Small but Mighty: Functional Peptides Encoded by Small ORFs in Plants

CRISPR/Cas9-mediated genome editing in plants

(2017) Xuejun Liu et al.   METHODS

Global translational reprogramming is a fundamental layer of immune regulation in plants

(2017) Guoyong Xu et al.   NATURE

uORF-mediated translation allows engineered plant disease resistance without fitness costs

(2017) Guoyong Xu et al.   NATURE

Translation regulation in plants: an interesting past, an exciting present and a promising future

(2017) Catharina Merchante et al.   PLANT JOURNAL

Insights into the adaptive response of Arabidopsis thaliana to prolonged thermal stress by ribosomal profiling and RNA-Seq

(2016) Radoslaw Lukoszek et al.   BMC PLANT BIOLOGY

Ribosome Footprint Profiling of Translation throughout the Genome

(2016) Nicholas T. Ingolia   CELL

Dynamics of ribosome scanning and recycling revealed by translation complex profiling

(2016) Stuart K. Archer et al.   NATURE

Global Analysis of Truncated RNA Ends Reveals New Insights into Ribosome Stalling in Plants

(2016) Cheng‐Yu Hou et al.   PLANT CELL

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

(2016) Mayuki Tanaka et al.   PLANT CELL

A Short Open Reading Frame Encompassing the MicroRNA173 Target Site Plays a Role in trans-Acting Small Interfering RNA Biogenesis

(2016) Manabu Yoshikawa et al.   PLANT PHYSIOLOGY

Super-resolution ribosome profiling reveals unannotated translation events inArabidopsis

(2016) Polly Yingshan Hsu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

The Emerging World of Small ORFs

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

Gene-Specific Translation Regulation Mediated by the Hormone-Signaling Molecule EIN2

(2015) Catharina Merchante et al.   CELL

A Negative Feedback Loop Controlling bHLH Complexes Is Involved in Vascular Cell Division and Differentiation in the Root Apical Meristem

(2015) Hirofumi Katayama et al.   CURRENT BIOLOGY

Expanding the repertoire of secretory peptides controlling root development with comparative genome analysis and functional assays

(2015) Sarieh Ghorbani et al.   JOURNAL OF EXPERIMENTAL BOTANY

Comparative analysis of the RTFL peptide family on the control of plant organogenesis

(2015) Pin Guo et al.   JOURNAL OF PLANT RESEARCH

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

Ribosome profiling reveals the what, when, where and how of protein synthesis

(2015) Gloria A. Brar et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

The expanding world of small RNAs in plants

(2015) Filipe Borges et al.   NATURE REVIEWS MOLECULAR CELL 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

A novel strategy to produce sweeter tomato fruits with high sugar contents by fruit-specific expression of a single bZIP transcription factor gene

(2015) G. H. M. Sagor et al.   PLANT BIOTECHNOLOGY JOURNAL

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

AtLa1 protein initiates IRES-dependent translation ofWUSCHELmRNA and regulates the stem cell homeostasis ofArabidopsisin response to environmental hazards

(2015) Yuchao Cui et al.   PLANT CELL AND ENVIRONMENT

Ribosome profiling reveals dynamic translational landscape in maize seedlings under drought stress

(2015) Lei Lei et al.   PLANT JOURNAL

Genome-wide analysis of thylakoid-bound ribosomes in maize reveals principles of cotranslational targeting to the thylakoid membrane

(2015) Reimo Zoschke et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The use of duplex-specific nuclease in ribosome profiling and a user-friendly software package for Ribo-seq data analysis

(2015) Betty Y. Chung et al.   RNA

Posttranslationally Modified Small-Peptide Signals in Plants

(2014) Yoshikatsu Matsubayashi   Annual Review of Plant Biology

Dom34 Rescues Ribosomes in 3′ Untranslated Regions

(2014) Nicholas R. Guydosh et al.   CELL

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

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

N-terminal Proteomics and Ribosome Profiling Provide a Comprehensive View of the Alternative Translation Initiation Landscape in Mice and Men

(2014) Petra Van Damme et al.   MOLECULAR & CELLULAR PROTEOMICS

Proteogenomics: concepts, applications and computational strategies

(2014) Alexey I Nesvizhskii   NATURE METHODS

Emerging evidence for functional peptides encoded by short open reading frames

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

Quantitative Peptidomics Study Reveals That a Wound-Induced Peptide from PR-1 Regulates Immune Signaling in Tomato

(2014) Y.-L. Chen et al.   PLANT CELL

Arabidopsis noncoding RNA mediates control of photomorphogenesis by red light

(2014) Y. Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Perception of root-derived peptides by shoot LRR-RKs mediates systemic N-demand signaling

(2014) R. Tabata 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

Long non-coding RNAs as a source of new peptides

(2014) Jorge Ruiz-Orera et al.   eLife

Detecting small plant peptides using SPADA (Small Peptide Alignment Discovery Application)

(2013) Peng Zhou et al.   BMC BIOINFORMATICS

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

Zm908p11, encoded by a short open reading frame (sORF) gene, functions in pollen tube growth as a profilin ligand in maize

(2013) Xue Dong et al.   JOURNAL OF EXPERIMENTAL BOTANY

Deep Proteome Coverage Based on Ribosome Profiling Aids Mass Spectrometry-based Protein and Peptide Discovery and Provides Evidence of Alternative Translation Products and Near-cognate Translation Initiation Events*

(2013) Gerben Menschaert et al.   MOLECULAR & CELLULAR PROTEOMICS

Translational Landscape of Photomorphogenic Arabidopsis

(2013) M.-J. Liu et al.   PLANT CELL

Regulation of plant translation by upstream open reading frames

(2013) Albrecht G. von Arnim et al.   PLANT SCIENCE

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

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

Detailed analysis of putative genes encoding small proteins in legume genomes

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

BAIUCAS: a novel BLAST-based algorithm for the identification of upstream open reading frames with conserved amino acid sequences and its application to the Arabidopsis thaliana genome

(2012) Hiro Takahashi et al.   BIOINFORMATICS

The HSF-like Transcription Factor TBF1 Is a Major Molecular Switch for Plant Growth-to-Defense Transition

(2012) Karolina M. Pajerowska-Mukhtar et al.   CURRENT BIOLOGY

Translational regulation of Arabidopsis XIPOTL1 is modulated by phosphocholine levels via the phylogenetically conserved upstream open reading frame 30

(2012) Fulgencio Alatorre-Cobos et al.   JOURNAL OF EXPERIMENTAL BOTANY

The ribosome profiling strategy for monitoring translation in vivo by deep sequencing of ribosome-protected mRNA fragments

(2012) Nicholas T Ingolia et al.   Nature Protocols

An inhibitory effect of the sequence-conserved upstream open-reading frame on the translation of the main open-reading frame ofHsfB1transcripts inArabidopsis

(2012) XUJUN ZHU et al.   PLANT CELL AND ENVIRONMENT

Arabidopsis ribosomal proteins control developmental programs through translational regulation of auxin response factors

(2012) A. Rosado et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Known and novel post-transcriptional regulatory sequences are conserved across plant families

(2012) J. N. Vaughn et al.   RNA

Coding vs non-coding: Translatability of short ORFs found in putative non-coding transcripts

(2011) Yuji Kageyama et al.   BIOCHIMIE

Dual RNAs in plants

(2011) Florian Bardou et al.   BIOCHIMIE

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

Discovery and annotation of small proteins using genomics, proteomics, and computational approaches

(2011) X. Yang et al.   GENOME RESEARCH

DVL genes play a role in the coordination of socket cell recruitment and differentiation

(2011) E. R. Valdivia et al.   JOURNAL OF EXPERIMENTAL BOTANY

When one is better than two: RNA with dual functions

(2010) Damien Ulveling et al.   BIOCHIMIE

Translation reinitiation and development are compromised in similar ways by mutations in translation initiation factor eIF3h and the ribosomal protein RPL24

(2010) Fujun Zhou et al.   BMC PLANT BIOLOGY

Value of Using Multiple Proteases for Large-Scale Mass Spectrometry-Based Proteomics

(2010) Danielle L. Swaney et al.   JOURNAL OF PROTEOME RESEARCH

The mechanism of eukaryotic translation initiation and principles of its regulation

(2010) Richard J. Jackson et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

ROTUNDIFOLIA4 Regulates Cell Proliferation Along the Body Axis in Arabidopsis Shoot

(2010) Momoko Ikeuchi et al.   PLANT AND CELL PHYSIOLOGY

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

(2009) Kousuke Hanada et al.   BIOINFORMATICS

Zm401p10, encoded by an anther-specific gene with short open reading frames, is essential for tapetum degeneration and anther development in maize

(2009) Dongxue Wang et al.   FUNCTIONAL PLANT BIOLOGY

The upstream open reading frame of the Arabidopsis AtMHX gene has a strong impact on transcript accumulation through the nonsense-mediated mRNA decay pathway

(2009) Helen Saul et al.   PLANT JOURNAL

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

(2009) F. Rahmani et al.   PLANT PHYSIOLOGY

Plant secretome: Unlocking secrets of the secreted proteins

(2009) Ganesh Kumar Agrawal et al.   PROTEOMICS

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

(2009) N. T. Ingolia et al.   SCIENCE

Alternative translation start sites and hidden coding potential of eukaryotic mRNAs

(2008) Alex V. Kochetov   BIOESSAYS

Identification of a biologically active, small, secreted peptide in Arabidopsis byin silicogene screening, followed by LC-MS-based structure analysis

(2008) Kentaro Ohyama et al.   PLANT JOURNAL

Discovery and revision of Arabidopsis genes by proteogenomics

(2008) N. E. Castellana et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA