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1. Adaptive Dynamic Programming for Human Postural Balance Control

Author

Mauro, Eric, Bian, Tao, Jiang, Zhong-Ping, Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Weikum, Gerhard, Series editor, Liu, Derong, editor, Xie, Shengli, editor, Li, Yuanqing, editor, Zhao, Dongbin, editor, and El-Alfy, El-Sayed M., editor

Published
2017
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3. Modulation of the intrinsic chromatin binding property of HIV-1 integrase by LEDGF/p75

Author

Lapaillerie, Delphine, primary, Lelandais, Benoît, additional, Mauro, Eric, additional, Lagadec, Floriane, additional, Tumiotto, Camille, additional, Miskey, Csaba, additional, Ferran, Guillaume, additional, Kuschner, Natacha, additional, Calmels, Christina, additional, Métifiot, Mathieu, additional, Rooryck, Caroline, additional, Ivics, Zoltan, additional, Ruff, Marc, additional, Zimmer, Christophe, additional, Lesbats, Paul, additional, Toutain, Jérôme, additional, and Parissi, Vincent, additional

Published
2021
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4. Two-long terminal repeat (LTR) DNA circles are a substrate for HIV-1 integrase

Author

Chaignepain, Stephane, Maillot, Benoit, Oladosu, Oyindamola, Robert, Xavier, Fiorini, Francesca, Kieffer, Bruno, Bouaziz, Serge, Gouet, Patrice, Ruff, Marc, Lee, Ga-Eun, Mauro, Eric, Shin, Cha-Gyun, Richetta, Clémence, Thierry, Sylvain, Thierry, Eloise, Lesbats, Paul, Lapaillerie, Delphine, Munir, Soundasse, Subra, Frédéric, Leh, Hervé, Deprez, Eric, Parissi, Vincent, Delelis, Olivier, Immunité infection vaccination (I2V), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-IFR128-Institut National de la Santé et de la Recherche Médicale (INSERM), Microbiologie cellulaire et moléculaire et pathogénicité (MCMP), Université Bordeaux Segalen - Bordeaux 2-Centre National de la Recherche Scientifique (CNRS), Centre génomique fonctionnelle, Université Bordeaux Segalen - Bordeaux 2, Department of Microbiology, Kohat University of Science and Technology (KUST), Laboratoire de Biotechnologie et Pharmacogénétique Appliquée (LBPA), École normale supérieure - Cachan (ENS Cachan)-Centre National de la Recherche Scientifique (CNRS), Bioalliancepharma, and Laboratoire de Biologie et de Pharmacologie Appliquée (LBPA)

Subjects
0301 basic medicine, Virus Integration, [SDV]Life Sciences [q-bio], HIV Integrase, Microbiology, Biochemistry, law.invention, 03 medical and health sciences, chemistry.chemical_compound, Retrovirus, law, Humans, Molecular Biology, ComputingMilieux_MISCELLANEOUS, HIV Long Terminal Repeat, 030102 biochemistry & molecular biology, biology, Chemistry, Cell Biology, Integrases, biology.organism_classification, Reverse transcriptase, Long terminal repeat, 3. Good health, Integrase, Cell biology, 030104 developmental biology, Viral replication, DNA, Viral, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, HIV-1, biology.protein, Recombinant DNA, DNA, Circular, DNA
Abstract

Integration of the HIV-1 DNA into the host genome is essential for viral replication and is catalyzed by the retroviral integrase. To date, the only substrate described to be involved in this critical reaction is the linear viral DNA produced in reverse transcription. However, during HIV-1 infection, two-long terminal repeat DNA circles (2-LTRcs) are also generated through the ligation of the viral DNA ends by the host cell's nonhomologous DNA end-joining pathway. These DNAs contain all the genetic information required for viral replication, but their role in HIV-1's life cycle remains unknown. We previously showed that both linear and circular DNA fragments containing the 2-LTR palindrome junction can be efficiently cleaved in vitro by recombinant integrases, leading to the formation of linear 3′-processed–like DNA. In this report, using in vitro experiments with purified proteins and DNAs along with DNA endonuclease and in vivo integration assays, we show that this circularized genome can also be efficiently used as a substrate in HIV-1 integrase-mediated integration both in vitro and in eukaryotic cells. Notably, we demonstrate that the palindrome cleavage occurs via a two-step mechanism leading to a blunt-ended DNA product, followed by a classical 3′-processing reaction; this cleavage leads to integrase-dependent integration, highlighted by a 5-bp duplication of the host genome. Our results suggest that 2-LTRc may constitute a reserve supply of HIV-1 genomes for proviral integration.

Published
2019
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5. Modulation of chromatin structure by the FACT histone chaperone complex regulates HIV-1 integration

Author

Matysiak, Julien, Lesbats, Paul, Mauro, Eric, Lapaillerie, Delphine, Dupuy, Jean-William, Lopez, Angelica P., Benleulmi, Mohamed Salah, Calmels, Christina, Andreola, Marie-Line, Ruff, Marc, Llano, Manuel, Delelis, Olivier, Lavigne, Marc, Parissi, Vincent, Microbiologie Fondamentale et Pathogénicité (MFP), Université Bordeaux Segalen - Bordeaux 2-Centre National de la Recherche Scientifique (CNRS), Centre Génomique Fonctionnelle Bordeaux [Bordeaux] (CGFB), Institut Polytechnique de Bordeaux-Université de Bordeaux Ségalen [Bordeaux 2], University of Texas [El Paso] (UTEP ), Institut de génétique et biologie moléculaire et cellulaire (IGBMC), Université Louis Pasteur - Strasbourg I-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Biologie et de Pharmacologie Appliquée (LBPA), École normale supérieure - Cachan (ENS Cachan)-Centre National de la Recherche Scientifique (CNRS), Virologie (CNRS - UMR3569), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Institut Cochin (IC UM3 (UMR 8104 / U1016)), Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), This work was supported by the French National Research Agency (ANR, RETROSelect, jcjc2011 program), the French National Research Agency against AIDS (ANRS, AO2016), SIDACTION (AO2016, VIH20160721002), the French Infrastructure for Integrated Structural Biology (FRISBI) ANR-10-INSB-05-01, Instruct, a part of the European Strategy Forum on Research Infrastructures (ESFRI), the Centre National de la Recherche Scientifique (CNRS), the University of Bordeaux., ANR-11-JSV3-0006,RetroSelect,Contrôle cellulaire de la sélectivité de l'intégration rétrovirale(2011), ANR-10-INBS-0005,FRISBI,Infrastructure Française pour la Biologie Structurale Intégrée(2010), ruff, marc, Jeunes Chercheuses et Jeunes Chercheurs - Contrôle cellulaire de la sélectivité de l'intégration rétrovirale - - RetroSelect2011 - ANR-11-JSV3-0006 - JCJC - VALID, and Infrastructure Française pour la Biologie Structurale Intégrée - - FRISBI2010 - ANR-10-INBS-0005 - INBS - VALID

Subjects
lcsh:Immunologic diseases. Allergy, Virus Integration, FACT, Retroviral integration, HIV Infections, HIV Integrase, Integrase, MESH: Chromatin, MESH: HIV-1, MESH: Nucleosomes, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Humans, MESH: Protein Binding, Histone Chaperones, MESH: Intercellular Signaling Peptides and Proteins, Cells, Cultured, [SDV.MP.VIR] Life Sciences [q-bio]/Microbiology and Parasitology/Virology, MESH: Humans, Research, MESH: Host-Pathogen Interactions, MESH: Chromatin Assembly and Disassembly, MESH: Histone Chaperones, MESH: HIV Infections, Chromatin Assembly and Disassembly, Chromatin, Nucleosomes, Nucleosome, Host-Pathogen Interactions, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, [SDV.MHEP.MI] Life Sciences [q-bio]/Human health and pathology/Infectious diseases, HIV-1, Intercellular Signaling Peptides and Proteins, MESH: HIV Integrase, lcsh:RC581-607, MESH: Virus Integration, Protein Binding, MESH: Cells, Cultured
Abstract

Background Insertion of retroviral genome DNA occurs in the chromatin of the host cell. This step is modulated by chromatin structure as nucleosomes compaction was shown to prevent HIV-1 integration and chromatin remodeling has been reported to affect integration efficiency. LEDGF/p75-mediated targeting of the integration complex toward RNA polymerase II (polII) transcribed regions ensures optimal access to dynamic regions that are suitable for integration. Consequently, we have investigated the involvement of polII-associated factors in the regulation of HIV-1 integration. Results Using a pull down approach coupled with mass spectrometry, we have selected the FACT (FAcilitates Chromatin Transcription) complex as a new potential cofactor of HIV-1 integration. FACT is a histone chaperone complex associated with the polII transcription machinery and recently shown to bind LEDGF/p75. We report here that a tripartite complex can be formed between HIV-1 integrase, LEDGF/p75 and FACT in vitro and in cells. Biochemical analyzes show that FACT-dependent nucleosome disassembly promotes HIV-1 integration into chromatinized templates, and generates highly favored nucleosomal structures in vitro. This effect was found to be amplified by LEDGF/p75. Promotion of this FACT-mediated chromatin remodeling in cells both increases chromatin accessibility and stimulates HIV-1 infectivity and integration. Conclusions Altogether, our data indicate that FACT regulates HIV-1 integration by inducing local nucleosomes dissociation that modulates the functional association between the incoming intasome and the targeted nucleosome. Electronic supplementary material The online version of this article (doi:10.1186/s12977-017-0363-4) contains supplementary material, which is available to authorized users.

Published
2017
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7. Human H4 tail stimulates HIV-1 integration through binding to the carboxy-terminal domain of integrase

Author

Mauro, Eric, primary, Lesbats, Paul, additional, Lapaillerie, Delphine, additional, Chaignepain, Stephane, additional, Maillot, Benoit, additional, Oladosu, Oyindamola, additional, Robert, Xavier, additional, Fiorini, Francesca, additional, Kieffer, Bruno, additional, Bouaziz, Serge, additional, Gouet, Patrice, additional, Ruff, Marc, additional, and Parissi, Vincent, additional

Published
2019
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8. MOESM1 of Modulation of the functional association between the HIV-1 intasome and the nucleosome by histone amino-terminal tails

Author

Benleulmi, Mohamed, Matysiak, Julien, Robert, Xavier, Miskey, Csaba, Mauro, Eric, Lapaillerie, Delphine, Lesbats, Paul, Chaignepain, Stéphane, Henriquez, Daniel, Calmels, Christina, Oyindamola Oladosu, Eloïse Thierry, Leon, Oscar, Lavigne, Marc, Marie-Line Andreola, Delelis, Olivier, Ivics, Zoltán, Ruff, Marc, Gouet, Patrice, and Parissi, Vincent

Abstract

Additional file 1: Figure S1. Structure of the native and tailless mononucleosomes used in the work. The globular structure of the nucleosomes was analyzed by loading 250 ng of native or tailless MN on 0.8% native agarose gel run 4 h at 50 V and 4 °C then stained with SYBR®Safe 20 min. Assembled MNs migrate between 600 and 700 bp and the naked 601 DNA fragment at 147 bp. Figure S2. A. Effect of LEDGF/p75 on HIV-1 integration in vitro. Integration assay was performed as done in Fig. 2 using naked 601 DNA coupled to magnetic beads and increasing concentration of LEDGF in the presence or absence of PEG and DMSO. B. Integration activity catalyzed by IN and IN/LEDGF complex on native or tail less nucleosomes in the absence of PEG and DMSO. Integration assay was performed as done in Fig. 2 using native or tail less nucleosomes coupled to magnetic beads and either IN or IN/LEDGF complex. All values are shown as the mean ± standard deviation (error bars) of three independent sets of experiments. The p values were calculated by Student’s t test and are shown as *p

Published
2017
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9. Modulation of the functional association between the HIV-1 intasome and the nucleosome by histone amino-terminal tails

Author

Benleulmi, Mohamed, Matysiak, Julien, Robert, Xavier, Miskey, Csaba, Mauro, Eric, Lapaillerie, Delphine, Lesbats, Paul, Chaignepain, Stéphane, Henriquez, Daniel, Calmels, Christina, Oladosu, Oyindamola, Thierry, Eloïse, Leon, Oscar, Lavigne, Marc, Andreola, Marie-Line, Delelis, Olivier, Ivics, Zoltán, Ruff, Marc, Gouet, Patrice, Parissi, Vincent, Microbiologie Fondamentale et Pathogénicité (MFP), Université Bordeaux Segalen - Bordeaux 2-Centre National de la Recherche Scientifique (CNRS), Microbiologie moléculaire et biochimie structurale / Molecular Microbiology and Structural Biochemistry (MMSB), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Paul-Ehrlich-Institute - Federal Institute for Vaccines and Biomedicines (EPI), Chimie et Biologie des Membranes et des Nanoobjets (CBMN), Université de Bordeaux (UB)-École Nationale d'Ingénieurs des Travaux Agricoles - Bordeaux (ENITAB)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Universidad de Chile = University of Chile [Santiago] (UCHILE), Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Université de Strasbourg (UNISTRA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Biologie et de Pharmacologie Appliquée (LBPA), École normale supérieure - Cachan (ENS Cachan)-Centre National de la Recherche Scientifique (CNRS), Virologie (CNRS - UMR3569), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), This work was supported by the French National Research Agency [ANR, RETROSelect program], the French National Research Agency against AIDS (ANRS, AO 2016-2, ECTZ18624), SIDACTION (AO-27-1 10465, 16-1-AEQ-10465), the French Infrastructure for Integrated Structural Biology (FRISBI) [ANR-10-INSB-05-01], Instruct, a part of the European Strategy Forum on Research Infrastructures (ESFRI), the Centre National de la Recherche Scientifique (CNRS), the University Victor Segalen Bordeaux 2, and the ECOS-CONICYT C12B03 program., ANR-11-JSV3-0006,RetroSelect,Contrôle cellulaire de la sélectivité de l'intégration rétrovirale(2011), ANR-10-INBS-0005,FRISBI,Infrastructure Française pour la Biologie Structurale Intégrée(2010), European Project: 654213,H2020,H2020-INFRASUPP-2014-2,STR- ESFRI(2015), ruff, marc, Jeunes Chercheuses et Jeunes Chercheurs - Contrôle cellulaire de la sélectivité de l'intégration rétrovirale - - RetroSelect2011 - ANR-11-JSV3-0006 - JCJC - VALID, Infrastructure Française pour la Biologie Structurale Intégrée - - FRISBI2010 - ANR-10-INBS-0005 - INBS - VALID, and Support to Reinforce the European Strategy Forum for Research Infrastructures - STR- ESFRI - - H20202015-03-01 - 2019-03-01 - 654213 - VALID

Subjects
lcsh:Immunologic diseases. Allergy, [SDV.MP.VIR] Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Chromatine, Virus Integration, Research, Retroviral integration, HIV Integrase, Integrase, Chromatin, Host-Parasite Interactions, Nucleosomes, Histones, HEK293 Cells, Nucleosome, DNA, Viral, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, HIV-1, Humans, Histone tails, lcsh:RC581-607, Cell Line, Transformed, Protein Binding
Abstract

Background Stable insertion of the retroviral DNA genome into host chromatin requires the functional association between the intasome (integrase·viral DNA complex) and the nucleosome. The data from the literature suggest that direct protein–protein contacts between integrase and histones may be involved in anchoring the intasome to the nucleosome. Since histone tails are candidates for interactions with the incoming intasomes we have investigated whether they could participate in modulating the nucleosomal integration process. Results We show here that histone tails are required for an optimal association between HIV-1 integrase (IN) and the nucleosome for efficient integration. We also demonstrate direct interactions between IN and the amino-terminal tail of human histone H4 in vitro. Structure/function studies enabled us to identify amino acids in the carboxy-terminal domain of IN that are important for this interaction. Analysis of the nucleosome-binding properties of catalytically active mutated INs confirmed that their ability to engage the nucleosome for integration in vitro was affected. Pseudovirus particles bearing mutations that affect the IN/H4 association also showed impaired replication capacity due to altered integration and re-targeting of their insertion sites toward dynamic regions of the chromatin with lower nucleosome occupancy. Conclusions Collectively, our data support a functional association between HIV-1 IN and histone tails that promotes anchoring of the intasome to nucleosomes and optimal integration into chromatin. Electronic supplementary material The online version of this article (10.1186/s12977-017-0378-x) contains supplementary material, which is available to authorized users.

Published
2017
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11. CORRESPONDENCE.

Author

Frank, Nathaniel, Neblo, Michael A., Mauro, Eric, and Harrison, Jeffrey

Subjects
LETTERS to the editor, POETRY (Literary form), GLOBALIZATION
Abstract

Presents letters to the editor referencing several articles published in previous issues. Views of a reader on the article "Teach In," by Peter Beinart published in the November 12, issue; Necessity of U.S. Central Investigation Agency; Emphasis on globalization in Muslim countries in the article "Poor Choice," by Brink Lindsey, published in the November 12, issue; Comments on the article "Things Done on Earth," by Glyn Maxwell, published in the November 12, issue; Opinion of a reader on comments on his article related to poems, published in a previous issue.

Published
2001

13. Modulation of the functional association between the HIV-1 intasome and the nucleosome by histone amino-terminal tails.

Author

Benleulmi MS, Matysiak J, Robert X, Miskey C, Mauro E, Lapaillerie D, Lesbats P, Chaignepain S, Henriquez DR, Calmels C, Oladosu O, Thierry E, Leon O, Lavigne M, Andreola ML, Delelis O, Ivics Z, Ruff M, Gouet P, and Parissi V

Subjects
Cell Line, Transformed, Chromatin virology, DNA, Viral metabolism, HEK293 Cells, HIV-1 genetics, Histones chemistry, Host-Parasite Interactions physiology, Humans, Protein Binding, HIV Integrase metabolism, HIV-1 metabolism, Histones metabolism, Nucleosomes metabolism, Virus Integration
Abstract

Background: Stable insertion of the retroviral DNA genome into host chromatin requires the functional association between the intasome (integrase·viral DNA complex) and the nucleosome. The data from the literature suggest that direct protein-protein contacts between integrase and histones may be involved in anchoring the intasome to the nucleosome. Since histone tails are candidates for interactions with the incoming intasomes we have investigated whether they could participate in modulating the nucleosomal integration process., Results: We show here that histone tails are required for an optimal association between HIV-1 integrase (IN) and the nucleosome for efficient integration. We also demonstrate direct interactions between IN and the amino-terminal tail of human histone H4 in vitro. Structure/function studies enabled us to identify amino acids in the carboxy-terminal domain of IN that are important for this interaction. Analysis of the nucleosome-binding properties of catalytically active mutated INs confirmed that their ability to engage the nucleosome for integration in vitro was affected. Pseudovirus particles bearing mutations that affect the IN/H4 association also showed impaired replication capacity due to altered integration and re-targeting of their insertion sites toward dynamic regions of the chromatin with lower nucleosome occupancy., Conclusions: Collectively, our data support a functional association between HIV-1 IN and histone tails that promotes anchoring of the intasome to nucleosomes and optimal integration into chromatin.

Published
2017
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