Revisiting sORFs: overcoming challenges to identify and characterize functional microproteins

A short ORF-encoded transcriptional regulator

(2021) Minseob Koh et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Alt-RPL36 downregulates the PI3K-AKT-mTOR signaling pathway by interacting with TMEM24

(2021) Xiongwen Cao et al.   Nature Communications

Pan-cancer analysis of transcripts encoding novel open-reading frames (nORFs) and their potential biological functions

(2021) Chaitanya Erady et al.   npj Genomic Medicine

Noncanonical open reading frames encode functional proteins essential for cancer cell survival

(2021) John R. Prensner et al.   NATURE BIOTECHNOLOGY

Pervasive functional translation of noncanonical human open reading frames

(2020) Jin Chen et al.   SCIENCE

DeepCPP: a deep neural network based on nucleotide bias information and minimum distribution similarity feature selection for RNA coding potential prediction

(2020) Yu Zhang et al.   BRIEFINGS IN BIOINFORMATICS

RiboToolkit: an integrated platform for analysis and annotation of ribosome profiling data to decode mRNA translation at codon resolution

(2020) Qi Liu et al.   NUCLEIC ACIDS RESEARCH

PsORF: a database of small ORFs in plants

(2020) Yanjun Chen et al.   PLANT BIOTECHNOLOGY JOURNAL

Mitochondrial peptide BRAWNIN is essential for vertebrate respiratory complex III assembly

(2020) Shan Zhang et al.   Nature Communications

A micropeptide encoded by lncRNA MIR155HG suppresses autoimmune inflammation via modulating antigen presentation

(2020) Liman Niu et al.   Science Advances

Uncovering small membrane proteins in pathogenic bacteria: Regulatory functions and therapeutic potential

(2020) Preeti Garai et al.   MOLECULAR MICROBIOLOGY

The coding capacity of SARS-CoV-2

(2020) Yaara Finkel et al.   NATURE

Identifying Small Proteins by Ribosome Profiling with Stalled Initiation Complexes

(2019) Jeremy Weaver et al.   mBio

LINC00116 codes for a mitochondrial peptide linking respiration and lipid metabolism

(2019) Anastasia Chugunova et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Small peptide–mediated self-recognition prevents cannibalism in predatory nematodes

(2019) James W. Lightfoot et al.   SCIENCE

The mlpt/Ubr3/Svb module comprises an ancient developmental switch for embryonic patterning

(2019) Suparna Ray et al.   eLife

MiTPeptideDB: a proteogenomic resource for the discovery of novel peptides

(2019) Elizabeth Guruceaga et al.   BIOINFORMATICS

The Translational Landscape of the Human Heart

(2019) Sebastiaan van Heesch et al.   CELL

A hidden human proteome encoded by ‘non-coding’ genes

(2019) Shaohua Lu et al.   NUCLEIC ACIDS RESEARCH

Cryo-EM structure of the mammalian ATP synthase tetramer bound with inhibitory protein IF1

(2019) Jinke Gu et al.   SCIENCE

Large-Scale Analyses of Human Microbiomes Reveal Thousands of Small, Novel Genes

(2019) Hila Sberro et al.   CELL

Discovery of high-confidence human protein-coding genes and exons by whole-genome PhyloCSF helps elucidate 118 GWAS loci

(2019) Jonathan M. Mudge et al.   GENOME RESEARCH

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

(2019) Igor Fesenko et al.   GENOME RESEARCH

MiPepid: MicroPeptide identification tool using machine learning

(2019) Mengmeng Zhu et al.   BMC BIOINFORMATICS

Regulation of the ER stress response by a mitochondrial microprotein

(2019) Qian Chu et al.   Nature Communications

LncRNA-encoded polypeptide ASRPS inhibits triple-negative breast cancer angiogenesis

(2019) Yirong Wang et al.   JOURNAL OF EXPERIMENTAL MEDICINE

A Mitochondrial Micropeptide Is Required for Activation of the Nlrp3 Inflammasome

(2019) Ankit Bhatta et al.   JOURNAL OF IMMUNOLOGY

Accurate annotation of human protein-coding small open reading frames

(2019) Thomas F. Martinez et al.   Nature Chemical Biology

Enrichment-Based Proteogenomics Identifies Microproteins, Missing Proteins, and Novel smORFs in Saccharomyces cerevisiae

(2018) Cuitong He et al.   JOURNAL OF PROTEOME RESEARCH

MRI Is a DNA Damage Response Adaptor during Classical Non-homologous End Joining

(2018) Putzer J. Hung et al.   MOLECULAR CELL

High-throughput creation and functional profiling of DNA sequence variant libraries using CRISPR–Cas9 in yeast

(2018) Xiaoge Guo et al.   NATURE BIOTECHNOLOGY

Improved Ribo-seq enables identification of cryptic translation events

(2018) Florian Erhard et al.   NATURE METHODS

De novo annotation and characterization of the translatome with ribosome profiling data

(2018) Zhengtao Xiao et al.   NUCLEIC ACIDS RESEARCH

Ribosome elongating footprints denoised by wavelet transform comprehensively characterize dynamic cellular translation events

(2018) Zhiyu Xu et al.   NUCLEIC ACIDS RESEARCH

The cancer-associated microprotein CASIMO1 controls cell proliferation and interacts with squalene epoxidase modulating lipid droplet formation

(2018) Maria Polycarpou-Schwarz et al.   ONCOGENE

The influence of transcript assembly on the proteogenomics discovery of microproteins

(2018) Jiao Ma et al.   PLoS One

Fusogenic micropeptide Myomixer is essential for satellite cell fusion and muscle regeneration

(2018) Pengpeng Bi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Comprehensive Peptide Analysis of Mouse Brain Striatum Identifies Novel sORF-Encoded Polypeptides

(2018) Harshavardhan Budamgunta et al.   PROTEOMICS

Discovery of coding regions in the human genome by integrated proteogenomics analysis workflow

(2018) Yafeng Zhu et al.   Nature Communications

MOXI Is a Mitochondrial Micropeptide That Enhances Fatty Acid β-Oxidation

(2018) Catherine A. Makarewich et al.   Cell Reports

Mitoregulin: A lncRNA-Encoded Microprotein that Supports Mitochondrial Supercomplexes and Respiratory Efficiency

(2018) Colleen S. Stein et al.   Cell Reports

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

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

Mutations in Disordered Regions Can Cause Disease by Creating Dileucine Motifs

(2018) Katrina Meyer et al.   CELL

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

The Ly6/uPAR protein Bouncer is necessary and sufficient for species-specific fertilization

(2018) Sarah Herberg et al.   SCIENCE

The Pfam protein families database in 2019

(2018) Sara El-Gebali 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

A peptide encoded by circular form of LINC-PINT suppresses oncogenic transcriptional elongation in glioblastoma

(2018) Maolei Zhang et al.   Nature Communications

The DWORF micropeptide enhances contractility and prevents heart failure in a mouse model of dilated cardiomyopathy

(2018) Catherine A Makarewich et al.   eLife

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

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

Translation from unconventional 5′ start sites drives tumour initiation

(2017) Ataman Sendoel et al.   NATURE

Regulation of DNA repair pathway choice in S and G2 phases by the NHEJ inhibitor CYREN

(2017) Nausica Arnoult et al.   NATURE

Classification and function of small open reading frames

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

The eukaryotic linear motif resource – 2018 update

(2017) Marc Gouw et al.   NUCLEIC ACIDS RESEARCH

An update on sORFs.org: a repository of small ORFs identified by ribosome profiling

(2017) Volodimir Olexiouk et al.   NUCLEIC ACIDS RESEARCH

Requirement of the fusogenic micropeptide myomixer for muscle formation in zebrafish

(2017) Jun Shi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

ELABELA deficiency promotes preeclampsia and cardiovascular malformations in mice

(2017) Lena Ho et al.   SCIENCE

Control of muscle formation by the fusogenic micropeptide myomixer

(2017) Pengpeng Bi et al.   SCIENCE

Structural Basis for Apelin Control of the Human Apelin Receptor

(2017) Yingli Ma et al.   STRUCTURE

Mining for Micropeptides

(2017) Catherine A. Makarewich et al.   TRENDS IN CELL BIOLOGY

Genome-wide identification and differential analysis of translational initiation

(2017) Peng Zhang et al.   Nature Communications

Long non-coding RNA Linc-RAM enhances myogenic differentiation by interacting with MyoD

(2017) Xiaohua Yu et al.   Nature Communications

The microprotein Minion controls cell fusion and muscle formation

(2017) Qiao Zhang et al.   Nature Communications

Myomerger induces fusion of non-fusogenic cells and is required for skeletal muscle development

(2017) Malgorzata E. Quinn et al.   Nature Communications

Loss of Apela Peptide in Mice Causes Low Penetrance Embryonic Lethality and Defects in Early Mesodermal Derivatives

(2017) Laina Freyer et al.   Cell Reports

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

(2017) Sondos Samandi et al.   eLife

Naturally occurring mitochondrial-derived peptides are age-dependent regulators of apoptosis, insulin sensitivity, and inflammatory markers

(2016) Laura J. Cobb et al.   Aging-US

Improved Identification and Analysis of Small Open Reading Frame Encoded Polypeptides

(2016) Jiao Ma et al.   ANALYTICAL CHEMISTRY

The contribution of intrinsically disordered regions to protein function, cellular complexity, and human disease

(2016) M. Madan Babu   BIOCHEMICAL SOCIETY TRANSACTIONS

SPECtre: a spectral coherence-­based classifier of actively translated transcripts from ribosome profiling sequence data

(2016) Sang Y. Chun et al.   BMC BIOINFORMATICS

Upstream ORFs are prevalent translational repressors in vertebrates

(2016) Timothy G Johnstone et al.   EMBO JOURNAL

Site-Specific Bioorthogonal Labeling for Fluorescence Imaging of Intracellular Proteins in Living Cells

(2016) Tao Peng et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

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 Minimum Open Reading Frame, AUG-Stop, Induces Boron-Dependent Ribosome Stalling and mRNA Degradation

(2016) Mayuki Tanaka et al.   PLANT CELL

Decoding sORF translation – from small proteins to gene regulation

(2016) Luis Enrique Cabrera-Quio et al.   RNA Biology

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

(2016) B. R. Nelson et al.   SCIENCE

Widespread control of calcium signaling by a family of SERCA-inhibiting micropeptides

(2016) D. M. Anderson et al.   Science Signaling

Improving GENCODE reference gene annotation using a high-stringency proteogenomics workflow

(2016) James C. Wright et al.   Nature Communications

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

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

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

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

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

(2016) Anil Raj et al.   eLife

Widespread control of calcium signaling by a family of SERCA-inhibiting micropeptides

(2016) D. M. Anderson et al.   Science Signaling

Exosome-driven transfer of tumor-associated Pioneer Translation Products (TA-PTPs) for the MHC class I cross-presentation pathway

(2016) Emilie Duvallet et al.   OncoImmunology

First description of small proteins encoded by spRNAs in Methanosarcina mazei strain Gö1

(2015) Daniela Prasse et al.   BIOCHIMIE

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

Primate-Specific ORF0 Contributes to Retrotransposon-Mediated Diversity

(2015) Ahmet M. Denli 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

Are Human Translated Pseudogenes Functional?

(2015) Jinrui Xu et al.   MOLECULAR BIOLOGY AND EVOLUTION

A Regression-Based Analysis of Ribosome-Profiling Data Reveals a Conserved Complexity to Mammalian Translation

(2015) Alexander P. Fields et al.   MOLECULAR CELL

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

Detecting actively translated open reading frames in ribosome profiling data

(2015) Lorenzo Calviello et al.   NATURE METHODS

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

sORFs.org: a repository of small ORFs identified by ribosome profiling

(2015) Volodimir Olexiouk et al.   NUCLEIC ACIDS RESEARCH

Pri sORF peptides induce selective proteasome-mediated protein processing

(2015) J. Zanet et al.   SCIENCE

Relevance of Viroporin Ion Channel Activity on Viral Replication and Pathogenesis

(2015) Jose Nieto-Torres et al.   Viruses-Basel

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

Selective inhibition of angiotensin receptor signaling through Erk1/2 pathway by a novel peptide

(2014) Jun Liu et al.   AMERICAN JOURNAL OF PHYSIOLOGY-REGULATORY INTEGRATIVE AND COMPARATIVE PHYSIOLOGY

The Scanning Mechanism of Eukaryotic Translation Initiation

(2014) Alan G. Hinnebusch   Annual Review of Biochemistry

Small Proteins Can No Longer Be Ignored

(2014) Gisela Storz et al.   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

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

A draft map of the human proteome

(2014) Min-Sik Kim et al.   NATURE

PROTEOFORMER: deep proteome coverage through ribosome profiling and MS integration

(2014) Jeroen Crappé 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

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

(2014) Nicholas T. Ingolia 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

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

Chemoproteomic Discovery of Cysteine-Containing Human Short Open Reading Frames

(2013) Adam G. Schwaid et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

The sarcolipin-bound calcium pump stabilizes calcium sites exposed to the cytoplasm

(2013) Anne-Marie L. Winther et al.   NATURE

HiRIEF LC-MS enables deep proteome coverage and unbiased proteogenomics

(2013) Rui M M Branca et al.   NATURE METHODS

uORFdb—a comprehensive literature database on eukaryotic uORF biology

(2013) Klaus Wethmar et al.   NUCLEIC ACIDS RESEARCH

TISdb: a database for alternative translation initiation in mammalian cells

(2013) Ji Wan 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

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

Translation of pre-spliced RNAs in the nuclear compartment generates peptides for the MHC class I pathway

(2013) S. Apcher 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

Pinstripe: a suite of programs for integrating transcriptomic and proteomic datasets identifies novel proteins and improves differentiation of protein-coding and non-coding genes

(2012) Dennis K. Gascoigne et al.   BIOINFORMATICS

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

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

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

(2012) Sarah A Slavoff et al.   Nature Chemical 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

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

(2012) S. R. Starck et al.   SCIENCE

Decoding Human Cytomegalovirus

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

Evolution of Bcl-2 homology motifs: homology versus homoplasy

(2012) Abdel Aouacheria et al.   TRENDS IN CELL BIOLOGY

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

Non-conventional sources of peptides presented by MHC class I

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

Intrinsically disordered proteins: regulation and disease

(2011) M Madan Babu et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

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

(2011) Benoît Vanderperre et al.   FASEB JOURNAL

RNAcode: Robust discrimination of coding and noncoding regions in comparative sequence data

(2011) S. Washietl et al.   RNA

Hundreds of putatively functional small open reading frames in Drosophila

(2011) Emmanuel Ladoukakis et al.   GENOME BIOLOGY

tsORFdb: Theoretical Small Open Reading Frames (ORFs) database and massProphet: Peptide Mass Fingerprinting (PMF) tool for unknown small functional ORFs

(2010) Hyoung-Sam Heo et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Small Peptides Switch the Transcriptional Activity of Shavenbaby During Drosophila Embryogenesis

(2010) T. Kondo et al.   SCIENCE

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

(2009) Kousuke Hanada et al.   BIOINFORMATICS

Noxa: at the tip of the balance between life and death

(2009) C Ploner et al.   ONCOGENE

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

Biogenesis of mitochondrial outer membrane proteins

(2008) Dirk M. Walther et al.   BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH

A Cryptic Vascular Endothelial Growth Factor T-Cell Epitope: Identification and Characterization by Mass Spectrometry and T-Cell Assays

(2008) A. O. Weinzierl et al.   CANCER RESEARCH

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

(2008) Jose Ignacio Pueyo et al.   DEVELOPMENTAL BIOLOGY

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

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

A Distinct Translation Initiation Mechanism Generates Cryptic Peptides for Immune Surveillance

(2008) Shelley R. Starck et al.   PLoS One