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14 results on '"MESH: Transcription Initiation Site"'

1. Antisense transcriptional interference mediates condition-specific gene repression in budding yeast

Author

Antonia Doyen, Alicia Nevers, Christophe Malabat, Bertrand Néron, Gwenael Badis, Thomas Kergrohen, Alain Jacquier, Génétique des Interactions macromoléculaires, Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris], Université Pierre et Marie Curie - Paris 6 (UPMC), Centre de Bioinformatique, Biostatistique et Biologie Intégrative (C3BI), Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Pasteur Institute, the Centre National de la Recherche Scientifique and the Agence Nationale pour la Recherche [ANR-14-CE-10-0014-01, 2014], A.N. received Fellowships from the French Ministry of Research and from the Fondation pour la Recherche Médicale [FDT20160435375, 2016]. Funding for open access charge: Agence Nationale pour la Recherche [ANR-14-CE-10-0014-01, 2014]., We thank Frank Feuerbach for providing strains LMA2811 and LMA2819. We thank Bernard Turcotte, Cosmin Saveanu and Micheline Fromont-Racine for discussions and critical reading of the manuscript. We acknowledge Jean Yves Coppee and Caroline Proux for the facilities and expertise of the Transcriptomic Platform (PF2) for cDNA libraries sequencing., Génétique des Interactions macromoléculaires / Genetics of Macromolecular Interactions, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Génétique des génomes - Genetics of Genomes (UMR 3525), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), and Institut Pasteur [Paris] (IP)

Subjects
0301 basic medicine, Saccharomyces cerevisiae Proteins, Mutant, MESH: Gene Expression Regulation, Fungal, Saccharomyces cerevisiae, Biology, Transcriptome, 03 medical and health sciences, 0302 clinical medicine, MESH: Saccharomyces cerevisiae/metabolism, Transcription (biology), Gene Expression Regulation, Fungal, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Sense (molecular biology), Gene expression, medicine, Genetics, RNA, Antisense, RNA, Messenger, MESH: RNA Polymerase II/metabolism, Gene, Psychological repression, 030304 developmental biology, Regulation of gene expression, MESH: Saccharomyces cerevisiae/genetics, 0303 health sciences, Messenger RNA, MESH: RNA Helicases/genetics, 030302 biochemistry & molecular biology, Gene regulation, Chromatin and Epigenetics, Promoter, medicine.disease, Chromatin, Cell biology, MESH: RNA, Antisense/biosynthesis, MESH: Saccharomyces cerevisiae Proteins/genetics, 030104 developmental biology, MESH: Gene Deletion, RNA Polymerase II, MESH: Transcription Initiation Site, Transcription Initiation Site, Transcriptional noise, 030217 neurology & neurosurgery, Gene Deletion, RNA Helicases
Abstract

Pervasive transcription generates many unstable non-coding transcripts in budding yeast. The transcription of such noncoding RNAs, in particular antisense RNAs (asRNAs), has been shown in a few examples to repress the expression of the associated mRNAs. Yet, such mechanism is not known to commonly contribute to the regulation of a given class of genes. Using a mutant context that stabilised pervasive transcripts, we observed that the least expressed mRNAs during the exponential phase were associated with high levels of asRNAs. These asRNAs also overlapped their corresponding gene promoters with a much higher frequency than average. Interrupting antisense transcription of a subset of genes corresponding to quiescence-enriched mRNAs restored their expression. The underlying mechanism acts in cis and involves several chromatin modifiers. Our results convey that transcription interference represses up to 30% of the 590 least expressed genes, which includes 163 genes with quiescence-enriched mRNAs. We also found that pervasive transcripts constitute a higher fraction of the transcriptome in quiescence relative to the exponential phase, consistent with gene expression itself playing an important role to suppress pervasive transcription. Accordingly, the HIS1 asRNA, normally only present in quiescence, is expressed in exponential phase upon HIS1 mRNA transcription interruption.

Published
2018
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2. ERK-Induced Activation of TCF Family of SRF Cofactors Initiates a Chromatin Modification Cascade Associated with Transcription

Author

Richard Treisman, Stuart Horswell, Aengus Stewart, Gavin Kelly, Phil East, Francesco Gualdrini, Nik Matthews, Cyril Esnault, Lincoln's Inn Fields Laboratories, and Cancer Research UK

Subjects
0301 basic medicine, MESH: Signal Transduction, Serum Response Factor, Transcription, Genetic, [SDV]Life Sciences [q-bio], Transcription coregulator, MESH: Mice, Knockout, Histones, Mice, Elk-1, Histone methylation, MESH: Early Growth Response Protein 1, Histone code, histone modification, MESH: Animals, Phosphorylation, Extracellular Signal-Regulated MAP Kinases, MESH: Extracellular Signal-Regulated MAP Kinases, Mice, Knockout, MESH: Histones, General transcription factor, biology, Activating transcription factor 2, ternary complex factor, 3. Good health, ERK, MESH: Serum Response Factor, H3 phosphorylation, embryonic structures, Tetradecanoylphorbol Acetate, RNA Interference, SRF, MESH: Transcription Initiation Site, Transcription Initiation Site, TCF Transcription Factors, transcription, Signal Transduction, MESH: Enzyme Activation, MESH: Mutation, MESH: RNA Interference, Transfection, immediate-early genes, Article, Cell Line, MESH: Chromatin, 03 medical and health sciences, Sp3 transcription factor, Animals, MESH: ets-Domain Protein Elk-1, Transcription factor, Molecular Biology, MESH: Mice, MESH: Tetradecanoylphorbol Acetate, Early Growth Response Protein 1, ets-Domain Protein Elk-1, MESH: Phosphorylation, MESH: Transcription, Genetic, MESH: Transfection, Pioneer factor, MESH: Chromatin Assembly and Disassembly, Cell Biology, Chromatin Assembly and Disassembly, Molecular biology, MESH: Cell Line, Enzyme Activation, 030104 developmental biology, Mutation, biology.protein, chromatin, MESH: TCF Transcription Factors
Abstract

Summary We investigated the relationship among ERK signaling, histone modifications, and transcription factor activity, focusing on the ERK-regulated ternary complex factor family of SRF partner proteins. In MEFs, activation of ERK by TPA stimulation induced a common pattern of H3K9acS10ph, H4K16ac, H3K27ac, H3K9acK14ac, and H3K4me3 at hundreds of transcription start site (TSS) regions and remote regulatory sites. The magnitude of the increase in histone modification correlated well with changes in transcription. H3K9acS10ph preceded the other modifications. Most induced changes were TCF dependent, but TCF-independent TSSs exhibited the same hierarchy, indicating that it reflects gene activation per se. Studies with TCF Elk-1 mutants showed that TCF-dependent ERK-induced histone modifications required Elk-1 to be phosphorylated and competent to activate transcription. Analysis of direct TCF-SRF target genes and chromatin modifiers confirmed this and showed that H3S10ph required only Elk-1 phosphorylation. Induction of histone modifications following ERK stimulation is thus directed by transcription factor activation and transcription., Graphical Abstract, Highlights • TPA-driven ERK activation induces a common pattern of histone modifications at TSSs • Most ERK-induced histone modifications are dependent on TCF family of SRF cofactors • At these TSSs, induced histone modifications require ERK-dependent TCF phosphorylation • TCF-dependent histone modifications require TCF to recruit the transcription machinery, In MEFs, TPA-induced ERK activation induces a common pattern of histone modifications at more than 2,000 TSSs. Modifications at most TSSs are dependent on the TCF family of ERK-regulated SRF cofactors. At these TSSs, induced modifications are dependent both on phosphorylation of TCF and on its ability to recruit the transcriptional machinery.

Published
2017
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3. Whole-genome mapping of 5' RNA ends in bacteria by tagged sequencing: a comprehensive view in Enterococcus faecalis

Author

Francis Repoila, Philippe Bouloc, Caroline Lacoux, Erik Aurell, Pascale Serror, Sean Kennedy, Nicolas Innocenti, Françoise Wessner, Aymeric Fouquier d'Hérouël, Rémy A. Bonnin, Monica Golumbeanu, MICrobiologie de l'ALImentation au Service de la Santé (MICALIS), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Royal Inst Technol, Dept Computat Biol, Albanova University Center, Department of Biosystems Science and Engineering [ETH Zürich] (D-BSSE), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology in Zürich [Zürich] (ETH Zürich), Luxembourg Centre for Systems Biomedicine, Institut de génétique et microbiologie [Orsay] (IGM), Université Paris-Sud - Paris 11 (UP11)-Centre National de la Recherche Scientifique (CNRS), INRA US1367 MetaGenoPolis, Signalisation et Réseaux de Régulations Bactériens (SRRB), Département Biologie des Génomes (DBG), Institut de Biologie Intégrative de la Cellule (I2BC), Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut de Biologie Intégrative de la Cellule (I2BC), Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Department of Information and Computer Science, Aalto University, MICrobiologie de l'ALImentation au Service de la Santé humaine ( MICALIS ), Institut National de la Recherche Agronomique ( INRA ) -AgroParisTech, Department of Biosystems Science and Engineering ( ETH-Z ), Swiss Federal Institute of Technology in Zürich ( ETH Zürich ), Institut de génétique et microbiologie [Orsay] ( IGM ), Université Paris-Sud - Paris 11 ( UP11 ) -Centre National de la Recherche Scientifique ( CNRS ), Signalisation et Réseaux de Régulations Bactériens ( SRRB ), Département Biologie des Génomes ( DBG ), Institut de Biologie Intégrative de la Cellule ( I2BC ), Université Paris-Sud - Paris 11 ( UP11 ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ) -Université Paris-Sud - Paris 11 ( UP11 ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ) -Institut de Biologie Intégrative de la Cellule ( I2BC ), Université Paris-Sud - Paris 11 ( UP11 ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ) -Université Paris-Sud - Paris 11 ( UP11 ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ), Royal Institute of Technology [Stockholm] (KTH ), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), Swiss Institute of Bioinformatics [Genève] (SIB), Luxembourg Centre For Systems Biomedicine (LCSB), University of Luxembourg [Luxembourg], MetaGenoPolis, Institut National de la Recherche Agronomique (INRA), This research was supported by the Swedish Science Council through grant 621-2012-2982 (E.A.), and by the Academy of Finland through Finland Distinguished Professor Programme and the Center of Excellence COIN (E.A.), and grant ANR-12-BSV6-0008 (ReadRNA) from the Agence Nationale pour la Recherche., We thank the eBIO computing platform of Orsay, particularly C. Drevet and C. Toffano-Nioche, for hosting the 'ppRNome browser.' We thank Ingemar Ernberg at Karolinska Institutet for his hospitality by providing laboratory space and equipment for A.F.d'H., and V. Cantoni for the suggestion to use edge detection algorithms. We are grateful to the 'CPE team,' A. Gruss, and D. Halpern for comments and discussions, and to S. Gaubert, L. Girbal, T. Esquerré, and M. Cocaign-Bousquet for communicating results prior to publication. Many thanks to our colleagues, P. Palcy, V. Bourgogne, N. Eberlin, and P. Régent for invaluable administrative, IT, and equipment-related support., ANR-12-BSV6-0008,ReadRNA,Les transcriptomes bactériens primaires et maturés pour décrypter les réseaux de régulation(2012), Department of Applied Physics, Department of Computer Science, and Aalto-yliopisto

Subjects
MESH: RNA, Bacterial/genetics, [SDV]Life Sciences [q-bio], Nucleic Acid Denaturation, medicine.disease_cause, MESH: Genome, Bacterial, Quantitative Biology - Quantitative Methods, MESH: Sequence Tagged Sites, Methods, Enterococcus faecalis, RNA Processing, Post-Transcriptional, Promoter Regions, Genetic, Quantitative Methods (q-bio.QM), Sequence Tagged Sites, 0303 health sciences, MESH: Gene Expression Regulation, Bacterial, ta214, Transcription start, biology, Chromosome Mapping, Bacterial RNA, MESH: Chromosome Mapping/methods, RNA, Bacterial, processed RNA, MESH: Transcription Initiation Site, Transcription Initiation Site, MESH: RNA Processing, Post-Transcriptional, MESH: 5' Untranslated Regions/genetics, ta221, Computational biology, MESH: Nucleic Acid Denaturation, Bioinformatik och systembiologi, Microbiology, 03 medical and health sciences, Gene mapping, RNA degradation, primary RNA, medicine, Genetics, Quantitative Biology - Genomics, Genetik, Molecular Biology, Escherichia coli, ta218, 030304 developmental biology, Genomics (q-bio.GN), promoter, ta114, Bioinformatics and Systems Biology, [ SDV ] Life Sciences [q-bio], Sequence Analysis, RNA, 030306 microbiology, MESH: Enterococcus faecalis/genetics, MESH: Transcriptome, RNA, Promoter, Biomolecules (q-bio.BM), Gene Expression Regulation, Bacterial, biology.organism_classification, MESH: Sequence Analysis, RNA/methods, Mikrobiologi, Quantitative Biology - Biomolecules, MESH: Promoter Regions, Genetic/genetics, FOS: Biological sciences, 5' Untranslated Regions, Transcriptome, Genome, Bacterial, Bacteria
Abstract

Enterococcus faecalis is the third cause of nosocomial infections. To obtain the first snapshot of transcriptional organizations in this bacterium, we used a modified RNA-seq approach enabling to discriminate primary from processed 5′ RNA ends. We also validated our approach by confirming known features in Escherichia coli. We mapped 559 transcription start sites (TSSs) and 352 processing sites (PSSs) in E. faecalis. A blind motif search retrieved canonical features of SigA- and SigN-dependent promoters preceding transcription start sites mapped. We discovered 85 novel putative regulatory RNAs, small- and antisense RNAs, and 72 transcriptional antisense organizations. Presented data constitute a significant insight into bacterial RNA landscapes and a step toward the inference of regulatory processes at transcriptional and post-transcriptional levels in a comprehensive manner.

Published
2015
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4. Promoter analysis of the gene encoding GDNF in murine Sertoli cells

Author

Elena Vicini, Dante Lamberti, Department of Anatomy, Histology, Forensic Medicine and Orthopedic [Roma] (DAHFMO), Institut Pasteur, Fondation Cenci Bolognetti - Istituto Pasteur Italia, Fondazione Cenci Bolognetti, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP)-Università degli Studi di Roma 'La Sapienza' = Sapienza University [Rome], and This work was supported by Grants from Italian Ministry of University (FIRB,Grant No.: RBIN06E9Z8_008) and Sapienza University (Ateno 2011).

Subjects
Male, Transcription, Genetic, 5' Flanking Region, animal diseases, Sertoli cells, [SDV]Life Sciences [q-bio], Spermatogonial stem cells, MESH: Base Sequence, Biochemistry, Mice, 0302 clinical medicine, Endocrinology, Transcription (biology), FSH, MESH: Gene Expression Regulation, Developmental, Cyclic AMP, Glial cell line-derived neurotrophic factor, MESH: Animals, Promoter Regions, Genetic, Luciferase activity, Conserved Sequence, MESH: Cyclic AMP, 0303 health sciences, MESH: Conserved Sequence, biology, Gene Expression Regulation, Developmental, Cell Differentiation, CRE, MESH: Transcription Factors, Seminiferous Tubules, Sertoli cell, GDNF, medicine.anatomical_structure, MESH: Transcription Initiation Site, Transcription Initiation Site, MESH: Glial Cell Line-Derived Neurotrophic Factor, MESH: Cell Differentiation, endocrine system, Molecular Sequence Data, Primary Cell Culture, MESH: Seminiferous Tubules, spermatogonial stem cells, cre, fsh, luciferase activity, sertoli cells, gdnf, DNA sequencing, MESH: Primary Cell Culture, 03 medical and health sciences, MESH: Sertoli Cells, MESH: Mice, Inbred C57BL, MESH: Promoter Regions, Genetic, medicine, Animals, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Glial Cell Line-Derived Neurotrophic Factor, Molecular Biology, Gene, MESH: Mice, 030304 developmental biology, MESH: 5' Flanking Region, Binding Sites, MESH: Molecular Sequence Data, Base Sequence, urogenital system, MESH: Transcription, Genetic, Promoter, Molecular biology, MESH: Male, Mice, Inbred C57BL, nervous system, MESH: Binding Sites, biology.protein, GDNF family of ligands, 030217 neurology & neurosurgery, Transcription Factors, Hormone
Abstract

International audience; GDNF is a Sertoli-cell-derived factor that controls the balance between self-renewal and differentiation of the spermatogonial stem cells. Although research in recent years has concentrated on the impact of GDNF on target germ cells rather little attention has been paid to the molecular control of GDNF expression in Sertoli cells. Here, we aimed to characterize the promoter region of the mouse gdnf gene active in Sertoli cells. We identified the transcriptional start sites and analyzed the promoter activity of the 5'-flanking regions. By in-silico analysis of evolutionarily conserved DNA sequences we identified several putative transcription factor-binding regions. Deletion analysis showed the involvement of the three CRE sites for basal and cAMP-induced expression of gdnf in murine Sertoli cells. These results provide the basis for future studies to analyze how hormonal or paracrine signals modulate the transcriptional activity of gdnf in Sertoli cells.

Published
2014
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5. Riboswitch Discovery by Combining RNA-Seq and Genome-Wide Identification of Transcriptional Start Sites

Author

Isabelle Rosinski-Chupin, Isabelle Martin-Verstraete, Olga Soutourina, Biologie des Bactéries pathogènes à Gram-positif, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Pathogénèse des Bactéries Anaérobies / Pathogenesis of Bacterial Anaerobes (PBA (U-Pasteur_6)), Institut Pasteur [Paris] (IP)-Université Paris Diderot - Paris 7 (UPD7), Cellule Pasteur, Université Paris Diderot - Paris 7 (UPD7)-PRES Sorbonne Paris Cité, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Institut Pasteur [Paris]-Université Paris Diderot - Paris 7 (UPD7), and PRES Sorbonne Paris Cité-Université Paris Diderot - Paris 7 (UPD7)

Subjects
Untranslated region, Riboswitch, Deep sequencing, In silico, RNA-Seq, Transcriptional start site mapping, Biology, Genome, 03 medical and health sciences, Transcription (biology), MESH: Sequence Analysis, RNA, natural sciences, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, MESH: High-Throughput Nucleotide Sequencing, 030304 developmental biology, MESH: RNA, Messenger, Genetics, 0303 health sciences, 030306 microbiology, RNA, 5′-untranslated region, cis-Acting regulatory RNA, MESH: Bacteria, Riboswitches, MESH: 5' Untranslated Regions, MESH: Transcription Initiation Site, RNA-seq, MESH: Riboswitch
Abstract

International audience; Deep-sequencing technologies applied to RNA have tremendous potential to identify novel transcripts with single-nucleotide resolution. By combining whole-transcript cDNA sequencing (RNA-seq) and genome-wide identification of transcription start sites (dRNA-seq), it is possible to characterize long 5'-untranslated regions potentially endowed with regulatory capacities and to detect premature termination of transcription. This can be used to identify new potential riboswitches. In this chapter, we provide a detailed protocol of the dRNA-seq method based on differential pretreatment of RNAs with tobacco acid pyrophosphatase to differentiate between 5'-ends of primary and processed RNAs. We also give a briefer protocol of the preparation of RNA-seq libraries and of how to go through data bioinformatics analysis and data visualization using genome browsers. This approach is powerful to identify novel riboswitches and to demonstrate the functionality of riboswitches predicted in silico.

Published
2014
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6. Characterization of the SigD regulon of C. difficile and its positive control of toxin production through the regulation of tcdR

Author

Marc Monot, Johann Peltier, Martine Pestel-Caron, Jean-Louis Pons, Olga Soutourina, Imane El Meouche, Bruno Dupuy, Groupe de Recherche sur les Antimicrobiens et les Micro-Organismes (GRAM 1.0), Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Normandie Université (NU), Pathogénèse des Bactéries Anaérobies / Pathogenesis of Bacterial Anaerobes (PBA (U-Pasteur_6)), Institut Pasteur [Paris]-Université Paris Diderot - Paris 7 (UPD7), Cellule Pasteur, PRES Sorbonne Paris Cité-Université Paris Diderot - Paris 7 (UPD7), Ecosystème intestinal, probiotiques, antibiotiques (EA 4065), Université Paris Descartes - Paris 5 (UPD5), Funding was provided by the University of Rouen., Université Paris Diderot - Paris 7 (UPD7)-PRES Sorbonne Paris Cité, Institut Pasteur [Paris] (IP)-Université Paris Diderot - Paris 7 (UPD7), Groupe de Recherche sur les Antimicrobiens et les Micro-Organismes ( GRAM 1.0 ), Université de Rouen Normandie ( UNIROUEN ), Normandie Université ( NU ) -Normandie Université ( NU ), Pathogénèse des Bactéries Anaérobies, Institut Pasteur [Paris], Université Paris Diderot - Paris 7 ( UPD7 ) -PRES Sorbonne Paris Cité, Ecosystème intestinal, probiotiques, antibiotiques ( EA 4065 ), and Université Paris Descartes - Paris 5 ( UPD5 )

Subjects
MESH : Protein Biosynthesis, Transcription, Genetic, Mutant, lcsh:Medicine, MESH : Transcriptome, MESH : Promoter Regions, Genetic, MESH: Base Sequence, Transcription (biology), Sigma factor, Gene expression, MESH : Bacterial Proteins, MESH: Gene Silencing, lcsh:Science, Promoter Regions, Genetic, MESH : Clostridium difficile, MESH: Bacterial Proteins, MESH : Consensus Sequence, Regulation of gene expression, Genetics, 0303 health sciences, MESH: Gene Expression Regulation, Bacterial, MESH: Genetic Complementation Test, Multidisciplinary, MESH : Protein Binding, DNA-Directed RNA Polymerases, MESH : Phenotype, Phenotype, Flagella, MESH: Protein Biosynthesis, MESH: Transcription Initiation Site, Transcription Initiation Site, MESH : Mutation, Research Article, Protein Binding, MESH : Gene Expression Regulation, Bacterial, MESH: Mutation, Bacterial Toxins, [ SDV.BBM.BM ] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, Biology, MESH: Phenotype, MESH: Flagella, 03 medical and health sciences, Bacterial Proteins, MESH : DNA-Directed RNA Polymerases, Consensus Sequence, MESH : Gene Silencing, MESH: Promoter Regions, Genetic, Consensus sequence, Position-Specific Scoring Matrices, MESH: Protein Binding, Gene Silencing, MESH: Consensus Sequence, Gene, MESH: Clostridium difficile, 030304 developmental biology, Binding Sites, Base Sequence, MESH : Genetic Complementation Test, Clostridioides difficile, 030306 microbiology, MESH: Transcription, Genetic, MESH: Transcriptome, lcsh:R, Genetic Complementation Test, MESH : Transcription, Genetic, MESH: Position-Specific Scoring Matrices, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, Gene Expression Regulation, Bacterial, MESH : Position-Specific Scoring Matrices, MESH: DNA-Directed RNA Polymerases, Regulon, MESH: Bacterial Toxins, MESH: Binding Sites, MESH : Transcription Initiation Site, Protein Biosynthesis, Mutation, MESH : Bacterial Toxins, lcsh:Q, MESH : Base Sequence, Transcriptome, MESH : Flagella, MESH : Binding Sites
Abstract

International audience; Clostridium difficile intestinal disease is mediated largely by the actions of toxins A (TcdA) and B (TcdB), whose production occurs after the initial steps of colonization involving different surface or flagellar proteins. In B. subtilis, the sigma factor SigD controls flagellar synthesis, motility, and vegetative autolysins. A homolog of SigD encoding gene is present in the C.difficile 630 genome. We constructed a sigD mutant in C. difficile 630 ∆erm to analyze the regulon of SigD using a global transcriptomic approach. A total of 103 genes were differentially expressed between the wild-type and the sigD mutant, including genes involved in motility, metabolism and regulation. In addition, the sigD mutant displayed decreased expression of genes involved in flagellar biosynthesis, and also of genes encoding TcdA and TcdB as well as TcdR, the positive regulator of the toxins. Genomic analysis and RACE-PCR experiments allowed us to characterize promoter sequences of direct target genes of SigD including tcdR and to identify the SigD consensus. We then established that SigD positively regulates toxin expression via direct control of tcdR transcription. Interestingly, the overexpression of FlgM, a putative anti-SigD factor, inhibited the positive regulation of motility and toxin synthesis by SigD. Thus, SigD appears to be the first positive regulator of the toxin synthesis in C. difficile.

Published
2013
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7. A role for SIRT2-dependent histone H3K18 deacetylation in bacterial infection

Author

Guillaume Soubigou, Haig A. Eskandarian, Francis Impens, Pascale Cossart, Melanie Hamon, Marie-Anne Nahori, Jean-Yves Coppée, Interactions Bactéries-Cellules (UIBC), Institut National de la Recherche Agronomique (INRA)-Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM), INSERM, Institut National de la Santé et de la Recherche Médicale (INSERM), Department of Medical Protein Research (VIB), Vlaams Instituut voor Biotechnologie, Department of Biochemistry, Universiteit Gent = Ghent University (UGENT), Transcriptome et Epigénome (PF2), Institut Pasteur [Paris] (IP), Work in the Cossart laboratory is funded by the Pasteur Institute, Inserm (U604), Institut National de la Recherche Agronomique (USC2020), the Fondation Louis Jeantet, the European Research Council (advanced grant 233348 MODELIST), the Fondation Le Roch Les Mousquetaires, and the Agence Nationale pour la Recherche grants (ERANET 'LISTRESS' and EPILIS), Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut Pasteur [Paris]-Institut National de la Recherche Agronomique (INRA), Unité Sous Contrat 2020, Institut National de la Recherche Agronomique (INRA), Ghent University [Belgium] (UGENT), Institut Pasteur [Paris], Institut National de la Recherche Agronomique (INRA)-Institut Pasteur [Paris]-Institut National de la Santé et de la Recherche Médicale (INSERM), and Universiteit Gent = Ghent University [Belgium] (UGENT)

Subjects
NF-KAPPA-B, MESH: Proto-Oncogene Proteins c-met, medicine.disease_cause, MESH: Listeria monocytogenes, MESH: Mice, Knockout, Histones, Mice, 0302 clinical medicine, Cytosol, Sirtuin 2, MESH: Cytosol, Transcription (biology), MESH: Sirtuin 2, Listeriosis, MESH: Animals, LISTERIA-MONOCYTOGENES, PHOSPHORYLATION, MESH: Bacterial Proteins, GENE-EXPRESSION, Mice, Knockout, MESH: Histones, 0303 health sciences, Mice, Inbred BALB C, Multidisciplinary, IFN-GAMMA, biology, IMMUNE-RESPONSES, Proto-Oncogene Proteins c-met, Chromatin, 3. Good health, Histone, Sirtuin, Host-Pathogen Interactions, MESH: Transcription Initiation Site, MESH: Membrane Proteins, Transcription Initiation Site, MESH: Acetylation, Transcriptional Activation, MESH: Cell Nucleus, ACETYLATION, MESH: Mice, Inbred BALB C, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, SIRT2, Microbiology, MESH: Chromatin, 03 medical and health sciences, Histone H3, Listeria monocytogenes, Bacterial Proteins, medicine, Animals, Humans, MESH: Lysine, MESH: Mice, 030304 developmental biology, Cell Nucleus, MESH: Humans, Lysine, MESH: Host-Pathogen Interactions, Membrane Proteins, Acetylation, SIRTUINS, MESH: Listeriosis, MESH: Protein Processing, Post-Translational, MESH: HeLa Cells, biology.protein, PATTERNS, MESH: Transcriptional Activation, Protein Processing, Post-Translational, 030217 neurology & neurosurgery, HeLa Cells
Abstract

Bacterial Subversion Tactics Intracellular bacterial pathogens such as Listeria monocytogenes can change host cell transcription programs to promote infection. Eskandarian et al. ( 1238858 ) found that during infection, the Listeria effector protein InlB promoted the movement of a host protein deacetylase, SIRT2, from its normal location in the cytosol to the nucleus. In the nucleus, SIRT2 helped to repress a number of host cell genes by deacetylating one of their associated histones. In mice, reduced levels of SIRT2 impaired bacterial infection.

Published
2013
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8. Genome-wide identification of Sox8-, and Sox9-dependent genes during early post-natal testis development in the mouse

Author

Bernard Jégou, Gerd Scherer, Michael Primig, Francisco J. Barrionuevo, Philippe Demougin, Ina Georg, Frédéric Chalmel, Aurélie Lardenois, Transcriptional networks in gametogenesis and cancer, Institut de recherche en santé, environnement et travail (Irset), Université d'Angers (UA)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-École des Hautes Études en Santé Publique [EHESP] (EHESP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique )-Université d'Angers (UA)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-École des Hautes Études en Santé Publique [EHESP] (EHESP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), Institute of Human Genetics, University of Freiburg [Freiburg], Biozentrum [Basel, Suisse], University of Basel (Unibas), Environnement viral et chimique & reproduction, and Université d'Angers (UA)-Université de Rennes (UR)-École des Hautes Études en Santé Publique [EHESP] (EHESP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique )-Université d'Angers (UA)-Université de Rennes (UR)-École des Hautes Études en Santé Publique [EHESP] (EHESP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique )

Subjects
Male, MESH: Sex Determination Processes, Sex Differentiation, Microarrays, Endocrinology, Diabetes and Metabolism, Cellular differentiation, Sertoli cells, Regulatory Sequences, Nucleic Acid, MESH: Mice, Knockout, MESH: Genotype, Mice, 0302 clinical medicine, Endocrinology, Testis, MESH: Animals, Genetics, Mice, Knockout, 0303 health sciences, SOXE Transcription Factors, MESH: Testis, MESH: Sex Differentiation, Cell Differentiation, SOX9 Transcription Factor, Sertoli cell, Cell biology, DNA-Binding Proteins, medicine.anatomical_structure, 030220 oncology & carcinogenesis, Female, MESH: Transcription Initiation Site, Transcription Initiation Site, Sox8, MESH: Spermatogenesis, Sox9, MESH: Cell Differentiation, Cell type, endocrine system, Genotype, Urology, SOX9, Biology, MESH: SOXE Transcription Factors, 03 medical and health sciences, MESH: Gene Expression Profiling, MESH: SOX9 Transcription Factor, FGF9, MESH: Sertoli Cells, MESH: Mice, Inbred C57BL, medicine, Animals, MESH: Regulatory Sequences, Nucleic Acid, RNA, Messenger, Spermatogenesis, Transcription factor, Gene, MESH: Mice, 030304 developmental biology, MESH: RNA, Messenger, Sexual differentiation, Binding Sites, urogenital system, Gene Expression Profiling, [SDV.BDLR]Life Sciences [q-bio]/Reproductive Biology, Sex Determination Processes, MESH: Male, Mice, Inbred C57BL, Reproductive Medicine, MESH: Binding Sites, MESH: Female, MESH: DNA-Binding Proteins
Abstract

test; International audience; The SOX8 and SOX9 transcription factors are involved in, among others, sex differentiation, male gonad development and adult maintenance of spermatogenesis. Sox8(-/-) mice lacking Sox9 in Sertoli cells fail to form testis cords and cannot establish spermatogenesis. Although genetic and histological data show an important role for these transcription factors in regulating spermatogenesis, it is not clear which genes depend upon them at a genome-wide level. To identify transcripts that respond to the absence of Sox8 in all cells and Sox9 in Sertoli cells we measured mRNA concentrations in testicular samples from mice at 0, 6 and 18 days post-partum. In total, 621 and 629 transcripts were found at decreased or increased levels, respectively, at different time points in the mutant as compared to the control samples. These mRNAs were categorized as preferentially expressed in Sertoli cells or germ cells using data obtained with male and female gonad samples and enriched testicular cell populations. Five candidate genes were validated at the protein level. Furthermore, we identified putative direct SOX8 and SOX9 target genes by integrating predicted SOX-binding sites present in potential regulatory regions upstream of the transcription start site. Finally, we used protein network data to gain insight into the effects on regulatory interactions that occur when Sox8 and Sox9 are absent in developing Sertoli cells. The integration of testicular samples with enriched Sertoli cells, germ cells and female gonads enabled us to broadly distinguish transcripts directly affected in Sertoli cells from others that respond to secondary events in testicular cell types. Thus, combined RNA profiling signals, motif predictions and network data identified putative SOX8/SOX9 target genes in Sertoli cells and yielded insight into regulatory interactions that depend upon these transcription factors. In addition, our results will facilitate the interpretation of genome-wide in vivo SOX8 and SOX9 DNA binding data.

Published
2013
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9. cDNA library construction for next-generation sequencing to determine the transcriptional landscape of Legionella pneumophila

Author

Tobias Sahr, Carmen Buchrieser, Biologie des bactéries intracellulaires, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), This work received support from the Institut Pasteur, the Centre national de la recherche scientifique (CNRS), and the Institut Carnot-Pasteur MI, the Labex project 'IBEID' and from the ANR-10-PATH-004 project, in the frame of ERA-Net PathoGenoMics., Carmen Buchrieser, Hubert Hilbi, ANR-10-LABX-0062,IBEID,Integrative Biology of Emerging Infectious Diseases(2010), ANR-10-PATH-0004,MobileGenomics(2010), and Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Small ncRNA, Computational biology, Transcriptional start site mapping, Biology, Genome, Legionella pneumophila, Deep sequencing, DNA sequencing, Microbiology, Transcriptome, 03 medical and health sciences, MESH: Gene Expression Profiling, MESH: Gene Library, Gene, MESH: High-Throughput Nucleotide Sequencing, 030304 developmental biology, 0303 health sciences, 030306 microbiology, cDNA library, MESH: Transcriptome, CDNA Library Construction, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, biology.organism_classification, bacterial infections and mycoses, MESH: Legionella pneumophila, Next-generation sequencing, MESH: Transcription Initiation Site, MESH: RNA, Bacterial
Abstract

International audience; The adaptation of Legionella pneumophila to the different conditions it encounters in the environment and in the host is governed by a complex regulatory system. Current knowledge of these regulatory networks and the transcriptome responses of L. pneumophila is mainly based on microarray analysis and limited to transcriptional products of annotated protein-coding genes. The application of the Next-Generation Sequencing (NGS) technology allows now genome-wide strand-specific sequencing and accurate determination of all expressed regions of the genome to reveal the complete transcriptional network and the dynamic interplay of specific regulators on a genome-wide level. NGS-based techniques promote deeper understanding of the global transcriptional organization of L. pneumophila by identifying transcription start sites (TSS), alternative TSS and operon organization, noncoding RNAs, antisense RNAs, and 5'-/3'-untranslated regions. In this chapter we describe the construction of cDNA libraries for (1) RNA deep sequencing (RNA-seq) and (2) TSS mapping using the Illumina technology.

Published
2013
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10. The nucleoid-associated protein Fis directly modulates the synthesis of cellulose, an essential component of pellicle-biofilms in the phytopathogenic bacterium Dickeya dadantii

Author

Claire Prigent-Combaret, Ouafa Zghidi-Abouzid, Géraldine Effantin, Philippe Lejeune, Sylvie Reverchon, William Nasser, Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Ecole Nationale Vétérinaire de Lyon (ENVL), Trafic et signalisation membranaires chez les bactéries (MTSB), Microbiologie, adaptation et pathogénie (MAP), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS), Chromatine et Régulation de la Pathogénie bactérienne (CRP), Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Vétérinaire de Lyon (ENVL)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS), Ecologie microbienne ( EM ), Centre National de la Recherche Scientifique ( CNRS ) -Ecole Nationale Vétérinaire de Lyon ( ENVL ) -Université Claude Bernard Lyon 1 ( UCBL ), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique ( INRA ) -VetAgro Sup ( VAS ), Microbiologie, adaptation et pathogénie ( MAP ), Université Claude Bernard Lyon 1 ( UCBL ), Université de Lyon-Université de Lyon-Institut National des Sciences Appliquées de Lyon ( INSA Lyon ), and Université de Lyon-Institut National des Sciences Appliquées ( INSA ) -Institut National des Sciences Appliquées ( INSA ) -Centre National de la Recherche Scientifique ( CNRS )

Subjects
MESH : Operator Regions, Genetic, Operator Regions, Genetic, MESH : Molecular Sequence Data, MESH : Operon, MESH : Solanum tuberosum, MESH: Base Sequence, MESH: Virulence, Chicory, MESH: Plant Diseases, Genes, Reporter, [ SDV.EE.IEO ] Life Sciences [q-bio]/Ecology, environment/Symbiosis, MESH: Cellulose, MESH: Gene Expression Regulation, Bacterial, Virulence, MESH : Plant Diseases, MESH : Virulence, MESH : beta-Galactosidase, MESH : Enterobacteriaceae, MESH : Genes, Reporter, MESH: beta-Galactosidase, MESH : Biofilms, MESH: Repressor Proteins, MESH: Transcription Initiation Site, Transcription Initiation Site, MESH : Repressor Proteins, MESH : Gene Expression Regulation, Bacterial, MESH: Operon, Molecular Sequence Data, MESH: Biofilms, MESH: Solanum tuberosum, MESH: Artificial Gene Fusion, MESH: Enterobacteriaceae, Enterobacteriaceae, Operon, Cellulose, Plant Diseases, Solanum tuberosum, MESH: Molecular Sequence Data, Base Sequence, MESH : Cellulose, MESH: Genes, Reporter, Gene Expression Regulation, Bacterial, beta-Galactosidase, Artificial Gene Fusion, MESH : Chicory, Repressor Proteins, MESH : Artificial Gene Fusion, MESH : Transcription Initiation Site, MESH: Operator Regions, Genetic, Biofilms, MESH: Chicory, MESH : Base Sequence, [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Abstract

International audience; Bacteria use biofilm structures to colonize surfaces and to survive in hostile conditions, and numerous bacteria produce cellulose as a biofilm matrix polymer. Hence, expression of the bcs operon, responsible for cellulose biosynthesis, must be finely regulated in order to allow bacteria to adopt the proper surface-associated behaviours. Here we show that in the phytopathogenic bacterium, Dickeya dadantii, production of cellulose is required for pellicle-biofilm formation and resistance to chlorine treatments. Expression of the bcs operon is growth phase-regulated and is stimulated in biofilms. Furthermore, we unexpectedly found that the nucleoid-associated protein and global regulator of virulence functions, Fis, directly represses bcs operon expression by interacting with an operator that is absent from the bcs operon of animal pathogenic bacteria and the plant pathogenic bacterium Pectobacterium. Moreover, production of cellulose enhances plant surface colonization by D. dadantii. Overall, these data suggest that cellulose production and biofilm formation may be important factors for surface colonization by D. dadantii and its subsequent survival in hostile environments. This report also presents a new example of how bacteria can modulate the action of a global regulator to co-ordinate basic metabolism, virulence and modifications of lifestyle.

Published
2012

11. Dual role of the PhoP approximately P response regulator: Bacillus amyloliquefaciens FZB45 phytase gene transcription is directed by positive and negative interactions with the phyC promoter

Author

Tarek Msadek, Rainer Borriss, Sarah Dubrac, Oliwia Makarewicz, Institut für Biologie [Berlin] (IFB), Humboldt University Of Berlin, Biologie des Bactéries Pathogènes à Gram-positif, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Partial financial support given for the genomic network sponsored by BMBF, the German ministry for education and research, is gratefully acknowledged. Sarah Dubrac's work was supported by research funds from the European Commission (Grant LSHG-CT-2004-503468 BACELL Health), the Centre National de la Recherche Scientifique, and the Institut Pasteur (Grand Programme Horizontal no. 9)., We thank Masaya Fujita for providing the Bacillus subtilis strain MF1 used for isolation of RNAP. We also thank Christiane Müller for technical support and sequencing and Markus Wilhelms for cloning pPHOR231 and purification of the proteins. Steffen Porwollik (Sidney Kimmel Cancer Center, San Diego, Calif.) is especially thanked for valuable hints for improving the manuscript., European Project: 26873,BACELL HEALTH, Humboldt-Universität zu Berlin, and Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS)

Subjects
Transcription, Genetic, DNA Footprinting, Bacillus, Electrophoretic Mobility Shift Assay, Transcription (biology), Genes, Reporter, MESH: 6-Phytase, MESH: DNA Footprinting, Promoter Regions, Genetic, MESH: Bacterial Proteins, Regulator gene, 0303 health sciences, 6-Phytase, MESH: Gene Expression Regulation, Bacterial, DNA-Binding Proteins, MESH: beta-Galactosidase, MESH: Promoter Regions (Genetics), MESH: Regulon, MESH: Transcription Initiation Site, Transcription Initiation Site, Protein Binding, DNA footprinting, Biology, Microbiology, Models, Biological, Regulon, MESH: Artificial Gene Fusion, 03 medical and health sciences, Bacterial Proteins, MESH: Bacillus, Consensus sequence, Point Mutation, MESH: Protein Binding, Gene Regulation, Binding site, Molecular Biology, 030304 developmental biology, MESH: Point Mutation, Binding Sites, 030306 microbiology, MESH: Transcription, Genetic, MESH: Genes, Reporter, MESH: Models, Biological, Promoter, Gene Expression Regulation, Bacterial, biochemical phenomena, metabolism, and nutrition, beta-Galactosidase, Molecular biology, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Artificial Gene Fusion, Response regulator, MESH: Binding Sites, MESH: Electrophoretic Mobility Shift Assay, bacteria, MESH: DNA-Binding Proteins
Abstract

Several Bacillus strains secrete phytase, an enzyme catalyzing dephosphorylation of myo -inositol hexakisphosphate (phytate). We identified the phyC (phytase) gene from environmental Bacillus amyloliquefaciens FZB45 as a member of the phosphate starvation-inducible PhoPR regulon. In vivo and in vitro assays revealed that PhoP∼P is essential for phy C transcription. The transcriptional start site was identified downstream of a σ A -like promoter region located 27 bp upstream of the probable translation ATG start codon. Inspection of the phyC promoter sequence revealed an unusual structure. The− 35 and −10 regions are separated by a window of 21 bp. A pair of tandemly repeated PhoP TT(T/A/C)ACA binding boxes was located within and upstream of the −35 consensus promoter region. A single PhoP box was found within the −10 consensus promoter region. DNase I footprinting experiments performed with isolated PhoP confirmed that PhoP∼P binds at two sites overlapping with the phy C −35 and −10 consensus promoter region. While binding of dimeric PhoP∼P at −35 is essential for activation of the phyC promoter, binding of PhoP∼P at− 10 suppresses promoter activity. A sixfold enhancement of phyC gene expression was registered after T:G substitution of nucleotide −13 (mutant MUT13), which eliminates PhoP binding at the single PhoP box without impairing the −10 consensus sequence. Moreover, MUT13 also expressed phyC during phosphate-replete growth, suggesting that the repressing effect due to binding of PhoP∼P at −10 was abolished. A model is presented in which transcription initiation of phyC is positively and negatively affected by the actual concentration of the PhoP∼P response regulator.

Published
2006
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12. Krox20 hindbrain cis-regulatory landscape: interplay between multiple long-range initiation and autoregulatory elements

Author

Diane Chomette, Julien Ghislain, Monique Frain, Patrick Charnay, Silvia Cereghini, Génétique moléculaire du développement, Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-IFR36-Institut National de la Santé et de la Recherche Médicale (INSERM), Laboratoire de Biologie du Développement (LBD), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut de Biologie Paris Seine (IBPS), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Centre Hospitalier de l'Université de Montréal (CHUM), Université de Montréal (UdeM), École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), and Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Indoles, Body Patterning, [SDV.NEU.NB]Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC]/Neurobiology, Chick Embryo, MESH: Base Sequence, Conserved sequence, Mice, 0302 clinical medicine, Genes, Reporter, Transcription (biology), MESH: Early Growth Response Protein 2, MESH: Gene Expression Regulation, Developmental, MESH: Animals, MESH: Models, Genetic, Promoter Regions, Genetic, Conserved Sequence, In Situ Hybridization, Genetics, MESH: Indoles, 0303 health sciences, MESH: Conserved Sequence, [SDV.NEU.PC]Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC]/Psychology and behavior, Gene Expression Regulation, Developmental, Neural crest, [SDV.NEU.SC]Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC]/Cognitive Sciences, MESH: Rhombencephalon, MESH: Transcription Factors, MESH: Lac Operon, MESH: Chick Embryo, Cell biology, MESH: Mutagenesis, Site-Directed, Enhancer Elements, Genetic, Lac Operon, Mice, Inbred DBA, MESH: Transcription Initiation Site, Transcription Initiation Site, Protein Binding, MESH: Body Patterning, MESH: Mice, Transgenic, Molecular Sequence Data, Rhombomere, Mice, Transgenic, Hindbrain, Biology, MESH: Sequence Homology, Nucleic Acid, 03 medical and health sciences, MESH: In Situ Hybridization, MESH: Mice, Inbred C57BL, Sequence Homology, Nucleic Acid, MESH: Promoter Regions, Genetic, Animals, Humans, MESH: Protein Binding, MESH: Galactosides, MESH: Hepatocyte Nuclear Factor 1-beta, Molecular Biology, Gene, Transcription factor, MESH: Mice, Early Growth Response Protein 2, MESH: Genome, Human, Hepatocyte Nuclear Factor 1-beta, 030304 developmental biology, Binding Sites, MESH: Molecular Sequence Data, MESH: Humans, Base Sequence, Models, Genetic, MESH: Mice, Inbred DBA, Genome, Human, MESH: Genes, Reporter, Galactosides, Mice, Inbred C57BL, Rhombencephalon, MESH: Binding Sites, Mutagenesis, Site-Directed, MESH: Enhancer Elements, Genetic, 030217 neurology & neurosurgery, Transcription Factors, Developmental Biology
Abstract

International audience; The vertebrate hindbrain is subject to a transient segmentation process leading to the formation of seven or eight metameric territories termed rhombomeres (r). This segmentation provides the basis for the subsequent establishment of hindbrain neuronal organization and participates in the patterning of the neural crest involved in craniofacial development. The zinc-finger gene Krox20 is expressed in r3 and r5, and encodes a transcription factor that plays a key role in hindbrain segmentation, coordinating segment formation, specification of odd- and even-numbered rhombomeres, and cell segregation between adjacent segments, through the regulation of numerous downstream genes. In order to further elucidate the genetic network underlying hindbrain segmentation, we have undertaken the analysis of the cis-regulatory sequences governing Krox20 expression. We have found that the control of Krox20 transcription relies on three very long-range (200 kb) enhancer elements (A, B and C) that are conserved between chick, mouse and human genomes. Elements B and C are activated at the earliest stage of Krox20 expression in r5 and r3-r5, respectively, and do not require the Krox20 protein. These elements are likely to function as initiators of Krox20 expression. Element B contains a binding site for the transcription factor vHNF1, the mutation of which abolishes its activity, suggesting that vHNF1 is a direct initiator of Krox20 expression in r5. Element A contains Krox20-binding sites, which are required, together with the Krox20 protein, for its activity. This element therefore allows the establishment of a direct positive autoregulatory loop, which takes the relay of the initiator elements and maintains Krox20 expression. Together, our studies provide a basis for a model of the molecular mechanisms controlling Krox20 expression in the developing hindbrain and neural crest.

Published
2006
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13. The complete mitochondrial genome of the yeast Kluyveromyces thermotolerans

Author

Lionel Frangeul, Emmanuel Talla, Christiane Bouchier, Véronique Anthouard, Bernard Dujon, Génétique Moléculaire des Levures, Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Génomique (Plate-Forme) - Genomics Platform, Institut Pasteur [Paris], This work is part of Genolevures Consortium (CNRS-GDR2345) and was supported by CNRS (Action genome). BD is a member of Institut Universitaire de France., Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), and Institut Pasteur [Paris] (IP)

Subjects
Mitochondrial DNA, MESH: Introns, Genetic code, Molecular Sequence Data, Biophysics, Biology, MESH: Base Sequence, DNA, Mitochondrial, Biochemistry, MESH: Kluyveromyces, MESH: Gene Order, Kluyveromyces, 03 medical and health sciences, RNA, Transfer, Structural Biology, Ribosomal protein, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Gene Order, Genetics, Intronic ORF, Group I catalytic intron, Codon, Molecular Biology, Gene, tRNA, 030304 developmental biology, 0303 health sciences, MESH: Molecular Sequence Data, Base Sequence, MESH: Codon, 030302 biochemistry & molecular biology, Nucleic acid sequence, MESH: DNA, Mitochondrial, RNA, Cell Biology, Ribosomal RNA, mitochondrial, MESH: RNA, Transfer, Introns, mt, Transfer RNA, MESH: Genome, Fungal, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Codon usage, MESH: Transcription Initiation Site, Genome, Fungal, Transcription Initiation Site, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM]
Abstract

International audience; We report here the complete nucleotide sequence of the 23.5-kb mitochondrial genome from the yeast Kluyveromyces thermotolerans. It encodes, all on the same DNA strand, three subunits of cytochrome oxidase (COX1, COX2 and COX3), three subunits of ATP synthetase (ATP6, ATP8 and ATP9), the apocytochrome b (COB), the ribosomal protein VAR1, 24 tRNAs, the small and large ribosomal RNAs, and the RNA subunit of RNase P. Three intronic ORFs are present within the COX1 gene group I introns. The K. thermotolerans mitochondrial genome is very similar to the Candida glabrata mitochondrial genome, as judged from clusters of gene order, gene transcription units and sequence similarities. Interestingly, the predicted secondary structure of the abnormal tRNAThr1 contains 10 nucleotides in its anticodon loop. This sequence is available under EMBL Accession No. AJ634268.

Published
2005
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14. Putative FLJ20436 gene characterisation in goat. Observed ubiquitous expression in goat and transgenic mice allowed to restrict the location of an hypothesised insulator element

Author

Mata, Xavier, Taourit, Sead, Le Provost, Fabienne, Unité de recherche Génétique Biochimique et Cytogénétique (LGBC), Institut National de la Recherche Agronomique (INRA), Génétique Animale et Biologie Intégrative (GABI), and Institut National de la Recherche Agronomique (INRA)-AgroParisTech

Subjects
Male, GENE EXPRESSION, MESH: Gene Expression, Transcription, Genetic, MESH: Mice, Transgenic, MESH: Introns, [SDV]Life Sciences [q-bio], Molecular Sequence Data, Mice, Transgenic, Response Elements, MESH: Goats, STRUCTURE DES GENES, GOATS, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], MESH: Promoter Regions, Genetic, Animals, Humans, MESH: Animals, Promoter Regions, Genetic, GENE STRUCTURE, MESH: Mice, Conserved Sequence, MESH: Molecular Sequence Data, MESH: Conserved Sequence, MESH: Humans, MESH: Alternative Splicing, MESH: Transcription, Genetic, Chromosome Mapping, Exons, Introns, MESH: Male, MESH: Genes, Alternative Splicing, MICE, Genes, MESH: Response Elements, MESH: Transcription Initiation Site, Transcription Initiation Site, MESH: Poly A, SPLICING, Poly A, MESH: Chromosome Mapping, MESH: Exons
Abstract

International audience; Eukaryotic genomes are organised into independent domains through the establishment of boundaries which allow to have distinct pattern of gene expression both during development and in differentiated cells. The previously reported site independent expression of the mammary-specific goat alpha-lactalbumin gene in transgenic mice suggested the existence of cis-regulatory elements located upstream of this gene. The nearby presence of a second ubiquitously expressed gene (the cyclin T1 gene) allowed to define two chromatin domains putatively separated by a boundary insulator-like element. In this study, the characterisation of a third putative gene (FLJ20436) present between the alpha-lactalbumin and the cyclin T1 loci is reported. It was found to be a functional gene, ubiquitously expressed both in goat and transgenic mice. A complex pattern of alternative splicing events was observed in several analysed tissues leading to various mRNAs and putative FLJ20436 proteins, as suggested in human and mouse species. This allowed us to assign this gene to one of the two hypothesised chromatin domains, refining the location of the potential insulator element.

Published
2003

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