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

Ribosome queuing enables non-AUG translation to be resistant to multiple protein synthesis inhibitors

(2019) Michael G. Kearse et al.   GENES & DEVELOPMENT

The endonuclease Cue2 cleaves mRNAs at stalled ribosomes during No Go Decay

(2019) Karole N D'Orazio et al.   eLife

Ribosome Collisions Result in +1 Frameshifting in the Absence of No-Go Decay

(2019) Carrie L. Simms et al.   Cell Reports

Pervasive Regulatory Functions of mRNA Structure Revealed by High-Resolution SHAPE Probing

(2018) Anthony M. Mustoe et al.   CELL

A Novel Amino Lipid Series for mRNA Delivery: Improved Endosomal Escape and Sustained Pharmacology and Safety in Non-human Primates

(2018) Staci Sabnis et al.   MOLECULAR THERAPY

Timing during translation matters: synonymous mutations in human pathologies influence protein folding and function

(2018) Robert Rauscher et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

ZNF598 Is a Quality Control Sensor of Collided Ribosomes

(2018) Szymon Juszkiewicz et al.   MOLECULAR CELL

Ribosome Collision Is Critical for Quality Control during No-Go Decay

(2017) Carrie L. Simms et al.   MOLECULAR CELL

N1-methyl-pseudouridine in mRNA enhances translation through eIF2α-dependent and independent mechanisms by increasing ribosome density

(2017) Yuri V. Svitkin et al.   NUCLEIC ACIDS RESEARCH

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

(2016) Aditya Radhakrishnan et al.   CELL

A novel translational control mechanism involving RNA structures within coding sequences

(2016) Jennifer Jungfleisch et al.   GENOME RESEARCH

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

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

Activation of GCN2 kinase by ribosome stalling links translation elongation with translation initiation

(2016) Ryuta Ishimura et al.   eLife

Codon Optimality Is a Major Determinant of mRNA Stability

(2015) Vladimir Presnyak et al.   CELL

Increased functional protein expression using nucleotide sequence features enriched in highly expressed genes in zebrafish

(2015) Eric J. Horstick et al.   NUCLEIC ACIDS RESEARCH

Reply to Simmonds et al.: Codon pair and dinucleotide bias have not been functionally distinguished

(2015) Bruce Futcher et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Attenuation of dengue (and other RNA viruses) with codon pair recoding can be explained by increased CpG/UpA dinucleotide frequencies: Table 1.

(2015) Peter Simmonds et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Landscape and variation of RNA secondary structure across the human transcriptome

(2014) Yue Wan et al.   NATURE

RNA motif discovery by SHAPE and mutational profiling (SHAPE-MaP)

(2014) Nathan A Siegfried et al.   NATURE METHODS

Insights into RNA structure and function from genome-wide studies

(2014) Stefanie A. Mortimer et al.   NATURE REVIEWS GENETICS

Multiple roles of the coding sequence 5′ end in gene expression regulation

(2014) Tamir Tuller et al.   NUCLEIC ACIDS RESEARCH

RNA virus attenuation by codon pair deoptimisation is an artefact of increases in CpG/UpA dinucleotide frequencies

(2014) Fiona Tulloch 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

In vivo genome-wide profiling of RNA secondary structure reveals novel regulatory features

(2013) Yiliang Ding et al.   NATURE

Thermodynamic contribution and nearest-neighbor parameters of pseudouridine-adenosine base pairs in oligoribonucleotides

(2013) G. A. Hudson et al.   RNA

Expression of therapeutic proteins after delivery of chemically modified mRNA in mice

(2011) Michael S D Kormann et al.   NATURE BIOTECHNOLOGY

Mechanisms of endonuclease-mediated mRNA decay

(2011) Daniel R. Schoenberg   Wiley Interdisciplinary Reviews-RNA

An Evolutionarily Conserved Mechanism for Controlling the Efficiency of Protein Translation

(2010) Tamir Tuller et al.   CELL

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

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

Architecture and secondary structure of an entire HIV-1 RNA genome

(2009) Joseph M. Watts et al.   NATURE

Design Parameters to Control Synthetic Gene Expression in Escherichia coli

(2009) Mark Welch et al.   PLoS One

Incorporation of Pseudouridine Into mRNA Yields Superior Nonimmunogenic Vector With Increased Translational Capacity and Biological Stability

(2008) Katalin Karikó et al.   MOLECULAR THERAPY

Following translation by single ribosomes one codon at a time

(2008) Jin-Der Wen et al.   NATURE