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Mao J, Huang L, Fan L, Chen F, Lou J, Shan X, Yu D, Zhou J. 60-nt DNA Direct Detection without Pretreatment by Surface-Enhanced Raman Scattering with Polycationic Modified Ag Microcrystal Derived from AgCl Cube. Molecules 2021; 26:molecules26226790. [PMID: 34833883 PMCID: PMC8620099 DOI: 10.3390/molecules26226790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 10/31/2021] [Accepted: 11/05/2021] [Indexed: 11/18/2022] Open
Abstract
Direct detection of long-strand DNA by surface-enhanced Raman scattering (SERS) is a valuable method for diagnosis of hereditary diseases, but it is currently limited to less than 25-nt DNA strand in pure water, which makes this approach unsuitable for many real-life applications. Here, we report a 60-nt DNA label-free detection strategy without pretreatment by SERS with polyquaternium-modified Ag microcrystals derived from an AgCl cube. Through the reduction-induced decomposition, the size of the about 3 × 3 × 3 μm3 AgCl cube is reduced to Ag, and the surface is distributed with the uniform size of 63 nm silver nanoparticles, providing a large area of a robust and highly electromagnetic enhancement region. The modified polycationic molecule enhances the non-specific electrostatic interaction with the phosphate group, thereby anchoring DNA strands firmly to the SERS enhanced region intactly. As a result, the single-base recognition ability of this strategy reaches 60-nt and is successfully applied to detect thalassemia-related mutation genes.
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Affiliation(s)
- Jikai Mao
- Research Center for Analytical Instrumentation, State Key Laboratory of Industrial Control Technology, Institute of Cyber-Systems and Control, Zhejiang University, Hangzhou 310027, China; (J.M.); (L.H.); (L.F.)
- Department of Chemistry, Zhejiang University, Hangzhou 310027, China;
| | - Lvtao Huang
- Research Center for Analytical Instrumentation, State Key Laboratory of Industrial Control Technology, Institute of Cyber-Systems and Control, Zhejiang University, Hangzhou 310027, China; (J.M.); (L.H.); (L.F.)
- Department of Chemistry, Zhejiang University, Hangzhou 310027, China;
| | - Li Fan
- Research Center for Analytical Instrumentation, State Key Laboratory of Industrial Control Technology, Institute of Cyber-Systems and Control, Zhejiang University, Hangzhou 310027, China; (J.M.); (L.H.); (L.F.)
| | - Fang Chen
- Department of Chemistry, Zhejiang University, Hangzhou 310027, China;
| | - Jingan Lou
- The Children’s Hospital Zhejiang University School of Medicine, Hangzhou 310000, China;
| | - Xuliang Shan
- Hangzhou Green Environment Science & Technology Co., Ltd., Hangzhou 310000, China;
| | - Dongdong Yu
- Hospital of Zhejiang University, Hangzhou 310027, China;
| | - Jianguang Zhou
- Research Center for Analytical Instrumentation, State Key Laboratory of Industrial Control Technology, Institute of Cyber-Systems and Control, Zhejiang University, Hangzhou 310027, China; (J.M.); (L.H.); (L.F.)
- Department of Chemistry, Zhejiang University, Hangzhou 310027, China;
- Correspondence:
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2
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The siRNA-mediated knockdown of GluN3A in 46C-derived neural stem cells affects mRNA expression levels of neural genes, including known iGluR interactors. PLoS One 2018; 13:e0192242. [PMID: 29438442 PMCID: PMC5811004 DOI: 10.1371/journal.pone.0192242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Accepted: 01/18/2018] [Indexed: 11/30/2022] Open
Abstract
For years, GluN3A was solely considered to be a dominant-negative modulator of NMDARs, since its incorporation into receptors alters hallmark features of conventional NMDARs composed of GluN1/GluN2 subunits. Only recently, increasing evidence has accumulated that GluN3A plays a more diversified role. It is considered to be critically involved in the maturation of glutamatergic synapses, and it might act as a molecular brake to prevent premature synaptic strengthening. Its expression pattern supports a putative role during neural development, since GluN3A is predominantly expressed in early pre- and postnatal stages. In this study, we used RNA interference to efficiently knock down GluN3A in 46C-derived neural stem cells (NSCs) both at the mRNA and at the protein level. Global gene expression profiling upon GluN3A knockdown revealed significantly altered expression of a multitude of neural genes, including genes encoding small GTPases, retinal proteins, and cytoskeletal proteins, some of which have been previously shown to interact with GluN3A or other iGluR subunits. Canonical pathway enrichment studies point at important roles of GluN3A affecting key cellular pathways involved in cell growth, proliferation, motility, and survival, such as the mTOR pathway. This study for the first time provides insights into transcriptome changes upon the specific knockdown of an NMDAR subunit in NSCs, which may help to identify additional functions and downstream pathways of GluN3A and GluN3A-containing NMDARs.
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3
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BIM and NOXA are mitochondrial effectors of TAF6δ-driven apoptosis. Cell Death Dis 2018; 9:70. [PMID: 29358700 PMCID: PMC5833734 DOI: 10.1038/s41419-017-0115-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Revised: 10/04/2017] [Accepted: 10/30/2017] [Indexed: 12/29/2022]
Abstract
TAF6δ is a pro-apoptotic splice variant of the RNA polymerase II general transcription factor, TAF6, that can dictate life vs. death decisions in animal cells. TAF6δ stands out from classical pro-apoptotic proteins because it is encoded by a gene that is essential at the cellular level, and because it functions as a component of the basal transcription machinery. TAF6δ has been shown to modulate the transcriptome landscape, but it is not known if changes in gene expression trigger apoptosis nor which TAF6δ-regulated genes contribute to cell death. Here we used microarrays to interrogate the genome-wide impact of TAF6δ on transcriptome dynamics at temporal resolution. The results revealed changes in pro-apoptotic BH3-only mitochondrial genes that correlate tightly with the onset of cell death. These results prompted us to test and validate a role for the mitochondrial pathway by showing that TAF6δ expression causes cytochrome c release into the cytoplasm. To further dissect the mechanism by which TAF6δ drives apoptosis, we pinpointed BIM and NOXA as candidate effectors. siRNA experiments showed that both BIM and NOXA contribute to TAF6δ-dependent cell death. Our results identify mitochondrial effectors of TAF6δ-driven apoptosis, thereby providing the first of mechanistic framework underlying the atypical TAF6δ apoptotic pathway's capacity to intersect with the classically defined apoptotic machinery to trigger cell death.
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4
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Eilebrecht S, Benecke BJ, Benecke AG. Latent HIV-1 TAR Regulates 7SK-responsive P-TEFb Target Genes and Targets Cellular Immune Responses in the Absence of Tat. GENOMICS PROTEOMICS & BIOINFORMATICS 2017; 15:313-323. [PMID: 29037489 PMCID: PMC5673678 DOI: 10.1016/j.gpb.2017.05.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/04/2017] [Revised: 05/10/2017] [Accepted: 05/24/2017] [Indexed: 01/04/2023]
Abstract
The transactivating response element (TAR) structure of the nascent HIV-1 transcript is critically involved in the recruitment of inactive positive transcription elongation factor b (P-TEFb) to the promoter proximal paused RNA polymerase II. The viral transactivator Tat is responsible for subsequent P-TEFb activation in order to start efficient viral transcription elongation. In the absence of the viral transactivator of transcription (Tat), e.g., during latency or in early stages of HIV transcription, TAR mediates an interaction of P-TEFb with its inhibitor hexamethylene bis-acetamide-inducible protein 1 (HEXIM1), keeping P-TEFb in its inactive form. In this study, we address the function of HIV-1 TAR in the absence of Tat by analyzing consequences of HIV-1 TAR overexpression on host cellular gene expression. An RNA chimera consisting of Epstein-Barr virus-expressed RNA 2 (EBER2) and HIV-1 TAR was developed to assure robust overexpression of TAR in HEK293 cells. The overexpression results in differential expression of more than 800 human genes. A significant proportion of these genes is involved in the suppression of cellular immune responses, including a significant set of 7SK-responsive P-TEFb target genes. Our findings identify a novel role for HIV-1 TAR in the absence of Tat, involving the interference with host cellular immune responses by targeting 7SK RNA-mediated gene expression and P-TEFb inactivation.
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Affiliation(s)
- Sebastian Eilebrecht
- CNRS UMR8246, Université Pierre et Marie Curie, Paris 75005, France; ACSIOMA GmbH, Technologiezentrum Ruhr, Bochum 44799, Germany.
| | | | - Arndt G Benecke
- CNRS UMR8246, Université Pierre et Marie Curie, Paris 75005, France; Center for Innate Immunity and Immune Disease, University of Washington School of Medicine, Seattle, WA 98195, USA.
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5
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Le Douce V, Forouzanfar F, Eilebrecht S, Van Driessche B, Ait-Ammar A, Verdikt R, Kurashige Y, Marban C, Gautier V, Candolfi E, Benecke AG, Van Lint C, Rohr O, Schwartz C. HIC1 controls cellular- and HIV-1- gene transcription via interactions with CTIP2 and HMGA1. Sci Rep 2016; 6:34920. [PMID: 27725726 PMCID: PMC5057145 DOI: 10.1038/srep34920] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 09/21/2016] [Indexed: 02/06/2023] Open
Abstract
Among many cellular transcriptional regulators, Bcl11b/CTIP2 and HGMA1 have been described to control the establishment and the persistence of HIV-1 latency in microglial cells, the main viral reservoir in the brain. In this present work, we identify and characterize a transcription factor i.e. HIC1, which physically interacts with both Bcl11b/CTIP2 and HMGA1 to co-regulate specific subsets of cellular genes and the viral HIV-1 gene. Our results suggest that HIC1 represses Tat dependent HIV-1 transcription. Interestingly, this repression of Tat function is linked to HIC1 K314 acetylation status and to SIRT1 deacetylase activity. Finally, we show that HIC1 interacts and cooperates with HGMA1 to regulate Tat dependent HIV-1 transcription. Our results also suggest that HIC1 repression of Tat function happens in a TAR dependent manner and that this TAR element may serve as HIC1 reservoir at the viral promoter to facilitate HIC1/TAT interaction.
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Affiliation(s)
- Valentin Le Douce
- University of Strasbourg, EA7292, DHPI, Institut of Parasitology and tropical pathology Strasbourg, France.,University of Strasbourg, IUT Louis Pasteur, Schiltigheim, France.,Institut des Hautes Etudes Scientifiques-Centre National de la Recherche Scientifique, 35 route de Chartres, 91440 Bures sur Yvette, France
| | - Faezeh Forouzanfar
- University of Strasbourg, EA7292, DHPI, Institut of Parasitology and tropical pathology Strasbourg, France
| | - Sebastian Eilebrecht
- Institut Universitaire de France, Paris, France.,Université Libre de Bruxelles (ULB), Service of Molecular Virology, Institute for Molecular Biology and Medicine (IBMM), 12 rue des Profs Jeener et Brachet, 6041 Gosselies, Belgium
| | - Benoit Van Driessche
- Deutsches Krebsforschungszentrum, Im Neuenheimer Feld 242, Heidelberg 69120, Germany
| | - Amina Ait-Ammar
- University of Strasbourg, EA7292, DHPI, Institut of Parasitology and tropical pathology Strasbourg, France
| | - Roxane Verdikt
- Deutsches Krebsforschungszentrum, Im Neuenheimer Feld 242, Heidelberg 69120, Germany
| | - Yoshihito Kurashige
- CNRS UMR 7224, Université Pierre et Marie Curie, 7 quai Saint Bernard, 75005 Paris, France
| | - Céline Marban
- CNRS UMR 7224, Université Pierre et Marie Curie, 7 quai Saint Bernard, 75005 Paris, France
| | - Virginie Gautier
- Institut des Hautes Etudes Scientifiques-Centre National de la Recherche Scientifique, 35 route de Chartres, 91440 Bures sur Yvette, France
| | - Ermanno Candolfi
- University of Strasbourg, EA7292, DHPI, Institut of Parasitology and tropical pathology Strasbourg, France
| | - Arndt G Benecke
- Université Libre de Bruxelles (ULB), Service of Molecular Virology, Institute for Molecular Biology and Medicine (IBMM), 12 rue des Profs Jeener et Brachet, 6041 Gosselies, Belgium.,UCD Centre for Research in Infectious Diseases (CRID) School of Medicine and Medical Science University College Dublin, Ireland
| | - Carine Van Lint
- Deutsches Krebsforschungszentrum, Im Neuenheimer Feld 242, Heidelberg 69120, Germany
| | - Olivier Rohr
- University of Strasbourg, EA7292, DHPI, Institut of Parasitology and tropical pathology Strasbourg, France.,University of Strasbourg, IUT Louis Pasteur, Schiltigheim, France.,Inserm UMR 1121 Faculté de Chirurgie Dentaire Pavillon Leriche 1, place de l'Hôpital Strasbourg, France
| | - Christian Schwartz
- University of Strasbourg, EA7292, DHPI, Institut of Parasitology and tropical pathology Strasbourg, France.,University of Strasbourg, IUT Louis Pasteur, Schiltigheim, France
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6
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Kamtchueng C, Stébenne MÉ, Delannoy A, Wilhelm E, Léger H, Benecke AG, Bell B. Alternative splicing of TAF6: downstream transcriptome impacts and upstream RNA splice control elements. PLoS One 2014; 9:e102399. [PMID: 25025302 PMCID: PMC4099370 DOI: 10.1371/journal.pone.0102399] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2013] [Accepted: 06/19/2014] [Indexed: 01/07/2023] Open
Abstract
The TAF6δ pathway of apoptosis can dictate life versus death decisions independently of the status of p53 tumor suppressor. TAF6δ is an inducible pro-apoptotic subunit of the general RNA polymerase II (Pol II) transcription factor TFIID. Alternative splice site choice of TAF6δ has been shown to be a pivotal event in triggering death via the TAF6δ pathway, yet nothing is currently known about the mechanisms that promote TAF6δ splicing. Furthermore the transcriptome impact of the gain of function of TAF6δ versus the loss of function of the major TAF6α splice form remains undefined. Here we employ comparative microarray analysis to show that TAF6δ drives a transcriptome profile distinct from that resulting from depletion of TAF6α. To define the cis-acting RNA elements responsible for TAF6δ alternative splicing we performed a mutational analysis of a TAF6 minigene system. The data point to several new RNA elements that can modulate TAF6δ and also reveal a role for RNA secondary structure in the selection of TAF6δ.
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Affiliation(s)
- Catherine Kamtchueng
- RNA Group, Département de microbiologie et d'infectiologie, Faculté de médecine et sciences de la santé, Université de Sherbrooke, and Centre de recherche du CHUS, Pavillon de recherche appliquée sur le cancer, 3201 rue Jean-Migneault, Sherbrooke, Québec, Canada
| | - Marie-Éve Stébenne
- RNA Group, Département de microbiologie et d'infectiologie, Faculté de médecine et sciences de la santé, Université de Sherbrooke, and Centre de recherche du CHUS, Pavillon de recherche appliquée sur le cancer, 3201 rue Jean-Migneault, Sherbrooke, Québec, Canada
| | - Aurélie Delannoy
- RNA Group, Département de microbiologie et d'infectiologie, Faculté de médecine et sciences de la santé, Université de Sherbrooke, and Centre de recherche du CHUS, Pavillon de recherche appliquée sur le cancer, 3201 rue Jean-Migneault, Sherbrooke, Québec, Canada
| | - Emmanuelle Wilhelm
- RNA Group, Département de microbiologie et d'infectiologie, Faculté de médecine et sciences de la santé, Université de Sherbrooke, and Centre de recherche du CHUS, Pavillon de recherche appliquée sur le cancer, 3201 rue Jean-Migneault, Sherbrooke, Québec, Canada
| | - Hélène Léger
- Institut des Hautes Etudes Scientifiques, Centre National de la Recherche Scientifique, 35 route de Chartres, Bures sur Yvette, France
| | - Arndt G. Benecke
- Institut des Hautes Etudes Scientifiques, Centre National de la Recherche Scientifique, 35 route de Chartres, Bures sur Yvette, France
- Université Pierre et Marie Curie, UMR8246 CNRS, 7 quai Saint Bernard, Paris, France
| | - Brendan Bell
- RNA Group, Département de microbiologie et d'infectiologie, Faculté de médecine et sciences de la santé, Université de Sherbrooke, and Centre de recherche du CHUS, Pavillon de recherche appliquée sur le cancer, 3201 rue Jean-Migneault, Sherbrooke, Québec, Canada
- * E-mail:
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7
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Airway structural cells regulate TLR5-mediated mucosal adjuvant activity. Mucosal Immunol 2014; 7:489-500. [PMID: 24064672 DOI: 10.1038/mi.2013.66] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2013] [Revised: 07/16/2013] [Accepted: 08/13/2013] [Indexed: 02/04/2023]
Abstract
Antigen-presenting cell (APC) activation is enhanced by vaccine adjuvants. Most vaccines are based on the assumption that adjuvant activity of Toll-like receptor (TLR) agonists depends on direct, functional activation of APCs. Here, we sought to establish whether TLR stimulation in non-hematopoietic cells contributes to flagellin's mucosal adjuvant activity. Nasal administration of flagellin enhanced T-cell-mediated immunity, and systemic and secretory antibody responses to coadministered antigens in a TLR5-dependent manner. Mucosal adjuvant activity was not affected by either abrogation of TLR5 signaling in hematopoietic cells or the presence of flagellin-specific, circulating neutralizing antibodies. We found that flagellin is rapidly degraded in conducting airways, does not translocate into lung parenchyma and stimulates an early immune response, suggesting that TLR5 signaling is regionalized. The flagellin-specific early response of lung was regulated by radioresistant cells expressing TLR5 (particularly the airway epithelial cells). Flagellin stimulated the epithelial production of a small set of mediators that included the chemokine CCL20, which is known to promote APC recruitment in mucosal tissues. Our data suggest that (i) the adjuvant activity of TLR agonists in mucosal vaccination may require TLR stimulation of structural cells and (ii) harnessing the effect of adjuvants on epithelial cells can improve mucosal vaccines.
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8
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Eilebrecht S, Le Douce V, Riclet R, Targat B, Hallay H, Van Driessche B, Schwartz C, Robette G, Van Lint C, Rohr O, Benecke AG. HMGA1 recruits CTIP2-repressed P-TEFb to the HIV-1 and cellular target promoters. Nucleic Acids Res 2014; 42:4962-71. [PMID: 24623795 PMCID: PMC4005653 DOI: 10.1093/nar/gku168] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Active positive transcription elongation factor b (P-TEFb) is essential for cellular and human immunodeficiency virus type 1 (HIV-1) transcription elongation. CTIP2 represses P-TEFb activity in a complex containing 7SK RNA and HEXIM1. Recently, the inactive 7SK/P-TEFb small nuclear RNP (snRNP) has been detected at the HIV-1 core promoter as well as at the promoters of cellular genes, but a recruiting mechanism still remains unknown to date. Here we show global synergy between CTIP2 and the 7SK-binding chromatin master-regulator HMGA1 in terms of P-TEFb–dependent endogenous and HIV-1 gene expression regulation. While CTIP2 and HMGA1 concordingly repress the expression of cellular 7SK-dependent P-TEFb targets, the simultaneous knock-down of CTIP2 and HMGA1 also results in a boost in Tat-dependent and independent HIV-1 promoter activity. Chromatin immunoprecipitation experiments reveal a significant loss of CTIP2/7SK/P-TEFb snRNP recruitment to cellular gene promoters and the HIV-1 promoter on HMGA1 knock-down. Our findings not only provide insights into a recruiting mechanism for the inactive 7SK/P-TEFb snRNP, but may also contribute to a better understanding of viral latency.
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Affiliation(s)
- Sebastian Eilebrecht
- Vaccine Research Institute, INSERM U955, Institut Mondor de Recherche Biomédicale, 8 rue du général Sarrail, 94011 Créteil, France, Institut des Hautes Études Scientifiques-Centre National de la Recherche Scientifique, 35 route de Chartres, 91440 Bures sur Yvette, France, Institut de Parasitologie et de Pathologie Tropicale, Fédération de Médecine Translationnelle, University of Strasbourg, 3 rue Koeberlé, 67000 Strasbourg, France, IUT Louis Pasteur, 1 Allée d'Athénes, 67300 Schiltigheim, France, Université Libre de Bruxelles (ULB), Service of Molecular Virology, Institute for Molecular Biology and Medicine (IBMM), 12 rue des Profs Jeener et Brachet, 6041 Gosselies, Belgium, Institut Universitaire de France-IUF, Paris, France and CNRS UMR 7224, Université Pierre et Marie Curie, 7 quai Saint Bernard, 75005 Paris, France
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9
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Léger H, Smet-Nocca C, Attmane-Elakeb A, Morley-Fletcher S, Benecke AG, Eilebrecht S. A TDG/CBP/RARα ternary complex mediates the retinoic acid-dependent expression of DNA methylation-sensitive genes. GENOMICS PROTEOMICS & BIOINFORMATICS 2014; 12:8-18. [PMID: 24394593 PMCID: PMC4411359 DOI: 10.1016/j.gpb.2013.11.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/12/2013] [Revised: 11/27/2013] [Accepted: 11/28/2013] [Indexed: 11/28/2022]
Abstract
The thymine DNA glycosylase (TDG) is a multifunctional enzyme, which is essential for embryonic development. It mediates the base excision repair (BER) of G:T and G:U DNA mismatches arising from the deamination of 5-methyl cytosine (5-MeC) and cytosine, respectively. Recent studies have pointed at a role of TDG during the active demethylation of 5-MeC within CpG islands. TDG interacts with the histone acetylase CREB-binding protein (CBP) to activate CBP-dependent transcription. In addition, TDG also interacts with the retinoic acid receptor α (RARα), resulting in the activation of RARα target genes. Here we provide evidence for the existence of a functional ternary complex containing TDG, CBP and activated RARα. Using global transcriptome profiling, we uncover a coupling of de novo methylation-sensitive and RA-dependent transcription, which coincides with a significant subset of CBP target genes. The introduction of a point mutation in TDG, which neither affects overall protein structure nor BER activity, leads to a significant loss in ternary complex stability, resulting in the deregulation of RA targets involved in cellular networks associated with DNA replication, recombination and repair. We thus demonstrate for the first time a direct coupling of TDG’s epigenomic and transcription regulatory function through ternary complexes with CBP and RARα.
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Affiliation(s)
- Hélène Léger
- Vaccine Research Institute, INSERM U955, Institut Mondor de Recherche Biomédicale, 94011 Créteil, France; Institut des Hautes Études Scientifiques, 91440 Bures sur Yvette, France
| | - Caroline Smet-Nocca
- Unité de Glycobiologie Structurale et Fonctionnelle - CNRS UMR 8576, Group of NMR and Structural Biology, Université Lille 1, 59655 Villeneuve d'Ascq, France
| | | | - Sara Morley-Fletcher
- Unité de Glycobiologie Structurale et Fonctionnelle - CNRS UMR 8576, Neuroplasticity Team, Université Lille 1, 59655 Villeneuve d'Ascq, France
| | - Arndt G Benecke
- Institut des Hautes Études Scientifiques, 91440 Bures sur Yvette, France; CNRS UMR 7224, Université Pierre et Marie Curie, 75005 Paris, France.
| | - Sebastian Eilebrecht
- Vaccine Research Institute, INSERM U955, Institut Mondor de Recherche Biomédicale, 94011 Créteil, France; Institut des Hautes Études Scientifiques, 91440 Bures sur Yvette, France
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10
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Moreno G, Errea A, Van Maele L, Roberts R, Léger H, Sirard JC, Benecke A, Rumbo M, Hozbor D. Toll-like receptor 4 orchestrates neutrophil recruitment into airways during the first hours of Bordetella pertussis infection. Microbes Infect 2013; 15:708-18. [DOI: 10.1016/j.micinf.2013.06.010] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2013] [Revised: 06/19/2013] [Accepted: 06/19/2013] [Indexed: 01/16/2023]
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11
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Cherrier T, Le Douce V, Eilebrecht S, Riclet R, Marban C, Dequiedt F, Goumon Y, Paillart JC, Mericskay M, Parlakian A, Bausero P, Abbas W, Herbein G, Kurdistani SK, Grana X, Van Driessche B, Schwartz C, Candolfi E, Benecke AG, Van Lint C, Rohr O. CTIP2 is a negative regulator of P-TEFb. Proc Natl Acad Sci U S A 2013; 110:12655-60. [PMID: 23852730 PMCID: PMC3732990 DOI: 10.1073/pnas.1220136110] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The positive transcription elongation factor b (P-TEFb) is involved in physiological and pathological events including inflammation, cancer, AIDS, and cardiac hypertrophy. The balance between its active and inactive form is tightly controlled to ensure cellular integrity. We report that the transcriptional repressor CTIP2 is a major modulator of P-TEFb activity. CTIP2 copurifies and interacts with an inactive P-TEFb complex containing the 7SK snRNA and HEXIM1. CTIP2 associates directly with HEXIM1 and, via the loop 2 of the 7SK snRNA, with P-TEFb. In this nucleoprotein complex, CTIP2 significantly represses the Cdk9 kinase activity of P-TEFb. Accordingly, we show that CTIP2 inhibits large sets of P-TEFb- and 7SK snRNA-sensitive genes. In hearts of hypertrophic cardiomyopathic mice, CTIP2 controls P-TEFb-sensitive pathways involved in the establishment of this pathology. Overexpression of the β-myosin heavy chain protein contributes to the pathological cardiac wall thickening. The inactive P-TEFb complex associates with CTIP2 at the MYH7 gene promoter to repress its activity. Taken together, our results strongly suggest that CTIP2 controls P-TEFb function in physiological and pathological conditions.
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Affiliation(s)
- Thomas Cherrier
- Institut de Parasitologie et de Pathologie Tropicale, Fédération de Médecine Translationnelle, University of Strasbourg, 67000 Strasbourg, France
- Laboratory of Protein Signaling and Interactions, University of Liège, Liège, Belgium
| | - Valentin Le Douce
- Institut de Parasitologie et de Pathologie Tropicale, Fédération de Médecine Translationnelle, University of Strasbourg, 67000 Strasbourg, France
| | - Sebastian Eilebrecht
- Vaccine Research Institute, Institut National de la Santé et de la Recherche Médicale, Unité 955, 94010 Créteil, France
- Institut des Hautes Études Scientifiques, Centre National de la Recherche Scientifique, 91440 Bures sur Yvette, France
| | - Raphael Riclet
- Institut de Parasitologie et de Pathologie Tropicale, Fédération de Médecine Translationnelle, University of Strasbourg, 67000 Strasbourg, France
| | - Céline Marban
- Institut de Parasitologie et de Pathologie Tropicale, Fédération de Médecine Translationnelle, University of Strasbourg, 67000 Strasbourg, France
- Department of Biological Chemistry, University of California, Los Angeles, CA 92093
| | - Franck Dequiedt
- Laboratory of Protein Signaling and Interactions, University of Liège, Liège, Belgium
| | - Yannick Goumon
- Institut des Neurosciences Cellulaires et Intégratives, University of Strasbourg, Centre National de la Recherche Scientifique, 67000 Strasbourg, France
| | - Jean-Christophe Paillart
- Architecture et Réactivité de l'ARN, Centre National de la Recherche Scientifique Unité Propre de Recherche 9002, Institut de Biologie Moléculaire et Cellulaire, Université de Strasbourg, 67000 Strasbourg, France
| | - Mathias Mericskay
- Unité de Recherche 4, Aging, Stress, Inflammation Department, Université Pierre et Marie Curie Université Paris 6, 75005 Paris, France
| | - Ara Parlakian
- Unité de Recherche 4, Aging, Stress, Inflammation Department, Université Pierre et Marie Curie Université Paris 6, 75005 Paris, France
| | - Pedro Bausero
- Unité de Recherche 4, Aging, Stress, Inflammation Department, Université Pierre et Marie Curie Université Paris 6, 75005 Paris, France
| | - Wasim Abbas
- Department of Virology, Institut Fédératif de Recherche 133, Institut National de la Santé et de la Recherche Médicale, University of Franche-Comté, 25000 Besançon, France
| | - Georges Herbein
- Department of Virology, Institut Fédératif de Recherche 133, Institut National de la Santé et de la Recherche Médicale, University of Franche-Comté, 25000 Besançon, France
| | | | - Xavier Grana
- Fels Institute for Cancer Research and Molecular Biology and Department of Biochemistry, Temple University School of Medicine, Philadelphia, PA 19140
| | - Benoit Van Driessche
- Institut de Biologie et de Médecine Moléculaires, Université Libre de Bruxelles, 6041 Gosselies, Belgium; and
| | - Christian Schwartz
- Institut de Parasitologie et de Pathologie Tropicale, Fédération de Médecine Translationnelle, University of Strasbourg, 67000 Strasbourg, France
| | - Ermanno Candolfi
- Institut de Parasitologie et de Pathologie Tropicale, Fédération de Médecine Translationnelle, University of Strasbourg, 67000 Strasbourg, France
| | - Arndt G. Benecke
- Vaccine Research Institute, Institut National de la Santé et de la Recherche Médicale, Unité 955, 94010 Créteil, France
- Institut des Hautes Études Scientifiques, Centre National de la Recherche Scientifique, 91440 Bures sur Yvette, France
| | - Carine Van Lint
- Institut de Biologie et de Médecine Moléculaires, Université Libre de Bruxelles, 6041 Gosselies, Belgium; and
| | - Olivier Rohr
- Institut de Parasitologie et de Pathologie Tropicale, Fédération de Médecine Translationnelle, University of Strasbourg, 67000 Strasbourg, France
- Institut Universitaire de France, 75005 Paris, France
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CDS: a fold-change based statistical test for concomitant identification of distinctness and similarity in gene expression analysis. GENOMICS PROTEOMICS & BIOINFORMATICS 2012; 10:127-35. [PMID: 22917185 PMCID: PMC5054499 DOI: 10.1016/j.gpb.2012.06.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/09/2012] [Revised: 06/08/2012] [Accepted: 06/10/2012] [Indexed: 11/23/2022]
Abstract
The problem of identifying differential activity such as in gene expression is a major defeat in biostatistics and bioinformatics. Equally important, however much less frequently studied, is the question of similar activity from one biological condition to another. The fold-change, or ratio, is usually considered a relevant criterion for stating difference and similarity between measurements. Importantly, no statistical method for concomitant evaluation of similarity and distinctness currently exists for biological applications. Modern microarray, digital PCR (dPCR), and Next-Generation Sequencing (NGS) technologies frequently provide a means of coefficient of variation estimation for individual measurements. Using fold-change, and by making the assumption that measurements are normally distributed with known variances, we designed a novel statistical test that allows us to detect concomitantly, thus using the same formalism, differentially and similarly expressed genes (http://cds.ihes.fr). Given two sets of gene measurements in different biological conditions, the probabilities of making type I and type II errors in stating that a gene is differentially or similarly expressed from one condition to the other can be calculated. Furthermore, a confidence interval for the fold-change can be delineated. Finally, we demonstrate that the assumption of normality can be relaxed to consider arbitrary distributions numerically. The Concomitant evaluation of Distinctness and Similarity (CDS) statistical test correctly estimates similarities and differences between measurements of gene expression. The implementation, being time and memory efficient, allows the use of the CDS test in high-throughput data analysis such as microarray, dPCR, and NGS experiments. Importantly, the CDS test can be applied to the comparison of single measurements (N = 1) provided the variance (or coefficient of variation) of the signals is known, making CDS a valuable tool also in biomedical analysis where typically a single measurement per subject is available.
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13
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Sonnenschein N, Golib Dzib JF, Lesne A, Eilebrecht S, Boulkroun S, Zennaro MC, Benecke A, Hütt MT. A network perspective on metabolic inconsistency. BMC SYSTEMS BIOLOGY 2012; 6:41. [PMID: 22583819 PMCID: PMC3579709 DOI: 10.1186/1752-0509-6-41] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2011] [Accepted: 04/14/2012] [Indexed: 11/10/2022]
Abstract
BACKGROUND Integrating gene expression profiles and metabolic pathways under different experimental conditions is essential for understanding the coherence of these two layers of cellular organization. The network character of metabolic systems can be instrumental in developing concepts of agreement between expression data and pathways. A network-driven interpretation of gene expression data has the potential of suggesting novel classifiers for pathological cellular states and of contributing to a general theoretical understanding of gene regulation. RESULTS Here, we analyze the coherence of gene expression patterns and a reconstruction of human metabolism, using consistency scores obtained from network and constraint-based analysis methods. We find a surprisingly strong correlation between the two measures, demonstrating that a substantial part of inconsistencies between metabolic processes and gene expression can be understood from a network perspective alone. Prompted by this finding, we investigate the topological context of the individual biochemical reactions responsible for the observed inconsistencies. On this basis, we are able to separate the differential contributions that bear physiological information about the system, from the unspecific contributions that unravel gaps in the metabolic reconstruction. We demonstrate the biological potential of our network-driven approach by analyzing transcriptome profiles of aldosterone producing adenomas that have been obtained from a cohort of Primary Aldosteronism patients. We unravel systematics in the data that could not have been resolved by conventional microarray data analysis. In particular, we discover two distinct metabolic states in the adenoma expression patterns. CONCLUSIONS The methodology presented here can help understand metabolic inconsistencies from a network perspective. It thus serves as a mediator between the topology of metabolic systems and their dynamical function. Finally, we demonstrate how physiologically relevant insights into the structure and dynamics of metabolic networks can be obtained using this novel approach.
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Affiliation(s)
- Nikolaus Sonnenschein
- School of Engineering and Science, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany.
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14
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Bécavin C, Tchitchek N, Mintsa-Eya C, Lesne A, Benecke A. Improving the efficiency of multidimensional scaling in the analysis of high-dimensional data using singular value decomposition. Bioinformatics 2011; 27:1413-21. [PMID: 21421551 DOI: 10.1093/bioinformatics/btr143] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
MOTIVATION Multidimensional scaling (MDS) is a well-known multivariate statistical analysis method used for dimensionality reduction and visualization of similarities and dissimilarities in multidimensional data. The advantage of MDS with respect to singular value decomposition (SVD) based methods such as principal component analysis is its superior fidelity in representing the distance between different instances specially for high-dimensional geometric objects. Here, we investigate the importance of the choice of initial conditions for MDS, and show that SVD is the best choice to initiate MDS. Furthermore, we demonstrate that the use of the first principal components of SVD to initiate the MDS algorithm is more efficient than an iteration through all the principal components. Adding stochasticity to the molecular dynamics simulations typically used for MDS of large datasets, contrary to previous suggestions, likewise does not increase accuracy. Finally, we introduce a k nearest neighbor method to analyze the local structure of the geometric objects and use it to control the quality of the dimensionality reduction. RESULTS We demonstrate here the, to our knowledge, most efficient and accurate initialization strategy for MDS algorithms, reducing considerably computational load. SVD-based initialization renders MDS methodology much more useful in the analysis of high-dimensional data such as functional genomics datasets.
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Eilebrecht S, Brysbaert G, Wegert T, Urlaub H, Benecke BJ, Benecke A. 7SK small nuclear RNA directly affects HMGA1 function in transcription regulation. Nucleic Acids Res 2010; 39:2057-72. [PMID: 21087998 PMCID: PMC3064786 DOI: 10.1093/nar/gkq1153] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Non-coding (nc) RNAs are increasingly recognized to play important regulatory roles in eukaryotic gene expression. The highly abundant and essential 7SK ncRNA has been shown to negatively regulate RNA Polymerase II transcription by inactivating the positive transcription elongation factor b (P-TEFb) in cellular and Tat-dependent HIV transcription. Here, we identify a more general, P-TEFb-independent role of 7SK RNA in directly affecting the function of the architectural transcription factor and chromatin regulator HMGA1. An important regulatory role of 7SK RNA in HMGA1-dependent cell differentiation and proliferation regulation is uncovered with the identification of over 1500 7SK-responsive HMGA1 target genes. Elevated HMGA1 expression is observed in nearly every type of cancer making the use of a 7SK substructure in the inhibition of HMGA1 activity, as pioneered here, potentially useful in therapy. The 7SK-HMGA1 interaction not only adds an essential facet to the comprehension of transcriptional plasticity at the coupling of initiation and elongation, but also might provide a molecular link between HIV reprogramming of cellular gene expression-associated oncogenesis.
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Affiliation(s)
- Sebastian Eilebrecht
- Institut des Hautes Études Scientifiques & Centre National de la Recherche Scientifique USR3078, 35 route de Chartres, 91440 Bures sur Yvette, France
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16
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Brysbaert G, Pellay FX, Noth S, Benecke A. Quality assessment of transcriptome data using intrinsic statistical properties. GENOMICS PROTEOMICS & BIOINFORMATICS 2010; 8:57-71. [PMID: 20451162 PMCID: PMC5054119 DOI: 10.1016/s1672-0229(10)60006-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
In view of potential application to biomedical diagnosis, tight transcriptome data quality control is compulsory. Usually, quality control is achieved using labeling and hybridization controls added at different stages throughout the processing of the biologic RNA samples. These control measures, however, only reflect the performance of the individual technical manipulations during the entire process and have no bearing as to the continued integrity of the RNA sample itself. Here we demonstrate that intrinsic statistical properties of the resulting transcriptome data signal and signal-variance distributions and their invariance can be identified independently of the animal species studied and the labeling protocol used. From these invariant properties we have developed a data model, the parameters of which can be estimated from individual experiments and used to compute relative quality measures based on similarity with large reference datasets. These quality measures add supplementary, non-redundant information to standard quality control estimates based on spike-in and hybridization controls, and are exploitable in data analysis. A software application for analyzing datasets as well as a reference dataset for AB1700 arrays are provided. They should allow AB1700 users to easily integrate this method into their analysis pipeline, and might instigate similar developments for other transcriptome platforms.
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Affiliation(s)
- Guillaume Brysbaert
- Institut des Hautes Etudes Scientifiques & Institut de Recherche Interdisciplinaire (CNRS USR3078, Université de Lille1), 91440 Bures-sur-Yvette, France
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17
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Hydroxycarbamide stimulates the production of proinflammatory cytokines by endothelial cells: relevance to sickle cell disease. Pharmacogenet Genomics 2010; 20:257-68. [PMID: 20216336 DOI: 10.1097/fpc.0b013e32833854d6] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
BACKGROUND AND OBJECTIVE The clinical hallmarks of sickle cell disease (SCD) are vaso-occlusive crises (VOC) triggered by red blood cells (RBC) stiffening and abnormal adhesion to vascular endothelial cells (VEC) in the context of chronic inflammation, cell activation, and vascular tone abnormalities. Hydroxycarbamide (HC) is the only drug with a proven efficacy in decreasing VOC frequency. HC decreases RBC stiffening, modulates adhesion protein expression by RBC and VEC, and reduces endothelin-1 production by VEC. Our objective was to test whether HC could also affect inflammation through its action on VEC. METHODS We used microarrays to study the effect of HC on the transcriptome of transformed human bone marrow endothelial cell, a cell line derived from bone marrow microcirculation (the predilection site of VOC), in basal and proinflammatory conditions. Microarray results were confirmed by real-time quantitative PCR and protein analysis on transformed human bone marrow endothelial cell (TrHBMEC) and on two other VEC types in the primary culture: human pulmonary microcirculation endothelial cell (HPMEC) and human umbilical vein endothelial cell (HUVEC a classical model for the macrocirculation). RESULTS HC had a significant effect on the expression of genes of the 'inflammation pathway'. Strikingly, it stimulates the expression of proinflammatory genes such as IL1A, IL1B, IL6, IL8, CCL2, CCL5, CCL20, and CCL8 in all the tested VEC types. CONCLUSION Our study confirms that VECs are significant targets of HC in the context of SCD and identifies its earlier unsuspected action on another major component of SCD pathophysiology, that is, the 'inflammation pathway'.
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18
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Jacquelin B, Mayau V, Targat B, Liovat AS, Kunkel D, Petitjean G, Dillies MA, Roques P, Butor C, Silvestri G, Giavedoni LD, Lebon P, Barré-Sinoussi F, Benecke A, Müller-Trutwin MC. Nonpathogenic SIV infection of African green monkeys induces a strong but rapidly controlled type I IFN response. J Clin Invest 2010; 119:3544-55. [PMID: 19959873 DOI: 10.1172/jci40093] [Citation(s) in RCA: 293] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2009] [Accepted: 10/19/2009] [Indexed: 01/12/2023] Open
Abstract
African green monkeys (AGMs) infected with the AGM type of SIV (SIVagm) do not develop chronic immune activation and AIDS, despite viral loads similar to those detected in humans infected with HIV-1 and rhesus macaques (RMs) infected with the RM type of SIV (SIVmac). Because chronic immune activation drives progressive CD4+ T cell depletion and immune cell dysfunctions, factors that characterize disease progression, we sought to understand the molecular basis of this AGM phenotype. To this end, we longitudinally assessed the gene expression profiles of blood- and lymph node-derived CD4+ cells from AGMs and RMs in response to SIVagm and SIVmac infection, respectively, using a genomic microarray platform. The molecular signature of acute infection was characterized, in both species, by strong upregulation of type I IFN-stimulated genes (ISGs). ISG expression returned to basal levels after postinfection day 28 in AGMs but was sustained in RMs, especially in the lymph node-derived cells. We also found that SIVagm induced IFN-alpha production by AGM cells in vitro and that low IFN-alpha levels were sufficient to induce strong ISG responses. In conclusion, SIV infection triggered a rapid and strong IFN-alpha response in vivo in both AGMs and RMs, with this response being efficiently controlled only in AGMs, possibly as a result of active regulatory mechanisms.
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Affiliation(s)
- Béatrice Jacquelin
- Institut Pasteur, Unité de Régulation des Infections Rétrovirales, Paris, France
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Eilebrecht S, Pellay FX, Odenwälder P, Brysbaert G, Benecke BJ, Benecke A. EBER2 RNA-induced transcriptome changes identify cellular processes likely targeted during Epstein Barr Virus infection. BMC Res Notes 2008; 1:100. [PMID: 18957101 PMCID: PMC2588618 DOI: 10.1186/1756-0500-1-100] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2008] [Accepted: 10/28/2008] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Little is known about the physiological role of the EBER1 and 2 nuclear RNAs during Epstein Barr viral infection. The EBERs are transcribed by cellular RNA Polymerase III and their strong expression results in 106 to 107 copies per EBV infected cell, making them reliable diagnostic markers for the presence of EBV. Although the functions of most of the proteins targeted by EBER RNAs have been studied, the role of EBERs themselves still remains elusive. FINDINGS The cellular transcription response to EBER2 expression using the wild-type and an internal deletion mutant was determined. Significant changes in gene expression patterns were observed. A functional meta-analysis of the regulated genes points to inhibition of stress and immune responses, as well as activation of cellular growth and cytoskeletal reorganization as potential targets for EBER2 RNA. Different functions can be assigned to different parts of the RNA. CONCLUSION These results provide new avenues to the understanding of EBER2 and EBV biology, and set the grounds for a more in depth functional analysis of EBER2 using transcriptome activity measurements.
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Affiliation(s)
- Sebastian Eilebrecht
- Department of Biochemistry; Ruhr University Bochum; Universitätsstr, 150; 44780 Bochum, Germany.
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20
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Wilhelm E, Pellay FX, Benecke A, Bell B. Determining the impact of alternative splicing events on transcriptome dynamics. BMC Res Notes 2008; 1:94. [PMID: 18950505 PMCID: PMC2584107 DOI: 10.1186/1756-0500-1-94] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2008] [Accepted: 10/24/2008] [Indexed: 11/10/2022] Open
Abstract
Background The complete sequencing of the human genome and its subsequent analysis revealed a predominant role for alternative splicing in the generation of proteome diversity. Splice switching oligonucleotides (SSOs) are a powerful and specific tool to experimentally control alternative splicing of endogenous messenger RNAs in living cells. SSOs also have therapeutic potential to treat diseases that are caused by aberrant splicing. The assignment of biological roles to alternative splicing events of currently unknown function promises to provide a largely untapped source of potential new therapeutic targets. Here we have developed a protocol that combines high sensitivity microarrays with the transfection of SSOs to monitor global changes in gene expression downstream of alternate, endogenous splice events. Results When applied to a well-characterized splicing event in the Bcl-x gene, the application of high sensitivity microarrays revealed a link between the induction of the Bcl-xS isoform and the repression of genes involved in protein synthesis. Conclusion The strategy introduced herein provides a useful approach to define the biological impact of any given alternative splicing event on global gene expression patterns. Furthermore, our data provide the first link between Bcl-xS expression and the repression of ribosomal protein gene expression.
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Affiliation(s)
- Emmanuelle Wilhelm
- RNA Group, Département de microbiologie et d'infectiologie, Faculté de médecine et sciences de la santé, Université de Sherbrooke, 3001 12e ave Nord, Sherbrooke, Québec J1H 5N4, Canada.
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21
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Firlej V, Ladam F, Brysbaert G, Dumont P, Fuks F, de Launoit Y, Benecke A, Chotteau-Lelievre A. Reduced tumorigenesis in mouse mammary cancer cells following inhibition of Pea3- or Erm-dependent transcription. J Cell Sci 2008; 121:3393-402. [PMID: 18827017 DOI: 10.1242/jcs.027201] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Pea3 and Erm are transcription factors expressed in normal developing branching organs such as the mammary gland. Deregulation of their expression is generally associated with tumorigenesis and particularly breast cancer. By using RNA interference (RNAi) to downregulate the expression of Pea3 and/or Erm in a mammary cancer cell line, we present evidence for a role of these factors in proliferation, migration and invasion capacity of cancer cells. We have used different small interfering RNAs (siRNAs) targeting pea3 and erm transcripts in transiently or stably transfected cells, and assessed the physiological behavior of these cells in in vitro assays. We also identified an in vivo alteration of tumor progression after injection of cells that overexpress pea3 and/or erm short hairpin RNAs (shRNAs) in immunodeficient mice. Using transcriptome profiling in Pea3- or Erm-targeted cells, two largely independent gene expression programs were identified on the basis of their shared phenotypic modifications. A statistically highly significant part of both sets of target genes had previously been already associated with the cellular signaling pathways of the ;proliferation, migration, invasion' class. These data provide the first evidence, by using endogenous knockdown, for pivotal and complementary roles of Pea3 and Erm transcription factors in events crucial to mammary tumorigenesis, and identify sets of downstream target genes whose expression during tumorigenesis is regulated by these transcription factors.
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Affiliation(s)
- Virginie Firlej
- UMR 8161, Institut de Biologie de Lille, CNRS Universités de Lille 1 and 2, Institut Pasteur de Lille, IFR 142, BP 447, 1 rue Calmette, 59021 Lille Cedex, France
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Wilhelm E, Pellay FX, Benecke A, Bell B. TAF6delta controls apoptosis and gene expression in the absence of p53. PLoS One 2008; 3:e2721. [PMID: 18628956 PMCID: PMC2444026 DOI: 10.1371/journal.pone.0002721] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2008] [Accepted: 06/18/2008] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Life and death decisions of metazoan cells hinge on the balance between the expression of pro- versus anti-apoptotic gene products. The general RNA polymerase II transcription factor, TFIID, plays a central role in the regulation of gene expression through its core promoter recognition and co-activator functions. The core TFIID subunit TAF6 acts in vitro as an essential co-activator of transcription for the p53 tumor suppressor protein. We previously identified a splice variant of TAF6, termed TAF6delta that can be induced during apoptosis. METHODOLOGY/PRINCIPAL FINDINGS To elucidate the impact of TAF6delta on cell death and gene expression, we have employed modified antisense oligonucleotides to enforce expression of endogenous TAF6delta. The induction of endogenous TAF6delta triggered apoptosis in tumor cell lines, including cells devoid of p53. Microarray experiments revealed that TAF6delta activates gene expression independently of cellular p53 status. CONCLUSIONS Our data define TAF6delta as a pivotal node in a signaling pathway that controls gene expression programs and apoptosis in the absence of p53.
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Affiliation(s)
- Emmanuelle Wilhelm
- RNA Group, Département de microbiologie et d'infectiologie, Faculté de médecine et sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - François-Xavier Pellay
- Institut des Hautes Études Scientifiques and Institut de Recherche Interdisciplinaire – CNRS USR3078 - Université de Lille, Bures sur Yvette, France
| | - Arndt Benecke
- Institut des Hautes Études Scientifiques and Institut de Recherche Interdisciplinaire – CNRS USR3078 - Université de Lille, Bures sur Yvette, France
| | - Brendan Bell
- RNA Group, Département de microbiologie et d'infectiologie, Faculté de médecine et sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec, Canada
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Brysbaert G, Noth S, Benecke A. Generation of synthetic transcriptome data with defined statistical properties for the development and testing of new analysis methods. GENOMICS PROTEOMICS & BIOINFORMATICS 2007; 5:45-52. [PMID: 17572363 PMCID: PMC5054096 DOI: 10.1016/s1672-0229(07)60013-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
We have previously developed a combined signal/variance distribution model that accounts for the particular statistical properties of datasets generated on the Applied Biosystems AB1700 transcriptome system. Here we show that this model can be efficiently used to generate synthetic datasets with statistical properties virtually identical to those of the actual data by aid of the JAVA application ace.map creator 1.0 that we have developed. The fundamentally different structure of AB1700 transcriptome profiles requires re-evaluation, adaptation, or even redevelopment of many of the standard microarray analysis methods in order to avoid misinterpretation of the data on the one hand, and to draw full benefit from their increased specificity and sensitivity on the other hand. Our composite data model and the ace.map creator 1.0 application thereby not only present proof of the correctness of our parameter estimation, but also provide a tool for the generation of synthetic test data that will be useful for further development and testing of analysis methods.
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24
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Jacquelin B, Mayau V, Brysbaert G, Regnault B, Diop OM, Arenzana-Seisdedos F, Rogge L, Coppée JY, Barré-Sinoussi F, Benecke A, Müller-Trutwin MC. Long oligonucleotide microarrays for African green monkey gene expression profile analysis. FASEB J 2007; 21:3262-71. [PMID: 17507667 DOI: 10.1096/fj.07-8271com] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Nonhuman primates, including African green monkey (AGM), are important models for biomedical research. The information on monkey genomes is still limited and no versatile gene expression screening tool is available. We tested human whole genome microarrays for cross-species reactivity with AGM transcripts using both long oligonucleotide arrays (60-mer probes) and short oligonucleotide arrays (25-mer). Using the long oligonucleotide arrays, we detected 4-fold more AGM transcripts than with the short oligonucleotide technology. The number of detected transcripts was comparable to that detected using human RNA, with 87% of the detected genes being shared between both species. The specificity of the signals obtained with the long oligonucleotide arrays was determined by analyzing the transcriptome of concanavalin A-activated CD4+ T cells vs. nonactivated T cells of two monkey species AGM and macaque. For both species, the genes showing the most significant changes in expression, such as IL-2R, were those known to be regulated in human CD4+ T cell activation. Finally, tissue specificity of the signals was established by comparing the transcription profiles of AGM brain and tonsil cells. In conclusion, the ABI human microarray platform provides a highly valuable tool for the assessment of AGM gene expression profiles.
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Affiliation(s)
- Béatrice Jacquelin
- Unité de Régulations des Infections Rétrovirales, Institut Pasteur, 25, rue du Docteur Roux, 75724 Paris cedex 15, France
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