Classification and function of small open reading frames

Secondary structure impacts patterns of selection in human lncRNAs

(2016) Cinta Pegueroles et al.   BMC BIOLOGY

Upstream ORFs are prevalent translational repressors in vertebrates

(2016) Timothy G Johnstone et al.   EMBO JOURNAL

Evaluating Phylostratigraphic Evidence for Widespread De Novo Gene Birth in Genome Evolution

(2016) Bryan A. Moyers et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

(2016) B. R. Nelson et al.   SCIENCE

New Peptides Under the s(ORF)ace of the Genome

(2016) Jose I. Pueyo et al.   TRENDS IN BIOCHEMICAL SCIENCES

Hemotin, a Regulator of Phagocytosis Encoded by a Small ORF and Conserved across Metazoans

(2016) José I. Pueyo et al.   PLOS BIOLOGY

MicroProtein-Mediated Recruitment of CONSTANS into a TOPLESS Trimeric Complex Represses Flowering in Arabidopsis

(2016) Moritz Graeff et al.   PLoS Genetics

Global Intersection of Long Non-Coding RNAs with Processed and Unprocessed Pseudogenes in the Human Genome

(2016) Michael J. Milligan et al.   Frontiers in Genetics

DRAMP: a comprehensive data repository of antimicrobial peptides

(2016) Linlin Fan et al.   Scientific Reports

Ribosomal profiling adds new coding sequences to the proteome

(2015) M. A. S. Mumtaz et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

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

(2015) Douglas M. Anderson et al.   CELL

The Mitochondrial-Derived Peptide MOTS-c Promotes Metabolic Homeostasis and Reduces Obesity and Insulin Resistance

(2015) Changhan Lee et al.   Cell Metabolism

Rat Humanin is encoded and translated in mitochondria and is localized to the mitochondrial compartment where it regulates ROS production

(2015) Vladislava Paharkova et al.   MOLECULAR AND CELLULAR ENDOCRINOLOGY

Primary transcripts of microRNAs encode regulatory peptides

(2015) Dominique Lauressergues et al.   NATURE

Discovery and characterization of smORF-encoded bioactive polypeptides

(2015) Alan Saghatelian et al.   Nature Chemical Biology

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

Ensembl 2016

(2015) Andrew Yates et al.   NUCLEIC ACIDS RESEARCH

Pri sORF peptides induce selective proteasome-mediated protein processing

(2015) J. Zanet et al.   SCIENCE

Genes from scratch – the evolutionary fate of de novo genes

(2015) Christian Schlötterer   TRENDS IN GENETICS

Partial protein domains: evolutionary insights and bioinformatics challenges

(2015) Lawrence A Kelley et al.   GENOME BIOLOGY

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

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

A Human Short Open Reading Frame (sORF)-encoded Polypeptide That Stimulates DNA End Joining

(2014) Sarah A. Slavoff et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

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

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

Emerging evidence for functional peptides encoded by short open reading frames

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

The translational landscape of fission-yeast meiosis and sporulation

(2014) Caia D S Duncan et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Small cationic antimicrobial peptides delocalize peripheral membrane proteins

(2014) M. Wenzel et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Origin and Spread of de Novo Genes in Drosophila melanogaster Populations

(2014) L. Zhao 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

Widespread Changes in the Posttranscriptional Landscape at the Drosophila Oocyte-to-Embryo Transition

(2014) Iva Kronja et al.   Cell Reports

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

Extensive localization of long noncoding RNAs to the cytosol and mono- and polyribosomal complexes

(2014) Sebastiaan van Heesch et al.   GENOME BIOLOGY

Phylogenetic patterns of emergence of new genes support a model of frequent de novo evolution

(2013) Rafik Neme et al.   BMC GENOMICS

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

Integration of New Genes into Cellular Networks, and Their Structural Maturation

(2013) G. Abrusan   GENETICS

Long non-coding RNAs: new players in cell differentiation and development

(2013) Alessandro Fatica et al.   NATURE REVIEWS GENETICS

Small open reading frames associated with morphogenesis are hidden in plant genomes

(2013) K. Hanada 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

De Novo ORFs in Drosophila Are Important to Organismal Fitness and Evolved Rapidly from Previously Non-coding Sequences

(2013) Josephine A. Reinhardt et al.   PLoS Genetics

Long noncoding RNAs are rarely translated in two human cell lines

(2012) B. Banfai 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

The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression

(2012) T. Derrien et al.   GENOME RESEARCH

Proto-genes and de novo gene birth

(2012) Anne-Ruxandra Carvunis et al.   NATURE

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

Mitochondrial dynamics in neurodegeneration

(2012) Kie Itoh et al.   TRENDS IN CELL BIOLOGY

Hominoid-Specific De Novo Protein-Coding Genes Originating from Long Non-Coding RNAs

(2012) Chen Xie et al.   PLoS Genetics

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

(2011) Nicholas T. Ingolia et al.   CELL

Tarsal-less peptides control Notch signalling through the Shavenbaby transcription factor

(2011) Jose I. Pueyo et al.   DEVELOPMENTAL BIOLOGY

Notch Ligand Ubiquitylation: What Is It Good For?

(2011) Gerry Weinmaster et al.   DEVELOPMENTAL CELL

Competitive inhibition of transcription factors by small interfering peptides

(2011) Pil Joon Seo et al.   TRENDS IN PLANT SCIENCE

Hundreds of putatively functional small open reading frames in Drosophila

(2011) Emmanuel Ladoukakis et al.   GENOME BIOLOGY

Regulation of protein function by ‘microProteins’

(2010) Annica-Carolin Staudt et al.   EMBO REPORTS

Ubiquitin-like protein activation by E1 enzymes: the apex for downstream signalling pathways

(2009) Brenda A. Schulman et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Detection of intergenic non-coding RNAs expressed in the main developmental stages in Drosophila melanogaster

(2009) Zheng Li et al.   NUCLEIC ACIDS RESEARCH

The Evolutionary History of Protein Domains Viewed by Species Phylogeny

(2009) Song Yang et al.   PLoS One

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

Targeting lipophilic cations to mitochondria

(2008) Michael P. Murphy   BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS

The 11-aminoacid long Tarsal-less peptides trigger a cell signal in Drosophila leg development

(2008) Jose Ignacio Pueyo et al.   DEVELOPMENTAL BIOLOGY

Trans-regulation of the expression of the transcription factor MtHAP2-1 by a uORF controls root nodule development

(2008) J. P. Combier et al.   GENES & DEVELOPMENT

eIF3a cooperates with sequences 5' of uORF1 to promote resumption of scanning by post-termination ribosomes for reinitiation on GCN4 mRNA

(2008) B. Szamecz et al.   GENES & DEVELOPMENT

On the origin of new genes in Drosophila

(2008) Q. Zhou et al.   GENOME RESEARCH

Reassessing the amyloid cascade hypothesis of Alzheimer's disease

(2008) Sanjay W. Pimplikar   INTERNATIONAL JOURNAL OF BIOCHEMISTRY & CELL BIOLOGY

Small membrane proteins found by comparative genomics and ribosome binding site models

(2008) Matthew R. Hemm et al.   MOLECULAR MICROBIOLOGY

Translational control of intron splicing in eukaryotes

(2008) Olivier Jaillon et al.   NATURE

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

(2008) Kazuko Hanyu-Nakamura et al.   NATURE

Predicting cell-penetrating peptides

(2007) Mats Hansen et al.   ADVANCED DRUG DELIVERY REVIEWS