Distinct types of short open reading frames are translated in plant cells

A methodology for discovering novel brain-relevant peptides: Combination of ribosome profiling and peptidomics

(2019) Ravi Tharakan et al.   NEUROSCIENCE RESEARCH

The loss of SMG1 causes defects in quality control pathways in Physcomitrella patens

(2018) James P B Lloyd et al.   NUCLEIC ACIDS RESEARCH

The Physcomitrella patens chromosome-scale assembly reveals moss genome structure and evolution

(2018) Daniel Lang et al.   PLANT JOURNAL

Short Open Reading Frames and Their Encoded Peptides

(2018) Joseph Rothnagel et al.   PROTEOMICS

Translation of neutrally evolving peptides provides a basis for de novo gene evolution

(2018) Jorge Ruiz-Orera et al.   Nature Ecology & Evolution

The protein coded by a short open reading frame, not by the annotated coding sequence is the main gene product of the dual-coding gene MIEF1

(2018) Vivian Delcourt et al.   MOLECULAR & CELLULAR PROTEOMICS

Protein encoded in human telomerase RNA is involved in cell protective pathways

(2018) Maria Rubtsova et al.   NUCLEIC ACIDS RESEARCH

OpenProt: a more comprehensive guide to explore eukaryotic coding potential and proteomes

(2018) Marie A Brunet et al.   NUCLEIC ACIDS RESEARCH

Translation of Small Open Reading Frames: Roles in Regulation and Evolutionary Innovation

(2018) Jorge Ruiz-Orera et al.   TRENDS IN GENETICS

Noncoding after All: Biases in Proteomics Data Do Not Explain Observed Absence of lncRNA Translation Products

(2017) Kenneth Verheggen et al.   JOURNAL OF PROTEOME RESEARCH

A Peptide Encoded by a Putative lncRNA HOXB-AS3 Suppresses Colon Cancer Growth

(2017) Jin-Zhou Huang et al.   MOLECULAR CELL

Classification and function of small open reading frames

(2017) Juan-Pablo Couso et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Alternative splicing shapes transcriptome but not proteome diversity in Physcomitrella patens

(2017) Igor Fesenko et al.   Scientific Reports

Deep transcriptome annotation enables the discovery and functional characterization of cryptic small proteins

(2017) Sondos Samandi et al.   eLife

Improved Identification and Analysis of Small Open Reading Frame Encoded Polypeptides

(2016) Jiao Ma et al.   ANALYTICAL CHEMISTRY

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

mTORC1 and muscle regeneration are regulated by the LINC00961-encoded SPAR polypeptide

(2016) Akinobu Matsumoto et al.   NATURE

A human microprotein that interacts with the mRNA decapping complex

(2016) Nadia G D'Lima et al.   Nature Chemical Biology

The MaxQuant computational platform for mass spectrometry-based shotgun proteomics

(2016) Stefka Tyanova et al.   Nature Protocols

2016 update of the PRIDE database and its related tools

(2016) Juan Antonio Vizcaíno et al.   NUCLEIC ACIDS RESEARCH

CRISPR-Cas9-mediated efficient directed mutagenesis and RAD51-dependent and RAD51-independent gene targeting in the mossPhyscomitrella patens

(2016) Cécile Collonnier et al.   PLANT BIOTECHNOLOGY JOURNAL

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

(2016) B. R. Nelson et al.   SCIENCE

The Emerging World of Small ORFs

(2016) Roger P. Hellens et al.   TRENDS IN PLANT SCIENCE

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

(2016) Moritz Graeff et al.   PLoS Genetics

Nonsense-mediated mRNA decay: novel mechanistic insights and biological impact

(2016) Evangelos D. Karousis et al.   Wiley Interdisciplinary Reviews-RNA

The Physcomitrella patens Chloroplast Proteome Changes in Response to Protoplastation

(2016) Igor Fesenko et al.   Frontiers in Plant Science

Specific pools of endogenous peptides are present in gametophore, protonema, and protoplast cells of the moss Physcomitrella patens

(2015) Igor A Fesenko et al.   BMC PLANT BIOLOGY

Small-peptide signals that control root nodule number, development, and symbiosis

(2015) Michael A. Djordjevic et al.   JOURNAL OF EXPERIMENTAL BOTANY

Primary transcripts of microRNAs encode regulatory peptides

(2015) Dominique Lauressergues et al.   NATURE

Detecting actively translated open reading frames in ribosome profiling data

(2015) Lorenzo Calviello et al.   NATURE METHODS

GREENC: a Wiki-based database of plant lncRNAs

(2015) Andreu Paytuví Gallart et al.   NUCLEIC ACIDS RESEARCH

New genes from non-coding sequence: the role of de novo protein-coding genes in eukaryotic evolutionary innovation

(2015) Aoife McLysaght et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

CANTATAdb: A Collection of Plant Long Non-Coding RNAs

(2015) Michał W. Szcześniak et al.   PLANT AND CELL PHYSIOLOGY

The Plant Peptidome: An Expanding Repertoire of Structural Features and Biological Functions

(2015) Patrizia Tavormina et al.   PLANT CELL

An Upstream Open Reading Frame Is Essential for Feedback Regulation of Ascorbate Biosynthesis in Arabidopsis

(2015) William A. Laing et al.   PLANT CELL

MicroProteins: small size – big impact

(2015) Tenai Eguen et al.   TRENDS IN PLANT SCIENCE

Contrasting expression patterns of coding and noncoding parts of the human genome upon oxidative stress

(2015) Antonis Giannakakis et al.   Scientific Reports

Classification of Intrinsically Disordered Regions and Proteins

(2014) Robin van der Lee et al.   CHEMICAL REVIEWS

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

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

Emerging evidence for functional peptides encoded by short open reading frames

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

Transcriptome analysis reveals novel regulatory mechanisms in a genome-reduced bacterium

(2014) Pavel V. Mazin et al.   NUCLEIC ACIDS RESEARCH

Genome-Wide Analysis of Heat-Sensitive Alternative Splicing in Physcomitrella patens

(2014) C.-Y. Chang et al.   PLANT PHYSIOLOGY

Quantitative profiling of peptides from RNAs classified as noncoding

(2014) Sudhakaran Prabakaran et al.   Nature Communications

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

(2014) Julie L Aspden et al.   eLife

Genome-wide analysis of light-regulated alternative splicing mediated by photoreceptors in Physcomitrella patens

(2014) Hshin-Ping Wu et al.   GENOME BIOLOGY

Organizing Principles of Mammalian Nonsense-Mediated mRNA Decay

(2013) Maximilian Wei-Lin Popp et al.   Annual Review of Genetics

The functional consequences of intron retention: Alternative splicing coupled to NMD as a regulator of gene expression

(2013) Ying Ge et al.   BIOESSAYS

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

(2013) Mitchell Guttman et al.   CELL

Mining the genome of Arabidopsis thaliana as a basis for the identification of novel bioactive peptides involved in oxidative stress tolerance

(2013) Barbara De Coninck et al.   JOURNAL OF EXPERIMENTAL BOTANY

De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis

(2013) Brian J Haas et al.   Nature Protocols

Alternative splicing of transcription factors in plant responses to low temperature stress: mechanisms and functions

(2013) Pil Joon Seo et al.   PLANTA

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

(2013) Benoît Vanderperre et al.   PLoS One

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

Gene Expression Regulation by Upstream Open Reading Frames and Human Disease

(2013) Cristina Barbosa et al.   PLoS Genetics

Detailed analysis of putative genes encoding small proteins in legume genomes

(2013) Gabriel Guillén et al.   Frontiers in Plant Science

Primer-BLAST: A tool to design target-specific primers for polymerase chain reaction

(2012) Jian Ye et al.   BMC BIOINFORMATICS

Proto-genes and de novo gene birth

(2012) Anne-Ruxandra Carvunis et al.   NATURE

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

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

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

(2011) Nicholas T. Ingolia et al.   CELL

TheArabidopsispeptide kiss of death is an inducer of programmed cell death

(2011) Robert Blanvillain et al.   EMBO JOURNAL

A Versatile Set of Ligation-Independent Cloning Vectors for Functional Studies in Plants

(2011) B. De Rybel et al.   PLANT PHYSIOLOGY

REVIGO Summarizes and Visualizes Long Lists of Gene Ontology Terms

(2011) Fran Supek et al.   PLoS One

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

Expression Level, Evolutionary Rate, and the Cost of Expression

(2010) J. L. Cherry   Genome Biology and Evolution

Small Peptides Switch the Transcriptional Activity of Shavenbaby During Drosophila Embryogenesis

(2010) T. Kondo et al.   SCIENCE

RNA polymerase mapping during stress responses reveals widespread nonproductive transcription in yeast

(2010) Tae Soo Kim et al.   GENOME BIOLOGY

sORF finder: a program package to identify small open reading frames with high coding potential

(2009) Kousuke Hanada et al.   BIOINFORMATICS

Biopython: freely available Python tools for computational molecular biology and bioinformatics

(2009) P. J. A. Cock et al.   BIOINFORMATICS