Article
Cell Biology
Yuchao Diao, Yingwei Li, Zixiang Wang, Shourong Wang, Peng Li, Beihua Kong
Summary: Studies have shown that overexpression of SF3B4 in ovarian cancer patients is associated with poor prognosis, and miR-509-3p negatively regulates SF3B4 expression which in turn promotes ovarian cancer progression. Additionally, SF3B4's splicing of RAD52 also impacts the development of ovarian cancer.
CELL DEATH & DISEASE
(2022)
Article
Biochemistry & Molecular Biology
Yinli Zheng, Jinjun Wu, Ru Deng, Censhan Lin, Yuhua Huang, Xia Yang, Chunhua Wang, Mingming Yang, Yangfan He, Jiabin Lu, Xiaodong Su, Qian Yan, Yinghui Zhu, Xinyuan Guan, Yan Li, Jingping Yun
Summary: The study revealed that upregulation of G3BP2 in ESCC is significantly correlated with lymph node metastasis, depth of tumor invasion, and unfavorable outcomes. G3BP2 enhances ESCC cell migration and invasion through interactions with LINC01554 and HDGF.
Article
Biotechnology & Applied Microbiology
Fan Ren, Quan Zhou, Yinglu Meng, Wenjie Guo, Qin Tang, Jie Mei
Summary: This study identified evaluation indicators for fish egg quality by combining the study of fertilization rate, hatching rate, embryo malformation rate and gene expression profile. A cluster of RNA-binding proteins were found to potentially regulate egg quality.
Article
Multidisciplinary Sciences
Francesco Camera, Isabel Romero-Camarero, Bradley H. Revell, Fabio M. R. Amaral, Oliver J. Sinclair, Fabrizio Simeoni, Daniel H. Wiseman, Lovorka Stojic, Tim C. P. Somervaille
Summary: The Iroquois transcription factor gene IRX3 is highly expressed in 20-30% of acute myeloid leukemia (AML) and contributes to the differentiation block. Intron 8 FTO sequences downstream of IRX3 show epigenetic modifications and contacts with the IRX3 promoter, indicating their role in regulating IRX3 expression. Deletion of these intronic elements confirms their positive regulation of IRX3. Knockdown of FTO-lncAML induces differentiation of AML cells and reduces FTO intron 8:IRX3 promoter contacts, suggesting a role for the long non-coding RNA in trans-regulation. FTO-lncAML(high) AML samples display altered expression of differentiation and HOXA genes.
Article
Multidisciplinary Sciences
Jiazhi Li, Longfei Wang, Quentin Hahn, Radoslaw P. Nowak, Thibault Viennet, Esteban A. Orellana, Shourya S. Roy Burman, Hong Yue, Moritz Hunkeler, Pietro Fontana, Hao Wu, Haribabu Arthanari, Eric S. Fischer, Richard I. Gregory
Summary: Chemical modifications of RNA play a crucial role in various biological processes. N-7-methylguanosine (m(7)G) is essential for the integrity and stability of a large group of tRNAs. The METTL1-WDR4 complex acts as a methyltransferase that modifies G46 in specific tRNAs, and its dysregulation is implicated in tumorigenesis. However, the mechanism of tRNA substrate recognition and regulation of METTL1-WDR4 remains unknown.
Article
Biochemistry & Molecular Biology
Wenqi Feng, Hongwanjun Zhang, Yang Cao, Cheng Yang, Muhammad Hayder Bin Khalid, Qingqing Yang, Wanchen Li, Yingge Wang, Fengling Fu, Haoqiang Yu
Summary: This study identified and classified 19 ZmPum genes in maize and found that they exhibit diversity in gene and protein architectures, physicochemical properties, and expression patterns. The research also revealed the involvement of ZmPum genes in kernel development, with certain genes showing significantly high expression levels during seed development. These findings provide valuable information for understanding the functions of ZmPum genes and offer insights for improving maize yield.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Cell Biology
Matilda Rehn, Anne Wenzel, Anne-Katrine Frank, Mikkel Bruhn Schuster, Sachin Pundhir, Nanna Jorgensen, Kristoffer Vitting-Seerup, Ying Ge, Johan Jendholm, Magali Michaut, Erwin M. Schoof, Tanja Lyholm Jensen, Nicolas Rapin, Russell T. Sapio, Kasper Langebjerg Andersen, Anders H. Lund, Michele Solimena, Martin Holzenberger, Dimitri G. Pestov, Bo Torben Porse
Summary: Ribosomopathies are a range of disorders that affect protein synthesis and primarily impact hematopoietic stem cells and erythroid development. This study demonstrates that the deletion of poly-pyrimidine-tract-binding protein 1 (PTBP1) in the hematopoietic compartment leads to a condition resembling ribosomopathy. The loss of PTBP1 results in reduced HSC self-renewal, erythroid differentiation, and protein synthesis, along with defects in splicing and ribosome biogenesis.
Article
Biochemistry & Molecular Biology
Nikolay Manavski, Sebastien Mathieu, Margarita Rojas, Louis-Valentin Meteignier, Andreas Brachmann, Alice Barkan, Kamel Hammani
Summary: An artificial PPR protein, built from consensus PPR motifs, demonstrated in vivo RNA binding specificity and substitution capabilities for natural PPR proteins, showing potential for mimicking native PPR proteins in serving as physical barriers against exoribonucleases.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biochemical Research Methods
Lei Xu, Shanshan Jiang, Jin Wu, Quan Zou
Summary: Exploring the function of proteins in protein-nucleic acid interactions is important for understanding related biological events and predicting these interactions. Establishing databases by collecting and identifying protein sequence information helps in predicting protein function, leading to improved prediction accuracy.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Biochemical Research Methods
Britta Velten, Jana M. Braunger, Ricard Argelaguet, Damien Arnol, Jakob Wirbel, Danila Bredikhin, Georg Zeller, Oliver Stegle
Summary: MEFISTO is a flexible and versatile toolbox for modeling high-dimensional data with spatial or temporal dependencies, enabling spatio-temporally informed dimensionality reduction, interpolation, and separation of smooth and non-smooth patterns of variation. It can also integrate underlying patterns of variation in multiple related datasets in a data-driven manner.
Article
Biochemistry & Molecular Biology
Renfu Shang, Dmitry A. Kretov, Scott Adamson, Thomas Treiber, Nora Treiber, Jeffrey Vedanayagam, Jeffrey H. Chuang, Gunter Meister, Daniel Cifuentes, Eric C. Lai
Summary: A study has revealed the important regulatory role of conserved loop sequences in the generation of miRNAs in vertebrates, particularly in the cleavage of pre-mir-144. This regulatory role involves the ILF3 complex and reshaping of the apical loop of pre-mir-144, allowing for cleavage by Dicer. Furthermore, these findings extend our understanding of nuclear and cytoplasmic regulatory events in miRNA maturation.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Cell Biology
Chungen Lan, Huikun Zhang, Kezhen Wang, Xiaoli Liu, Yawen Zhao, Zhifang Guo, Ning Zhang, Yongxia Zhou, Manzhi Gao, Feng Gu, Yongjie Ma
Summary: The study demonstrates that PTBP1 modulates the alternative splicing of ITSN1, promoting glioma proliferation and motility by up-regulating the ratio of ITSN1-S/ITSN1-L, suggesting that PTBP1 may be a promising therapeutic target for gliomas.
CELL DEATH & DISEASE
(2022)
Review
Biochemistry & Molecular Biology
Bernhard Dumoulin, Christoph Ufer, Hartmut Kuhn, Sajad Sofi
Summary: GRSF1, a widely distributed RNA-binding protein in eukaryotic cells, is involved in various physiological processes and the pathogenesis of diseases.
JOURNAL OF MOLECULAR BIOLOGY
(2021)
Article
Cell & Tissue Engineering
Marcos Plana-Carmona, Gregoire Stik, Romain Bulteau, Carolina Segura-Morales, Noelia Alcazar, Chris D. R. Wyatt, Antonios Klonizakis, Luisa de Andres-Aguayo, Maxime Gasnier, Tian Tian, Guillem Torcal Garcia, Maria Vila-Casadesus, Nicolas Plachta, Manuel Serrano, Mirko Francesconi, Thomas Graf
Summary: IL-6 is necessary for somatic cell reprogramming into iPSCs, and C/EBP alpha enhances the reprogramming process of B cells into iPSCs. The expression of IL-6 is regulated by Cebp alpha, and IL-6 secretion plays a crucial role in the development of blastocysts.
Article
Cell Biology
Valeria Savoca, Julieta Rivosecchi, Alice Gaiatto, Annalisa Rossi, Riccardo Mosca, Irene Gialdini, Lorena Zubovic, Toma Tebaldi, Paolo Macchi, Emilio Cusanelli
Summary: This study reveals that the stability of TERRA transcripts is regulated by the RNA-binding protein associated with lethal yellow mutation (RALY). Depletion of RALY leads to decreased levels of TERRA, impaired localization of TERRA at telomeres, and ultimately telomere damage. Furthermore, TERRA interacts with the poly(A)-binding protein nuclear 1 (PABPN1), suggesting an interplay between RALY and PABPN1 in regulating TERRA stability.
Article
Biochemistry & Molecular Biology
Andrea Vandelli, Fernando Cid Samper, Marc Torrent Burgas, Natalia Sanchez De Groot, Gian Gaetano Tartaglia
Summary: Condensation, or liquid-like phase separation, is an important phenomenon for the spatiotemporal regulation of molecules within the cell. Recent studies have shown that components of phase-separated organelles like Stress Granules (SGs) and Processing Bodies (PBs) exhibit high variability and dynamics in their composition and molecular organization. The formation of SGs and PBs is regulated by a dense contact network involving both RNAs and proteins, and the molecular architecture of these organelles is not yet fully understood.
JOURNAL OF MOLECULAR BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Giovanni Pascarella, Chung Chau Hon, Kosuke Hashimoto, Annika Busch, Joachim Luginbuhl, Callum Parr, Wing Hin Yip, Kazumi Abe, Anton Kratz, Alessandro Bonetti, Federico Agostini, Jessica Severin, Shigeo Murayama, Yutaka Suzuki, Stefano Gustincich, Martin Frith, Piero Carninci
Summary: This study reveals the somatic recombination of repeat elements, such as Alu and L1, in the human genome. It also identifies tissue-specific non-allelic homologous recombination hallmarks and retroelements as potential recombination hotspots. The study further shows that neuron-specific recombination of repeat elements accompanies chromatin changes during cell-fate determination. Moreover, somatic recombination profiles are altered in Parkinson's and Alzheimer's disease, indicating a link between retroelement recombination and genomic instability in neurodegeneration.
Article
Biochemistry & Molecular Biology
Lu Chen, Caitlin M. Roake, Paolo Maccallini, Francesca Bavasso, Roozbeh Dehghannasiri, Pamela Santonicola, Natalia Mendoza-Ferreira, Livia Scatolini, Ludovico Rizzuti, Alessandro Esposito, Ivan Gallotta, Sofia Francia, Stefano Cacchione, Alessandra Galati, Valeria Palumbo, Marie A. Kobin, Gian Gaetano Tartaglia, Alessio Colantoni, Gabriele Proietti, Yunming Wu, Matthias Hammerschmidt, Cristiano De Pitta, Gabriele Sales, Julia Salzman, Livio Pellizzoni, Brunhilde Wirth, Elia Di Schiavi, Maurizio Gatti, Steven E. Artandi, Grazia D. Raffa
Summary: This study identifies a neuroprotective role for TGS1 and highlights the impact of defective snRNA maturation on neuronal viability and function.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Multidisciplinary Sciences
Elsa Zacco, Owen Kantelberg, Edoardo Milanetti, Alexandros Armaos, Francesco Paolo Panei, Jenna Gregory, Kiani Jeacock, David J. Clarke, Siddharthan Chandran, Giancarlo Ruocco, Stefano Gustincich, Mathew H. Horrocks, Annalisa Pastore, Gian Gaetano Tartaglia
Summary: In this study, aptamers specific for Amyotrophic Lateral Sclerosis protein TDP-43 were successfully designed and used to track TDP-43 phase transition in vitro and in cells.
NATURE COMMUNICATIONS
(2022)
Article
Multidisciplinary Sciences
Roberto Ballarino, Britta A. M. Bouwman, Federico Agostini, Luuk Harbers, Constantin Diekmann, Erik Wernersson, Magda Bienko, Nicola Crosetto
Summary: This study has mapped the genomic landscape of endogenous DNA double-strand breaks (DSBs) occurring in neural cells and found that DSBs are enriched at the promoter and along the gene body of transcriptionally active genes. NDD risk genes are more affected by DSBs, especially in post-mitotic neural cells. The datasets and tools provided in this study can be utilized to investigate the role of genome fragility in the pathogenesis of NDDs.
Article
Biochemistry & Molecular Biology
Riccardo Delli Ponti, Laura Broglia, Andrea Vandelli, Alexandros Armaos, Marc Torrent Burgas, Natalia Sanchez de Groot, Gian Gaetano Tartaglia
Summary: RNA molecules undergo chemical modifications that can alter their structure and molecular interactions. This study introduces a predictor of A-to-I effects on RNA structure and finds enrichment of double-stranded regions caused by A-to-I in long intergenic noncoding RNAs. Investigation of specific cases suggests that A-to-I editing is linked to the alteration of interaction sites with proteins involved in phase separation.
Article
Multidisciplinary Sciences
Nicolas J. Walker, Mamunur Rashid, Shirong Yu, Helen Bignell, Casper K. Lumby, Carmen M. Livi, Kate Howell, David J. Morley, Sandro Morganella, Daniel Barrell, Shabhonam Caim, Walraj Gosal, Jens Fullgrabe, Thomas J. Charlesworth, Louella Vasquez, Miika Ahdesmaki, Jordan Eizenga, Parul Prabhat, Vitali Proutski, Marie Laurie Murat-Onana, Catherine J. Greenwood, Lisa Kirkwood, Meeta Maisuria-Armer, Mengjie Li, Emma Coats, Victoria Winfield, Lachlan MacBean, Toby Stock, Alice Tome-Fernandez, Yat Chan, Nasir Sheikh, Paula Golder, Michael Steward, Tobias W. B. Ost, Douglas Stewart, Albert Vilella, Mojtaba Noursalehi, Benedict Paten, Debora Lucarelli, Joanne Mason, Gareth Ridge, Jason Mellad, Suman Shirodkar, Shankar Balasubaramanian, Joanna D. Holbrook
Summary: Early detection of cancer using the blood biomarker 5-hydroxymethylcytosine can improve survival rates. The classifier based on this biomarker can accurately discriminate colorectal cancer, including early-stage disease, with high sensitivity.
SCIENTIFIC REPORTS
(2022)
Article
Biochemistry & Molecular Biology
Alessio Colantoni, Davide Capauto, Vincenzo Alfano, Eleonora D'Ambra, Sara D'Uva, Gian Gaetano Tartaglia, Mariangela Morlando
Summary: Deregulation of RNA metabolism, specifically mutations on RNA-binding proteins (RBPs) or on proteins involved in RNA metabolism, is a key factor in the degeneration of motor neurons in ALS. The ALS-linked mutation of the RBP FUS greatly affects various RNA-related processes, including splicing regulation and circRNA formation. In this study, the impact of the FUS mutation on circRNA levels and its binding preferences were investigated using in vitro-derived human motor neurons. The findings suggest potential implications of cytoplasmic circRNAs as miRNA sponges in ALS pathogenesis.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Multidisciplinary Sciences
Nuria Crua Asensio, Stefano Rizzieri, Alessandro Cuomo, Gian Gaetano Tartaglia, Elsa Zacco
Summary: Protein-RNA interactions are crucial for gene expression and cellular functions. To efficiently identify the binding partners of RNA molecules, especially non-canonical ones, an improved method was developed. This method involves pull-down and characterization of interacting proteins using biotinylated RNA loaded on streptavidin-coated beads. The protocol was validated by quantifying the enrichment of a known RNA binder compared to a negative control using mass spectrometry and confirming the selective interactions of computationally predicted protein binders by western blot. This protocol allows for the study of protein-RNA interactions in near-physiological conditions, aiding in the discovery of unique and unpredicted interactions.
JOVE-JOURNAL OF VISUALIZED EXPERIMENTS
(2023)
Editorial Material
Biochemistry & Molecular Biology
Andre P. Gerber, Gian Gaetano Tartaglia
FRONTIERS IN MOLECULAR BIOSCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Jakob Rupert, Michele Monti, Elsa Zacco, Gian Gaetano Tartaglia
Summary: This study characterizes the physico-chemical properties of regions involved in amyloid aggregation using a computational approach, and investigates the influence of RNA on protein assembly. Experimental data shows that while the core region is hydrophobic and highly ordered, external regions exhibit a distinct tendency to interact with nucleic acids. RNA is found to accelerate aggregation, especially in a mutant truncated protein with a higher propensity for RNA interaction. The findings suggest that RNA sequestration might be a common phenomenon linked to protein aggregation.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Multidisciplinary Sciences
Chiara Pederiva, Davide M. Trevisan, Dimitra Peirasmaki, Shan Chen, Sharon A. Savage, Ola Larsson, Jernej Ule, Laura Baranello, Federico Agostini, Marianne Farnebo
Summary: Posttranscriptional modifications of mRNA, including pseudouridylation, play a crucial role in gene expression regulation. In this study, dyskerin, a pseudouridine synthase, was found to bind to RNA polymerase II and be responsible for pseudouridylation of thousands of mRNAs. Dyskerin-mediated pseudouridylation was shown to interfere with translation and reduction of the modification led to enhanced protein synthesis. Furthermore, dyskeratosis congenita patients with mutations in the dyskerin-encoding gene showed severe reduction in mRNA pseudouridylation.
Article
Biochemical Research Methods
Andrea Vandelli, Magdalena Arnal Segura, Michele Monti, Jonathan Fiorentino, Laura Broglia, Alessio Colantoni, Natalia Sanchez de Groot, Marc Torrent Burgas, Alexandros Armaos, Gian Gaetano Tartaglia
Summary: PRALINE is a database that provides information on protein-protein, protein-RNA, and RNA-RNA interactions in stress granules, processing bodies, and other assemblies. It also reports the liquid-liquid and liquid-solid phase separation propensities of proteins and provides predicted secondary structure content of RNAs.
Article
Biochemistry & Molecular Biology
Thomas Schwarzl, Sudeep Sahadevan, Benjamin Lang, Milad Miladi, Rolf Backofen, Wolfgang Huber, Matthias W. Hentze, Gian Gaetano Tartaglia
Summary: Enhanced crosslinking and immunoprecipitation sequencing (eCLIP-seq) is a method for detecting RNA-binding protein binding sites. However, current analysis strategies have low replication and high false positive rates. DEWSeq, a R/Bioconductor package, improves the detection of binding regions by utilizing replicate information and size-matched input controls. It has been shown to significantly increase the number and quality of binding sites.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Clinical Neurology
Magdalena Arnal Segura, Giorgio Bini, Dietmar Fernandez Orth, Eleftherios Samaras, Maya Kassis, Fotis Aisopos, Jordi Rambla De Argila, George Paliouras, Peter Garrard, Claudia Giambartolomei, Gian Gaetano Tartaglia
Summary: In this study, tree-based machine learning algorithms were used to discriminate Alzheimer's disease from unaffected individuals, leading to the identification of specific genomic profiles defined by interactions among single nucleotide variants in gene regions such as PVRL2, TOMM40, APOE, and APOC1.
ALZHEIMER'S & DEMENTIA: DIAGNOSIS, ASSESSMENT & DISEASE MONITORING
(2022)