Codon usage is an important determinant of gene expression levels largely through its effects on transcription

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

(2016) Ariel A Bazzini et al.   EMBO JOURNAL

Codon Usage and 3′ UTR Length Determine Maternal mRNA Stability in Zebrafish

(2016) Yuichiro Mishima et al.   MOLECULAR CELL

Codon influence on protein expression in E. coli correlates with mRNA levels

(2016) Grégory Boël et al.   NATURE

Differences in codon bias and GC content contribute to the balanced expression of TLR7 and TLR9

(2016) Zachary R. Newman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Codon Optimality Is a Major Determinant of mRNA Stability

(2015) Vladimir Presnyak et al.   CELL

Mechanism of siRNA production from repetitive DNA

(2015) Qiuying Yang et al.   GENES & DEVELOPMENT

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

Causal signals between codon bias, mRNA structure, and the efficiency of translation and elongation

(2014) C. Pop et al.   Molecular Systems Biology

Transcriptional interference by antisense RNA is required for circadian clock function

(2014) Zhihong Xue et al.   NATURE

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

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

CpG domains downstream of TSSs promote high levels of gene expression

(2014) Simone Krinner et al.   NUCLEIC ACIDS RESEARCH

Mapping and Dynamics of Regulatory DNA and Transcription Factor Networks in A. thaliana

(2014) Alessandra M. Sullivan et al.   Cell Reports

CATP is a critical component of the Neurospora circadian clock by regulating the nucleosome occupancy rhythm at the frequency locus

(2013) Joonseok Cha et al.   EMBO REPORTS

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

(2013) Mian Zhou et al.   NATURE

Suppression of WC-independent frequency transcription by RCO-1 is essential for Neurospora circadian clock

(2013) Z. Zhou et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Exonic Transcription Factor Binding Directs Codon Choice and Affects Protein Evolution

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

Convergent Transcription Induces Dynamic DNA Methylation at disiRNA Loci

(2013) Yunkun Dang et al.   PLoS Genetics

The RNA polymerase II CTD coordinates transcription and RNA processing

(2012) J.-P. Hsin et al.   GENES & DEVELOPMENT

Silent Substitutions Predictably Alter Translation Elongation Rates and Protein Folding Efficiencies

(2012) Paige S. Spencer et al.   JOURNAL OF MOLECULAR BIOLOGY

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

Evolutionary conservation of codon optimality reveals hidden signatures of cotranslational folding

(2012) Sebastian Pechmann et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Nascent RNA structure modulates the transcriptional dynamics of RNA polymerases

(2012) B. Zamft et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Light-Inducible System for Tunable Protein Expression in Neurospora crassa

(2012) Jennifer M. Hurley et al.   G3-Genes Genomes Genetics

Neurospora COP9 Signalosome Integrity Plays Major Roles for Hyphal Growth, Conidial Development, and Circadian Function

(2012) Zhipeng Zhou et al.   PLoS Genetics

Balanced Codon Usage Optimizes Eukaryotic Translational Efficiency

(2012) Wenfeng Qian et al.   PLoS Genetics

Regulation of the Activity and Cellular Localization of the Circadian Clock Protein FRQ

(2011) Joonseok Cha et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Determinants of translation efficiency and accuracy

(2011) H. Gingold et al.   Molecular Systems Biology

An Evolutionarily Conserved Mechanism for Controlling the Efficiency of Protein Translation

(2010) Tamir Tuller et al.   CELL

DNA methylation and the formation of heterochromatin in Neurospora crassa

(2010) M R Rountree et al.   HEREDITY

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

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

Identification of DIM-7, a protein required to target the DIM-5 H3 methyltransferase to chromatin

(2010) Z. A. Lewis et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

DCAF26, an Adaptor Protein of Cul4-Based E3, Is Essential for DNA Methylation in Neurospora crassa

(2010) Hui Xu et al.   PLoS Genetics

The Exosome Regulates Circadian Gene Expression in a Posttranscriptional Negative Feedback Loop

(2009) Jinhu Guo et al.   CELL

Codon usage bias is correlated with gene expression levels in the fission yeastSchizosaccharomyces pombe

(2009) Yasushi Hiraoka et al.   GENES TO CELLS

Tools for Fungal Proteomics: Multifunctional Neurospora Vectors for Gene Replacement, Protein Expression and Protein Purification

(2009) S. Honda et al.   GENETICS

Translationally Optimal Codons Associate with Structurally Sensitive Sites in Proteins

(2009) T. Zhou et al.   MOLECULAR BIOLOGY AND EVOLUTION

Relationship between Phylogenetic Distribution and Genomic Features in Neurospora crassa

(2009) Takao Kasuga et al.   PLoS One

Coding-Sequence Determinants of Gene Expression in Escherichia coli

(2009) G. Kudla et al.   SCIENCE

Selection on Codon Bias

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

Mistranslation-Induced Protein Misfolding as a Dominant Constraint on Coding-Sequence Evolution

(2008) D. Allan Drummond et al.   CELL

Relics of repeat-induced point mutation direct heterochromatin formation in Neurospora crassa

(2008) Z. A. Lewis et al.   GENOME RESEARCH