Codon usage biases co-evolve with transcription termination machinery to suppress premature cleavage and polyadenylation

Comparative analysis of alternative polyadenylation in S. cerevisiae and S. pombe

(2017) Xiaochuan Liu et al.   GENOME RESEARCH

Codon usage regulates protein structure and function by affecting translation elongation speed in Drosophila cells

(2017) Fangzhou Zhao et al.   NUCLEIC ACIDS RESEARCH

Transcription elongation rate has a tissue-specific impact on alternative cleavage and polyadenylation in Drosophila melanogaster

(2017) Xiaochuan Liu et al.   RNA

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

(2016) Ariel A Bazzini et al.   EMBO JOURNAL

Codon usage affects the structure and function of theDrosophilacircadian clock protein PERIOD

(2016) Jingjing Fu et al.   GENES & DEVELOPMENT

The Nrd1-like protein Seb1 coordinates cotranscriptional 3′ end processing and polyadenylation site selection

(2016) Jean-François Lemay et al.   GENES & DEVELOPMENT

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

Alternative polyadenylation of mRNA precursors

(2016) Bin Tian et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Backmasking in the yeast genome: encoding overlapping information for protein-coding and RNA degradation

(2016) S. Aylin Cakiroglu et al.   NUCLEIC ACIDS RESEARCH

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

(2016) Zhipeng Zhou et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Transcriptional termination in mammals: Stopping the RNA polymerase II juggernaut

(2016) N. J. Proudfoot   SCIENCE

PAF Complex Plays Novel Subunit-Specific Roles in Alternative Cleavage and Polyadenylation

(2016) Yan Yang et al.   PLoS Genetics

Codon Optimality Is a Major Determinant of mRNA Stability

(2015) Vladimir Presnyak et al.   CELL

The end of the message: multiple protein–RNA interactions define the mRNA polyadenylation site

(2015) Yongsheng Shi 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

Nonoptimal codon usage influences protein structure in intrinsically disordered regions

(2015) Mian Zhou et al.   MOLECULAR MICROBIOLOGY

Transcription termination and the control of the transcriptome: why, where and how to stop

(2015) Odil Porrua et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Premature termination ofGAT1transcription explains paradoxical negative correlation between nitrogen-responsive mRNA, but constitutive low-level protein production

(2015) Georis Isabelle et al.   RNA Biology

A journey to the end of the message

(2015) James L. Manley   RNA

Rare codons capacitate Kras-driven de novo tumorigenesis

(2014) Nicole L.K. Pershing et al.   JOURNAL OF CLINICAL INVESTIGATION

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

3' UTR-isoform choice has limited influence on the stability and translational efficiency of most mRNAs in mouse fibroblasts

(2013) N. Spies et al.   GENOME RESEARCH

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

Species-specific factors mediate extensive heterogeneity of mRNA 3' ends in yeasts

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

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

Genome-wide mapping of polyadenylation sites in fission yeast reveals widespread alternative polyadenylation

(2013) Juan Mata   RNA Biology

Genome-wide analysis of poly(A) site selection in Schizosaccharomyces pombe

(2013) M. Schlackow et al.   RNA

The Conserved Intronic Cleavage and Polyadenylation Site of CstF-77 Gene Imparts Control of 3′ End Processing Activity through Feedback Autoregulation and by U1 snRNP

(2013) Wenting Luo et al.   PLoS Genetics

Convergent Transcription Induces Dynamic DNA Methylation at disiRNA Loci

(2013) Yunkun Dang et al.   PLoS Genetics

U1 snRNP Determines mRNA Length and Regulates Isoform Expression

(2012) Michael G. Berg et al.   CELL

Rare Codons Regulate KRas Oncogenesis

(2012) Benjamin L. Lampson et al.   CURRENT BIOLOGY

Extensive alternative polyadenylation during zebrafish development

(2012) I. Ulitsky et al.   GENOME RESEARCH

Silent Substitutions Predictably Alter Translation Elongation Rates and Protein Folding Efficiencies

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

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

(2012) Zhipeng Zhou et al.   PLoS Genetics

Ending the message: poly(A) signals then and now

(2011) N. J. Proudfoot   GENES & DEVELOPMENT

Unravelling the means to an end: RNA polymerase II transcription termination

(2011) Jason N. Kuehner et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

CHD1 Remodels Chromatin and Influences Transient DNA Methylation at the Clock Gene frequency

(2011) William J. Belden et al.   PLoS Genetics

Signals for pre-mRNA cleavage and polyadenylation

(2011) Bin Tian et al.   Wiley Interdisciplinary Reviews-RNA

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Comprehensive Polyadenylation Site Maps in Yeast and Human Reveal Pervasive Alternative Polyadenylation

(2010) Fatih Ozsolak et al.   CELL

An Evolutionarily Conserved Mechanism for Controlling the Efficiency of Protein Translation

(2010) Tamir Tuller et al.   CELL

Poly(A) Signals Located near the 5' End of Genes Are Silenced by a General Mechanism That Prevents Premature 3'-End Processing

(2010) J. Guo et al.   MOLECULAR AND CELLULAR BIOLOGY

U1 snRNP protects pre-mRNAs from premature cleavage and polyadenylation

(2010) Daisuke Kaida et al.   NATURE

Formation, regulation and evolution of Caenorhabditis elegans 3′UTRs

(2010) Calvin H. Jan et al.   NATURE

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

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

Nuclear quality control of RNA polymerase II transcripts

(2010) Manfred Schmid et al.   Wiley Interdisciplinary Reviews-RNA

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Widespread Shortening of 3′UTRs by Alternative Cleavage and Polyadenylation Activates Oncogenes in Cancer Cells

(2009) Christine Mayr 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

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

Codon Optimization Increases Steady-State mRNA Levels in Aspergillus oryzae Heterologous Gene Expression

(2008) M. Tokuoka et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

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

(2008) D. Allan Drummond et al.   CELL