Decoding sORF translation – from small proteins to gene regulation

Improved Identification and Analysis of Small Open Reading Frame Encoded Polypeptides

(2016) Jiao Ma et al.   ANALYTICAL CHEMISTRY

Mapping the non-standardized biases of ribosome profiling

(2016) Alexander Bartholomäus et al.   BIOLOGICAL CHEMISTRY

Ribosome Footprint Profiling of Translation throughout the Genome

(2016) Nicholas T. Ingolia   CELL

Upstream ORFs are prevalent translational repressors in vertebrates

(2016) Timothy G Johnstone et al.   EMBO JOURNAL

DHX29 reduces leaky scanning through an upstream AUG codon regardless of its nucleotide context

(2016) Vera P. Pisareva et al.   NUCLEIC ACIDS RESEARCH

In-depth analysis ofcis-determinants that either promote or inhibit reinitiation onGCN4mRNA after translation of its four short uORFs

(2016) Stanislava Gunišová et al.   RNA

A peptide encoded by a transcript annotated as long noncoding RNA enhances SERCA activity in muscle

(2016) B. R. Nelson et al.   SCIENCE

Translation from the 5' untranslated region shapes the integrated stress response

(2016) S. R. Starck et al.   SCIENCE

Conservation of uORF repressiveness and sequence features in mouse, human and zebrafish

(2016) Guo-Liang Chew et al.   Nature Communications

Tunable protein synthesis by transcript isoforms in human cells

(2016) Stephen N Floor et al.   eLife

Thousands of novel translated open reading frames in humans inferred by ribosome footprint profiling

(2016) Anil Raj et al.   eLife

The effect of heterogeneous Transcription Start Sites (TSS) on the translatome: implications for the mammalian cellular phenotype

(2015) Francois-Xavier Dieudonné et al.   BMC GENOMICS

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

(2015) Douglas M. Anderson et al.   CELL

Plant peptide hormone signalling

(2015) A. Motomitsu et al.   Essays in Biochemistry

Ribosome profiling reveals the rhythmic liver translatome and circadian clock regulation by upstream open reading frames

(2015) Peggy Janich et al.   GENOME RESEARCH

Phytosulfokine peptide signalling

(2015) Margret Sauter   JOURNAL OF EXPERIMENTAL BOTANY

Allosteric receptor activation by the plant peptide hormone phytosulfokine

(2015) Jizong Wang et al.   NATURE

Discovery and characterization of smORF-encoded bioactive polypeptides

(2015) Alan Saghatelian et al.   Nature Chemical Biology

Detecting actively translated open reading frames in ribosome profiling data

(2015) Lorenzo Calviello et al.   NATURE METHODS

Sliding of a 43S ribosomal complex from the recognized AUG codon triggered by a delay in eIF2-bound GTP hydrolysis

(2015) Ilya M. Terenin et al.   NUCLEIC ACIDS RESEARCH

Identification of novel Arabidopsis thaliana upstream open reading frames that control expression of the main coding sequences in a peptide sequence-dependent manner

(2015) Isao Ebina et al.   NUCLEIC ACIDS RESEARCH

Assessing the translational landscape of myogenic differentiation by ribosome profiling

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

Comprehensive translational control of tyrosine kinase expression by upstream open reading frames

(2015) K Wethmar et al.   ONCOGENE

The awesome power of ribosome profiling

(2015) Richard Jackson et al.   RNA

Pri sORF peptides induce selective proteasome-mediated protein processing

(2015) J. Zanet et al.   SCIENCE

The hormonal peptide Elabela guides angioblasts to the midline during vasculogenesis

(2015) Christian SM Helker et al.   eLife

Quality control of transcription start site selection by nonsense-mediated-mRNA decay

(2015) Christophe Malabat et al.   eLife

Many lncRNAs, 5’UTRs, and pseudogenes are translated and some are likely to express functional proteins

(2015) Zhe Ji et al.   eLife

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

(2015) Dmitry E Andreev et al.   eLife

Identifying (non-)coding RNAs and small peptides: Challenges and opportunities

(2014) Andrea Pauli et al.   BIOESSAYS

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

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

Everything old is new again: (linc)RNAs make proteins!

(2014) S. M. Cohen   EMBO JOURNAL

Progranulin Transcripts with Short and Long 5′ Untranslated Regions (UTRs) Are Differentially Expressed via Posttranscriptional and Translational Repression

(2014) Anja Capell et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

A draft map of the human proteome

(2014) Min-Sik Kim et al.   NATURE

Mass-spectrometry-based draft of the human proteome

(2014) Mathias Wilhelm et al.   NATURE

Two independent transcription initiation codes overlap on vertebrate core promoters

(2014) Vanja Haberle et al.   NATURE

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

(2014) Sibylle Schleich et al.   NATURE

Emerging evidence for functional peptides encoded by short open reading frames

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

Translation inhibitors cause abnormalities in ribosome profiling experiments

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

Central Cell-Derived Peptides Regulate Early Embryo Patterning in Flowering Plants

(2014) L. M. Costa et al.   SCIENCE

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

(2014) A. Pauli et al.   SCIENCE

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

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

Translation of Small Open Reading Frames within Unannotated RNA Transcripts in Saccharomyces cerevisiae

(2014) Jenna E. Smith et al.   Cell Reports

Long Open Reading Frame Transcripts Escape Nonsense-Mediated mRNA Decay in Yeast

(2014) Laurence Decourty et al.   Cell Reports

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

(2014) Klaus Wethmar   Wiley Interdisciplinary Reviews-RNA

Combining in silico prediction and ribosome profiling in a genome-wide search for novel putatively coding sORFs

(2013) Jeroen Crappé et al.   BMC GENOMICS

Ribosome Profiling Provides Evidence that Large Noncoding RNAs Do Not Encode Proteins

(2013) Mitchell Guttman et al.   CELL

Ribosome profiling reveals resemblance between long non-coding RNAs and 5′ leaders of coding RNAs

(2013) Guo-Liang Chew et al.   DEVELOPMENT

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

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

TOR and S6K1 promote translation reinitiation of uORF-containing mRNAs via phosphorylation of eIF3h

(2013) Mikhail Schepetilnikov et al.   EMBO JOURNAL

Dynamic regulation of the transcription initiation landscape at single nucleotide resolution during vertebrate embryogenesis

(2013) Chirag Nepal et al.   GENOME RESEARCH

Global analyses of UPF1 binding and function reveal expanded scope of nonsense-mediated mRNA decay

(2013) J. A. Hurt et al.   GENOME RESEARCH

Roles for transcript leaders in translation and mRNA decay revealed by transcript leader sequencing

(2013) J. A. Arribere et al.   GENOME RESEARCH

The apelin receptor APJ: journey from an orphan to a multifaceted regulator of homeostasis

(2013) Anne-Marie O'Carroll et al.   JOURNAL OF ENDOCRINOLOGY

Extensive transcriptional heterogeneity revealed by isoform profiling

(2013) Vicent Pelechano et al.   NATURE

Translational dynamics revealed by genome-wide profiling of ribosome footprints in Arabidopsis

(2013) P. Juntawong et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Conserved Regulation of Cardiac Calcium Uptake by Peptides Encoded in Small Open Reading Frames

(2013) E. G. Magny et al.   SCIENCE

Gene Expression Regulation by Upstream Open Reading Frames and Human Disease

(2013) Cristina Barbosa et al.   PLoS Genetics

Alternative Splicing within the elk-1 5' Untranslated Region Serves To Modulate Initiation Events Downstream of the Highly Conserved Upstream Open Reading Frame 2

(2012) G. Rahim et al.   MOLECULAR AND CELLULAR BIOLOGY

Modular regulatory principles of large non-coding RNAs

(2012) Mitchell Guttman et al.   NATURE

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

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

APC15 mediates CDC20 autoubiquitylation by APC/CMCC and disassembly of the mitotic checkpoint complex

(2012) Kristina Uzunova et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

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

Alternative transcription start site selection leads to large differences in translation activity in yeast

(2012) M. F. Rojas-Duran et al.   RNA

Leucine-tRNA Initiates at CUG Start Codons for Protein Synthesis and Presentation by MHC Class I

(2012) S. R. Starck et al.   SCIENCE

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

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

Translational Control via Protein-Regulated Upstream Open Reading Frames

(2011) Jan Medenbach et al.   CELL

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

(2011) Nicholas T. Ingolia et al.   CELL

Non-conventional sources of peptides presented by MHC class I

(2011) Shelley R. Starck et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

APC15 drives the turnover of MCC-CDC20 to make the spindle assembly checkpoint responsive to kinetochore attachment

(2011) Jörg Mansfeld et al.   NATURE CELL BIOLOGY

Alternative splicing and nonsense-mediated decay modulate expression of important regulatory genes in Arabidopsis

(2011) Maria Kalyna et al.   NUCLEIC ACIDS RESEARCH

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

(2011) G. A. Brar et al.   SCIENCE

Quantitative proteomics combined with BAC TransgeneOmics reveals in vivo protein interactions

(2010) Nina C. Hubner et al.   JOURNAL OF CELL BIOLOGY

Small Peptides Switch the Transcriptional Activity of Shavenbaby During Drosophila Embryogenesis

(2010) T. Kondo et al.   SCIENCE

Systematic Analysis of Human Protein Complexes Identifies Chromosome Segregation Proteins

(2010) J. R. A. Hutchins et al.   SCIENCE

Ubiquitin–proteasome-mediated degradation and synthesis of MyoD is modulated by αB-crystallin, a small heat shock protein, during muscle differentiation

(2009) Bhairab N. Singh et al.   BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH

Evolution of alternative and constitutive regions of mammalian 5'UTRs

(2009) Alissa M Resch et al.   BMC GENOMICS

Regulation of Translation Initiation in Eukaryotes: Mechanisms and Biological Targets

(2009) Nahum Sonenberg et al.   CELL

Execution of nonsense-mediated mRNA decay: what defines a substrate?

(2009) Indrani Rebbapragada et al.   CURRENT OPINION IN CELL BIOLOGY

Sucrose Control of Translation Mediated by an Upstream Open Reading Frame-Encoded Peptide

(2009) F. Rahmani et al.   PLANT PHYSIOLOGY

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 isoform regulation in human tissue transcriptomes

(2008) Eric T. Wang et al.   NATURE

Drosophila Pgc protein inhibits P-TEFb recruitment to chromatin in primordial germ cells

(2008) Kazuko Hanyu-Nakamura et al.   NATURE

Repression of RNA Polymerase II Transcription by a Drosophila Oligopeptide

(2008) Gyula Timinszky et al.   PLoS One

Genome-Scale Proteomics Reveals Arabidopsis thaliana Gene Models and Proteome Dynamics

(2008) K. Baerenfaller et al.   SCIENCE

The functional consequences of alternative promoter use in mammalian genomes

(2008) Ramana V. Davuluri et al.   TRENDS IN GENETICS