Article
Biology
Manon Fallet, Rachel Wilson, Peter Sarkies
Summary: The study reveals that cisplatin exposure has limited effects on small non-coding RNA epimutations and gene expression levels in Caenorhabditis elegans, but leads to increased fluctuations in tRNA-derived small RNAs. These changes may be associated with gene expression alterations induced by genotoxic stress.
Article
Biochemistry & Molecular Biology
Yue Sun, Xiaolong Shao, Yingchao Zhang, Liangliang Han, Jiadai Huang, Yingpeng Xie, Jingui Liu, Xin Deng
Summary: Adequate nutrition is crucial for rapid translational elongation and protein synthesis in both eukaryotic cells and prokaryotic bacteria. The translational elongation rates of T3SS proteins in pathogenic bacteria are negatively regulated by nutrient concentration and culture duration. Rapid translational elongation and synthesis of T3SS proteins require sufficient tRNAs and elongation factors under nutrient-limiting conditions.
CELL AND BIOSCIENCE
(2022)
Article
Multidisciplinary Sciences
Ryota Yamagami, Jacob P. Sieg, Sarah M. Assmann, Philip C. Bevilacqua
Summary: RNA structure is crucial for cellular events, and the study of tRNA structure is challenging. The tRNA structure-seq workflow accurately determines the in vivo secondary structure of tRNA and provides insights into tRNA abundance and natural modifications.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biochemistry & Molecular Biology
Karl Jurgenstein, Mari Tagel, Heili Ilves, Margus Leppik, Maia Kivisaar, Jaanus Remme
Summary: Variations in the translational machinery affect protein synthesis efficiency in different organisms. The study shows that species more prone to translational frameshifting are not necessarily more prone to stop codon readthrough. The presence of pseudouridines in the anticodon stem-loop of tRNA influences translational fidelity in a context-specific manner, but this effect differs between species.
Review
Biochemistry & Molecular Biology
Gerald Soslau
Summary: It was widely believed in the scientific community that mammalian anucleate platelets were incapable of protein biosynthesis until the 1960s. However, evidence started to challenge this belief and showed that platelets had the ability to synthesize proteins. It is now known that platelet protein synthesis has significant implications in various physiological and pathological processes, and this review aims to provide an updated understanding of this field.
CRITICAL REVIEWS IN BIOCHEMISTRY AND MOLECULAR BIOLOGY
(2023)
Article
Biotechnology & Applied Microbiology
Ajeet Singh, Shafaque Zahra, Durdam Das, Shailesh Kumar
Summary: In this study, a plant-exclusive tRNA database PtRNAdb has been developed, containing 113,849 tRNA gene sequences from phylogenetically diverse plant species. This resource is believed to be highly useful for plant researchers and molecular biologists to conduct extensive research on the plant tRNAome as well as comparative and evolutionary studies related to tRNAs and their derivatives.
Article
Oncology
Yijie He, Lidan Wang, Jing Tang, Zhijie Han
Summary: This study analyzed the methylation and lncRNAs of 537 glioma patients from TCGA and TANRIC databases, identifying 18 key lncRNAs associated with the pathogenesis of glioma, which were shown to be high-risk factors for clinical prognosis. The findings provided insight into the influence of lncRNA methylation on glioma and improved understanding of its pathogenesis.
FRONTIERS IN ONCOLOGY
(2021)
Article
Genetics & Heredity
Jingjing Wang, Qi Chen, Wenyi Wu, Yujie Chen, Yincong Zhou, Guoji Guo, Ming Chen
Summary: Nutrient stress is the most important environmental stress that limits plant growth, and this study identified and characterized lncRNAs under seven different nutrient stress conditions in Arabidopsis thaliana. It was found that lncRNAs are more sensitive to nutrient stress and exhibit stress-specific expression patterns. The study also constructed ceRNA network and lncRNA-mRNA co-expression network to explore the potential function of lncRNAs under nutrient stress conditions.
FUNCTIONAL & INTEGRATIVE GENOMICS
(2021)
Article
Medical Laboratory Technology
Dandan Yi, Fazhan Xu, Ru Wang, Chaoyu Jiang, Jiabo Qin, YiHsuan Lee, Xianbiao Shi, Jianfeng Sang
Summary: This study demonstrates the importance of METTL14-mediated m6A modification of lncRNAs in breast cancer and identifies a set of differentially expressed lncRNAs associated with breast cancer. These findings provide valuable insights for future research on tumor intervention.
JOURNAL OF CLINICAL LABORATORY ANALYSIS
(2022)
Article
Genetics & Heredity
Juzuo Li, Ning Li, Ling Zhu, Zhibin Zhang, Xiaochong Li, Jinbin Wang, Hongwei Xun, Jing Zhao, Xiaofei Wang, Tianya Wang, Hongyan Wang, Bao Liu, Yu Li, Lei Gong
Summary: The study demonstrates that CG methylation negatively regulates the TE-related expression of lncRNA, while CHH methylation is also involved in the regulation of lncRNA expression.
G3-GENES GENOMES GENETICS
(2021)
Article
Genetics & Heredity
Juzuo Li, Ning Li, Ling Zhu, Zhibin Zhang, Xiaochong Li, Jinbin Wang, Hongwei Xun, Jing Zhao, Xiaofei Wang, Tianya Wang, Hongyan Wang, Bao Liu, Yu Li, Lei Gong
Summary: In this study, the profiles of genome-wide lncRNA of a rice DNA methyltransferase mutant and its wild type were characterized and compared, revealing that erasure of CG methylation leads to increased production of specific lncRNAs and CHH hypermethylation is involved in the regulation of lncRNA expression.
G3-GENES GENOMES GENETICS
(2021)
Article
Biotechnology & Applied Microbiology
Wietje Nolte, Rosemarie Weikard, Elke Albrecht, Harald M. Hammon, Christa Kuhn
Summary: By combining transcriptomic and metabolomic analyses, long non-coding RNAs (lncRNAs) were identified to have potential regulatory functions in livestock, especially in divergent nutrient partitioning. These lncRNAs may play important roles in fine-tuning gene expression involved in metabolic pathways associated with different nutrient partitioning phenotypes.
Article
Agriculture, Dairy & Animal Science
Godstime Taiwo, Taylor Sidney, Modoluwamu Idowu, Francisca Eichie, Theodore P. Karnezos, Ibukun M. Ogunade
Summary: This study evaluated the effects of dietary supplementation of fenugreek seed extract (SAP) on dry matter intake, blood metabolites, nutrient digestibility, and transcriptome in Holstein dairy heifers. Supplementing SAP increased intake and digestibility, reduced blood urea nitrogen, and increased blood glucose concentration. Transcriptome analysis revealed improved energy and amino acid metabolism, enhanced antiviral immune status, and reduced oxidative stress damage in heifers fed SAP.
TRANSLATIONAL ANIMAL SCIENCE
(2022)
Review
Biochemistry & Molecular Biology
Haneul Yoo, Catherine Triandafillou, D. Allan Drummond
JOURNAL OF BIOLOGICAL CHEMISTRY
(2019)
Article
Biology
Edward Wallace
Article
Biochemistry & Molecular Biology
Edward W. J. Wallace, Corinne Maufrais, Jade Sales-Lee, Laura R. Tuck, Luciana de Oliveira, Frank Feuerbach, Frederique Moyrand, Prashanthi Natarajan, Hiten D. Madhani, Guilhem Janbon
NUCLEIC ACIDS RESEARCH
(2020)
Article
Biology
Catherine G. Triandafillou, Christopher D. Katanski, Aaron R. Dinner, D. Allan Drummond
Article
Cell Biology
Gopal K. Pattanayak, Yi Liao, Edward W. J. Wallace, Bogdan Budnik, D. Allan Drummond, Michael J. Rust
Article
Biochemistry & Molecular Biology
Elizabeth R. Ballou, Atlanta G. Cook, Edward W. J. Wallace
Summary: The RNase II family of 3'-5' exoribonucleases is found across all domains of life, with eukaryotic members Dis3 and Dis3L2 playing essential roles in RNA degradation. Some yeasts contain both active Dis3 and inactive pseudonucleases, which function as RNA-binding proteins affecting cell growth, cytokinesis, and fungal pathogenicity. The evolutionary origins of these pseudonucleases remain unknown, with their non-nuclease functions requiring specific structural domains across diverse fungal lineages.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Biochemical Research Methods
Michael Jackson, Kostas Kavoussanakis, Edward W. J. Wallace
Summary: Data analysis involves multiple steps, and workflow management systems can help scientists process data more efficiently and provide various benefits, such as enhancing reproducibility and supporting portability. Researchers select a suitable workflow management system for their project through prototyping, emphasizing it as a cost-effective decision-making approach.
PLOS COMPUTATIONAL BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Rosemary A. Bayne, Uma Jayachandran, Aleksandra Kasprowicz, Stefan Bresson, David Tollervey, Edward W. J. Wallace, Atlanta G. Cook
Summary: Ssd1, a conserved fungal RNA-binding protein, plays important roles in stress responses, cell division, and virulence. Through in vivo cross-linking and cDNA analysis, precise binding sites of Ssd1 on RNA were identified, particularly enriched in the 5' untranslated regions of mRNAs encoding cell wall proteins. The structure-guided mutations of Ssd1 prevent its binding to RNA, providing insights into the evolution of regulatory elements in the RNase II family.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Cell Biology
Gea Cereghetti, Caroline Wilson-Zbinden, Vera M. Kissling, Maren Diether, Alexandra Arm, Haneul Yoo, Ilaria Piazza, Shady Saad, Paola Picotti, D. Allan Drummond, Uwe Sauer, Reinhard Dechant, Matthias Peter
Summary: The glycolytic metabolite fructose-1,6-bisphosphate is able to initiate the disassembly of inactive amyloids formed by Cdc19 during stress, leading to the restoration of ATP production and disassembly of stress granules (SGs) in yeast cells. This mechanism directly links cellular metabolism with SG dynamics, and plays a critical role in stress recovery by promoting Cdc19 re-solubilization and enhancing ATP production.
NATURE CELL BIOLOGY
(2021)
Correction
Cell Biology
Gea Cereghetti, Caroline Wilson-Zbinden, Vera M. Kissling, Maren Diether, Alexandra Arm, Haneul Yoo, Ilaria Piazza, Shady Saad, Paola Picotti, D. Allan Drummond, Uwe Sauer, Reinhard Dechant, Matthias Peter
NATURE CELL BIOLOGY
(2022)
Article
Biochemical Research Methods
Stevie A. Bain, Heleen Plaisier, Felicity Anderson, Nicola Cook, Kathryn Crouch, Thomas R. Meagher, Michael G. Ritchie, Edward W. J. Wallace, Daniel Barker
Summary: The nature of life sciences research has changed, creating a demand for a workforce with computational skills. However, bioinformatics education has not kept up with research advancements. The 4273pi Bioinformatics at School project aims to address this issue by providing hands-on bioinformatics workshops for secondary school students and has reached over 180 schools in Scotland.
PLOS COMPUTATIONAL BIOLOGY
(2022)
Review
Biochemistry & Molecular Biology
Hendrik Glauninger, Caitlin J. Wong Hickernell, Jared A. M. Bard, D. Allan Drummond
Summary: Stress-induced condensation of mRNA and protein into massive cytosolic clusters, known as stress granules, is a conserved phenomenon in eukaryotes. However, the biological function, mechanism of formation and dispersal, and molecular composition of these structures remain poorly understood.
Article
Cell Biology
Asif Ali, Rania Garde, Olivia C. Schaffer, Jared A. M. Bard, Kabir Husain, Samantha Keyport Kik, Kathleen A. Davis, Sofia Luengo-Woods, Maya G. Igarashi, D. Allan Drummond, Allison H. Squires, David Pincus
Summary: During stress, cells halt ribosome biogenesis, leading to accumulation of aggregation-prone orphan ribosomal proteins (oRPs). A study shows that these oRPs form reversible peri-nucleolar condensates recognized by Hsp70 co-chaperone Sis1/DnaJB6 during heat shock. These condensates remain in a liquid-like state through Hsp70 and its co-chaperones. Upon recovery, these condensates disperse in a Sis1- and Hsp70-dependent manner, with the oRPs being incorporated back into functional ribosomes in the cytosol.
NATURE CELL BIOLOGY
(2023)
Meeting Abstract
Cell Biology
C. G. Triandafillou, C. D. Katanski, A. R. Dinner, D. A. Drummond
MOLECULAR BIOLOGY OF THE CELL
(2018)
Article
Biology
Catherine G. Triandafillou, D. Allan Drummond