Article
Multidisciplinary Sciences
Sohail Khoshnevis, R. Elizabeth Dreggors-Walker, Virginie Marchand, Yuri Motorin, Homa Ghalei
Summary: Protein synthesis by ribosomes is crucial for gene expression in cells, and 2'-O-methylation is a common modification on ribosomal RNAs. This study reveals that changes in the biogenesis of snoRNPs, which guide 2'-O-methylation, lead to the production of ribosomes with distinct translational properties. The hypo-2'-O-methylated ribosomes show translational defects and affect ribosome dynamics and ligand binding. This highlights the importance of 2'-O-methylation in regulating cellular translation.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Oncology
Zhiyong Liu, Yanan Pang, Yin Jia, Qin Qin, Rui Wang, Wei Li, Jie Jing, Haidong Liu, Shanrong Liu
Summary: This study found that SNORA23 regulates ribosome biogenesis in hepatocellular carcinoma (HCC) by impairing the 2'-O-ribose methylation of 28S rRNA. SNORA23 inhibits the proliferation, migration, and invasion of HCC cells in vitro and in vivo. It is regulated by the PI3K/Akt/mTOR signaling pathway and inhibits the phosphorylation of 4E binding protein 1.
CANCER BIOLOGY & MEDICINE
(2022)
Review
Plant Sciences
Deniz Streit, Enrico Schleiff
Summary: The translation delves into ribosome assembly in eukaryotes, focusing on the processes in Arabidopsis thaliana and the significance of ribosome biogenesis factors and small nucleolar RNAs. It also discusses the various types of rRNA modifications and the role of snoRNPs in directing these modifications. The study compares plant-specific modifications in Arabidopsis thaliana with those in humans and yeast, shedding light on the diversity in ribosome biogenesis.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Plant Sciences
Zi-Yuan Wang, Wan-Tong Qu, Tong Mei, Nan Zhang, Nai-Ying Yang, Xiao-Feng Xu, Hai-Bo Xiong, Zhong-Nan Yang, Qing-Bo Yu
Summary: This study further analyzed the function of AtRsmD in chloroplast development and photosynthesis, revealing its distinct regulatory roles in chloroplast translation.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Biochemistry & Molecular Biology
Elan A. Shatoff, Bryan T. Gemler, Ralf Bundschuh, Kurt Fredrick
Summary: In most bacteria, the three ribosomal RNAs are encoded together in near-identical operons, and ribosome assembly begins as soon as the nascent precursor rRNA emerges from RNA polymerase. Despite differences in the cohort of RNases involved, rRNA processing in model organisms results in similar mature rRNAs. Recent studies have shown that mature ribosomes from various bacterial lineages lack structures like H1 and H98, which are predicted to form in precursor rRNA but are lost during maturation of the 50S subunit.
Review
Genetics & Heredity
Chiara Barozzi, Federico Zacchini, Sidra Asghar, Lorenzo Montanaro
Summary: This article provides a summary of the methods currently available for studying rRNA pseudouridylation and discusses the perspectives offered by newly developed approaches.
FRONTIERS IN GENETICS
(2022)
Article
Multidisciplinary Sciences
Pooja Srinivas, Meisam Nosrati, Natalia Zelinskaya, Debayan Dey, Lindsay R. Comstock, Christine M. Dunham, Graeme L. Conn
Summary: Acquired ribosomal RNA (rRNA) methylation is an important mechanism of aminoglycoside resistance in pathogenic bacterial infections. The recognition and modification of a nucleotide in the ribosome decoding center by a specific methyltransferase enzyme has been studied, revealing the critical role of the enzyme's N-terminal domain in recognition and binding to the ribosome.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Biochemical Research Methods
Chunyan Ao, Quan Zou, Liang Yu
Summary: This study developed a predictor based on machine learning to identify 2'-O-methylation modification sites in RNA. The predictor showed high efficiency and accuracy in identifying modification sites across multiple species, outperforming existing tools.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Biochemistry & Molecular Biology
Minju Joo, Ji-Hyun Yeom, Younkyung Choi, Hyeon Jun, Wooseok Song, Hyun-Lee Kim, Kangseok Lee, Eunkyoung Shin
Summary: The ribosome, once considered homogeneous, is now known to be highly heterogeneous and plays specialized roles in translational regulation. This review provides an overview of the current understanding of ribosome heterogeneity and their specialized functions, as well as discussions on specific translation systems that utilize orthogonal ribosomes.
Article
Biochemical Research Methods
Ximei Luo, Qun Li, Yifan Tang, Yan Liu, Quan Zou, Jie Zheng, Ying Zhang, Lei Xu
Summary: Our method effectively reduces the false positives in eRNA identification by adjusting the statistical distribution of expression levels. Additionally, our eRNA prediction models, which incorporate joint gene expressions, DNA methylation, and histone modification, achieved impressive performance with an AUC value of approximately 0.95 for intra-cell prediction and 0.9 for cross-cell prediction.
BMC BIOINFORMATICS
(2023)
Review
Biochemistry & Molecular Biology
Christian Trahan, Marlene Oeffinger
Summary: For over 40 years, ribosomes were believed to be homogeneous machines that translate genetic code without distinction. However, recent studies have suggested that ribosomes have compositional and functional adaptability in response to various factors. They play an active role in translation regulation through their intrinsic adaptability, providing an additional layer of gene expression regulation. Despite the identification of sources of ribosomal heterogeneity, its functional relevance and many questions remain unanswered. This article reviews the evolutionary aspects of ribosome heterogeneity and reframes it as an adaptive and dynamic process of plasticity.
Article
Cell Biology
Hongyu Li, Li Chen, Zaoli Huang, Xiaotong Luo, Huiqin Li, Jian Ren, Yubin Xie
Summary: 2'-O-methylations play a crucial role in regulating gene expression, and a novel hybrid deep-learning algorithm named DeepOMe has been proposed to accurately predict 2'-O-Me sites in human transcriptome, showing high performance in cross-validation and outperforming existing methods.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Article
Microbiology
Yansha Wu, Xinxin Pang, Xiayu Liu, Yajing Wu, Xinglin Zhang
Summary: This study comprehensively identified the genetic determinants involved in the low-temperature growth of Listeria monocytogenes (Lm) using a functional genomics method. The novel gene lmo1366 and gene lmo2301 were found to play essential roles in Lm growth at low temperatures, with lmo1366 promoting growth and lmo2301 inhibiting growth. Transcriptomic analysis revealed potential mechanisms underlying these effects. These findings contribute to a better understanding of bacterial survival and multiplication at low temperatures and have implications for the development of antibacterial strategies.
MICROBIOLOGY SPECTRUM
(2022)
Article
Agriculture, Dairy & Animal Science
Hanwen Gu, Yu H. Sun, Xin Zhiguo Li
Summary: Deep sequencing of RNA has revolutionized transcriptome research, but efficiently enriching mRNA species is a challenge. This study introduces a cost-effective method for depleting rRNAs, using chickens as a model species. The method not only removes rRNAs for RNA-seq library construction, but also for ribosome profiling.
Article
Biochemistry & Molecular Biology
J. Azevedo-Favory, C. Gaspin, L. Ayadi, C. Montacie, V Marchand, E. Jobet, M. Rompais, C. Carapito, Y. Motorin, J. Saez-Vasquez
Summary: This study used RiboMethSeq to explore rRNA 2'MODIFIER LETTER PRIME-O-methylation sites in A. thaliana plants, discovering new C/D snoRNA-guided methylation sites and some orphan sites. Moreover, disruption of Nucleolin 1 gene was found to decrease 2'MODIFIER LETTER PRIME-O-methylation at specific rRNA sites, suggesting a functional/structural interconnection with nucleolus organization and plant development.
Article
Oncology
Oriane Lie, Thierry Virolle, Mathieu Gabut, Claude Pasquier, Ilyess Zemmoura, Corinne Auge-Gouillou
Summary: This study investigates the expression of SETMAR protein in glioblastoma tissues and its potential as a prognostic marker. The results suggest that the level of S-SETMAR in the perilesional brain is associated with better survival outcomes in glioblastoma patients.
FRONTIERS IN ONCOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Danny Bergeron, Hermes Paraqindes, Etienne Fafard-Couture, Gabrielle Deschamps-Francoeur, Laurence Faucher-Giguere, Philia Bouchard-Bourelle, Sherif Abou Elela, Frederic Catez, Virginie Marcel, Michelle S. Scott
Summary: snoDB is an interactive database providing up-to-date information on human small nucleolar RNAs (snoRNAs), including features, genomic location, conservation, host gene, snoRNA-RNA targets, and abundance. The second edition of snoDB introduces a new section on ribosomal RNA (rRNA) chemical modifications guided by snoRNAs, with easy navigation between different rRNA versions used in literature and experimentally measured modification levels. Additional information including snoRNA motifs, secondary structure prediction, snoRNA-protein interactions, and expression data in various tissues and cell lines has been included to enhance functional probing of snoRNA biology. Version 2.0 also features updated identifiers, more external resource links, and duplicate entry resolution.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Pathology
Thiebaud Picart, Delphine Poncet, Marc Barritault, Luc Bauchet, Sonia Zouaoui, Jacques Guyotat, Mathieu Gabut, Frederic Fina, Jerome Honnorat, Dominique Figarella-Branger, Johan Pallud, Francois Ducray, David Meyronet
Summary: The aim of this study was to identify subgroups of cerebellar glioblastoma (cGBM) based on targeted molecular analysis. Eighty-three cGBM cases were included and classified into 6 mutually exclusive subgroups associated with age at diagnosis and prognosis. MAPK pathway-activating alterations were found to be associated with a better outcome.
AMERICAN JOURNAL OF SURGICAL PATHOLOGY
(2023)
Article
Oncology
Nour-El-Houda Mourksi, Cecile Dalban, Amelie Colombe-Vermorel, Laetitia Odeyer, Valentin Simioni, Jean-Sebastien Frenel, Michel Fabbro, Fernando Bazan, Sophie Abadie-Lacourtoisie, Elodie Coquan, Severine Martinez, Gwenaelle Garin, Severine Tabone-Eglinger, Isabelle Treilleux, Sylvie Chabaud, David Perol, Isabelle Ray-Coquard, Pierre-Etienne Heudel, Jean-Jacques Diaz, Virginie Marcel
Summary: The resistance of advanced hormone-dependent endometrial carcinoma to endocrine therapy is a global clinical issue. A recent study found that the combination of Vistusertib (a mTOR inhibitor) and Anastrozole (an aromatase inhibitor) improves progression-free rate compared to Anastrozole alone. This study evaluates the potential use of ribosome biogenesis (RiBi) factors as innovative markers for patient selection and treatment response prediction.
MOLECULAR ONCOLOGY
(2023)
Article
Multidisciplinary Sciences
Sebastien Durand, Marion Bruelle, Fleur Bourdelais, Bigitha Bennychen, Juliana Blin-Gonthier, Caroline Isaac, Aurelia Huyghe, Sylvie Martel, Antoine Seyve, Christophe Vanbelle, Annie Adrait, Yohann Coute, David Meyronet, Frederic Catez, Jean-Jacques Diaz, Fabrice Lavial, Emiliano P. Ricci, Francois Ducray, Mathieu Gabut
Summary: The study reveals that RSL24D1 is highly expressed in both mouse and human pluripotent stem cells and is involved in the biogenesis of 60S subunits. Depletion of RSL24D1 impairs global translation, particularly of pluripotency factors and components from the Polycomb Repressive Complex 2 (PRC2), leading to altered self-renewal and lineage commitment choices in embryonic stem cells.
NATURE COMMUNICATIONS
(2023)
Article
Multidisciplinary Sciences
Alexis J. Chambost, Nabila Berabez, Olivier Cochet-Escartin, Francois Ducray, Mathieu Gabut, Caroline Isaac, Sylvie Martel, Ahmed Idbaih, David Rousseau, David Meyronet, Sylvain Monnier
Summary: This study utilized microfluidics to optimize a deep learning algorithm for the accurate and rapid monitoring of isolated cancer stem-like cells under non-adherent conditions. The results demonstrate that the algorithm outperforms classical computer vision and shallow learning-based algorithms in terms of accuracy, while also being faster than cutting-edge convolutional neural networks (CNNs).
SCIENTIFIC REPORTS
(2022)
Review
Oncology
Margherita Puppo, Mariam Jaafar, Jean-Jacques Diaz, Virginie Marcel, Philippe Clezardin
Summary: This review discusses the roles of microRNAs and snoRNAs in the metastatic progression of cancer in bone. Dysregulation of microRNA and snoRNA expression in primary cancer cells leads to the acquisition of metastatic properties. Additionally, microRNAs and snoRNAs can act as intercellular mediators and remotely modulate the function of resident bone cells. Furthermore, the review explores the potential of microRNAs and snoRNAs as biomarkers and therapeutic targets in cancer treatments.
Article
Psychiatry
Marie Alexandra Albaret, Julien Textoris, Bastien Dalzon, Jeremy Lambert, Morgane Linard, Catherine Helmer, Sabine Hacot, Sandra E. Ghayad, Martial Ferreol, Hichem C. Mertani, Jean-Jacques Diaz
Summary: Many studies suggest a potential link between Alzheimer's disease and HSV-1 infection, but the molecular mechanisms behind this process are not yet fully understood.
TRANSLATIONAL PSYCHIATRY
(2023)
Review
Oncology
Andreas Bikfalvi, Cristine Alves da Costa, Tony Avril, Jean-Vianney Barnier, Luc Bauchet, Lucie Brisson, Pierre Francois Cartron, Helene Castel, Eric Chevet, Herve Chneiweiss, Anne Clavreul, Bruno Constantin, Valerie Coronas, Thomas Daubon, Monique Dontenwill, Francois Ducray, Natacha Entz-Werle, Dominique Figarella-Branger, Isabelle Fournier, Jean-Sebastien Frenel, Mathieu Gabut, Thierry Galli, Julie Gavard, Gilles Huberfeld, Jean-Philippe Hugnot, Ahmed Idbaih, Marie-Pierre Junier, Thomas Mathivet, Philippe Menei, David Meyronet, Celine Mirjolet, Fabrice Morin, Jean Mosser, Elisabeth Cohen-Jonathan Moyal, Veronique Rousseau, Michel Salzet, Marc Sanson, Giorgio Seano, Emeline Tabouret, Aurelie Tchoghandjian, Laurent Turchi, Francois M. Vallette, Somya Vats, Maite Verreault, Thierry Virolle
Summary: Glioblastoma (GBM) is a highly lethal brain tumor, and recent studies have emphasized the importance of the tumor microenvironment (TME) as a therapeutic target. However, a comprehensive understanding of the different cellular and molecular components involved in the GBM TME and their interactions is still needed for the development of more effective treatments. This review presents a comprehensive report on the GBM TME, combining the contributions of researchers and physicians in France, and provides a holistic view of the subject by describing the specific features of the GBM TME at the cellular, molecular, and therapeutic levels.
Correction
Oncology
Hermes Paraqindes, Nour-El-Houda Mourksi, Samantha Ballesta, Jordan Hedjam, Fleur Bourdelais, Tanguy Fenouil, Thiebaud Picart, Frederic Catez, Theo Combe, Anthony Ferrari, Janice Kielbassa, Emilie Thomas, Laurie Tonon, Alain Viari, Valery Attignon, Marjorie Carrere, Jessie Perrossier, Stephane Giraud, Christophe Vanbelle, Mathieu Gabut, Danny Bergeron, Michelle S. Scott, Luis Castro Vega, Nathalie Magne, Emmanuelle Huillard, Marc Sanson, David Meyronet, Jean-Jacques Diaz, Francois Ducray, Virginie Marcel, Sebastien Durand