECULAR CELL BIOLOGY (2018)

Article Physics, Multidisciplinary

Deciphering mRNA Sequence Determinants of Protein Production Rate

Juraj Szavits-Nossan et al.

PHYSICAL REVIEW LETTERS (2018)

Article Multidisciplinary Sciences

Deciphering the reading of the genetic code by near-cognate tRNA

Sandra Blanchet et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2018)

Article Cell Biology

Genome-wide Translation Profiling by Ribosome-Bound tRNA Capture

Chien-Wen Chen et al.

CELL REPORTS (2018)

Article Biochemical Research Methods

The extent of ribosome queuing in budding yeast

Alon Diament et al.

PLOS COMPUTATIONAL BIOLOGY (2018)

Review Biochemistry & Molecular Biology

How Messenger RNA and Nascent Chain Sequences Regulate Translation Elongation

Junhong Choi et al.

ANNUAL REVIEW OF BIOCHEMISTRY, VOL 87 (2018)

Article Biochemistry & Molecular Biology

Queuosine-modified tRNAs confer nutritional control of protein translation

Francesca Tuorto et al.

EMBO JOURNAL (2018)

Review Biochemistry & Molecular Biology

Hypusine, a polyamine-derived amino acid critical for eukaryotic translation

Myung Hee Park et al.

JOURNAL OF BIOLOGICAL CHEMISTRY (2018)

Article Multidisciplinary Sciences

mRNA circularization by METTL3-eIF3h enhances translation and promotes oncogenesis

Junho Choe et al.

NATURE (2018)

Article Biochemical Research Methods

riboWaltz: Optimization of ribosome P-site positioning in ribosome profiling data

Fabio Lauria et al.

PLOS COMPUTATIONAL BIOLOGY (2018)

Article Biochemistry & Molecular Biology

ZNF598 Is a Quality Control Sensor of Collided Ribosomes

Szymon Juszkiewicz et al.

MOLECULAR CELL (2018)

Article Cell Biology

Quantifying Single mRNA Translation Kinetics in Living Cells

Tatsuya Morisaki et al.

COLD SPRING HARBOR PERSPECTIVES IN BIOLOGY (2018)

Article Physics, Fluids & Plasmas

Power series solution of the inhomogeneous exclusion process

Juraj Szavits-Nossan et al.

PHYSICAL REVIEW E (2018)

Review Biochemistry & Molecular Biology

More than just scanning: the importance of cap-independent mRNA translation initiation for cellular stress response and cancer

Rafaela Lacerda et al.

CELLULAR AND MOLECULAR LIFE SCIENCES (2017)

Article Biochemistry & Molecular Biology

Insights into the mechanisms of eukaryotic translation gained with ribosome profiling

Dmitry E. Andreev et al.

NUCLEIC ACIDS RESEARCH (2017)

Article Physics, Condensed Matter

Cluster approximations for the TASEP: stationary state and dynamical transition

A. Pelizzola et al.

EUROPEAN PHYSICAL JOURNAL B (2017)

Article Biochemical Research Methods

Accurate Recovery of Ribosome Positions Reveals Slow Translation of Wobble-Pairing Codons in Yeast

Hao Wang et al.

JOURNAL OF COMPUTATIONAL BIOLOGY (2017)

Article Biochemistry & Molecular Biology

Initiation of Quality Control during Poly(A) Translation Requires Site-Specific Ribosome Ubiquitination

Szymon Juszkiewicz et al.

MOLECULAR CELL (2017)

Article Biochemistry & Molecular Biology

eIF5A Functions Globally in Translation Elongation and Termination

Anthony P. Schuller et al.

MOLECULAR CELL (2017)

Review Biochemistry & Molecular Biology

Emerging Themes in Regulation of Global mRNA Turnover in cis

Chyi-Ying A. Chen et al.

TRENDS IN BIOCHEMICAL SCIENCES (2017)

Article Multidisciplinary Sciences

Effects of cycloheximide on the interpretation of ribosome profiling experiments in Schizosaccharomyces pombe

Caia D. S. Duncan et al.

SCIENTIFIC REPORTS (2017)

Review Cell Biology

Ribosome profiling and dynamic regulation of translation in mammals

Cedric Gobet et al.

CURRENT OPINION IN GENETICS & DEVELOPMENT (2017)

Review Biochemistry & Molecular Biology

tRNA Modifications: Impact on Structure and Thermal Adaptation

Christian Lorenz et al.

BIOMOLECULES (2017)

Review Biochemistry & Molecular Biology

Mapping the non-standardized biases of ribosome profiling

Alexander Bartholomaeus et al.

BIOLOGICAL CHEMISTRY (2016)

Article Biotechnology & Applied Microbiology

Plastid: nucleotide-resolution analysis of next-generation sequencing and genomics data

Joshua G. Dunn et al.

BMC GENOMICS (2016)

Article Biochemistry & Molecular Biology

Dynamics of Translation of Single mRNA Molecules In Vivo

Xiaowei Yan et al.

Article Biochemistry & Molecular Biology

Adjacent Codons Act in Concert to Modulate Translation Efficiency in Yeast

Caitlin E. Gamble et al.

Article Biochemistry & Molecular Biology

Modulated Expression of Specific tRNAs Drives Gene Expression and Cancer Progression

Hani Goodarzi et al.

Article Biochemistry & Molecular Biology

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

Ariel A. Bazzini et al.

EMBO JOURNAL (2016)

Article Biochemistry & Molecular Biology

Codon Usage and 30 UTR Length Determine Maternal mRNA Stability in Zebrafish

Yuichiro Mishima et al.

MOLECULAR CELL (2016)

Article Biochemistry & Molecular Biology

The m6A Methyltransferase METTL3 Promotes Translation in Human Cancer Cells

Shuibin Lin et al.

MOLECULAR CELL (2016)

Article Multidisciplinary Sciences

Tumour-specific proline vulnerability uncovered by differential ribosome codon reading

Fabricio Loayza-Puch et al.

NATURE (2016)

Article Biochemistry & Molecular Biology

Codon optimality controls differential mRNA translation during amino acid starvation

Mridusmita Saikia et al.

Article Multidisciplinary Sciences

Translation dynamics of single mRNAs in live cells and neurons

Bin Wu et al.

SCIENCE (2016)

Article Multidisciplinary Sciences

Comparative survey of the relative impact of mRNA features on local ribosome profiling read density

Patrick B. F. O'Connor et al.

NATURE COMMUNICATIONS (2016)

Article Genetics & Heredity

Codon-Driven Translational Efficiency Is Stable across Diverse Mammalian Cell States

Konrad L. M. Rudolph et al.

PLOS GENETICS (2016)

Review Cell Biology

tRNA wobble modifications and protein homeostasis

Namit Ranjan et al.

TRANSLATION (2016)

Review Biophysics

Roles for Synonymous Codon Usage in Protein Biogenesis

Julie L. Chaney et al.

ANNUAL REVIEW OF BIOPHYSICS, VOL 44 (2015)

Article Biochemistry & Molecular Biology

The translation factor eIF5A and human cancer

Michael B. Mathews et al.

BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS (2015)

Article Biochemistry & Molecular Biology

Optimization of Codon Translation Rates via tRNA Modifications Maintains Proteome Integrity

Danny D. Nedialkova et al.

Article Biochemistry & Molecular Biology

Codon Optimality Is a Major Determinant of mRNA Stability

Vladimir Presnyak et al.

Article Biochemistry & Molecular Biology

N6-methyladenosine Modulates Messenger RNA Translation Efficiency

Xiao Wang et al.

Article Biochemistry & Molecular Biology

The tRNA methyltransferase Dnmt2 is required for accurate polypeptide synthesis during haematopoiesis

Francesca Tuorto et al.

EMBO JOURNAL (2015)

Article Biochemistry & Molecular Biology

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

Chien-Hung Yu et al.

MOLECULAR CELL (2015)

Article Biochemistry & Molecular Biology

Structure and Assembly Pathway of the Ribosome Quality Control Complex

Sichen Shao et al.

MOLECULAR CELL (2015)

Article Biochemical Research Methods

Efficient and quantitative high-throughput tRNA sequencing

Guanqun Zheng et al.

NATURE METHODS (2015)

Article Biochemistry & Molecular Biology

Ribosome A and P sites revealed by length analysis of ribosome profiling data

Andrew T. Martens et al.

NUCLEIC ACIDS RESEARCH (2015)

Article Multidisciplinary Sciences

Translation initiation mediated by RNA looping

Ki Young Paek et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2015)

Article Multidisciplinary Sciences

Rqc2p and 60S ribosomal subunits mediate mRNA-independent elongation of nascent chains

Peter S. Shen et al.

SCIENCE (2015)

Article Biochemical Research Methods

Unbiased Quantitative Models of Protein Translation Derived from Ribosome Profiling Data

Alexey A. Gritsenko et al.

PLOS COMPUTATIONAL BIOLOGY (2015)

Article Biochemistry & Molecular Biology

A Dual Program for Translation Regulation in Cellular Proliferation and Differentiation

Hila Gingold et al.

Article Biochemistry & Molecular Biology

Dom34 Rescues Ribosomes in 3′ Untranslated Regions

Nicholas R. Guydosh et al.

Article Biochemistry & Molecular Biology

A Protein-Tagging System for Signal Amplification in Gene Expression and Fluorescence Imaging

Marvin E. Tanenbaum et al.

Review Biochemistry & Molecular Biology

The hypusine-containing translation factor eIF5A

Thomas E. Dever et al.

CRITICAL REVIEWS IN BIOCHEMISTRY AND MOLECULAR BIOLOGY (2014)

Article Biochemistry & Molecular Biology

Co-translational mechanisms of protein maturation

Felix Gloge et al.

CURRENT OPINION IN STRUCTURAL BIOLOGY (2014)

Review Oncology

Library preparation methods for next-generation sequencing: Tone down the bias

Erwin L. van Dijk et al.

EXPERIMENTAL CELL RESEARCH (2014)

Article Biochemistry & Molecular Biology

Accounting for biases in riboprofiling data indicates a major role for proline in stalling translation

Carlo G. Artieri et al.

GENOME RESEARCH (2014)

Article Multidisciplinary Sciences

Structural basis for translational surveillance by the large ribosomal subunit-associated protein quality control complex

Dmitry Lyumkis et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2014)

Article Biochemistry & Molecular Biology

elF5A Promotes Translation of Polyproline Motifs

Erik Gutierrez et al.

MOLECULAR CELL (2013)

Article Multidisciplinary Sciences

Cdc48-associated complex bound to 60S particles is required for the clearance of aberrant translation products

Quentin Defenouillere et al.

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

Article Biochemistry & Molecular Biology

A Role for tRNA Modifications in Genome Structure and Codon Usage

Eva Maria Novoa et al.

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)

Review Cell Biology

Structure of transfer RNAs: similarity and variability

Richard Giege et al.

WILEY INTERDISCIPLINARY REVIEWS-RNA (2012)

Article Physics, Mathematical

Modeling Translation in Protein Synthesis with TASEP: A Tutorial and Recent Developments

R. K. P. Zia et al.

JOURNAL OF STATISTICAL PHYSICS (2011)

Review Physics, Multidisciplinary

Non-equilibrium statistical mechanics: from a paradigmatic model to biological transport

T. Chou et al.

REPORTS ON PROGRESS IN PHYSICS (2011)

Article Multidisciplinary Sciences

Real-Time Observation of Transcription Initiation and Elongation on an Endogenous Yeast Gene

Daniel R. Larson et al.

SCIENCE (2011)

Article Biochemical Research Methods

Genome-Scale Analysis of Translation Elongation with a Ribosome Flow Model

Shlomi Reuveni et al.

PLOS COMPUTATIONAL BIOLOGY (2011)

Review Biochemistry & Molecular Biology

Regulation of mRNA Translation and Stability by microRNAs

Marc Robert Fabian et al.

ANNUAL REVIEW OF BIOCHEMISTRY, VOL 79 (2010)

Article Biochemistry & Molecular Biology

The Pioneer Round of Translation: Features and Functions

Lynne E. Maquat et al.

Article Biochemistry & Molecular Biology

An Evolutionarily Conserved Mechanism for Controlling the Efficiency of Protein Translation

Tamir Tuller et al.

Article Multidisciplinary Sciences

Role of a ribosome-associated E3 ubiquitin ligase in protein quality control

Mario H. Bengtson et al.

NATURE (2010)

Article Biochemistry & Molecular Biology

Genome-wide analysis of N1-methyl-adenosine modification in human tRNAs

Mridusmita Saikia et al.

Article Multidisciplinary Sciences

Co-translational mRNA decay in Saccharomyces cerevisiae

Wenqian Hu et al.

NATURE (2009)

Article Physics, Fluids & Plasmas

Competition between multiple totally asymmetric simple exclusion processes for a finite pool of resources

L. Jonathan Cook et al.

PHYSICAL REVIEW E (2009)

Article Multidisciplinary Sciences

A mouse forward genetics screen identifies LISTERIN as an E3 ubiquitin ligase involved in neurodegeneration

Jessie Chu et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (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 Genetics & Heredity

Selection on Codon Bias

Ruth Hershberg et al.

ANNUAL REVIEW OF GENETICS (2008)

Article Mechanics

Far-from-equilibrium transport with constrained resources

D. A. Adams et al.

JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT (2008)

Article Genetics & Heredity

Tissue-specific differences in human transfer RNA expression

Kimberly A. Dittmar et al.

PLOS GENETICS (2006)

Article Physics, Multidisciplinary

The asymmetric simple exclusion process: an integrable model for non-equilibrium statistical mechanics

Olivier Golinelli et al.

JOURNAL OF PHYSICS A-MATHEMATICAL AND GENERAL (2006)

Article Biochemistry & Molecular Biology

Differential expression of eIF5A-1 and eIF5A-2 in human cancer cells

PMJ Clement et al.

FEBS JOURNAL (2006)

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 Physics, Multidisciplinary

Totally asymmetric exclusion processes with particles of arbitrary size

G Lakatos et al.

JOURNAL OF PHYSICS A-MATHEMATICAL AND GENERAL (2003)

Review Physics, Multidisciplinary

Statistical physics of vehicular traffic and some related systems

D Chowdhury et al.

PHYSICS REPORTS-REVIEW SECTION OF PHYSICS LETTERS (2000)