Augmented genetic decoding: global, local and temporal alterations of decoding processes and codon meaning

Expanding and Reprogramming the Genetic Code of Cells and Animals

(2014) Jason W. Chin   Annual Review of Biochemistry

Programmed Translational Readthrough Generates Antiangiogenic VEGF-Ax

(2014) Sandeepa M. Eswarappa et al.   CELL

Comprehensive Analysis of Stop Codon Usage in Bacteria and Its Correlation with Release Factor Abundance

(2014) Gürkan Korkmaz et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Promiscuous methionyl-tRNA synthetase mediates adaptive mistranslation to protect cells against oxidative stress

(2014) J. Y. Lee et al.   JOURNAL OF CELL SCIENCE

Pseudouridine profiling reveals regulated mRNA pseudouridylation in yeast and human cells

(2014) Thomas M. Carlile et al.   NATURE

Ribosomal frameshifting in the CCR5 mRNA is regulated by miRNAs and the NMD pathway

(2014) Ashton Trey Belew et al.   NATURE

Ribosome profiling: new views of translation, from single codons to genome scale

(2014) Nicholas T. Ingolia   NATURE REVIEWS GENETICS

Repeat-Associated Non-AUG Translation and Its Impact in Neurodegenerative Disease

(2014) Michael G. Kearse et al.   Neurotherapeutics

Analysis of tetra- and hepta-nucleotides motifs promoting -1 ribosomal frameshifting in Escherichia coli

(2014) V. Sharma et al.   NUCLEIC ACIDS RESEARCH

RAN translation and frameshifting as translational challenges at simple repeats of human neurodegenerative disorders

(2014) Marzena Wojciechowska et al.   NUCLEIC ACIDS RESEARCH

The tmRNA website

(2014) Corey M. Hudson et al.   NUCLEIC ACIDS RESEARCH

Evidence of efficient stop codon readthrough in four mammalian genes

(2014) Gary Loughran et al.   NUCLEIC ACIDS RESEARCH

Selenoproteins: Molecular Pathways and Physiological Roles

(2014) Vyacheslav M. Labunskyy et al.   PHYSIOLOGICAL REVIEWS

Massive programmed translational jumping in mitochondria

(2014) B. F. Lang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A frameshifting stimulatory stem loop destabilizes the hybrid state and impedes ribosomal translocation

(2014) H.-K. Kim et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Transactivation of programmed ribosomal frameshifting by a viral protein

(2014) Y. Li et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Adjustments, extinction, and remains of selenocysteine incorporation machinery in the nematode lineage

(2014) L. Otero et al.   RNA

Stop codon reassignments in the wild

(2014) N. N. Ivanova et al.   SCIENCE

Orsay virus utilizes ribosomal frameshifting to express a novel protein that is incorporated into virions

(2014) Hongbing Jiang et al.   VIROLOGY

High-efficiency translational bypassing of non-coding nucleotides specified by mRNA structure and nascent peptide

(2014) Ekaterina Samatova et al.   Nature Communications

Ribosomal Readthrough at a Short UGA Stop Codon Context Triggers Dual Localization of Metabolic Enzymes in Fungi and Animals

(2014) Alina C. Stiebler et al.   PLoS Genetics

Ribosome Rescue and Translation Termination at Non-Standard Stop Codons by ICT1 in Mammalian Mitochondria

(2014) Shiori Akabane et al.   PLoS Genetics

Peroxisomal lactate dehydrogenase is generated by translational readthrough in mammals

(2014) Fabian Schueren et al.   eLife

Ends of the line for tmRNA-SmpB

(2014) Corey M. Hudson et al.   Frontiers in Microbiology

tmRNA-mediated trans-translation as the major ribosome rescue system in a bacterial cell

(2014) Hyouta Himeno et al.   Frontiers in Genetics

Unusual −1 Ribosomal Frameshift Caused by Stable RNA G-Quadruplex in Open Reading Frame

(2013) Tamaki Endoh et al.   ANALYTICAL CHEMISTRY

Repeat-associated non-ATG (RAN) translation in neurological disease

(2013) J. D. Cleary et al.   HUMAN MOLECULAR GENETICS

Evolutionary Relationships among Actinophages and a Putative Adaptation for Growth in Streptomyces spp.

(2013) M. C. M. Smith et al.   JOURNAL OF BACTERIOLOGY

Regulation of Gene Expression by Macrolide-Induced Ribosomal Frameshifting

(2013) Pulkit Gupta et al.   MOLECULAR CELL

Stimulation of ribosomal frameshifting by RNA G-quadruplex structures

(2013) Chien-Hung Yu et al.   NUCLEIC ACIDS RESEARCH

Identification of the nature of reading frame transitions observed in prokaryotic genomes

(2013) Ivan Antonov et al.   NUCLEIC ACIDS RESEARCH

UGA is an additional glycine codon in uncultured SR1 bacteria from the human microbiota

(2013) J. H. Campbell et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Depletion of Cognate Charged Transfer RNA Causes Translational Frameshifting within the Expanded CAG Stretch in Huntingtin

(2013) Hannah Girstmair et al.   Cell Reports

Ribosome profiling reveals pervasive and regulated stop codon readthrough in Drosophila melanogaster

(2013) Joshua G Dunn et al.   eLife

A-to-I editing of protein coding and noncoding RNAs

(2012) Arka Mallela et al.   CRITICAL REVIEWS IN BIOCHEMISTRY AND MOLECULAR BIOLOGY

Translational recoding in archaea

(2012) Beatrice Cobucci-Ponzano et al.   EXTREMOPHILES

Observation of dually decoded regions of the human genome using ribosome profiling data

(2012) A. M. Michel et al.   GENOME RESEARCH

Expanded ATXN3 frameshifting events are toxic in Drosophila and mammalian neuron models

(2012) Shawn J. Stochmanski et al.   HUMAN MOLECULAR GENETICS

Non-canonical translation in RNA viruses

(2012) A. E. Firth et al.   JOURNAL OF GENERAL VIROLOGY

Evolution and Diversification of the Organellar Release Factor Family

(2012) Isabel Duarte et al.   MOLECULAR BIOLOGY AND EVOLUTION

GeneTack database: genes with frameshifts in prokaryotic genomes and eukaryotic mRNA sequences

(2012) Ivan Antonov et al.   NUCLEIC ACIDS RESEARCH

Carbon source-dependent expansion of the genetic code in bacteria

(2012) L. Prat et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Efficient -2 frameshifting by mammalian ribosomes to synthesize an additional arterivirus protein

(2012) Y. Fang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

An Overlapping Protein-Coding Region in Influenza A Virus Segment 3 Modulates the Host Response

(2012) B. W. Jagger et al.   SCIENCE

Identification of A-to-I RNA editing: Dotting the i’s in the human transcriptome

(2011) A. Kiran et al.   BIOCHEMISTRY-MOSCOW

Bifunctional transfer-messenger RNA

(2011) Kenneth C. Keiler et al.   BIOCHIMIE

Evidence of abundant stop codon readthrough in Drosophila and other metazoa

(2011) I. Jungreis et al.   GENOME RESEARCH

The Interplay of mRNA Stimulatory Signals Required for AUU-Mediated Initiation and Programmed -1 Ribosomal Frameshifting in Decoding of Transposable Element IS911

(2011) M.-F. Prere et al.   JOURNAL OF BACTERIOLOGY

A Pilot Study of Bacterial Genes with Disrupted ORFs Reveals a Surprising Profusion of Protein Sequence Recoding Mediated by Ribosomal Frameshifting and Transcriptional Realignment

(2011) V. Sharma et al.   MOLECULAR BIOLOGY AND EVOLUTION

Converting nonsense codons into sense codons by targeted pseudouridylation

(2011) John Karijolich et al.   NATURE

Polyamine sensing by nascent ornithine decarboxylase antizyme stimulates decoding of its mRNA

(2011) Leo Kurian et al.   NATURE

Stem-loop structures can effectively substitute for an RNA pseudoknot in -1 ribosomal frameshifting

(2011) C.-H. Yu et al.   NUCLEIC ACIDS RESEARCH

Stimulation of stop codon readthrough: frequent presence of an extended 3′ RNA structural element

(2011) Andrew E. Firth et al.   NUCLEIC ACIDS RESEARCH

Identification of evolutionarily conserved non-AUG-initiated N-terminal extensions in human coding sequences

(2011) Ivaylo P. Ivanov et al.   NUCLEIC ACIDS RESEARCH

Ribosomal frameshifting into an overlapping gene in the 2B-encoding region of the cardiovirus genome

(2011) G. Loughran et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Programmed ribosomal frameshifting in the expression of the regulator of intestinal stem cell proliferation, adenomatous polyposis coli (APC)

(2011) Pavel V. Baranov et al.   RNA Biology

A long-distance RNA–RNA interaction plays an important role in programmed −1 ribosomal frameshifting in the translation of p88 replicase protein of Red clover necrotic mosaic virus

(2011) Yuri Tajima et al.   VIROLOGY

The Distinction Between Recoding and Codon Reassignment

(2010) J. F. Atkins et al.   GENETICS

Frameshifting in Alphaviruses: A Diversity of 3′ Stimulatory Structures

(2010) Betty Y.-W. Chung et al.   JOURNAL OF MOLECULAR BIOLOGY

Achieving a Golden Mean: Mechanisms by Which Coronaviruses Ensure Synthesis of the Correct Stoichiometric Ratios of Viral Proteins

(2010) E. P. Plant et al.   JOURNAL OF VIROLOGY

Two groups of phenylalanine biosynthetic operon leader peptides genes: a high level of apparently incidental frameshifting in decoding Escherichia coli pheL

(2010) Olga L. Gurvich et al.   NUCLEIC ACIDS RESEARCH

Endogenous ribosomal frameshift signals operate as mRNA destabilizing elements through at least two molecular pathways in yeast

(2010) Ashton T. Belew et al.   NUCLEIC ACIDS RESEARCH

Targeted insertion of cysteine by decoding UGA codons with mammalian selenocysteine machinery

(2010) X.-M. Xu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Bioinformatic, structural, and functional analyses support release factor-like MTRF1 as a protein able to decode nonstandard stop codons beginning with adenine in vertebrate mitochondria

(2010) D. J. Young et al.   RNA

Hungry Codons Promote Frameshifting in Human Mitochondrial Ribosomes

(2010) R. Temperley et al.   SCIENCE

Evidence for ribosomal frameshifting and a novel overlapping gene in the genomes of insect-specific flaviviruses

(2010) Andrew E. Firth et al.   VIROLOGY

The many levels of control on bacterial selenoprotein synthesis

(2009) Satoko Yoshizawa et al.   BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS

NS1' of Flaviviruses in the Japanese Encephalitis Virus Serogroup Is a Product of Ribosomal Frameshifting and Plays a Role in Viral Neuroinvasiveness

(2009) E. B. Melian et al.   JOURNAL OF VIROLOGY

Innate immune and chemically triggered oxidative stress modifies translational fidelity

(2009) Nir Netzer et al.   NATURE

An intermolecular RNA triplex provides insight into structural determinants for the pseudoknot stimulator of −1 ribosomal frameshifting

(2009) Ming-Yuan Chou et al.   NUCLEIC ACIDS RESEARCH

Triplex structures in an RNA pseudoknot enhance mechanical stability and increase efficiency of -1 ribosomal frameshifting

(2009) G. Chen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Connection between stop codon reassignment and frequent use of shifty stop frameshifting

(2009) H. Vallabhaneni et al.   RNA

Genetic Code Supports Targeted Insertion of Two Amino Acids by One Codon

(2009) A. A. Turanov et al.   SCIENCE

A conserved predicted pseudoknot in the NS2A-encoding sequence of West Nile and Japanese encephalitis flaviviruses suggests NS1' may derive from ribosomal frameshifting

(2009) Andrew E Firth et al.   Virology Journal

Origin of an Alternative Genetic Code in the Extremely Small and GC–Rich Genome of a Bacterial Symbiont

(2009) John P. McCutcheon et al.   PLoS Genetics

RNA pseudoknots and the regulation of protein synthesis

(2008) Ian Brierley et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

PRFdb: A database of computationally predicted eukaryotic programmed -1 ribosomal frameshift signals

(2008) Ashton T Belew et al.   BMC GENOMICS

Translational bypassing without peptidyl-tRNA anticodon scanning of coding gap mRNA

(2008) Norma M Wills et al.   EMBO JOURNAL

Eukaryotic selenoprotein synthesis: Mechanistic insight incorporating new factors and new functions for old factors

(2008) Jeffrey E. Squires et al.   IUBMB LIFE

Apical Loop-Internal Loop RNA Pseudoknots

(2008) Marie-Hélène Mazauric et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

The use of the rare UUA codon to define “Expression Space” for genes involved in secondary metabolism, development and environmental adaptation in Streptomyces

(2008) Keith F. Chater et al.   JOURNAL OF MICROBIOLOGY

Relaxation of Selective Constraints Causes Independent Selenoprotein Extinction in Insect Genomes

(2008) Charles E. Chapple et al.   PLoS One

Adaptive antioxidant methionine accumulation in respiratory chain complexes explains the use of a deviant genetic code in mitochondria

(2008) A. Bender et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Discovery of frameshifting in Alphavirus 6K resolves a 20-year enigma

(2008) Andrew E Firth et al.   Virology Journal

Frameshifting RNA pseudoknots: Structure and mechanism

(2008) David P. Giedroc et al.   VIRUS RESEARCH

Reduced reliance on the trace element selenium during evolution of mammals

(2008) Alexey V Lobanov et al.   GENOME BIOLOGY