Translation of noncoding RNAs and cancer

The LINC00961 transcript and its encoded micropeptide, small regulatory polypeptide of amino acid response, regulate endothelial cell function

(2020) Helen L Spencer et al.   CARDIOVASCULAR RESEARCH

m6A-dependent biogenesis of circular RNAs in male germ cells

(2020) Chong Tang et al.   CELL RESEARCH

ncEP: a manually curated database for experimentally validated ncRNA-encoded proteins or peptides

(2020) Haizhou Liu et al.   JOURNAL OF MOLECULAR BIOLOGY

Peptide SMIM30 promotes HCC development by inducing SRC/YES1 membrane anchoring and MAPK pathway activation

(2020) Yanan Pang et al.   JOURNAL OF HEPATOLOGY

A novel protein encoded by circFNDC3B inhibits tumor progression and EMT through regulating Snail in colon cancer

(2020) Zihao Pan et al.   Molecular Cancer

The micropeptide LEMP plays an evolutionarily conserved role in myogenesis

(2020) Lantian Wang et al.   Cell Death & Disease

An oncopeptide regulates m6A recognition by the m6A reader IGF2BP1 and tumorigenesis

(2020) Song Zhu et al.   Nature Communications

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

RNA Circularization Diminishes Immunogenicity and Can Extend Translation Duration In Vivo

(2019) R. Alexander Wesselhoeft et al.   MOLECULAR CELL

A novel protein encoded by a circular RNA circPPP1R12A promotes tumor pathogenesis and metastasis of colon cancer via Hippo-YAP signaling

(2019) Xiao Zheng et al.   Molecular Cancer

PROTEOFORMER 2.0: further developments in the ribosome profiling-assisted proteogenomic hunt for new proteoforms

(2019) Steven Verbruggen et al.   MOLECULAR & CELLULAR PROTEOMICS

The Translational Landscape of the Human Heart

(2019) Sebastiaan van Heesch et al.   CELL

circLgr4 drives colorectal tumorigenesis and invasion through Lgr4‐targeting peptide

(2019) Xiaofei Zhi et al.   INTERNATIONAL JOURNAL OF CANCER

Transforming activity of an oncoprotein-encoding circular RNA from human papillomavirus

(2019) Jiawei Zhao et al.   Nature Communications

A novel tumor suppressor protein encoded by circular AKT3 RNA inhibits glioblastoma tumorigenicity by competing with active phosphoinositide-dependent Kinase-1

(2019) Xin Xia et al.   Molecular Cancer

Programmable RNA N6-methyladenosine editing by CRISPR-Cas9 conjugates

(2019) Xiao-Min Liu et al.   Nature Chemical Biology

The biogenesis, biology and characterization of circular RNAs

(2019) Lasse S. Kristensen et al.   NATURE REVIEWS GENETICS

Micropeptide CIP 2A‐ BP encoded by LINC 00665 inhibits triple‐negative breast cancer progression

(2019) Binbin Guo et al.   EMBO JOURNAL

CircCode: A Powerful Tool for Identifying circRNA Coding Ability

(2019) Peisen Sun et al.   Frontiers in Genetics

circFBXW7 Inhibits Malignant Progression by Sponging miR-197-3p and Encoding a 185-aa Protein in Triple-Negative Breast Cancer

(2019) Feng Ye et al.   Molecular Therapy-Nucleic Acids

Highly parallel direct RNA sequencing on an array of nanopores

(2018) Daniel R Garalde et al.   NATURE METHODS

Novel tumour suppressive protein encoded by circular RNA, circ-SHPRH, in glioblastomas

(2018) S Begum et al.   ONCOGENE

A novel protein encoded by the circular form of the SHPRH gene suppresses glioma tumorigenesis

(2018) Maolei Zhang et al.   ONCOGENE

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

(2018) Yafeng Zhu et al.   Nature Communications

Engineering circular RNA for potent and stable translation in eukaryotic cells

(2018) R. Alexander Wesselhoeft et al.   Nature Communications

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

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

Tissue-Dependent Expression and Translation of Circular RNAs with Recombinant AAV Vectors In Vivo

(2018) Rita M. Meganck et al.   Molecular Therapy-Nucleic Acids

LncBook: a curated knowledgebase of human long non-coding RNAs

(2018) Lina Ma et al.   NUCLEIC ACIDS RESEARCH

RPFdb v2.0: an updated database for genome-wide information of translated mRNA generated from ribosome profiling

(2018) Hongwei Wang et al.   NUCLEIC ACIDS RESEARCH

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

(2018) Maolei Zhang et al.   Nature Communications

circGprc5a Promoted Bladder Oncogenesis and Metastasis through Gprc5a-Targeting Peptide

(2018) Chaohui Gu et al.   Molecular Therapy-Nucleic Acids

Novel Role of FBXW7 Circular RNA in Repressing Glioma Tumorigenesis

(2017) Yibing Yang et al.   JNCI-Journal of the National Cancer Institute

Translation of CircRNAs

(2017) Nagarjuna Reddy Pamudurti et al.   MOLECULAR CELL

Circ-ZNF609 Is a Circular RNA that Can Be Translated and Functions in Myogenesis

(2017) Ivano Legnini et al.   MOLECULAR CELL

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

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

CPC2: a fast and accurate coding potential calculator based on sequence intrinsic features

(2017) Yu-Jian Kang et al.   NUCLEIC ACIDS RESEARCH

NONCODEV5: a comprehensive annotation database for long non-coding RNAs

(2017) ShuangSang Fang et al.   NUCLEIC ACIDS RESEARCH

Novel Role of FBXW7 Circular RNA in Repressing Glioma Tumorigenesis

(2017) Yibing Yang et al.   JNCI-Journal of the National Cancer Institute

LncRNA-Six1 Encodes a Micropeptide to Activate Six1 in Cis and Is Involved in Cell Proliferation and Muscle Growth

(2017) Bolin Cai et al.   Frontiers in Physiology

Viral Infection Identifies Micropeptides Differentially Regulated in smORF-Containing lncRNAs

(2017) Brandon Razooky et al.   Genes

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

Use of microRNA-encoded peptide miPEP172c to stimulate nodulation in soybean

(2016) Jean-Malo Couzigou et al.   NEW PHYTOLOGIST

COME: a robust coding potential calculation tool for lncRNA identification and characterization based on multiple features

(2016) Long Hu et al.   NUCLEIC ACIDS RESEARCH

Non-coding RNAs in Development and Disease: Background, Mechanisms, and Therapeutic Approaches

(2016) Julia Beermann et al.   PHYSIOLOGICAL REVIEWS

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

Identifying and annotating human bifunctional RNAs reveals their versatile functions

(2016) Geng Chen et al.   Science China-Life Sciences

Global proteogenomic analysis of human MHC class I-associated peptides derived from non-canonical reading frames

(2016) Céline M. Laumont et al.   Nature Communications

circRNADb: A comprehensive database for human circular RNAs with protein-coding annotations

(2016) Xiaoping Chen et al.   Scientific Reports

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

(2015) Douglas M. Anderson et al.   CELL

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

Detecting actively translated open reading frames in ribosome profiling data

(2015) Lorenzo Calviello et al.   NATURE METHODS

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

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

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

(2015) Volodimir Olexiouk et al.   NUCLEIC ACIDS RESEARCH

miRNA-encoded peptides (miPEPs): A new tool to analyze the roles of miRNAs in plant biology

(2015) Jean-Malo Couzigou et al.   RNA Biology

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

(2015) Zhe Ji et al.   eLife

The Novel Gene CRNDE Encodes a Nuclear Peptide (CRNDEP) Which Is Overexpressed in Highly Proliferating Tissues

(2015) Lukasz Michal Szafron et al.   PLoS One

lncRNAtor: a comprehensive resource for functional investigation of long non-coding RNAs

(2014) Charny Park et al.   BIOINFORMATICS

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

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

A draft map of the human proteome

(2014) Min-Sik Kim et al.   NATURE

The multilayered complexity of ceRNA crosstalk and competition

(2014) Yvonne Tay et al.   NATURE

lncRNAdb v2.0: expanding the reference database for functional long noncoding RNAs

(2014) Xiu Cheng Quek et al.   NUCLEIC ACIDS RESEARCH

Cryptic MHC class I-binding peptides are revealed by aminoglycoside-induced stop codon read-through into the 3' UTR

(2014) E. Goodenough et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Novel coding, translation, and gene expression of a replicating covalently closed circular RNA of 220 nt

(2014) Mounir Georges AbouHaidar et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

circBase: a database for circular RNAs

(2014) Petar Glažar et al.   RNA

Efficient backsplicing produces translatable circular mRNAs

(2014) Yang Wang et al.   RNA

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

(2014) A. Pauli et al.   SCIENCE

The Pan-Cancer analysis of pseudogene expression reveals biologically and clinically relevant tumour subtypes

(2014) Leng Han et al.   Nature Communications

Quantitative profiling of peptides from RNAs classified as noncoding

(2014) Sudhakaran Prabakaran et al.   Nature Communications

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

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

Long non-coding RNAs as a source of new peptides

(2014) Jorge Ruiz-Orera et al.   eLife

The Somatic Genomic Landscape of Glioblastoma

(2013) Cameron W. Brennan et al.   CELL

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

TISdb: a database for alternative translation initiation in mammalian cells

(2013) Ji Wan et al.   NUCLEIC ACIDS RESEARCH

CPAT: Coding-Potential Assessment Tool using an alignment-free logistic regression model

(2013) Liguo Wang et al.   NUCLEIC ACIDS RESEARCH

miRBase: annotating high confidence microRNAs using deep sequencing data

(2013) Ana Kozomara et al.   NUCLEIC ACIDS RESEARCH

Expressed Pseudogenes in the Transcriptional Landscape of Human Cancers

(2012) Shanker Kalyana-Sundaram et al.   CELL

Long noncoding RNAs are rarely translated in two human cell lines

(2012) B. Banfai 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

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

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

A ceRNA Hypothesis: The Rosetta Stone of a Hidden RNA Language?

(2011) Leonardo Salmena 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

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

(2011) S. Washietl et al.   RNA

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

(2009) Kousuke Hanada et al.   BIOINFORMATICS

Screening non-coding RNAs in transcriptomes from neglected species using PORTRAIT: case study of the pathogenic fungus Paracoccidioides brasiliensis

(2009) Roberto T Arrial et al.   BMC BIOINFORMATICS

Origin, Biogenesis, and Activity of Plant MicroRNAs

(2009) Olivier Voinnet   CELL

IRESite—a tool for the examination of viral and cellular internal ribosome entry sites

(2009) Martin Mokrejš et al.   NUCLEIC ACIDS RESEARCH

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

(2009) N. T. Ingolia et al.   SCIENCE

Real-Time DNA Sequencing from Single Polymerase Molecules

(2008) J. Eid et al.   SCIENCE