Article
Biochemistry & Molecular Biology
Deepshikha Verma, Veena Hegde, John Kirkpatrick, Teresa Carlomagno
Summary: The discovery of a fuzzy protein-RNA complex formed by the intrinsically unfolded protein PYM and RNA suggests that specific interactions can occur without well-defined intermolecular interfaces. The first 160 amino acids of PYM (PYM1-160) were shown to be intrinsically disordered and capable of binding RNA independently of its nucleotide sequence. This fuzzy protein-RNA complex down-regulates PYM activity by blocking its interaction with the exon junction complex (EJC), thus enabling PYM to bind to a variety of diverse interaction partners.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Xiaolei Cheng, Xiaoping Gu, Tianjiao Xia, Zhengliang Ma, Zhongzhou Yang, Helen Lechen Feng, Yong Zhao, Wenbin Ma, Zhenyu Ju, Myriam Gorospe, Xia Yi, Hao Tang, Wengong Wang
Summary: HuB and HuD in human neuroblastoma cells repress telomerase activity by associating with TERC, competing with HuR and interfering with its function.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Neurosciences
Daniel Sobrido-Camean, Matthew C. W. Oswald, David M. D. Bailey, Amrita Mukherjee, Matthias Landgraf
Summary: Neurons respond to changes in activity levels through structural changes at pre- and postsynaptic terminals, which are regulated by reactive oxygen species (ROS). In a Drosophila larval neuromuscular junction model, NADPH oxidases Nox and Duox are essential for the growth of presynaptic motor terminals, while Nox is excluded from postsynaptic dendrites. Aquaporins Bib and Drip serve as ROS conduits in the presynaptic motoneuron, and different sources of ROS may regulate different aspects of activity-regulated structural changes in neurons.
FRONTIERS IN CELLULAR NEUROSCIENCE
(2023)
Article
Multidisciplinary Sciences
Rachel Waymack, Mario Gad, Zeba Wunderlich
Summary: Transgenic reporters are valuable tools for studying enhancers, but they may inhibit the expression of other genes. Competition for transcription factors is thought to be partially responsible for this inhibition of gene expression.
Article
Multidisciplinary Sciences
Sarah M. Morgan, Hideki Tanizawa, Lisa Beatrice Caruso, Michael Hulse, Andrew Kossenkov, Jozef Madzo, Kelsey Keith, Yinfei Tan, Sarah Boyle, Paul M. Lieberman, Italo Tempera
Summary: This study demonstrates the essential role of PARP1 in regulating the chromatin structure and gene expression of EBV. PARP inhibition leads to decreased intragenomic interactions within the EBV episome, but also forms new chromatin loops. Additionally, PARP inhibition alters the binding of chromatin looping factor CTCF and gene expression.
NATURE COMMUNICATIONS
(2022)
Article
Cell Biology
Kaiming Cao, Shixuan Li, Yu Wang, Hongze Hu, Sijia Xiang, Qianling Zhang, Yangzhong Liu
Summary: Recently, it has been discovered that bacterial cells contain membrane-less organelles formed by liquid-liquid phase separation of proteins or nucleic acids. In this study, it was found that the bacterial nickel-responsive regulatory protein, NikR, exhibits liquid-liquid phase separation in both solution and cells. Furthermore, disrupting the phase separation promotes the expression of nickel transporter genes, suggesting that the formation of these membrane-less compartments is a regulatory mechanism in bacterial cells.
Article
Developmental Biology
Yoshitomo Kurogi, Eisuke Imura, Yosuke Mizuno, Ryo Hoshino, Marcela Nouzova, Shigeru Matsuyama, Akira Mizoguchi, Shu Kondo, Hiromu Tanimoto, Fernando G. Noriega, Ryusuke Niwa
Summary: This study demonstrates that the neuropeptide Diuretic hormone 31 (DH31), produced by brain neurons, plays a crucial role in regulating reproductive dormancy in Drosophila melanogaster.
Article
Entomology
Xinyu Wang, Ying Zhou, Jianwen Guan, Yang Cheng, Yingying Lu, Youheng Wei
Summary: The study reveals the high expression of FKBP39 and its role in controlling JH activity in fruit flies. In addition, it is shown that FKBP39 regulates the expression of the rp49 gene, potentially affecting ribosome assembly.
Article
Biochemistry & Molecular Biology
Humberto Itriago, Rishi K. Jaiswal, Susanne Philipp, Marita Cohn
Summary: In budding yeast telomeres, two specific permutations of the 5' end correspond to a terminal adenine nucleotide. The proteins Rap1 and Cdc13 have complementary roles in protecting both 5' ends and 3' overhangs of telomeres from degradation.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Chemistry, Multidisciplinary
Anna Grochmal, Ben Woods, Lilia Milanesi, Manuel Perez-Soto, Salvador Tomas
Summary: Research on mimicking biological systems reveals that minimal environmental changes can trigger high avidity membrane receptor assembly, which can be modulated by weakly binding divalent ligands. Mathematical models and equations can predict the modulation intensity of the ligand-messenger on the ligand-receptor ON signal, providing valuable tools for studying membrane receptors in biological and biomimetic systems.
Article
Cell Biology
Ludmila Mamon, Anna Yakimova, Daria Kopytova, Elena Golubkova
Summary: In Drosophila, RNA-binding protein SBR is not only responsible for nuclear export, but also plays a role in specific processes in neurons and glial cells.
Article
Neurosciences
Serene Dhawan, Philip Myers, David M. D. Bailey, Aaron D. Ostrovsky, Jan Felix Evers, Matthias Landgraf
Summary: The study reveals the role of reactive oxygen species (ROS) in regulating the size of neuronal dendritic arbors. It shows that activity-regulated ROS are transmitted between cells through NADPH oxidase and aquaporins, ultimately negatively regulating dendritic arbor size.
FRONTIERS IN CELLULAR NEUROSCIENCE
(2021)
Article
Biochemistry & Molecular Biology
Csaba Bajusz, Ildiko Kristo, Csilla Abonyi, Tomas Venit, Viktor Vedelek, Tamas Lukacsovich, Attila Farkas, Peter Borkuti, Zoltan Kovacs, Izabella Bajusz, Annamaria Marton, Csaba Vizler, Zoltan Lipinszki, Rita Sinka, Piergiorgio Percipalle, Peter Vilmos
Summary: By reducing the amount of Moesin in the nuclei of Drosophila, the study demonstrated the importance of ERM proteins in the nucleus, resulting in developmental defects and revealing their regulatory role in gene expression.
Article
Neurosciences
Lulu Schulz, Paulino Ramirez, Adrienne Lemieux, Elias Gonzalez, Travis Thomson, Bess Frost
Summary: Alzheimer's disease and other tauopathies are neurodegenerative disorders characterized by aggregated forms of tau protein in the brain. The mechanisms by which pathogenic tau protein drives synaptic dysfunction are not fully understood. This study using a Drosophila model found that pathogenic tau significantly increases the multimeric forms of Arc1 protein in the brain, suggesting that elevated ARC protein in Alzheimer's disease is a consequence of tau pathology and contributes to neuronal death.
Review
Biochemistry & Molecular Biology
Oscar Munoz, Mlana Lore, Sujatha Jagannathan
Summary: NMD is an RNA surveillance mechanism that recognizes abnormal transcripts with premature termination codons and functions as a gene regulatory mechanism. It can recognize its substrates through the presence of exon-junction complexes (EJCs) or through a less efficient EJC-independent mechanism triggered by long 3' untranslated regions (UTRs). While EJC-independent NMD plays a crucial role in gene regulation, its mechanism in mammalian cells remains poorly understood.
BIOCHEMICAL SOCIETY TRANSACTIONS
(2023)
Article
Multidisciplinary Sciences
Matthias Heiss, Felix Hagelskamp, Virginie Marchand, Yuri Motorin, Stefanie Kellner
Summary: The study introduces a new technique called nucleic acid isotope labeling coupled mass spectrometry (NAIL-MS) for efficient, monoisotopic stable isotope labeling in both RNA and DNA in standard cell culture. The research results show that the loss of modified nucleosides in existing RNAs is time-dependent and can only be detected with the NAIL-MS technique.
NATURE COMMUNICATIONS
(2021)
Article
Genetics & Heredity
Florian Pichot, Virginie Marchand, Mark Helm, Yuri Motorin
Summary: Deep-sequencing approaches for RNA analysis have widespread applications in modern biology, particularly for mapping and quantifying RNA modifications. The major challenge in tRNA examination lies in duplicated and point-mutated genes encoding those RNA molecules, as well as the complications caused by multiple isoacceptors/isodecoders.
Review
Biochemistry & Molecular Biology
Yasemin Yoluc, Gregor Ammann, Pierre Barraud, Manasses Jora, Patrick A. Limbach, Yuri Motorin, Virginie Marchand, Carine Tisne, Kayla Borland, Stefanie Kellner
Summary: Organisms invest significant energy in introducing RNA modifications into transcripts, with instrumental analysis focusing on modified residues to reveal the function of epitranscriptomic marks. Recent advances and breakthroughs in the study of the epitranscriptome have been made through NMR spectroscopy, sequencing, and mass spectrometry.
CRITICAL REVIEWS IN BIOCHEMISTRY AND MOLECULAR BIOLOGY
(2021)
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.
Review
Genetics & Heredity
Yuri Motorin, Virginie Marchand
Summary: Exploring and quantifying RNA modifications in different types of RNAs remains a significant challenge in the field of epitranscriptomics. Various deep sequencing-based methods have been proposed to extend the list of detectable modified residues, with approaches including reverse transcription signatures in cDNA and labeling at RNA abasic sites. Recent advancements also involve direct single-molecule sequencing of RNA using nanopores for mapping RNA modifications.
Article
Biochemistry & Molecular Biology
Yuri Motorin, Marc Quinternet, Wassim Rhalloussi, Virginie Marchand
Summary: The epitranscriptomic modifications of stable RNAs, specifically 2′-O-methylation in rRNA, have been associated with distinct cancer types. These modifications suggest the existence of 'specialized ribosomes' with stable and variable residues, which can modulate translational properties depending on the physiological state of the cell. Mapping these modifications on the human ribosome structure shows that stable positions are located in important functional sites, while variable residues are mostly distributed to the ribosome periphery.
Article
Biochemistry & Molecular Biology
Vaishali, Lyudmila Dimitrova-Paternoga, Kevin Haubrich, Mai Sun, Anne Ephrussi, Janosch Hennig
Summary: Study uncovered novel mRNA interacting proteins lacking canonical RNA binding domains and recommended initial and simple in vitro RNA binding experiments for validating their functions.
Article
Genetics & Heredity
Jonathan Delhermite, Lionel Tafforeau, Sunny Sharma, Virginie Marchand, Ludivine Wacheul, Ruben Lattuca, Simon Desiderio, Yuri Motorin, Eric Bellefroid, Denis L. J. Lafontaine
Summary: Ribosomes are essential nanomachines responsible for protein production. Ribosomopathies, which are diseases caused by improper ribosome formation, impact specific tissues. In this study, the importance of fibrillarin, an enzyme that modifies ribosomal RNA, in the early embryonic development of Xenopus laevis is evaluated. The research reveals that fibrillarin depletion leads to defects in eye and craniofacial skeleton development due to a lack of neural crest cell survival caused by apoptosis. The study also investigates ribosomal RNA methylation during development and identifies potential roles in developmental transitions.
Article
Biochemistry & Molecular Biology
R. Elizabeth Dreggors-Walker, Lauren N. Cohen, Sohail Khoshnevis, Virginie Marchand, Yuri Motorin, Homa Ghalei
Summary: Regulation of protein synthesis is essential for gene expression control in cells. Defects in ribosome production, function, or regulation can lead to cellular damage and human diseases such as PEHO syndrome. This study reveals that mutations in the ZNHIT3 gene, which encodes a nuclear protein, cause a decrease in protein levels and defects in rRNA processing and translation in yeast, providing insights into the molecular basis of PEHO syndrome.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2022)
Article
Multidisciplinary Sciences
Lucia Cassella, Anne Ephrussi
Summary: In this study, the authors use spatial transcriptomics to identify localized RNAs in the Drosophila follicular epithelium and analyze the mechanisms underlying their localization. They find that apical RNA localization is mediated by the dynein/BicD/Egl machinery, while basally-targeted RNAs require kinesin-1. They also discover a non-canonical, translation- and dynein-dependent mechanism for the apical localization of a subgroup of dynein-activating adaptor-encoding RNAs.
NATURE COMMUNICATIONS
(2022)
Article
Orthopedics
A. Chabronova, G. G. H. van den Akker, B. A. C. Housmans, M. M. J. Caron, A. Cremers, D. A. M. Surtel, K. Wichapong, M. M. J. Peffers, L. W. van Rhijn, V. Marchand, Y. Motorin, T. J. M. Welting
Summary: This study investigates the role of ribosomes in chondrocyte translation regulation and its relevance for osteoarthritis. Using RiboMethSeq analysis, the researchers found that osteoarthritic synovial fluid induces site-specific changes in the rRNA 2'-O-me profile of primary human articular chondrocytes. These changes alter the translation mode and promote the translation of COL1A1 mRNA, leading to increased levels of COL1A1 protein and suggesting the involvement of rRNA epitranscriptomic mechanisms in osteoarthritis development.
OSTEOARTHRITIS AND CARTILAGE
(2023)
Article
Biochemistry & Molecular Biology
Florian Pichot, Marion C. Hogg, Virginie Marchand, Valerie Bourguignon, Elisabeth Jirstrom, Cliona Farrell, Hesham A. Gibriel, Jochen H. M. Prehn, Yuri Motorin, Mark Helm
Summary: Modification of tRNA is crucial for generating RNA expression diversity. In this study, the stoichiometry of incompletely modified sites in human tRNAs was investigated, and it was found that up to 75% of sites can be incompletely modified. The modification patterns of tRNA populations can provide information to differentiate different cell lines.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2023)
Article
Biology
Mira Brazane, Dilyana G. Dimitrova, Julien Pigeon, Chiara Paolantoni, Tao Ye, Virginie Marchand, Bruno Da Silva, Elise Schaefer, Margarita T. Angelova, Zornitza Stark, Martin Delatycki, Tracy Dudding-Byth, Jozef Gecz, Pierre-Yves Placais, Laure Teysset, Thomas Preat, Amelie Piton, Bassem A. Hassan, Jean-Yves Roignant, Yuri Motorin, Clement Carre
Summary: This study reports a novel pathogenic variant of FTSJ1 associated with X-linked intellectual disability (XLID). Using RiboMethSeq analysis, the researchers identified ribose methylation on all human tRNAs and novel targets. Transcriptome analysis revealed deregulation of genes associated with intellectual disability and cancers. The study also uncovered changes in the miRNA population and demonstrated defects in neuron morphology associated with FTSJ1 depletion.
LIFE SCIENCE ALLIANCE
(2023)
Article
Cell Biology
Imre Gaspar, Ly Jane Phea, Mark A. McClintock, Simone Heber, Simon L. Bullock, Anne Ephrussi
Summary: Gaspar et al. discovered that the sequential activity of dynein and kinesin-1 motors during the transport of oskar mRNA in Drosophila oocytes is regulated by the competition between two double-stranded RNA-binding proteins, Egl and Staufen, and this process is controlled by dynein-mediated localization of staufen mRNA. Regulating the recruitment and activity of motor proteins is crucial for intracellular transport of cargoes, including RNPs.
JOURNAL OF CELL BIOLOGY
(2023)
Article
Biotechnology & Applied Microbiology
Morghan C. Lucas, Leszek P. Pryszcz, Rebeca Medina, Ivan Milenkovic, Noelia Camacho, Virginie Marchand, Yuri Motorin, Lluis Ribas de Pouplana, Eva Maria Novoa
Summary: Nano-tRNAseq is a nanopore-based method that allows for simultaneous quantification of tRNA abundance and chemical modifications, providing a new tool for studying tRNA. Re-processing of raw nanopore current intensity signals leads to more accurate tRNA abundance information. Nano-tRNAseq can reveal changes in tRNA populations in response to oxidative stress.
NATURE BIOTECHNOLOGY
(2023)