Codon bias confers stability to human mRNA s

Cycloheximide can distort measurements of mRNA levels and translation efficiency

(2019) Daniel A Santos et al.   NUCLEIC ACIDS RESEARCH

Translation affects mRNA stability in a codon-dependent manner in human cells

(2019) Qiushuang Wu et al.   eLife

SARNAclust: Semi-automatic detection of RNA protein binding motifs from immunoprecipitation data

(2018) Ivan Dotu et al.   PLoS Computational Biology

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

(2018) Zhipeng Zhou et al.   eLife

Codon choice directs constitutive mRNA levels in trypanosomes

(2018) Janaina de Freitas Nascimento et al.   eLife

Codon usage bias controls mRNA and protein abundance in trypanosomatids

(2018) Laura Jeacock et al.   eLife

Attenuated Codon Optimality Contributes to Neural-Specific mRNA Decay in Drosophila

(2018) Dana A. Burow et al.   Cell Reports

Non-invasive measurement of mRNA decay reveals translation initiation as the major determinant of mRNA stability

(2018) Leon Y Chan et al.   eLife

Decoupling the impact of microRNAs on translational repression versus RNA degradation in embryonic stem cells

(2018) Jacob W Freimer et al.   eLife

Codon usage regulates human KRAS expression at both transcriptional and translational levels

(2018) Jingjing Fu et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Cap-specific terminal N6-methylation of RNA by an RNA polymerase II–associated methyltransferase

(2018) Shinichiro Akichika et al.   SCIENCE

An NF-κB Transcription-Factor-Dependent Lineage-Specific Transcriptional Program Promotes Regulatory T Cell Identity and Function

(2017) Hyunju Oh et al.   IMMUNITY

Transcriptome-wide measurement of translation by ribosome profiling

(2017) Nicholas J. McGlincy et al.   METHODS

Functional 5′ UTR mRNA structures in eukaryotic translation regulation and how to find them

(2017) Kathrin Leppek et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Ensembl 2018

(2017) Daniel R Zerbino et al.   NUCLEIC ACIDS RESEARCH

Cis -regulatory elements explain most of the mRNA stability variation across genes in yeast

(2017) Jun Cheng et al.   RNA

DHX15 is associated with poor prognosis in acute myeloid leukemia (AML) and regulates cell apoptosis via the NF-kB signaling pathway

(2017) Lili Pan et al.   Oncotarget

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

(2017) Caia D. S. Duncan et al.   Scientific Reports

Regnase-1 Maintains Iron Homeostasis via the Degradation of Transferrin Receptor 1 and Prolyl-Hydroxylase-Domain-Containing Protein 3 mRNAs

(2017) Masanori Yoshinaga et al.   Cell Reports

Analysis of the association between codon optimality and mRNA stability in Schizosaccharomyces pombe

(2016) Yuriko Harigaya et al.   BMC GENOMICS

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

(2016) Aditya Radhakrishnan et al.   CELL

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

Role of mRNA structure in the control of protein folding

(2016) Guilhem Faure 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

Seeing translation

(2016) S. Iwasaki et al.   SCIENCE

Mechanical insights into ribosomal progression overcoming RNA G-quadruplex from periodical translation suppression in cells

(2016) Tamaki Endoh et al.   Scientific Reports

Multiple Transcript Properties Related to Translation Affect mRNA Degradation Rates in Saccharomyces cerevisiae

(2016) B. Neymotin et al.   G3-Genes Genomes Genetics

Regnase-1 and Roquin Regulate a Common Element in Inflammatory mRNAs by Spatiotemporally Distinct Mechanisms

(2015) Takashi Mino et al.   CELL

Codon Optimality Is a Major Determinant of mRNA Stability

(2015) Vladimir Presnyak et al.   CELL

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

(2015) Chien-Hung Yu et al.   MOLECULAR CELL

Efficient and quantitative high-throughput tRNA sequencing

(2015) Guanqun Zheng et al.   NATURE METHODS

Accurate transcriptome-wide prediction of microRNA targets and small interfering RNA off-targets with MIRZA-G: Figure 2.

(2015) Rafal Gumienny et al.   NUCLEIC ACIDS RESEARCH

Nucleotide sequence composition adjacent to intronic splice sites improves splicing efficiency via its effect on pre-mRNA local folding in fungi

(2015) Zohar Zafrir et al.   RNA

RC3H1 post-transcriptionally regulates A20 mRNA and modulates the activity of the IKK/NF-κB pathway

(2015) Yasuhiro Murakawa et al.   Nature Communications

Aven recognition of RNA G-quadruplexes regulates translation of the mixed lineage leukemia protooncogenes

(2015) Palaniraja Thandapani et al.   eLife

A Dual Program for Translation Regulation in Cellular Proliferation and Differentiation

(2014) Hila Gingold et al.   CELL

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

(2014) Carlo G. Artieri et al.   GENOME RESEARCH

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

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

Translation inhibitors cause abnormalities in ribosome profiling experiments

(2014) Maxim V. Gerashchenko et al.   NUCLEIC ACIDS RESEARCH

ZFP36L1 and ZFP36L2 control LDLR mRNA stability via the ERK–RSK pathway

(2014) Shungo Adachi et al.   NUCLEIC ACIDS RESEARCH

The effect of tRNA levels on decoding times of mRNA codons

(2014) Alexandra Dana et al.   NUCLEIC ACIDS RESEARCH

Quantifying the Effect of Ribosomal Density on mRNA Stability

(2014) Shlomit Edri et al.   PLoS One

Mean of the Typical Decoding Rates: A New Translation Efficiency Index Based on the Analysis of Ribosome Profiling Data

(2014) Alexandra Dana et al.   G3-Genes Genomes Genetics

Measurement of average decoding rates of the 61 sense codons in vivo

(2014) Justin Gardin et al.   eLife

Distinct stages of the translation elongation cycle revealed by sequencing ribosome-protected mRNA fragments

(2014) Liana F Lareau et al.   eLife

Positively Charged Residues Are the Major Determinants of Ribosomal Velocity

(2013) Catherine A. Charneski et al.   PLOS BIOLOGY

Rare Codons Regulate KRas Oncogenesis

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

Insights into the regulation of protein abundance from proteomic and transcriptomic analyses

(2012) Christine Vogel et al.   NATURE REVIEWS GENETICS

Evolutionary conservation of codon optimality reveals hidden signatures of cotranslational folding

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

NF45 dimerizes with NF90, Zfr and SPNR via a conserved domain that has a nucleotidyltransferase fold

(2012) Urszula M. Wolkowicz et al.   NUCLEIC ACIDS RESEARCH

Differential GC Content between Exons and Introns Establishes Distinct Strategies of Splice-Site Recognition

(2012) Maayan Amit et al.   Cell Reports

The DEAD-Box Protein Dhh1 Promotes Decapping by Slowing Ribosome Movement

(2012) Thomas Sweet et al.   PLOS BIOLOGY

GC content around splice sites affects splicing through pre-mRNA secondary structures

(2011) Jing Zhang et al.   BMC GENOMICS

Ribosome Profiling of Mouse Embryonic Stem Cells Reveals the Complexity and Dynamics of Mammalian Proteomes

(2011) Nicholas T. Ingolia et al.   CELL

RNA Homeostasis Governed by Cell Type-Specific and Branched Feedback Loops Acting on NMD

(2011) Lulu Huang et al.   MOLECULAR CELL

Composite effects of gene determinants on the translation speed and density of ribosomes

(2011) Tamir Tuller et al.   GENOME BIOLOGY

Phosphorylation of the NFAR proteins by the dsRNA-dependent protein kinase PKR constitutes a novel mechanism of translational regulation and cellular defense

(2010) A. Harashima et al.   GENES & DEVELOPMENT

Translationally optimal codons associate with aggregation-prone sites in proteins

(2010) Yaelim Lee et al.   PROTEOMICS

The role of AUF1 in regulated mRNA decay

(2010) Frances M. Gratacós et al.   Wiley Interdisciplinary Reviews-RNA

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

NF45 functions as an IRES trans-acting factor that is required for translation of cIAP1 during the unfolded protein response

(2009) T E Graber et al.   CELL DEATH AND DIFFERENTIATION

Translationally Optimal Codons Associate with Structurally Sensitive Sites in Proteins

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

Hypusine-containing protein eIF5A promotes translation elongation

(2009) Preeti Saini et al.   NATURE

NF90 selectively represses the translation of target mRNAs bearing an AU-rich signature motif

(2009) Yuki Kuwano et al.   NUCLEIC ACIDS RESEARCH

MEME SUITE: tools for motif discovery and searching

(2009) T. L. Bailey et al.   NUCLEIC ACIDS RESEARCH

Genome-Wide Analysis in Vivo of Translation with Nucleotide Resolution Using Ribosome Profiling

(2009) N. T. Ingolia et al.   SCIENCE

CAIcal: A combined set of tools to assess codon usage adaptation

(2008) Pere Puigbò et al.   Biology Direct

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

(2008) D. Allan Drummond et al.   CELL

Nuclear Factor 45 (NF45) Is a Regulatory Subunit of Complexes with NF90/110 Involved in Mitotic Control

(2008) D. Guan et al.   MOLECULAR AND CELLULAR BIOLOGY

NFAR-1 and -2 modulate translation and are required for efficient host defense

(2008) I. Pfeifer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA