Review
Plant Sciences
Yong Feng, Mengyun Jiang, Weichang Yu, Jiannan Zhou
Summary: The increasing recognition of the roles of short/small open reading frames (sORFs) in recent years is attributed to the development and application of the Ribo-Seq technique, which allows for the identification of sORFs in various organisms. However, caution should be exercised when using RPFs to identify sORFs in plants, particularly for polyploidy species, due to the small size and complexity of the plant genome. This study compares different approaches to the identification of plant sORFs, discusses their advantages and disadvantages, and provides a guide for researchers in choosing the appropriate method for plant sORF studies.
FRONTIERS IN PLANT SCIENCE
(2023)
Review
Biochemistry & Molecular Biology
Yihan Liu, Shan Zeng, Minghua Wu
Summary: With the advancement of technology, the study of noncanonical open reading frames (nORFs) is gaining increasing attention. However, the translation potential of many putative nORFs remains unclear, and the functions of noncanonical peptides have not been systematically summarized. In this review, we highlight the recent technological advances that have facilitated the research on noncanonical peptides, such as ribosome profiling, bioinformatics approaches, and CRISPR/Cas9. We also summarize the diverse functions of noncanonical peptides in cancer and explore their potential in clinical applications.
BIOCHIMICA ET BIOPHYSICA ACTA-REVIEWS ON CANCER
(2022)
Article
Biochemical Research Methods
Mengyun Jiang, Weidong Ning, Shishi Wu, Xingwei Wang, Kun Zhu, Aomei Li, Yongyao Li, Shifeng Cheng, Bo Song
Summary: Accurate prediction of ORFs is essential for studying and utilizing genome sequences. This study introduces a novel approach utilizing nucleotide periodicity in populational genomic variants to predict ORFs and develops the OrfPP software package for validation. The method demonstrates high accuracy and reliability in various complex genomes.
BRIEFINGS IN BIOINFORMATICS
(2022)
Review
Cell Biology
Alyssa Zi-Xin Leong, Pey Yee Lee, M. Aiman Mohtar, Saiful Effendi Syafruddin, Yuh-Fen Pung, Teck Yew Low
Summary: This review discusses the history, development, and strategies used for identifying, validating, and characterizing sORFs and microproteins. Methods such as ribosome profiling, mass spectrometry-based proteomics, CRISPR/Cas9 screening, and protein-protein interaction studies are employed for detection and functional characterization. The review also highlights the challenges and potential solutions in identifying and validating these novel entities.
JOURNAL OF BIOMEDICAL SCIENCE
(2022)
Review
Biochemistry & Molecular Biology
Tatiana N. Erokhina, Dmitriy Y. Ryazantsev, Sergey K. Zavriev, Sergey Y. Morozov
Summary: This review provides a retrospective overview of the coding properties of pri-microRNAs and the regulatory functions of their ORFs and miPEPs. It discusses the identification and analysis of miPEPs and their functional activities, as well as the methods to identify pri-miRNA ORFs and encoded proteins. The differences in molecular mechanisms of miPEP action between flowering plants and metazoan species are emphasized, along with the need for further studies on the regulation of pri-miRNA/miRNA expression by miPEPs. The distribution of miPEPs in non-flowering plant taxa and their evolutionary origin are considered important questions that require extensive research.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Matthew D. C. Neville, Robin Kohze, Chaitanya Erady, Narendra Meena, Matthew Hayden, David N. Cooper, Matthew Mort, Sudhakaran Prabakaran
Summary: Recent studies have shown that there are significant numbers of uncharacterized open reading frames (ORFs) in eukaryotic genomes, particularly in humans, which are mostly distributed in diverse regions of the genome. It is important to evaluate the potential functional importance of these unannotated transcripts and proteins at a larger scale. The creation of a valuable nORFs data set with experimental evidence of translation, along with measures of heritability and selection, has implications for reinterpreting genetic variants previously classified as benign or of uncertain significance.
Article
Cell Biology
Thao P. Phan, Christina A. Boatwright, Chelsea G. Drown, Marnie W. Skinner, Margaret A. Strong, Philip W. Jordan, Andrew J. Holland
Summary: This study reveals the translational control of PLK4 through uORFs and its crucial role in preventing centriole amplification and preserving genomic integrity in germ cells. Knockout of Plk4 uORFs leads to reduced fertility and increased mitotic errors in mice, which can be rescued by reducing Plk4 mRNA levels. These findings highlight the importance of uORF-mediated translational suppression of PLK4 in maintaining proper cell division and preventing disease progression.
GENES & DEVELOPMENT
(2022)
Article
Biochemical Research Methods
Meng Zhang, Jian Zhao, Chen Li, Fang Ge, Jing Wu, Bin Jiang, Jiangning Song, Xiaofeng Song
Summary: Short open reading frames (sORFs) are small nucleic acid fragments that may encode small peptides and play important roles in biological processes. We developed an ensemble model called csORF-finder to accurately characterize the coding potential of sORFs. By integrating Efficient-CapsNet and LightGBM, csORF-finder outperformed existing methods in predicting coding sORFs across multiple species. We also introduced a novel feature encoding scheme and computed various in-frame sequence-based features to improve the performance of csORF-finder. Our results demonstrated the effectiveness of csORF-finder in high-throughput identification of coding sORFs and functional characterization of encoded peptides.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Biochemical Research Methods
Noe Guilloy, Marie A. Brunet, Sebastien Leblanc, Jean-Francois Jacques, Marie-Pierre Hardy, Gregory Ehx, Joel Lanoix, Pierre Thibault, Claude Perreault, Xavier Roucou
Summary: Proteomic diversity in biological samples can be characterized using mass spectrometry (MS)-based proteomics and customized protein databases generated from RNA-seq data. The recent discovery of translated alternative open reading frames in mRNAs and ncRNAs has increased this diversity. To fill the gap in current computational workflows, OpenCustomDB is a bioinformatics tool that identifies genomic variants in both canonical and alternative open reading frames using sample-specific RNA-seq data. It has been shown to detect a significant number of peptides from alternative proteins in a cohort of acute myeloid leukemia patients.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Computer Science, Interdisciplinary Applications
Ales Varabyou, Beril Erdogdu, Steven L. Salzberg, Mihaela Pertea
Summary: ORFanage is a system that analyzes RNA-seq data to discover novel protein variants and enhance gene annotations. It is fast, scalable, and effectively filters out noise to improve the quality of transcriptome assemblies.
NATURE COMPUTATIONAL SCIENCE
(2023)
Article
Virology
Morgan Monaghan, Joshua Munger
Summary: Transposon-based insertional mutagenesis screens have shown that disruption of HCMV UL30 gene inhibits viral replication. Deletion of the canonical UL30 ORF reduces production of infectious virus, while comutation of methionines in the UL30 region and mutation of the TATA box lead to viral replication defects. The UL30-associated ORFs play an important role in HCMV infection and further research could provide insights for therapeutic interventions.
JOURNAL OF VIROLOGY
(2021)
Article
Biochemistry & Molecular Biology
Hitesh Kore, Keshava K. Datta, Shivashankar H. Nagaraj, Harsha Gowda
Summary: Recent studies have discovered many proteins encoded by noncoding regions in the human genome. These proteins are often encoded by small open reading frames in the UTRs of mRNAs and lncRNAs, and show poor evolutionary conservation. Some of them have been functionally characterized and play important roles in fundamental biological processes and human diseases. The number of novel protein coding regions in the human genome and their functional importance remain unknown.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2023)
Review
Cardiac & Cardiovascular Systems
Omar Soukarieh, Caroline Meguerditchian, Carole Proust, Dylan Aissi, Melanie Eyries, Aurelie Goyenvalle, David-Alexandre Tregouet
Summary: HTS technologies are transforming research and molecular diagnostics by exploring millions of nucleotide sequences, focusing on identifying genetic variations contributing to rare and common human diseases. The study highlights the importance of 5'UTR variants altering upORFs and their association with rare cardiovascular disorders.
FRONTIERS IN CARDIOVASCULAR MEDICINE
(2022)
Article
Geriatrics & Gerontology
Alexandros Frydas, Rita Cacace, Julie van der Zee, Christine Van Broeckhoven, Eline Wauters
Summary: Genetic variants within the uORF regions of the GRN gene may alter PGRN expression levels and contribute to frontotemporal lobar degeneration. The functional uORFs present in the alternative 5' UTR act as potential regulators of PGRN expression, indicating a role for genetic variation in modulating gene function.
NEUROBIOLOGY OF AGING
(2022)
Article
Cell Biology
Ying Yang, Damian Gatica, Xu Liu, Runliu Wu, Rui Kang, Daolin Tang, Daniel J. Klionsky
Summary: This study reports the role of uORF-mediated translational control in regulating multiple Atg proteins in yeast and human cells. These findings suggest that uORF-mediated translational control is a widely used mechanism among ATG genes and provide a model for how some ATG genes bypass translational suppression under stress conditions to maintain proper autophagy levels.
Article
Cell Biology
Benoit Vanderperre, Tom Bender, Edmund R. S. Kunji, Jean-Claude Martinou
CURRENT OPINION IN CELL BIOLOGY
(2015)
Article
Biochemistry & Molecular Biology
Vincent Compan, Sandra Pierredon, Benoit Vanderperre, Petra Krznar, Ibtissam Marchiq, Nicola Zamboni, Jacques Pouyssegur, Jean-Claude Martinou
Article
Biochemistry & Molecular Biology
Benoit Vanderperre, Kristina Cermakova, Jessica Escoffier, Mayis Kaba, Tom Bender, Serge Nef, Jean-Claude Martinou
JOURNAL OF BIOLOGICAL CHEMISTRY
(2016)
Article
Genetics & Heredity
Benoit Vanderperre, Sebastien Herzig, Petra Krznar, Manuel Horl, Zeinab Ammar, Sylvie Montessuit, Sandra Pierredon, Nicola Zamboni, Jean-Claude Martinou
Review
Neurosciences
Destiny-Love Manecka, Benoit Vanderperre, Edward A. Fon, Thomas M. Durcan
FRONTIERS IN MOLECULAR NEUROSCIENCE
(2017)
Article
Biochemistry & Molecular Biology
Simon Beaudoin, Benoit Vanderperre, Catherine Grenier, Isabelle Tremblay, Frederic Leduc, Xavier Roucou
BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH
(2009)
Article
Biochemistry & Molecular Biology
Benoit Vanderperre, Antanas B. Staskevicius, Guillaume Tremblay, Marie McCoy, Megan A. O'Neill, Neil R. Cashman, Xavier Roucou
Article
Multidisciplinary Sciences
Benoit Vanderperre, Jean-Francois Lucier, Cyntia Bissonnette, Julie Motard, Guillaume Tremblay, Solene Vanderperre, Maxence Wisztorski, Michel Salzet, Francois-Michel Boisvert, Xavier Roucou
Article
Clinical Neurology
Roy N. Alcalay, Victoria Mallett, Benot Vanderperre, Omid Tavassoly, Yves Dauvillier, Richard Y. J. Wu, Jennifer A. Ruskey, Claire S. Leblond, Amirthagowri Ambalavanan, Sandra B. Laurent, Dan Spiegelman, Alexandre Dionne-Laporte, Christopher Liong, Oren A. Levy, Stanley Fahn, Cheryl Waters, Sheng-Han Kuo, Wendy K. Chung, Blair Ford, Karen S. Marder, Un Jung Kang, Sharon Hassin-Baer, Lior Greenbaum, Jean-Francois Trempe, Pavlina Wolf, Petra Oliva, Xiaokui Kate Zhang, Lorraine N. Clark, Melanie Langlois, Patrick A. Dion, Edward A. Fon, Nicolas Dupre, Guy A. Rouleau, Ziv Gan-Or
MOVEMENT DISORDERS
(2019)
Article
Clinical Neurology
Lynne Krohn, Tugba Nur Ozturk, Benoit Vanderperre, Bouchra Ouled Amar Bencheikh, Jennifer A. Ruskey, Sandra B. Laurent, Dan Spiegelman, Ronald B. Postuma, Isabelle Arnulf, Michele T. M. Hu, Yves Dauvilliers, Birgit Hogl, Ambra Stefani, Christelle Charley Monaca, Giuseppe Plazzi, Elena Antelmi, Luigi Ferini-Strambi, Anna Heidbreder, Uladzislau Rudakou, Valerie Cochen De Cock, Peter Young, Pavlina Wolf, Petra Oliva, Xiaokui Kate Zhang, Lior Greenbaum, Christopher Liong, Jean-Francois Gagnon, Alex Desautels, Sharon Hassin-Baer, Jacques Y. Montplaisir, Nicolas Dupre, Guy A. Rouleau, Edward A. Fon, Jean-Francois Trempe, Guillaume Lamoureux, Roy N. Alcalay, Ziv Gan-Or
ANNALS OF NEUROLOGY
(2020)
Article
Biology
Sondos Samandi, Annie V. Roy, Vivian Delcourt, Jean-Francois Lucier, Jules Gagnon, Maxime C. Beaudoin, Benoit Vanderperre, Marc-Andre Breton, Julie Motard, Jean-Francois Jacques, Mylene Brunelle, Isabelle Gagnon-Arsenault, Isabelle Fournier, Aida Ouangraoua, Darel J. Hunting, Alan A. Cohen, Christian R. Landry, Michelle S. Scott, Xavier Roucou