Death of a dogma: eukaryotic mRNAs can code for more than one protein

A Micropeptide Encoded by a Putative Long Noncoding RNA Regulates Muscle Performance

(2015) Douglas M. Anderson et al.   CELL

Rli1/ABCE1 Recycles Terminating Ribosomes and Controls Translation Reinitiation in 3′UTRs In Vivo

(2015) David J. Young et al.   CELL

Found in translation: functions and evolution of a recently discovered alternative proteome

(2015) Christian R Landry et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

A 5′-upstream short open reading frame encoded peptide regulates angiotensin type 1a receptor production and signalling via the β-arrestin pathway

(2015) Gina L.C. Yosten et al.   JOURNAL OF PHYSIOLOGY-LONDON

Ribosome profiling reveals the what, when, where and how of protein synthesis

(2015) Gloria A. Brar et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Assessing the translational landscape of myogenic differentiation by ribosome profiling

(2015) Eleonora de Klerk et al.   NUCLEIC ACIDS RESEARCH

RPFdb: a database for genome wide information of translated mRNA generated from ribosome profiling

(2015) Shang-Qian Xie et al.   NUCLEIC ACIDS RESEARCH

Translation initiation mediated by RNA looping

(2015) Ki Young Paek et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

HIV-1 Replication and the Cellular Eukaryotic Translation Apparatus

(2015) Santiago Guerrero et al.   Viruses-Basel

Translation of 5′ leaders is pervasive in genes resistant to eIF2 repression

(2015) Dmitry E Andreev et al.   eLife

Oxygen and glucose deprivation induces widespread alterations in mRNA translation within 20 minutes

(2015) Dmitry E Andreev et al.   GENOME BIOLOGY

The Scanning Mechanism of Eukaryotic Translation Initiation

(2014) Alan G. Hinnebusch   Annual Review of Biochemistry

uPEPperoni: An online tool for upstream open reading frame location and analysis of transcript conservation

(2014) Adam Skarshewski et al.   BMC BIOINFORMATICS

The small protein floodgates are opening; now the functional analysis begins

(2014) Kumaran S Ramamurthi et al.   BMC BIOLOGY

Identification of small ORFs in vertebrates using ribosome footprinting and evolutionary conservation

(2014) A. A. Bazzini et al.   EMBO JOURNAL

Discovery of Human sORF-Encoded Polypeptides (SEPs) in Cell Lines and Tissue

(2014) Jiao Ma et al.   JOURNAL OF PROTEOME RESEARCH

A draft map of the human proteome

(2014) Min-Sik Kim et al.   NATURE

DENR–MCT-1 promotes translation re-initiation downstream of uORFs to control tissue growth

(2014) Sibylle Schleich et al.   NATURE

Quantitative profiling of initiating ribosomes in vivo

(2014) Xiangwei Gao et al.   NATURE METHODS

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

(2014) Nicholas T. Ingolia   NATURE REVIEWS GENETICS

Emerging evidence for functional peptides encoded by short open reading frames

(2014) Shea J. Andrews et al.   NATURE REVIEWS GENETICS

Modified ribosome profiling reveals high abundance of ribosome protected mRNA fragments derived from 3′ untranslated regions

(2014) Teemu P. Miettinen et al.   NUCLEIC ACIDS RESEARCH

PROTEOFORMER: deep proteome coverage through ribosome profiling and MS integration

(2014) Jeroen Crappé et al.   NUCLEIC ACIDS RESEARCH

Ensembl 2015

(2014) Fiona Cunningham et al.   NUCLEIC ACIDS RESEARCH

A proteogenomics approach integrating proteomics and ribosome profiling increases the efficiency of protein identification and enables the discovery of alternative translation start sites

(2014) Alexander Koch et al.   PROTEOMICS

Toddler: An Embryonic Signal That Promotes Cell Movement via Apelin Receptors

(2014) A. Pauli et al.   SCIENCE

Exposing synonymous mutations

(2014) Ryan C. Hunt et al.   TRENDS IN GENETICS

Ribosome Profiling Reveals Pervasive Translation Outside of Annotated Protein-Coding Genes

(2014) Nicholas T. Ingolia et al.   Cell Reports

The regulatory potential of upstream open reading frames in eukaryotic gene expression

(2014) Klaus Wethmar   Wiley Interdisciplinary Reviews-RNA

Extensive translation of small Open Reading Frames revealed by Poly-Ribo-Seq

(2014) Julie L Aspden et al.   eLife

Long non-coding RNAs as a source of new peptides

(2014) Jorge Ruiz-Orera et al.   eLife

ELABELA: A Hormone Essential for Heart Development Signals via the Apelin Receptor

(2013) Serene C. Chng et al.   DEVELOPMENTAL CELL

The A2AAdenosine Receptor Is a Dual Coding Gene

(2013) Chien-fei Lee et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

An Out-of-frame Overlapping Reading Frame in the Ataxin-1 Coding Sequence Encodes a Novel Ataxin-1 Interacting Protein

(2013) Danny Bergeron et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Reinitiation and Other Unconventional Posttermination Events during Eukaryotic Translation

(2013) Maxim A. Skabkin et al.   MOLECULAR CELL

The Vertebrate Genome Annotation browser 10 years on

(2013) Jennifer L. Harrow et al.   NUCLEIC ACIDS RESEARCH

uORFdb—a comprehensive literature database on eukaryotic uORF biology

(2013) Klaus Wethmar et al.   NUCLEIC ACIDS RESEARCH

GWIPS-viz: development of a ribo-seq genome browser

(2013) Audrey M. Michel et al.   NUCLEIC ACIDS RESEARCH

TISdb: a database for alternative translation initiation in mammalian cells

(2013) Ji Wan et al.   NUCLEIC ACIDS RESEARCH

RefSeq: an update on mammalian reference sequences

(2013) Kim D. Pruitt et al.   NUCLEIC ACIDS RESEARCH

Current status and new features of the Consensus Coding Sequence database

(2013) Catherine M. Farrell et al.   NUCLEIC ACIDS RESEARCH

Direct Detection of Alternative Open Reading Frames Translation Products in Human Significantly Expands the Proteome

(2013) Benoît Vanderperre et al.   PLoS One

ZFN, TALEN, and CRISPR/Cas-based methods for genome engineering

(2013) Thomas Gaj et al.   TRENDS IN BIOTECHNOLOGY

The Current Status of Vertebrate Cellular mRNA IRESs

(2013) R. J. Jackson   Cold Spring Harbor Perspectives in Biology

Ribosome profiling: a Hi-Def monitor for protein synthesis at the genome-wide scale

(2013) Audrey M. Michel et al.   Wiley Interdisciplinary Reviews-RNA

Translational repression of the McKusick–Kaufman syndrome transcript by unique upstream open reading frames encoding mitochondrial proteins with alternative polyadenylation sites

(2012) Chizuru Akimoto et al.   BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS

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

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

Genome-wide search for novel human uORFs and N-terminal protein extensions using ribosomal footprinting

(2012) C. Fritsch et al.   GENOME RESEARCH

GENCODE: The reference human genome annotation for The ENCODE Project

(2012) J. Harrow et al.   GENOME RESEARCH

Non-canonical translation in RNA viruses

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

Ribosomal Protein S25 Dependency Reveals a Common Mechanism for Diverse Internal Ribosome Entry Sites and Ribosome Shunting

(2012) M. I. Hertz et al.   MOLECULAR AND CELLULAR BIOLOGY

Peptidomic discovery of short open reading frame–encoded peptides in human cells

(2012) Sarah A Slavoff et al.   Nature Chemical Biology

A beginner's guide to eukaryotic genome annotation

(2012) Mark Yandell et al.   NATURE REVIEWS GENETICS

Global mapping of translation initiation sites in mammalian cells at single-nucleotide resolution

(2012) S. Lee et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Decoding Human Cytomegalovirus

(2012) N. Stern-Ginossar et al.   SCIENCE

HAltORF: a database of predicted out-of-frame alternative open reading frames in human

(2012) B. Vanderperre et al.   Database-The Journal of Biological Databases and Curation

PhyloCSF: a comparative genomics method to distinguish protein coding and non-coding regions

(2011) M. F. Lin et al.   BIOINFORMATICS

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

(2011) Nicholas T. Ingolia et al.   CELL

An overlapping reading frame in the PRNP gene encodes a novel polypeptide distinct from the prion protein

(2011) Benoît Vanderperre et al.   FASEB JOURNAL

Cap-Assisted Internal Initiation of Translation of Histone H4

(2011) Franck Martin et al.   MOLECULAR CELL

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

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

High-Resolution View of the Yeast Meiotic Program Revealed by Ribosome Profiling

(2011) G. A. Brar et al.   SCIENCE

UniProt Knowledgebase: a hub of integrated protein data

(2011) M. Magrane et al.   Database-The Journal of Biological Databases and Curation

Length of the ORF, position of the first AUG and the Kozak motif are important factors in potential dual-coding transcripts

(2010) Heng Xu et al.   CELL RESEARCH

A Eukaryotic (Insect) Tricistronic mRNA Encodes Three Proteins Selected by Context-dependent Scanning

(2010) Yasushi Kanamori et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Alternative Ways to Think about Cellular Internal Ribosome Entry

(2010) Wendy V. Gilbert   JOURNAL OF BIOLOGICAL CHEMISTRY

Facilitated leaky scanning and atypical ribosome shunting direct downstream translation initiation on the tricistronic S1 mRNA of avian reovirus

(2010) T. Racine et al.   NUCLEIC ACIDS RESEARCH

Meeting report: a workshop on Best Practices in Genome Annotation

(2010) R. Madupu et al.   Database-The Journal of Biological Databases and Curation

Bridging IRES elements in mRNAs to the eukaryotic translation apparatus

(2009) Kerry D. Fitzgerald et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Cellular immune response to cryptic epitopes during therapeutic gene transfer

(2009) C. Li et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Upstream open reading frames cause widespread reduction of protein expression and are polymorphic among humans

(2009) S. E. Calvo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2009) N. T. Ingolia et al.   SCIENCE

Alternative translation start sites and hidden coding potential of eukaryotic mRNAs

(2008) Alex V. Kochetov   BIOESSAYS

Bioinformatics prediction of overlapping frameshifted translation products in mammalian transcripts

(2008) Sebastien Ribrioux et al.   BMC GENOMICS

Translation of cIAP2 mRNA Is Mediated Exclusively by a Stress-Modulated Ribosome Shunt

(2008) K. W. Sherrill et al.   MOLECULAR AND CELLULAR BIOLOGY

An ancient genetic link between vertebrate mitochondrial fatty acid synthesis and RNA processing

(2007) Kaija J. Autio et al.   FASEB JOURNAL