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2. Tyramine induces dynamic RNP granule remodeling and translation activation in the Drosophila brain

Author

Nadia Formicola, Marjorie Heim, Jérémy Dufourt, Anne-Sophie Lancelot, Akira Nakamura, Mounia Lagha, and Florence Besse

Subjects
RNP condensates, RNA binding proteins, neuron, live-imaging, Drosophila, translation, Medicine, Science, Biology (General), QH301-705.5
Abstract

Ribonucleoprotein (RNP) granules are dynamic condensates enriched in regulatory RNA binding proteins (RBPs) and RNAs under tight spatiotemporal control. Extensive recent work has investigated the molecular principles underlying RNP granule assembly, unraveling that they form through the self-association of RNP components into dynamic networks of interactions. How endogenous RNP granules respond to external stimuli to regulate RNA fate is still largely unknown. Here, we demonstrate through high-resolution imaging of intact Drosophila brains that Tyramine induces a reversible remodeling of somatic RNP granules characterized by the decondensation of granule-enriched RBPs (e.g. Imp/ZBP1/IGF2BP) and helicases (e.g. Me31B/DDX-6/Rck). Furthermore, our functional analysis reveals that Tyramine signals both through its receptor TyrR and through the calcium-activated kinase CamkII to trigger RNP component decondensation. Finally, we uncover that RNP granule remodeling is accompanied by the rapid and specific translational activation of associated mRNAs. Thus, this work sheds new light on the mechanisms controlling cue-induced rearrangement of physiological RNP condensates.

Published
2021
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3. Detecting Stress Granules in Drosophila Neurons

Author

Fabienne, De Graeve, Nadia, Formicola, Kavya Vinayan, Pushpalatha, Akira, Nakamura, Eric, Debreuve, Xavier, Descombes, and Florence, Besse

Subjects
Neurons, Ribonucleoproteins, Stress, Physiological, Animals, Drosophila, Cytoplasmic Granules, Stress Granules
Abstract

Stress granules (SGs) are cytoplasmic ribonucleoprotein condensates that dynamically and reversibly assemble in response to stress. They are thought to contribute to the adaptive stress response by storing translationally inactive mRNAs as well as signaling molecules. Recent work has shown that SG composition and properties depend on both stress and cell types, and that neurons exhibit a complex SG proteome and a strong vulnerability to mutations in SG proteins. Drosophila has emerged as a powerful genetically tractable organism where to study the physiological regulation and functions of SGs in normal and pathological contexts. In this chapter, we describe a protocol enabling quantitative analysis of SG properties in both larval and adult Drosophila CNS samples. In this protocol, fluorescently tagged SGs are induced upon acute ex vivo stress or chronic in vivo stress, imaged at high-resolution via confocal microscopy and detected automatically, using a dedicated software.

Published
2022

4. Correction: Tyramine induces dynamic RNP granule remodeling and translation activation in the Drosophila brain

Author

Akira Nakamura, Florence Besse, Marjorie Heim, Anne-Sophie Lancelot, Nadia Formicola, Jeremy Dufourt, and Mounia Lagha

Subjects
Male, QH301-705.5, Science, Tyramine, Cytoplasmic Granules, General Biochemistry, Genetics and Molecular Biology, chemistry.chemical_compound, Animals, Drosophila Proteins, Drosophila (subgenus), Biology (General), Neurotransmitter Agents, General Immunology and Microbiology, biology, Chemistry, General Neuroscience, Correction, Brain, RNA-Binding Proteins, Translation (biology), RNP granule, General Medicine, Cell Biology, biology.organism_classification, Cell biology, Drosophila melanogaster, Ribonucleoproteins, Medicine, Female, Protein Processing, Post-Translational
Abstract

Ribonucleoprotein (RNP) granules are dynamic condensates enriched in regulatory RNA binding proteins (RBPs) and RNAs under tight spatiotemporal control. Extensive recent work has investigated the molecular principles underlying RNP granule assembly, unraveling that they form through the self-association of RNP components into dynamic networks of interactions. How endogenous RNP granules respond to external stimuli to regulate RNA fate is still largely unknown. Here, we demonstrate through high-resolution imaging of intact

Published
2021

5. Tyramine induces dynamic RNP granule remodeling and translation activation in the Drosophila brain

Author

Florence Besse, Nadia Formicola, Anne-Sophie Lancelot, Mounia Lagha, Jeremy Dufourt, Akira Nakamura, Marjorie Heim, Institut de Biologie Valrose (IBV), Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA), Institut de Génétique Moléculaire de Montpellier (IGMM), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Kumamoto University, RUIZ, Caroline, Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Côte d'Azur (UCA)-Centre National de la Recherche Scientifique (CNRS), and Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)

Subjects
ZBP1, QH301-705.5, Science, translation, RNA-binding protein, General Biochemistry, Genetics and Molecular Biology, RNP condensates, 03 medical and health sciences, 0302 clinical medicine, Ca2+/calmodulin-dependent protein kinase, [SDV.BBM] Life Sciences [q-bio]/Biochemistry, Molecular Biology, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Biology (General), 030304 developmental biology, Ribonucleoprotein, 0303 health sciences, D. melanogaster, General Immunology and Microbiology, biology, Chemistry, General Neuroscience, Helicase, RNA, Translation (biology), Cell Biology, General Medicine, neuron, Cell biology, live-imaging, biology.protein, Medicine, Translational Activation, Drosophila, RNA binding proteins, 030217 neurology & neurosurgery, Research Article
Abstract

Ribonucleoprotein (RNP) granules are dynamic condensates enriched in regulatory RNA binding proteins (RBPs) and RNAs under tight spatiotemporal control. Extensive recent work has investigated the molecular principles underlying RNP granule assembly, unraveling that they form through the self-association of RNP components into dynamic networks of interactions. How endogenous RNP granules respond to external stimuli to regulate RNA fate is still largely unknown. Here, we demonstrate through high-resolution imaging of intact Drosophila brains that Tyramine induces a reversible remodeling of somatic RNP granules characterized by the decondensation of granule-enriched RBPs (e.g. Imp/ZBP1/IGF2BP) and helicases (e.g. Me31B/DDX-6/Rck). Furthermore, our functional analysis reveals that Tyramine signals both through its receptor TyrR and through the calcium-activated kinase CamkII to trigger RNP component decondensation. Finally, we uncover that RNP granule remodeling is accompanied by the rapid and specific translational activation of associated mRNAs. Thus, this work sheds new light on the mechanisms controlling cue-induced rearrangement of physiological RNP condensates.

Published
2021
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6. Subunits of the PBAP Chromatin Remodeler Are Capable of Mediating Enhancer-Driven Transcription in Drosophila

Author

Paul Schedl, Ennio Giordano, Giovanna De Simone, Oleg V. Bylino, Valeria V. Kolesnik, Diego Amendola, Nadia Formicola, Filomena Anna Digilio, A. V. Shaposhnikov, Yulii V. Shidlovskii, Zaur M. Kachaev, Lyubov A. Lebedeva, Shidlovskii, Yulii V, Bylino, Oleg V, Shaposhnikov, Alexander V, Kachaev, Zaur M, Lebedeva, Lyubov A, Kolesnik, Valeria V, Amendola, Diego, De Simone, Giovanna, Formicola, Nadia, Schedl, Paul, Digilio, Filomena Anna, Giordano, Ennio, Shidlovskii, Yulii V., Bylino, Oleg V., Shaposhnikov, Alexander V., Kachaev, Zaur M., Lebedeva, Lyubov A., and Kolesnik, Valeria V.

Subjects
Transcriptional Activation, Transcription, Genetic, Transgene, Biology, Article, Catalysis, Chromatin remodeling, chromatin remodeling, Animals, Genetically Modified, Inorganic Chemistry, lcsh:Chemistry, Chromatin remodeling,Enhancer,PBAP,Promoter,SWI/SNF, Transcription (biology), SWI/SNF, PBAP, promoter, enhancer, Animals, Drosophila Proteins, Humans, Physical and Theoretical Chemistry, Fluorescent Antibody Technique, Indirect, Promoter Regions, Genetic, Enhancer, Molecular Biology, lcsh:QH301-705.5, In Situ Hybridization, Spectroscopy, Regulation of gene expression, Models, Genetic, Organic Chemistry, Promoter, General Medicine, Chromatin Assembly and Disassembly, Computer Science Applications, Chromatin, Cell biology, Protein Subunits, Drosophila melanogaster, Enhancer Elements, Genetic, lcsh:Biology (General), lcsh:QD1-999, Transcription Factors
Abstract

The chromatin remodeler SWI/SNF is an important participant in gene activation, functioning predominantly by opening the chromatin structure on promoters and enhancers. Here, we describe its novel mode of action in which SWI/SNF factors mediate the targeted action of an enhancer. We studied the functions of two signature subunits of PBAP subfamily, BAP170 and SAYP, in Drosophila. These subunits were stably tethered to a transgene reporter carrying the hsp70 core promoter. The tethered subunits mediate transcription of the reporter in a pattern that is generated by enhancers close to the insertion site in multiple loci throughout the genome. Both tethered SAYP and BAP170 recruit the whole PBAP complex to the reporter promoter. However, we found that BAP170-dependent transcription is more resistant to the depletion of other PBAP subunits, suggesting that BAP170 may play a more critical role in establishing enhancer-dependent transcription.

Published
2021
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8. Detecting Stress Granules in Drosophila Neurons

Author

Fabienne De Graeve, Nadia Formicola, Kavya Vinayan Pushpalatha, Akira Nakamura, Eric Debreuve, Xavier Descombes, Florence Besse, Institut de Biologie Valrose (IBV), Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Côte d'Azur (UCA)-Centre National de la Recherche Scientifique (CNRS), Department of Germline Development, Institute of Molecular Embryology and Genetics, and Graduate School of Pharmaceutical Sciences, Kumamoto University, Kumamoto University, Morphologie et Images (MORPHEME), Inria Sophia Antipolis - Méditerranée (CRISAM), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Institut de Biologie Valrose (IBV), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Côte d'Azur (UCA)-Centre National de la Recherche Scientifique (CNRS)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Côte d'Azur (UCA)-Centre National de la Recherche Scientifique (CNRS)-Signal, Images et Systèmes (Laboratoire I3S - SIS), Laboratoire d'Informatique, Signaux, et Systèmes de Sophia Antipolis (I3S), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA)-Laboratoire d'Informatique, Signaux, et Systèmes de Sophia Antipolis (I3S), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA)-Centre National de la Recherche Scientifique (CNRS), Development of this protocol was also supported by Fondation pour la Recherche Médicale (Equipe FRM, grant #DEQ20180339161) to F.B. Part of this work was also supported by the Joint Usage/Research Center for Developmental Medicine, IMEG, Kumamoto University. K.P. was inaddition supported by a one year- La Ligue contre le cancer fellowship., ANR-15-CE12-0016,RNAGRIMP,Recherche de facteurs contrôlant l'assemblage de granules ARN par crible génomique(2015), ANR-11-LABX-0028,SIGNALIFE,Réseau d'Innovation sur les Voies de Signalisation en Sciences de la Vie(2011), Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA)-Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA)-Signal, Images et Systèmes (Laboratoire I3S - SIS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA)-Université Nice Sophia Antipolis (1965 - 2019) (UNS), Debreuve, Eric, Recherche de facteurs contrôlant l'assemblage de granules ARN par crible génomique - - RNAGRIMP2015 - ANR-15-CE12-0016 - AAPG2015 - VALID, and Centres d'excellences - Réseau d'Innovation sur les Voies de Signalisation en Sciences de la Vie - - SIGNALIFE2011 - ANR-11-LABX-0028 - LABX - VALID

Subjects
Drosophila melanogaster, automated detection, [SDV.BC.BC] Life Sciences [q-bio]/Cellular Biology/Subcellular Processes [q-bio.SC], fluorescent stress granule proteins, [SDV.BC.BC]Life Sciences [q-bio]/Cellular Biology/Subcellular Processes [q-bio.SC], central nervous system, confocal imaging, [SPI.SIGNAL]Engineering Sciences [physics]/Signal and Image processing, [SPI.SIGNAL] Engineering Sciences [physics]/Signal and Image processing
Abstract

International audience; Stress granules (SGs) are cytoplasmic ribonucleoprotein condensates that dynamically and reversibly assemble in response to acute or chronic stress. They are thought to contribute to the adaptive stress response by storing translationally inactive mRNAs as well as signaling molecules. Recent work has shown that SG composition and properties depend on both stress and cell types, and that neurons exhibit a complex SG proteome and a strong vulnerability to mutations in SG proteins. Drosophila has emerged as a powerful genetically tractable organism where to study the physiological regulation and functions of SGs in normal and pathological contexts. In this chapter, we describe a protocol enabling quantitative analysis of SG properties in both larval and adult Drosophila CNS samples. In this protocol, fluorescently-tagged SGs are induced upon acute ex vivo stress or chronic in vivo stress, imaged at high-resolution via confocal microscopy and detected automatically, usinusing a dedicated software.

Published
2021

9. Neuronal ribonucleoprotein granules: Dynamic sensors of localized signals

Author

Nadia Formicola, Jeshlee Vijayakumar, and Florence Besse

Subjects
Context (language use), Biology, Cytoplasmic Granules, Biochemistry, 03 medical and health sciences, 0302 clinical medicine, Stress, Physiological, Structural Biology, Organelle, Genetics, Protein biosynthesis, Extracellular, Animals, Humans, Molecular Biology, Rapid response, 030304 developmental biology, Ribonucleoprotein, Neurons, 0303 health sciences, Translation (biology), RNP granule, Cell Biology, Cell biology, Ribonucleoproteins, 030217 neurology & neurosurgery, Signal Transduction
Abstract

Membrane-less organelles, because of their capacity to dynamically, selectively and reversibly concentrate molecules, are very well adapted for local information processing and rapid response to environmental fluctuations. These features are particularly important in the context of neuronal cells, where synapse-specific activation, or localized extracellular cues, induce signaling events restricted to specialized axonal or dendritic subcompartments. Neuronal ribonucleoprotein (RNP) particles, or granules, are nonmembrane bound macromolecular condensates that concentrate specific sets of mRNAs and regulatory proteins, promoting their long-distance transport to axons or dendrites. Neuronal RNP granules also have a dual function in regulating the translation of associated mRNAs: while preventing mRNA translation at rest, they fuel local protein synthesis upon activation. As revealed by recent work, rapid and reversible switches between these two functional modes are triggered by modifications of the networks of interactions underlying RNP granule assembly. Such flexible properties also come with a cost, as neuronal RNP granules are prone to transition into pathological aggregates in response to mutations, aging, or cellular stresses, further emphasizing the need to better understand the mechanistic principles governing their dynamic assembly and regulation in living systems.

Published
2019
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